--- _id: '7864' abstract: - lang: eng text: "Purpose of review: Cancer is one of the leading causes of death and the incidence rates are constantly rising. The heterogeneity of tumors poses a big challenge for the treatment of the disease and natural antibodies additionally affect disease progression. The introduction of engineered mAbs for anticancer immunotherapies has substantially improved progression-free and overall survival of cancer patients, but little efforts have been made to exploit other antibody isotypes than IgG.\r\nRecent findings: In order to improve these therapies, ‘next-generation antibodies’ were engineered to enhance a specific feature of classical antibodies and form a group of highly effective and precise therapy compounds. Advanced antibody approaches include among others antibody-drug conjugates, glyco-engineered and Fc-engineered antibodies, antibody fragments, radioimmunotherapy compounds, bispecific antibodies and alternative (non-IgG) immunoglobulin classes, especially IgE.\r\nSummary: The current review describes solutions for the needs of next-generation antibody therapies through different approaches. Careful selection of the best-suited engineering methodology is a key factor in developing personalized, more specific and more efficient mAbs against cancer to improve the outcomes of cancer patients. We highlight here the large evidence of IgE exploiting a highly cytotoxic effector arm as potential next-generation anticancer immunotherapy." article_processing_charge: No article_type: original author: - first_name: Judit full_name: Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Singer orcid: 0000-0002-8777-3502 - first_name: Josef full_name: Singer, Josef last_name: Singer - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: 'Singer J, Singer J, Jensen-Jarolim E. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current opinion in allergy and clinical immunology. 2020;20(3):282-289. doi:10.1097/ACI.0000000000000637' apa: 'Singer, J., Singer, J., & Jensen-Jarolim, E. (2020). Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current Opinion in Allergy and Clinical Immunology. Wolters Kluwer. https://doi.org/10.1097/ACI.0000000000000637' chicago: 'Singer, Judit, Josef Singer, and Erika Jensen-Jarolim. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” Current Opinion in Allergy and Clinical Immunology. Wolters Kluwer, 2020. https://doi.org/10.1097/ACI.0000000000000637.' ieee: 'J. Singer, J. Singer, and E. Jensen-Jarolim, “Precision medicine in clinical oncology: the journey from IgG antibody to IgE,” Current opinion in allergy and clinical immunology, vol. 20, no. 3. Wolters Kluwer, pp. 282–289, 2020.' ista: 'Singer J, Singer J, Jensen-Jarolim E. 2020. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current opinion in allergy and clinical immunology. 20(3), 282–289.' mla: 'Singer, Judit, et al. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” Current Opinion in Allergy and Clinical Immunology, vol. 20, no. 3, Wolters Kluwer, 2020, pp. 282–89, doi:10.1097/ACI.0000000000000637.' short: J. Singer, J. Singer, E. Jensen-Jarolim, Current Opinion in Allergy and Clinical Immunology 20 (2020) 282–289. date_created: 2020-05-17T22:00:44Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-08-21T06:28:52Z day: '01' department: - _id: Bio doi: 10.1097/ACI.0000000000000637 external_id: isi: - '000561358300010' intvolume: ' 20' isi: 1 issue: '3' language: - iso: eng month: '06' oa_version: None page: 282-289 publication: Current opinion in allergy and clinical immunology publication_identifier: eissn: - '14736322' publication_status: published publisher: Wolters Kluwer quality_controlled: '1' scopus_import: '1' status: public title: 'Precision medicine in clinical oncology: the journey from IgG antibody to IgE' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2020' ... --- _id: '7876' abstract: - lang: eng text: 'In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. ' article_processing_charge: No article_type: original author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann citation: ama: 'Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp. Immunity. 2020;52(5):721-723. doi:10.1016/j.immuni.2020.04.020' apa: 'Sixt, M. K., & Lämmermann, T. (2020). T cells: Bridge-and-channel commute to the white pulp. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2020.04.020' chicago: 'Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity. Elsevier, 2020. https://doi.org/10.1016/j.immuni.2020.04.020.' ieee: 'M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the white pulp,” Immunity, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.' ista: 'Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white pulp. Immunity. 52(5), 721–723.' mla: 'Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity, vol. 52, no. 5, Elsevier, 2020, pp. 721–23, doi:10.1016/j.immuni.2020.04.020.' short: M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723. date_created: 2020-05-24T22:00:57Z date_published: 2020-05-19T00:00:00Z date_updated: 2023-08-21T06:27:18Z day: '19' department: - _id: MiSi doi: 10.1016/j.immuni.2020.04.020 external_id: isi: - '000535371100002' intvolume: ' 52' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf month: '05' oa: 1 oa_version: Published Version page: 721-723 publication: Immunity publication_identifier: eissn: - '10974180' issn: - '10747613' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'T cells: Bridge-and-channel commute to the white pulp' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2020' ... --- _id: '7909' abstract: - lang: eng text: Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration. article_number: e55351 article_processing_charge: No article_type: original author: - first_name: Julia full_name: Damiano-Guercio, Julia last_name: Damiano-Guercio - first_name: Laëtitia full_name: Kurzawa, Laëtitia last_name: Kurzawa - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Matthias full_name: Schaks, Matthias last_name: Schaks - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Thomas full_name: Pokrant, Thomas last_name: Pokrant - first_name: Stefan full_name: Brühmann, Stefan last_name: Brühmann - first_name: Joern full_name: Linkner, Joern last_name: Linkner - first_name: Laurent full_name: Blanchoin, Laurent last_name: Blanchoin - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Jan full_name: Faix, Jan last_name: Faix citation: ama: Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 2020;9. doi:10.7554/eLife.55351 apa: Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova, M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.55351 chicago: Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev, Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.55351. ieee: J. Damiano-Guercio et al., “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M, Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 9, e55351. mla: Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife, vol. 9, e55351, eLife Sciences Publications, 2020, doi:10.7554/eLife.55351. short: J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova, T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix, ELife 9 (2020). date_created: 2020-05-31T22:00:49Z date_published: 2020-05-11T00:00:00Z date_updated: 2023-08-21T06:32:25Z day: '11' ddc: - '570' department: - _id: MiSi doi: 10.7554/eLife.55351 ec_funded: 1 external_id: isi: - '000537208000001' file: - access_level: open_access checksum: d33bd4441b9a0195718ce1ba5d2c48a6 content_type: application/pdf creator: dernst date_created: 2020-06-02T10:35:37Z date_updated: 2020-07-14T12:48:05Z file_id: '7914' file_name: 2020_eLife_Damiano_Guercio.pdf file_size: 10535713 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '05' oa: 1 oa_version: Published Version project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '7908' abstract: - lang: eng text: Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses. article_processing_charge: No article_type: original author: - first_name: Han Ying full_name: Wang, Han Ying last_name: Wang - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Takayuki full_name: Yamashita, Takayuki last_name: Yamashita - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 2020;40(21):4103-4115. doi:10.1523/JNEUROSCI.2946-19.2020 apa: Wang, H. Y., Eguchi, K., Yamashita, T., & Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2946-19.2020 chicago: Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.2946-19.2020. ieee: H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” Journal of Neuroscience, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020. ista: Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 40(21), 4103–4115. mla: Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:10.1523/JNEUROSCI.2946-19.2020. short: H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115. date_created: 2020-05-31T22:00:48Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-21T06:31:25Z day: '20' ddc: - '570' department: - _id: RySh doi: 10.1523/JNEUROSCI.2946-19.2020 external_id: isi: - '000535694700004' file: - access_level: open_access checksum: 6571607ea9036154b67cc78e848a7f7d content_type: application/pdf creator: dernst date_created: 2020-06-02T09:12:16Z date_updated: 2020-07-14T12:48:05Z file_id: '7912' file_name: 2020_JourNeuroscience_Wang.pdf file_size: 3817360 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '21' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 4103-4115 publication: Journal of Neuroscience publication_identifier: eissn: - '15292401' publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2020' ... --- _id: '7931' abstract: - lang: eng text: In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data. article_number: '8635' article_processing_charge: No article_type: original author: - first_name: Leonid A. full_name: Uroshlev, Leonid A. last_name: Uroshlev - first_name: Eldar T. full_name: Abdullaev, Eldar T. last_name: Abdullaev - first_name: Iren R. full_name: Umarova, Iren R. last_name: Umarova - first_name: Irina A. full_name: Il’Icheva, Irina A. last_name: Il’Icheva - first_name: Larisa A. full_name: Panchenko, Larisa A. last_name: Panchenko - first_name: Robert V. full_name: Polozov, Robert V. last_name: Polozov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Yury D. full_name: Nechipurenko, Yury D. last_name: Nechipurenko - first_name: Sergei L. full_name: Grokhovsky, Sergei L. last_name: Grokhovsky citation: ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1 apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1 chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1. ieee: L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020. ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635. mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1. short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020). date_created: 2020-06-07T22:00:51Z date_published: 2020-05-25T00:00:00Z date_updated: 2023-08-21T07:00:17Z day: '25' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41598-020-65406-1 external_id: isi: - '000560774200007' file: - access_level: open_access checksum: 099e51611a5b7ca04244d03b2faddf33 content_type: application/pdf creator: dernst date_created: 2020-06-08T06:27:32Z date_updated: 2020-07-14T12:48:05Z file_id: '7947' file_name: 2020_ScientificReports_Uroshlev.pdf file_size: 1001724 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A method for identification of the methylation level of CpG islands from NGS data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '7933' abstract: - lang: eng text: We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance. article_number: '184104 ' article_processing_charge: No article_type: original author: - first_name: Mikhail full_name: Maslov, Mikhail id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87 last_name: Maslov orcid: 0000-0003-4074-2570 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 citation: ama: Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 2020;101(18). doi:10.1103/PhysRevB.101.184104 apa: Maslov, M., Lemeshko, M., & Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.184104 chicago: Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.184104. ieee: M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” Physical Review B, vol. 101, no. 18. American Physical Society, 2020. ista: Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104. mla: Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:10.1103/PhysRevB.101.184104. short: M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020). date_created: 2020-06-07T22:00:52Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-21T07:05:15Z day: '01' department: - _id: MiLe doi: 10.1103/PhysRevB.101.184104 ec_funded: 1 external_id: arxiv: - '1912.03092' isi: - '000530754700003' intvolume: ' 101' isi: 1 issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.03092 month: '05' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Review B publication_identifier: eissn: - '24699969' issn: - '24699950' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Synthetic spin-orbit coupling mediated by a bosonic environment type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 101 year: '2020' ... --- _id: '7942' abstract: - lang: eng text: An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18. acknowledgement: M.H., Y.-T.H. and S.E.S. acknowledge support from the Royal Society, the Winton Programme for the Physics of Sustainability, EPSRC (studentship, grant no. EP/P024947/1 and EPSRC Strategic Equipment grant no. EP/M000524/1) and the European Research Council (grant no. 772891). S.E.S. acknowledges support from the Leverhulme Trust by way of the award of a Philip Leverhulme Prize. H.Z., J.W. and Z.Z. acknowledge support from the National Key Research and Development Program of China (grant no. 2016YFA0401704). A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by the National Science Foundation Cooperative Agreement no. DMR-1644779, the state of Florida and the US Department of Energy. Work performed by M.K.C., R.D.M. and N.H. was supported by the US DOE BES ‘Science of 100 T’ programme. article_processing_charge: No article_type: letter_note author: - first_name: Máté full_name: Hartstein, Máté last_name: Hartstein - first_name: Yu Te full_name: Hsu, Yu Te last_name: Hsu - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Juan full_name: Porras, Juan last_name: Porras - first_name: Toshinao full_name: Loew, Toshinao last_name: Loew - first_name: Matthieu Le full_name: Tacon, Matthieu Le last_name: Tacon - first_name: Huakun full_name: Zuo, Huakun last_name: Zuo - first_name: Jinhua full_name: Wang, Jinhua last_name: Wang - first_name: Zengwei full_name: Zhu, Zengwei last_name: Zhu - first_name: Mun K. full_name: Chan, Mun K. last_name: Chan - first_name: Ross D. full_name: Mcdonald, Ross D. last_name: Mcdonald - first_name: Gilbert G. full_name: Lonzarich, Gilbert G. last_name: Lonzarich - first_name: Bernhard full_name: Keimer, Bernhard last_name: Keimer - first_name: Suchitra E. full_name: Sebastian, Suchitra E. last_name: Sebastian - first_name: Neil full_name: Harrison, Neil last_name: Harrison citation: ama: Hartstein M, Hsu YT, Modic KA, et al. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 2020;16:841-847. doi:10.1038/s41567-020-0910-0 apa: Hartstein, M., Hsu, Y. T., Modic, K. A., Porras, J., Loew, T., Tacon, M. L., … Harrison, N. (2020). Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-0910-0 chicago: Hartstein, Máté, Yu Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0910-0. ieee: M. Hartstein et al., “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors,” Nature Physics, vol. 16. Springer Nature, pp. 841–847, 2020. ista: Hartstein M, Hsu YT, Modic KA, Porras J, Loew T, Tacon ML, Zuo H, Wang J, Zhu Z, Chan MK, Mcdonald RD, Lonzarich GG, Keimer B, Sebastian SE, Harrison N. 2020. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 16, 841–847. mla: Hartstein, Máté, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature Physics, vol. 16, Springer Nature, 2020, pp. 841–47, doi:10.1038/s41567-020-0910-0. short: M. Hartstein, Y.T. Hsu, K.A. Modic, J. Porras, T. Loew, M.L. Tacon, H. Zuo, J. Wang, Z. Zhu, M.K. Chan, R.D. Mcdonald, G.G. Lonzarich, B. Keimer, S.E. Sebastian, N. Harrison, Nature Physics 16 (2020) 841–847. date_created: 2020-06-07T22:00:56Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-21T07:06:49Z day: '01' department: - _id: KiMo doi: 10.1038/s41567-020-0910-0 external_id: arxiv: - '2005.14123' isi: - '000535464400005' intvolume: ' 16' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2005.14123 month: '08' oa: 1 oa_version: Preprint page: 841-847 publication: Nature Physics publication_identifier: eissn: - '17452481' issn: - '17452473' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '9708' relation: research_data status: public scopus_import: '1' status: public title: Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2020' ... --- _id: '7948' abstract: - lang: eng text: In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture. article_processing_charge: No article_type: original author: - first_name: A full_name: Maghiaoui, A last_name: Maghiaoui - first_name: E full_name: Bouguyon, E last_name: Bouguyon - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: F full_name: Perrine-Walker, F last_name: Perrine-Walker - first_name: C full_name: Alcon, C last_name: Alcon - first_name: G full_name: Krouk, G last_name: Krouk - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: P full_name: Nacry, P last_name: Nacry - first_name: A full_name: Gojon, A last_name: Gojon - first_name: L full_name: Bach, L last_name: Bach citation: ama: Maghiaoui A, Bouguyon E, Cuesta C, et al. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 2020;71(15):4480-4494. doi:10.1093/jxb/eraa242 apa: Maghiaoui, A., Bouguyon, E., Cuesta, C., Perrine-Walker, F., Alcon, C., Krouk, G., … Bach, L. (2020). The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa242 chicago: Maghiaoui, A, E Bouguyon, Candela Cuesta, F Perrine-Walker, C Alcon, G Krouk, Eva Benková, P Nacry, A Gojon, and L Bach. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa242. ieee: A. Maghiaoui et al., “The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate,” Journal of Experimental Botany, vol. 71, no. 15. Oxford University Press, pp. 4480–4494, 2020. ista: Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A, Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 71(15), 4480–4494. mla: Maghiaoui, A., et al. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany, vol. 71, no. 15, Oxford University Press, 2020, pp. 4480–94, doi:10.1093/jxb/eraa242. short: A. Maghiaoui, E. Bouguyon, C. Cuesta, F. Perrine-Walker, C. Alcon, G. Krouk, E. Benková, P. Nacry, A. Gojon, L. Bach, Journal of Experimental Botany 71 (2020) 4480–4494. date_created: 2020-06-08T10:10:28Z date_published: 2020-07-25T00:00:00Z date_updated: 2023-08-21T07:07:30Z day: '25' department: - _id: EvBe doi: 10.1093/jxb/eraa242 external_id: isi: - '000553127600013' pmid: - '32428238' intvolume: ' 71' isi: 1 issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.inrae.fr/hal-02619371 month: '07' oa: 1 oa_version: Submitted Version page: 4480-4494 pmid: 1 publication: Journal of Experimental Botany publication_identifier: eissn: - 1460-2431 issn: - 0022-0957 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 71 year: '2020' ... --- _id: '7940' abstract: - lang: eng text: We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18]. acknowledgement: Gufang Zhao is affiliated to IST Austria, Hausel group until July of 2018. Supported by the Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593 of the European Research Council. article_processing_charge: No article_type: original author: - first_name: Yaping full_name: Yang, Yaping id: 360D8648-F248-11E8-B48F-1D18A9856A87 last_name: Yang - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao citation: ama: Yang Y, Zhao G. The PBW theorem for affine Yangians. Transformation Groups. 2020;25:1371-1385. doi:10.1007/s00031-020-09572-6 apa: Yang, Y., & Zhao, G. (2020). The PBW theorem for affine Yangians. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-020-09572-6 chicago: Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups. Springer Nature, 2020. https://doi.org/10.1007/s00031-020-09572-6. ieee: Y. Yang and G. Zhao, “The PBW theorem for affine Yangians,” Transformation Groups, vol. 25. Springer Nature, pp. 1371–1385, 2020. ista: Yang Y, Zhao G. 2020. The PBW theorem for affine Yangians. Transformation Groups. 25, 1371–1385. mla: Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups, vol. 25, Springer Nature, 2020, pp. 1371–85, doi:10.1007/s00031-020-09572-6. short: Y. Yang, G. Zhao, Transformation Groups 25 (2020) 1371–1385. date_created: 2020-06-07T22:00:55Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-08-21T07:06:21Z day: '01' department: - _id: TaHa doi: 10.1007/s00031-020-09572-6 ec_funded: 1 external_id: arxiv: - '1804.04375' isi: - '000534874300003' intvolume: ' 25' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.04375 month: '12' oa: 1 oa_version: Preprint page: 1371-1385 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Transformation Groups publication_identifier: eissn: - 1531586X issn: - '10834362' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The PBW theorem for affine Yangians type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2020' ... --- _id: '9708' abstract: - lang: eng text: This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided. article_processing_charge: No author: - first_name: Mate full_name: Hartstein, Mate last_name: Hartstein - first_name: Yu-Te full_name: Hsu, Yu-Te last_name: Hsu - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Juan full_name: Porras, Juan last_name: Porras - first_name: Toshinao full_name: Loew, Toshinao last_name: Loew - first_name: Matthieu full_name: Le Tacon, Matthieu last_name: Le Tacon - first_name: Huakun full_name: Zuo, Huakun last_name: Zuo - first_name: Jinhua full_name: Wang, Jinhua last_name: Wang - first_name: Zengwei full_name: Zhu, Zengwei last_name: Zhu - first_name: Mun full_name: Chan, Mun last_name: Chan - first_name: Ross full_name: McDonald, Ross last_name: McDonald - first_name: Gilbert full_name: Lonzarich, Gilbert last_name: Lonzarich - first_name: Bernhard full_name: Keimer, Bernhard last_name: Keimer - first_name: Suchitra full_name: Sebastian, Suchitra last_name: Sebastian - first_name: Neil full_name: Harrison, Neil last_name: Harrison citation: ama: Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169 apa: Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169 chicago: Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169. ieee: M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020. ista: Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169. mla: Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169. short: M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020). date_created: 2021-07-23T10:00:35Z date_published: 2020-05-29T00:00:00Z date_updated: 2023-08-21T07:06:48Z day: '29' department: - _id: KiMo doi: 10.17863/cam.50169 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.17863/CAM.50169 month: '05' oa: 1 oa_version: Published Version publisher: Apollo - University of Cambridge related_material: record: - id: '7942' relation: used_in_publication status: public status: public title: Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '7955' abstract: - lang: eng text: Simple stochastic games are turn-based 2½-player games with a reachability objective. The basic question asks whether one player can ensure reaching a given target with at least a given probability. A natural extension is games with a conjunction of such conditions as objective. Despite a plethora of recent results on the analysis of systems with multiple objectives, the decidability of this basic problem remains open. In this paper, we present an algorithm approximating the Pareto frontier of the achievable values to a given precision. Moreover, it is an anytime algorithm, meaning it can be stopped at any time returning the current approximation and its error bound. acknowledgement: "Pranav Ashok, Jan Křetínský and Maximilian Weininger were funded in part by TUM IGSSE Grant 10.06 (PARSEC) and the German Research Foundation (DFG) project KR 4890/2-1\r\n“Statistical Unbounded Verification”. Krishnendu Chatterjee was supported by the ERC CoG 863818 (ForM-SMArt) and Vienna Science and Technology Fund (WWTF) Project ICT15-\r\n003. Tobias Winkler was supported by the RTG 2236 UnRAVe." article_processing_charge: No author: - first_name: Pranav full_name: Ashok, Pranav last_name: Ashok - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jan full_name: Kretinsky, Jan last_name: Kretinsky - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler citation: ama: 'Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. Approximating values of generalized-reachability stochastic games. In: Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . Association for Computing Machinery; 2020:102-115. doi:10.1145/3373718.3394761' apa: 'Ashok, P., Chatterjee, K., Kretinsky, J., Weininger, M., & Winkler, T. (2020). Approximating values of generalized-reachability stochastic games. In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 102–115). Saarbrücken, Germany: Association for Computing Machinery. https://doi.org/10.1145/3373718.3394761' chicago: Ashok, Pranav, Krishnendu Chatterjee, Jan Kretinsky, Maximilian Weininger, and Tobias Winkler. “Approximating Values of Generalized-Reachability Stochastic Games.” In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , 102–15. Association for Computing Machinery, 2020. https://doi.org/10.1145/3373718.3394761. ieee: P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, and T. Winkler, “Approximating values of generalized-reachability stochastic games,” in Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Saarbrücken, Germany, 2020, pp. 102–115. ista: 'Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. 2020. Approximating values of generalized-reachability stochastic games. Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . LICS: Symposium on Logic in Computer Science, 102–115.' mla: Ashok, Pranav, et al. “Approximating Values of Generalized-Reachability Stochastic Games.” Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–15, doi:10.1145/3373718.3394761. short: P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, T. Winkler, in:, Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–115. conference: end_date: 2020-07-11 location: Saarbrücken, Germany name: 'LICS: Symposium on Logic in Computer Science' start_date: 2020-07-08 date_created: 2020-06-14T22:00:48Z date_published: 2020-07-08T00:00:00Z date_updated: 2023-08-21T08:24:36Z day: '08' ddc: - '000' department: - _id: KrCh doi: 10.1145/3373718.3394761 ec_funded: 1 external_id: arxiv: - '1908.05106' isi: - '000665014900010' file: - access_level: open_access checksum: d0d0288fe991dd16cf5f02598b794240 content_type: application/pdf creator: dernst date_created: 2020-11-25T09:38:14Z date_updated: 2020-11-25T09:38:14Z file_id: '8804' file_name: 2020_LICS_Ashok.pdf file_size: 1001395 relation: main_file success: 1 file_date_updated: 2020-11-25T09:38:14Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 102-115 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: 'Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science ' publication_identifier: isbn: - '9781450371049' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Approximating values of generalized-reachability stochastic games type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '7957' abstract: - lang: eng text: "Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of\r\nmutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches." acknowledgement: We wish to thank Jasmin Morandell for generously sharing Figure 2. This work was supported by the European Research Council Starting Grant (grant 715508 ) to G.N. article_processing_charge: No article_type: original author: - first_name: Ilaria full_name: Parenti, Ilaria id: D93538B0-5B71-11E9-AC62-02EBE5697425 last_name: Parenti - first_name: Luis E full_name: Garcia Rabaneda, Luis E id: 33D1B084-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Rabaneda - first_name: Hanna full_name: Schön, Hanna id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425 last_name: Schön - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 2020;43(8):608-621. doi:10.1016/j.tins.2020.05.004' apa: 'Parenti, I., Garcia Rabaneda, L. E., Schön, H., & Novarino, G. (2020). Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2020.05.004' chicago: 'Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences. Elsevier, 2020. https://doi.org/10.1016/j.tins.2020.05.004.' ieee: 'I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental disorders: From genetics to functional pathways,” Trends in Neurosciences, vol. 43, no. 8. Elsevier, pp. 608–621, 2020.' ista: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8), 608–621.' mla: 'Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences, vol. 43, no. 8, Elsevier, 2020, pp. 608–21, doi:10.1016/j.tins.2020.05.004.' short: I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences 43 (2020) 608–621. date_created: 2020-06-14T22:00:49Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-21T08:25:31Z day: '01' ddc: - '570' department: - _id: GaNo doi: 10.1016/j.tins.2020.05.004 ec_funded: 1 external_id: isi: - '000553090600008' pmid: - '32507511' file: - access_level: open_access checksum: 67db0251b1d415ae59005f876fcf9e34 content_type: application/pdf creator: dernst date_created: 2020-11-25T09:43:40Z date_updated: 2020-11-25T09:43:40Z file_id: '8805' file_name: 2020_TrendsNeuroscience_Parenti.pdf file_size: 1439550 relation: main_file success: 1 file_date_updated: 2020-11-25T09:43:40Z has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 608-621 pmid: 1 project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models publication: Trends in Neurosciences publication_identifier: eissn: - 1878108X issn: - '01662236' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Neurodevelopmental disorders: From genetics to functional pathways' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 43 year: '2020' ... --- _id: '7960' abstract: - lang: eng text: Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces. acknowledgement: "We are very grateful to Pavel Paták for many helpful discussions and remarks. We also thank the referees for helpful comments, which greatly improved the presentation.\r\nThe project was supported by ERC Advanced Grant 320924. GK was also partially supported by NSF grant DMS1300120. The research stay of ZP at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF." article_processing_charge: No article_type: original author: - first_name: Gil full_name: Kalai, Gil last_name: Kalai - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 citation: ama: Kalai G, Patakova Z. Intersection patterns of planar sets. Discrete and Computational Geometry. 2020;64:304-323. doi:10.1007/s00454-020-00205-z apa: Kalai, G., & Patakova, Z. (2020). Intersection patterns of planar sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00205-z chicago: Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00205-z. ieee: G. Kalai and Z. Patakova, “Intersection patterns of planar sets,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 304–323, 2020. ista: Kalai G, Patakova Z. 2020. Intersection patterns of planar sets. Discrete and Computational Geometry. 64, 304–323. mla: Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 304–23, doi:10.1007/s00454-020-00205-z. short: G. Kalai, Z. Patakova, Discrete and Computational Geometry 64 (2020) 304–323. date_created: 2020-06-14T22:00:50Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-21T08:26:34Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-020-00205-z external_id: arxiv: - '1907.00885' isi: - '000537329400001' intvolume: ' 64' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.00885 month: '09' oa: 1 oa_version: Preprint page: 304-323 publication: Discrete and Computational Geometry publication_identifier: eissn: - '14320444' issn: - '01795376' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Intersection patterns of planar sets type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 64 year: '2020' ... --- _id: '7962' abstract: - lang: eng text: 'A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.' article_processing_charge: No article_type: original author: - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach - first_name: Bruce full_name: Reed, Bruce last_name: Reed - first_name: Yelena full_name: Yuditsky, Yelena last_name: Yuditsky citation: ama: Pach J, Reed B, Yuditsky Y. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 2020;63(4):888-917. doi:10.1007/s00454-020-00213-z apa: Pach, J., Reed, B., & Yuditsky, Y. (2020). Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00213-z chicago: Pach, János, Bruce Reed, and Yelena Yuditsky. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00213-z. ieee: J. Pach, B. Reed, and Y. Yuditsky, “Almost all string graphs are intersection graphs of plane convex sets,” Discrete and Computational Geometry, vol. 63, no. 4. Springer Nature, pp. 888–917, 2020. ista: Pach J, Reed B, Yuditsky Y. 2020. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 63(4), 888–917. mla: Pach, János, et al. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry, vol. 63, no. 4, Springer Nature, 2020, pp. 888–917, doi:10.1007/s00454-020-00213-z. short: J. Pach, B. Reed, Y. Yuditsky, Discrete and Computational Geometry 63 (2020) 888–917. date_created: 2020-06-14T22:00:51Z date_published: 2020-06-05T00:00:00Z date_updated: 2023-08-21T08:49:18Z day: '05' department: - _id: HeEd doi: 10.1007/s00454-020-00213-z external_id: arxiv: - '1803.06710' isi: - '000538229000001' intvolume: ' 63' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.06710 month: '06' oa: 1 oa_version: Preprint page: 888-917 project: - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize publication: Discrete and Computational Geometry publication_identifier: eissn: - '14320444' issn: - '01795376' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Almost all string graphs are intersection graphs of plane convex sets type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 63 year: '2020' ... --- _id: '13460' abstract: - lang: eng text: Binary interaction can cause stellar envelopes to be stripped, which significantly reduces the radius of the star. The orbit of a binary composed of a stripped star and a compact object can therefore be so tight that the gravitational radiation the system produces reaches frequencies accessible to the Laser Interferometer Space Antenna (LISA). Two such stripped stars in tight orbits with white dwarfs are known so far (ZTF J2130+4420 and CD−30°11223), but many more are expected to exist. These binaries provide important constraints for binary evolution models and may be used as LISA verification sources. We develop a Monte Carlo code that uses detailed evolutionary models to simulate the Galactic population of stripped stars in tight orbits with either neutron star or white dwarf companions. We predict 0–100 stripped star + white dwarf binaries and 0–4 stripped star + neutron star binaries with a signal-to-noise ratio >5 after 10 yr of observations with LISA. More than 90% of these binaries are expected to show large radial velocity shifts of ≳200 $\,\mathrm{km}\,{{\rm{s}}}^{-1}$, which are spectroscopically detectable. Photometric variability due to tidal deformation of the stripped star is also expected and has been observed in ZTF J2130+4420 and CD−30°11223. In addition, the stripped star + neutron star binaries are expected to be X-ray bright with LX ≳ 1033–1036 $\,\mathrm{erg}\,{{\rm{s}}}^{-1}$. Our results show that stripped star binaries are promising multimessenger sources for the upcoming electromagnetic and gravitational wave facilities. article_number: '56' article_processing_charge: No article_type: original author: - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: V. full_name: Korol, V. last_name: Korol - first_name: A. full_name: Lamberts, A. last_name: Lamberts - first_name: T. full_name: Kupfer, T. last_name: Kupfer - first_name: K. full_name: Breivik, K. last_name: Breivik - first_name: B. full_name: Ludwig, B. last_name: Ludwig - first_name: M. R. full_name: Drout, M. R. last_name: Drout citation: ama: 'Götberg YLL, Korol V, Lamberts A, et al. Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. 2020;904(1). doi:10.3847/1538-4357/abbda5' apa: 'Götberg, Y. L. L., Korol, V., Lamberts, A., Kupfer, T., Breivik, K., Ludwig, B., & Drout, M. R. (2020). Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/abbda5' chicago: 'Götberg, Ylva Louise Linsdotter, V. Korol, A. Lamberts, T. Kupfer, K. Breivik, B. Ludwig, and M. R. Drout. “Stars Stripped in Binaries: The Living Gravitational-Wave Sources.” The Astrophysical Journal. American Astronomical Society, 2020. https://doi.org/10.3847/1538-4357/abbda5.' ieee: 'Y. L. L. Götberg et al., “Stars stripped in binaries: The living gravitational-wave sources,” The Astrophysical Journal, vol. 904, no. 1. American Astronomical Society, 2020.' ista: 'Götberg YLL, Korol V, Lamberts A, Kupfer T, Breivik K, Ludwig B, Drout MR. 2020. Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical Journal. 904(1), 56.' mla: 'Götberg, Ylva Louise Linsdotter, et al. “Stars Stripped in Binaries: The Living Gravitational-Wave Sources.” The Astrophysical Journal, vol. 904, no. 1, 56, American Astronomical Society, 2020, doi:10.3847/1538-4357/abbda5.' short: Y.L.L. Götberg, V. Korol, A. Lamberts, T. Kupfer, K. Breivik, B. Ludwig, M.R. Drout, The Astrophysical Journal 904 (2020). date_created: 2023-08-03T10:12:07Z date_published: 2020-11-20T00:00:00Z date_updated: 2023-08-21T11:32:40Z day: '20' doi: 10.3847/1538-4357/abbda5 extern: '1' external_id: arxiv: - '2006.07382' intvolume: ' 904' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2006.07382 month: '11' oa: 1 oa_version: Preprint publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Stars stripped in binaries: The living gravitational-wave sources' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 904 year: '2020' ... --- _id: '7999' abstract: - lang: eng text: 'Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal. ' article_number: '2865' article_processing_charge: No article_type: original author: - first_name: D full_name: Trejo Banos, D last_name: Trejo Banos - first_name: DL full_name: McCartney, DL last_name: McCartney - first_name: M full_name: Patxot, M last_name: Patxot - first_name: L full_name: Anchieri, L last_name: Anchieri - first_name: T full_name: Battram, T last_name: Battram - first_name: C full_name: Christiansen, C last_name: Christiansen - first_name: R full_name: Costeira, R last_name: Costeira - first_name: RM full_name: Walker, RM last_name: Walker - first_name: SW full_name: Morris, SW last_name: Morris - first_name: A full_name: Campbell, A last_name: Campbell - first_name: Q full_name: Zhang, Q last_name: Zhang - first_name: DJ full_name: Porteous, DJ last_name: Porteous - first_name: AF full_name: McRae, AF last_name: McRae - first_name: NR full_name: Wray, NR last_name: Wray - first_name: PM full_name: Visscher, PM last_name: Visscher - first_name: CS full_name: Haley, CS last_name: Haley - first_name: KL full_name: Evans, KL last_name: Evans - first_name: IJ full_name: Deary, IJ last_name: Deary - first_name: AM full_name: McIntosh, AM last_name: McIntosh - first_name: G full_name: Hemani, G last_name: Hemani - first_name: JT full_name: Bell, JT last_name: Bell - first_name: RE full_name: Marioni, RE last_name: Marioni - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Trejo Banos D, McCartney D, Patxot M, et al. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-16520-1 apa: Trejo Banos, D., McCartney, D., Patxot, M., Anchieri, L., Battram, T., Christiansen, C., … Robinson, M. R. (2020). Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16520-1 chicago: Trejo Banos, D, DL McCartney, M Patxot, L Anchieri, T Battram, C Christiansen, R Costeira, et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16520-1. ieee: D. Trejo Banos et al., “Bayesian reassessment of the epigenetic architecture of complex traits,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Trejo Banos D, McCartney D, Patxot M, Anchieri L, Battram T, Christiansen C, Costeira R, Walker R, Morris S, Campbell A, Zhang Q, Porteous D, McRae A, Wray N, Visscher P, Haley C, Evans K, Deary I, McIntosh A, Hemani G, Bell J, Marioni R, Robinson MR. 2020. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 11, 2865. mla: Trejo Banos, D., et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications, vol. 11, 2865, Springer Nature, 2020, doi:10.1038/s41467-020-16520-1. short: D. Trejo Banos, D. McCartney, M. Patxot, L. Anchieri, T. Battram, C. Christiansen, R. Costeira, R. Walker, S. Morris, A. Campbell, Q. Zhang, D. Porteous, A. McRae, N. Wray, P. Visscher, C. Haley, K. Evans, I. Deary, A. McIntosh, G. Hemani, J. Bell, R. Marioni, M.R. Robinson, Nature Communications 11 (2020). date_created: 2020-06-22T11:18:25Z date_published: 2020-06-08T00:00:00Z date_updated: 2023-08-22T07:13:09Z day: '08' ddc: - '570' department: - _id: MaRo doi: 10.1038/s41467-020-16520-1 external_id: isi: - '000541702400004' pmid: - '32513961' file: - access_level: open_access checksum: 4c96babd4cfb0d153334f6c598c0bacb content_type: application/pdf creator: dernst date_created: 2020-06-22T11:24:32Z date_updated: 2020-07-14T12:48:07Z file_id: '8000' file_name: 2020_NatureComm_Bayesian.pdf file_size: 1475657 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-020-19099-9 scopus_import: '1' status: public title: Bayesian reassessment of the epigenetic architecture of complex traits tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '7995' abstract: - lang: eng text: When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. acknowledgement: We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747. article_processing_charge: No article_type: original author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027 apa: Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027 chicago: Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027. ieee: S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020. ista: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497. mla: Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027. short: S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497. date_created: 2020-06-22T09:14:21Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:13:38Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.14027 ec_funded: 1 external_id: isi: - '000539780800001' file: - access_level: open_access checksum: 56235bf1e2a9e25f96196bb13b6b754d content_type: application/pdf creator: dernst date_created: 2020-11-25T10:49:48Z date_updated: 2020-11-25T10:49:48Z file_id: '8808' file_name: 2020_Evolution_Perini.pdf file_size: 1080810 relation: main_file success: 1 file_date_updated: 2020-11-25T10:49:48Z has_accepted_license: '1' intvolume: ' 74' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1482-1497 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Evolution publication_identifier: eissn: - '15585646' issn: - '00143820' publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '8809' relation: research_data status: public scopus_import: '1' status: public title: Assortative mating, sexual selection, and their consequences for gene flow in Littorina tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 74 year: '2020' ... --- _id: '8809' abstract: - lang: eng text: When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. article_processing_charge: No author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Marina full_name: Rafajlovic, Marina last_name: Rafajlovic - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger full_name: Butlin, Roger last_name: Butlin citation: ama: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn' apa: 'Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn' chicago: 'Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.' ieee: 'S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.' ista: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.' mla: 'Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.' short: S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020). date_created: 2020-11-25T11:07:25Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:13:37Z day: '01' department: - _id: NiBa doi: 10.5061/dryad.qrfj6q5cn has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.qrfj6q5cn month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '7995' relation: used_in_publication status: public status: public title: 'Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '8001' abstract: - lang: eng text: Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network. acknowledged_ssus: - _id: SSU acknowledgement: This project received funding from the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation Program (grant agreement 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung ( Z 312-B27 , Wittgenstein award to P.J. and V 739-B27 to C.B.-M.). We thank Drs. Jozsef Csicsvari, Jose Guzman, Erwin Neher, and Ryuichi Shigemoto for commenting on earlier versions of the manuscript. We are grateful to Walter Kaufmann, Daniel Gütl, and Vanessa Zheden for EM training; Alois Schlögl for programming; Florian Marr for excellent technical assistance and cell reconstruction; Christina Altmutter for technical help; Eleftheria Kralli-Beller for manuscript editing; Taija Makinen for providing the Prox1-CreERT2 mouse line; and the Scientific Service Units of IST Austria for support. article_processing_charge: No article_type: original author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vandael DH, Borges Merjane C, Zhang X, Jonas PM. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 2020;107(3):509-521. doi:10.1016/j.neuron.2020.05.013 apa: Vandael, D. H., Borges Merjane, C., Zhang, X., & Jonas, P. M. (2020). Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.05.013 chicago: Vandael, David H, Carolina Borges Merjane, Xiaomin Zhang, and Peter M Jonas. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.013. ieee: D. H. Vandael, C. Borges Merjane, X. Zhang, and P. M. Jonas, “Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation,” Neuron, vol. 107, no. 3. Elsevier, pp. 509–521, 2020. ista: Vandael DH, Borges Merjane C, Zhang X, Jonas PM. 2020. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 107(3), 509–521. mla: Vandael, David H., et al. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron, vol. 107, no. 3, Elsevier, 2020, pp. 509–21, doi:10.1016/j.neuron.2020.05.013. short: D.H. Vandael, C. Borges Merjane, X. Zhang, P.M. Jonas, Neuron 107 (2020) 509–521. date_created: 2020-06-22T13:29:05Z date_published: 2020-08-05T00:00:00Z date_updated: 2023-08-22T07:45:25Z day: '05' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2020.05.013 ec_funded: 1 external_id: isi: - '000556135600004' pmid: - '32492366' file: - access_level: open_access checksum: 4030b2be0c9625d54694a1e9fb00305e content_type: application/pdf creator: dernst date_created: 2020-11-25T11:23:02Z date_updated: 2020-11-25T11:23:02Z file_id: '8811' file_name: 2020_Neuron_Vandael.pdf file_size: 4390833 relation: main_file success: 1 file_date_updated: 2020-11-25T11:23:02Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '08' oa: 1 oa_version: Published Version page: 509-521 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 2696E7FE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: V00739 name: Structural plasticity at mossy fiber-CA3 synapses publication: Neuron publication_identifier: eissn: - '10974199' issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/possible-physical-trace-of-short-term-memory-found/ scopus_import: '1' status: public title: Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2020' ... --- _id: '13998' abstract: - lang: eng text: The interaction of strong near-infrared (NIR) laser pulses with wide-bandgap dielectrics produces high harmonics in the extreme ultraviolet (XUV) wavelength range. These observations have opened up the possibility of attosecond metrology in solids, which would benefit from a precise measurement of the emission times of individual harmonics with respect to the NIR laser field. Here we show that, when high-harmonics are detected from the input surface of a magnesium oxide crystal, a bichromatic probing of the XUV emission shows a clear synchronization largely consistent with a semiclassical model of electron–hole recollisions in bulk solids. On the other hand, the bichromatic spectrogram of harmonics originating from the exit surface of the 200 μm-thick crystal is strongly modified, indicating the influence of laser field distortions during propagation. Our tracking of sub-cycle electron and hole re-collisions at XUV energies is relevant to the development of solid-state sources of attosecond pulses. article_number: '144003' article_processing_charge: No article_type: original author: - first_name: Giulio full_name: Vampa, Giulio last_name: Vampa - first_name: Jian full_name: Lu, Jian last_name: Lu - first_name: Yong Sing full_name: You, Yong Sing last_name: You - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Mengxi full_name: Wu, Mengxi last_name: Wu - first_name: Hanzhe full_name: Liu, Hanzhe last_name: Liu - first_name: Kenneth J full_name: Schafer, Kenneth J last_name: Schafer - first_name: Mette B full_name: Gaarde, Mette B last_name: Gaarde - first_name: David A full_name: Reis, David A last_name: Reis - first_name: Shambhu full_name: Ghimire, Shambhu last_name: Ghimire citation: ama: 'Vampa G, Lu J, You YS, et al. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. 2020;53(14). doi:10.1088/1361-6455/ab8e56' apa: 'Vampa, G., Lu, J., You, Y. S., Baykusheva, D. R., Wu, M., Liu, H., … Ghimire, S. (2020). Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/1361-6455/ab8e56' chicago: 'Vampa, Giulio, Jian Lu, Yong Sing You, Denitsa Rangelova Baykusheva, Mengxi Wu, Hanzhe Liu, Kenneth J Schafer, Mette B Gaarde, David A Reis, and Shambhu Ghimire. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2020. https://doi.org/10.1088/1361-6455/ab8e56.' ieee: 'G. Vampa et al., “Attosecond synchronization of extreme ultraviolet high harmonics from crystals,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 53, no. 14. IOP Publishing, 2020.' ista: 'Vampa G, Lu J, You YS, Baykusheva DR, Wu M, Liu H, Schafer KJ, Gaarde MB, Reis DA, Ghimire S. 2020. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. 53(14), 144003.' mla: 'Vampa, Giulio, et al. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 53, no. 14, 144003, IOP Publishing, 2020, doi:10.1088/1361-6455/ab8e56.' short: 'G. Vampa, J. Lu, Y.S. You, D.R. Baykusheva, M. Wu, H. Liu, K.J. Schafer, M.B. Gaarde, D.A. Reis, S. Ghimire, Journal of Physics B: Atomic, Molecular and Optical Physics 53 (2020).' date_created: 2023-08-09T13:09:51Z date_published: 2020-06-17T00:00:00Z date_updated: 2023-08-22T07:36:36Z day: '17' doi: 10.1088/1361-6455/ab8e56 extern: '1' external_id: arxiv: - '2001.09951' intvolume: ' 53' issue: '14' keyword: - Condensed Matter Physics - Atomic and Molecular Physics - and Optics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2001.09951 month: '06' oa: 1 oa_version: Preprint publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics' publication_identifier: eissn: - 1361-6455 issn: - 0953-4075 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Attosecond synchronization of extreme ultraviolet high harmonics from crystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2020' ... --- _id: '13999' abstract: - lang: eng text: Attosecond chronoscopy has revealed small but measurable delays in photoionization, characterized by the ejection of an electron on absorption of a single photon. Ionization-delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect, resonances, electron correlations and transport. However, extending this approach to molecules presents challenges, such as identifying the correct ionization channels and the effect of the anisotropic molecular landscape on the measured delays. Here, we measure ionization delays from ethyl iodide around a giant dipole resonance. By using the theoretical value for the iodine atom as a reference, we disentangle the contribution from the functional ethyl group, which is responsible for the characteristic chemical reactivity of a molecule. We find a substantial additional delay caused by the presence of a functional group, which encodes the effect of the molecular potential on the departing electron. Such information is inaccessible to the conventional approach of measuring photoionization cross-sections. The results establish ionization-delay measurements as a valuable tool in investigating the electronic properties of molecules. article_processing_charge: No article_type: original author: - first_name: Shubhadeep full_name: Biswas, Shubhadeep last_name: Biswas - first_name: Benjamin full_name: Förg, Benjamin last_name: Förg - first_name: Lisa full_name: Ortmann, Lisa last_name: Ortmann - first_name: Johannes full_name: Schötz, Johannes last_name: Schötz - first_name: Wolfgang full_name: Schweinberger, Wolfgang last_name: Schweinberger - first_name: Tomáš full_name: Zimmermann, Tomáš last_name: Zimmermann - first_name: Liangwen full_name: Pi, Liangwen last_name: Pi - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Hafiz A. full_name: Masood, Hafiz A. last_name: Masood - first_name: Ioannis full_name: Liontos, Ioannis last_name: Liontos - first_name: Amgad M. full_name: Kamal, Amgad M. last_name: Kamal - first_name: Nora G. full_name: Kling, Nora G. last_name: Kling - first_name: Abdullah F. full_name: Alharbi, Abdullah F. last_name: Alharbi - first_name: Meshaal full_name: Alharbi, Meshaal last_name: Alharbi - first_name: Abdallah M. full_name: Azzeer, Abdallah M. last_name: Azzeer - first_name: Gregor full_name: Hartmann, Gregor last_name: Hartmann - first_name: Hans J. full_name: Wörner, Hans J. last_name: Wörner - first_name: Alexandra S. full_name: Landsman, Alexandra S. last_name: Landsman - first_name: Matthias F. full_name: Kling, Matthias F. last_name: Kling citation: ama: Biswas S, Förg B, Ortmann L, et al. Probing molecular environment through photoemission delays. Nature Physics. 2020;16(7):778-783. doi:10.1038/s41567-020-0887-8 apa: Biswas, S., Förg, B., Ortmann, L., Schötz, J., Schweinberger, W., Zimmermann, T., … Kling, M. F. (2020). Probing molecular environment through photoemission delays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-0887-8 chicago: Biswas, Shubhadeep, Benjamin Förg, Lisa Ortmann, Johannes Schötz, Wolfgang Schweinberger, Tomáš Zimmermann, Liangwen Pi, et al. “Probing Molecular Environment through Photoemission Delays.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0887-8. ieee: S. Biswas et al., “Probing molecular environment through photoemission delays,” Nature Physics, vol. 16, no. 7. Springer Nature, pp. 778–783, 2020. ista: Biswas S, Förg B, Ortmann L, Schötz J, Schweinberger W, Zimmermann T, Pi L, Baykusheva DR, Masood HA, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM, Hartmann G, Wörner HJ, Landsman AS, Kling MF. 2020. Probing molecular environment through photoemission delays. Nature Physics. 16(7), 778–783. mla: Biswas, Shubhadeep, et al. “Probing Molecular Environment through Photoemission Delays.” Nature Physics, vol. 16, no. 7, Springer Nature, 2020, pp. 778–83, doi:10.1038/s41567-020-0887-8. short: S. Biswas, B. Förg, L. Ortmann, J. Schötz, W. Schweinberger, T. Zimmermann, L. Pi, D.R. Baykusheva, H.A. Masood, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi, A.M. Azzeer, G. Hartmann, H.J. Wörner, A.S. Landsman, M.F. Kling, Nature Physics 16 (2020) 778–783. date_created: 2023-08-09T13:10:07Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:38:04Z day: '01' doi: 10.1038/s41567-020-0887-8 extern: '1' intvolume: ' 16' issue: '7' keyword: - General Physics and Astronomy language: - iso: eng month: '07' oa_version: None page: 778-783 publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Probing molecular environment through photoemission delays type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '8038' abstract: - lang: eng text: Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications. article_number: '034011' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: M. full_name: Kalaee, M. last_name: Kalaee - first_name: R. full_name: Norte, R. last_name: Norte - first_name: A. full_name: Pitanti, A. last_name: Pitanti - first_name: O. full_name: Painter, O. last_name: Painter citation: ama: Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 2020;5(3). doi:10.1088/2058-9565/ab8dce apa: Fink, J. M., Kalaee, M., Norte, R., Pitanti, A., & Painter, O. (2020). Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab8dce chicago: Fink, Johannes M, M. Kalaee, R. Norte, A. Pitanti, and O. Painter. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab8dce. ieee: J. M. Fink, M. Kalaee, R. Norte, A. Pitanti, and O. Painter, “Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator,” Quantum Science and Technology, vol. 5, no. 3. IOP Publishing, 2020. ista: Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. 2020. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 5(3), 034011. mla: Fink, Johannes M., et al. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology, vol. 5, no. 3, 034011, IOP Publishing, 2020, doi:10.1088/2058-9565/ab8dce. short: J.M. Fink, M. Kalaee, R. Norte, A. Pitanti, O. Painter, Quantum Science and Technology 5 (2020). date_created: 2020-06-29T07:59:35Z date_published: 2020-05-25T00:00:00Z date_updated: 2023-08-22T07:49:01Z day: '25' ddc: - '530' department: - _id: JoFi doi: 10.1088/2058-9565/ab8dce ec_funded: 1 external_id: isi: - '000539300800001' file: - access_level: open_access checksum: 8f25f05053f511f892ae8fa93f341e61 content_type: application/pdf creator: cziletti date_created: 2020-06-30T10:29:10Z date_updated: 2020-07-14T12:48:08Z file_id: '8072' file_name: 2020_QuantumSciTechnol_Fink.pdf file_size: 2600967 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 2622978C-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices publication: Quantum Science and Technology publication_identifier: eissn: - '20589565' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2020' ... --- _id: '8037' abstract: - lang: eng text: 'Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics.' article_number: '3105' article_processing_charge: No article_type: original author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Booshini full_name: Fernando, Booshini last_name: Fernando - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Lukacisinova M, Fernando B, Bollenbach MT. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-16932-z apa: Lukacisinova, M., Fernando, B., & Bollenbach, M. T. (2020). Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16932-z chicago: Lukacisinova, Marta, Booshini Fernando, and Mark Tobias Bollenbach. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16932-z. ieee: M. Lukacisinova, B. Fernando, and M. T. Bollenbach, “Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Lukacisinova M, Fernando B, Bollenbach MT. 2020. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 11, 3105. mla: Lukacisinova, Marta, et al. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications, vol. 11, 3105, Springer Nature, 2020, doi:10.1038/s41467-020-16932-z. short: M. Lukacisinova, B. Fernando, M.T. Bollenbach, Nature Communications 11 (2020). date_created: 2020-06-29T07:59:35Z date_published: 2020-06-19T00:00:00Z date_updated: 2023-08-22T07:48:30Z day: '19' ddc: - '570' doi: 10.1038/s41467-020-16932-z extern: '1' external_id: isi: - '000545685100002' pmid: - '32561723' file: - access_level: open_access checksum: 4f5f49d63add331d5eb8a2bae477b396 content_type: application/pdf creator: cziletti date_created: 2020-06-30T09:58:50Z date_updated: 2020-07-14T12:48:08Z file_id: '8071' file_name: 2020_NatureComm_Lukacisinova.pdf file_size: 1546491 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8040' abstract: - lang: eng text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form—a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I. article_processing_charge: No article_type: original author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun Kit full_name: Chan, Chun Kit last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M. R. full_name: Gunner, M. R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan CK, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 2020;142(20):9220-9230. doi:10.1021/jacs.9b13450 apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b13450 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450. ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I,” Journal of the American Chemical Society, vol. 142, no. 20. American Chemical Society, pp. 9220–9230, 2020. ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 142(20), 9220–9230. mla: Gupta, Chitrak, et al. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society, vol. 142, no. 20, American Chemical Society, 2020, pp. 9220–30, doi:10.1021/jacs.9b13450. short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, Journal of the American Chemical Society 142 (2020) 9220–9230. date_created: 2020-06-29T07:59:35Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:38Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450 external_id: isi: - '000537415600020' pmid: - '32347721' intvolume: ' 142' isi: 1 issue: '20' language: - iso: eng month: '05' oa_version: None page: 9220-9230 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - '15205126' issn: - '00027863' publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '9326' relation: research_data status: public - id: '9713' relation: research_data status: public - id: '9878' relation: research_data status: public scopus_import: '1' status: public title: Charge transfer and chemo-mechanical coupling in respiratory complex I type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 142 year: '2020' ... --- _id: '8036' abstract: - lang: eng text: When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves. article_number: '112' article_processing_charge: No article_type: original author: - first_name: Ylona full_name: Collard, Ylona last_name: Collard - first_name: Galien M full_name: Grosjean, Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X - first_name: Nicolas full_name: Vandewalle, Nicolas last_name: Vandewalle citation: ama: Collard Y, Grosjean GM, Vandewalle N. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 2020;3. doi:10.1038/s42005-020-0380-9 apa: Collard, Y., Grosjean, G. M., & Vandewalle, N. (2020). Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-0380-9 chicago: Collard, Ylona, Galien M Grosjean, and Nicolas Vandewalle. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-0380-9. ieee: Y. Collard, G. M. Grosjean, and N. Vandewalle, “Magnetically powered metachronal waves induce locomotion in self-assemblies,” Communications Physics, vol. 3. Springer Nature, 2020. ista: Collard Y, Grosjean GM, Vandewalle N. 2020. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 3, 112. mla: Collard, Ylona, et al. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics, vol. 3, 112, Springer Nature, 2020, doi:10.1038/s42005-020-0380-9. short: Y. Collard, G.M. Grosjean, N. Vandewalle, Communications Physics 3 (2020). date_created: 2020-06-29T07:59:35Z date_published: 2020-06-19T00:00:00Z date_updated: 2023-08-22T07:47:30Z day: '19' ddc: - '530' department: - _id: ScWa doi: 10.1038/s42005-020-0380-9 ec_funded: 1 external_id: isi: - '000543328000002' file: - access_level: open_access checksum: ed984f7a393f19140b5279a54a3336ad content_type: application/pdf creator: cziletti date_created: 2020-06-29T13:21:24Z date_updated: 2020-07-14T12:48:08Z file_id: '8045' file_name: 2020_CommunicationsPhysics_Collard.pdf file_size: 1907821 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 3' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Communications Physics publication_identifier: eissn: - '23993650' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Magnetically powered metachronal waves induce locomotion in self-assemblies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 3 year: '2020' ... --- _id: '8043' abstract: - lang: eng text: With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain. acknowledgement: The authors thank S. Zammert and B. Budanur for useful discussions. J. F. Gibson is gratefully acknowledged for the development and the maintenance of the code Channelflow. Y.D. would like to thank P. Schlatter and D. S. Henningson for an early collaboration on a similar topic in the case of plane Couette flow during the years 2008–2013. article_number: A7 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Chaitanya S full_name: Paranjape, Chaitanya S id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87 last_name: Paranjape - first_name: Yohann full_name: Duguet, Yohann last_name: Duguet - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Paranjape CS, Duguet Y, Hof B. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 2020;897. doi:10.1017/jfm.2020.322 apa: Paranjape, C. S., Duguet, Y., & Hof, B. (2020). Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2020.322 chicago: Paranjape, Chaitanya S, Yohann Duguet, and Björn Hof. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2020. https://doi.org/10.1017/jfm.2020.322. ieee: C. S. Paranjape, Y. Duguet, and B. Hof, “Oblique stripe solutions of channel flow,” Journal of Fluid Mechanics, vol. 897. Cambridge University Press, 2020. ista: Paranjape CS, Duguet Y, Hof B. 2020. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 897, A7. mla: Paranjape, Chaitanya S., et al. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics, vol. 897, A7, Cambridge University Press, 2020, doi:10.1017/jfm.2020.322. short: C.S. Paranjape, Y. Duguet, B. Hof, Journal of Fluid Mechanics 897 (2020). date_created: 2020-06-29T07:59:35Z date_published: 2020-08-25T00:00:00Z date_updated: 2023-08-22T07:48:02Z day: '25' ddc: - '530' department: - _id: BjHo doi: 10.1017/jfm.2020.322 external_id: isi: - '000539132300001' file: - access_level: open_access checksum: 3f487bf6d9286787096306eaa18702e8 content_type: application/pdf creator: cziletti date_created: 2020-06-30T08:37:37Z date_updated: 2020-07-14T12:48:08Z file_id: '8070' file_name: 2020_JournalOfFluidMech_Paranjape.pdf file_size: 767873 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 897' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '08' oa: 1 oa_version: Published Version publication: Journal of Fluid Mechanics publication_identifier: eissn: - '14697645' issn: - '00221120' publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Oblique stripe solutions of channel flow tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 897 year: '2020' ... --- _id: '9326' abstract: - lang: eng text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I. article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun full_name: Chan, Chun last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M. R. full_name: Gunner, M. R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002 apa: Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002. ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020. ista: Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002. mla: Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002. short: C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-04-14T12:05:20Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:37Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s002 license: https://creativecommons.org/licenses/by-nc/4.0/ main_file_link: - open_access: '1' month: '05' oa: 1 oa_version: Published Version publisher: American Chemical Society related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Charge transfer and chemo-mechanical coupling in respiratory complex I tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8042' abstract: - lang: eng text: We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N. article_processing_charge: No article_type: original author: - first_name: Chiara full_name: Boccato, Chiara id: 342E7E22-F248-11E8-B48F-1D18A9856A87 last_name: Boccato - first_name: Christian full_name: Brennecke, Christian last_name: Brennecke - first_name: Serena full_name: Cenatiempo, Serena last_name: Cenatiempo - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein citation: ama: Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966 apa: Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/966 chicago: Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society. European Mathematical Society, 2020. https://doi.org/10.4171/JEMS/966. ieee: C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum of Bose gases interacting through singular potentials,” Journal of the European Mathematical Society, vol. 22, no. 7. European Mathematical Society, pp. 2331–2403, 2020. ista: Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 22(7), 2331–2403. mla: Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society, vol. 22, no. 7, European Mathematical Society, 2020, pp. 2331–403, doi:10.4171/JEMS/966. short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403. date_created: 2020-06-29T07:59:35Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:47:04Z day: '01' department: - _id: RoSe doi: 10.4171/JEMS/966 external_id: arxiv: - '1704.04819' isi: - '000548174700006' intvolume: ' 22' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.04819 month: '07' oa: 1 oa_version: Preprint page: 2331-2403 publication: Journal of the European Mathematical Society publication_identifier: issn: - '14359855' publication_status: published publisher: European Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: The excitation spectrum of Bose gases interacting through singular potentials type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2020' ... --- _id: '9713' abstract: - lang: eng text: Additional analyses of the trajectories article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun Kit full_name: Chan, Chun Kit last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M.R. full_name: Gunner, M.R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001 apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001. ieee: C. Gupta et al., “Supporting information.” American Chemical Society , 2020. ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001. mla: Gupta, Chitrak, et al. Supporting Information. American Chemical Society , 2020, doi:10.1021/jacs.9b13450.s001. short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-07-23T12:02:39Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:38Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s001 month: '05' oa_version: Published Version publisher: 'American Chemical Society ' related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Supporting information type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9878' article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun Kit full_name: Chan, Chun Kit last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M.R. full_name: Gunner, M.R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan CK, et al. Movies. 2020. doi:10.1021/jacs.9b13450.s002 apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Movies. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002. ieee: C. Gupta et al., “Movies.” American Chemical Society, 2020. ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Movies, American Chemical Society, 10.1021/jacs.9b13450.s002. mla: Gupta, Chitrak, et al. Movies. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002. short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-08-11T09:18:54Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:38Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s002 month: '05' oa_version: Published Version publisher: American Chemical Society related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Movies type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '8093' abstract: - lang: eng text: "Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy." acknowledgement: "The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia." article_processing_charge: No article_type: original author: - first_name: Andreas full_name: Hippe, Andreas last_name: Hippe - first_name: Stephan Alexander full_name: Braun, Stephan Alexander last_name: Braun - first_name: Péter full_name: Oláh, Péter last_name: Oláh - first_name: Peter Arne full_name: Gerber, Peter Arne last_name: Gerber - first_name: Anne full_name: Schorr, Anne last_name: Schorr - first_name: Stephan full_name: Seeliger, Stephan last_name: Seeliger - first_name: Stephanie full_name: Holtz, Stephanie last_name: Holtz - first_name: Katharina full_name: Jannasch, Katharina last_name: Jannasch - first_name: Andor full_name: Pivarcsi, Andor last_name: Pivarcsi - first_name: Bettina full_name: Buhren, Bettina last_name: Buhren - first_name: Holger full_name: Schrumpf, Holger last_name: Schrumpf - first_name: Andreas full_name: Kislat, Andreas last_name: Kislat - first_name: Erich full_name: Bünemann, Erich last_name: Bünemann - first_name: Martin full_name: Steinhoff, Martin last_name: Steinhoff - first_name: Jens full_name: Fischer, Jens last_name: Fischer - first_name: Sérgio A. full_name: Lira, Sérgio A. last_name: Lira - first_name: Petra full_name: Boukamp, Petra last_name: Boukamp - first_name: Peter full_name: Hevezi, Peter last_name: Hevezi - first_name: Nikolas Hendrik full_name: Stoecklein, Nikolas Hendrik last_name: Stoecklein - first_name: Thomas full_name: Hoffmann, Thomas last_name: Hoffmann - first_name: Frauke full_name: Alves, Frauke last_name: Alves - first_name: Jonathan full_name: Sleeman, Jonathan last_name: Sleeman - first_name: Thomas full_name: Bauer, Thomas last_name: Bauer - first_name: Jörg full_name: Klufa, Jörg last_name: Klufa - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Maria full_name: Sibilia, Maria last_name: Sibilia - first_name: Albert full_name: Zlotnik, Albert last_name: Zlotnik - first_name: Anja full_name: Müller-Homey, Anja last_name: Müller-Homey - first_name: Bernhard full_name: Homey, Bernhard last_name: Homey citation: ama: Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 2020;123:942-954. doi:10.1038/s41416-020-0943-2 apa: Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2 chicago: Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer. Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2. ieee: A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” British Journal of Cancer, vol. 123. Springer Nature, pp. 942–954, 2020. ista: Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954. mla: Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature, 2020, pp. 942–54, doi:10.1038/s41416-020-0943-2. short: A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954. date_created: 2020-07-05T22:00:46Z date_published: 2020-09-15T00:00:00Z date_updated: 2023-08-22T07:51:12Z day: '15' ddc: - '610' department: - _id: SiHi doi: 10.1038/s41416-020-0943-2 external_id: isi: - '000544152500001' pmid: - '32601464' file: - access_level: open_access checksum: 05a8e65d49c3f5b8e37ac4afe68287e2 content_type: application/pdf creator: cchlebak date_created: 2021-12-02T12:35:12Z date_updated: 2021-12-02T12:35:12Z file_id: '10398' file_name: 2020_BrJournalCancer_Hippe.pdf file_size: 3620691 relation: main_file success: 1 file_date_updated: 2021-12-02T12:35:12Z has_accepted_license: '1' intvolume: ' 123' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 942-954 pmid: 1 publication: British Journal of Cancer publication_identifier: eissn: - 1532-1827 issn: - 0007-0920 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41416-021-01563-y record: - id: '10170' relation: later_version status: deleted scopus_import: '1' status: public title: EGFR/Ras-induced CCL20 production modulates the tumour microenvironment tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 123 year: '2020' ... --- _id: '8091' abstract: - lang: eng text: In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level. acknowledgement: "Open access funding provided by Institute of Science and Technology (IST Austria).\r\nThe work of R.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. " article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 2020;181:448-464. doi:10.1007/s10955-020-02586-0 apa: Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-020-02586-0 chicago: Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics. Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0. ieee: R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems with short-range interactions,” Journal of Statistical Physics, vol. 181. Springer, pp. 448–464, 2020. ista: Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 181, 448–464. mla: Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics, vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0. short: R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464. date_created: 2020-07-05T22:00:46Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T07:51:47Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s10955-020-02586-0 ec_funded: 1 external_id: arxiv: - '2001.07144' isi: - '000543030000002' file: - access_level: open_access checksum: 5cbeef52caf18d0d952f17fed7b5545a content_type: application/pdf creator: dernst date_created: 2020-11-25T15:05:04Z date_updated: 2020-11-25T15:05:04Z file_id: '8812' file_name: 2020_JourStatPhysics_Seiringer.pdf file_size: 404778 relation: main_file success: 1 file_date_updated: 2020-11-25T15:05:04Z has_accepted_license: '1' intvolume: ' 181' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 448-464 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Journal of Statistical Physics publication_identifier: eissn: - '15729613' issn: - '00224715' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Emergence of Haldane pseudo-potentials in systems with short-range interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 181 year: '2020' ... --- _id: '8077' abstract: - lang: eng text: The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods. acknowledgement: The authors are grateful to the two anonymous referees for their insightful comments and suggestions which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union Seventh Framework Programme (FP7 - 2007-2013) (Grant agreement No. 616160). article_processing_charge: No article_type: original author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Olaniyi S. full_name: Iyiola, Olaniyi S. last_name: Iyiola citation: ama: 'Shehu Y, Iyiola OS. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 2020;157:315-337. doi:10.1016/j.apnum.2020.06.009' apa: 'Shehu, Y., & Iyiola, O. S. (2020). Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2020.06.009' chicago: 'Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.apnum.2020.06.009.' ieee: 'Y. Shehu and O. S. Iyiola, “Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence,” Applied Numerical Mathematics, vol. 157. Elsevier, pp. 315–337, 2020.' ista: 'Shehu Y, Iyiola OS. 2020. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 157, 315–337.' mla: 'Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics, vol. 157, Elsevier, 2020, pp. 315–37, doi:10.1016/j.apnum.2020.06.009.' short: Y. Shehu, O.S. Iyiola, Applied Numerical Mathematics 157 (2020) 315–337. date_created: 2020-07-02T09:02:33Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-08-22T07:50:43Z day: '01' ddc: - '510' department: - _id: VlKo doi: 10.1016/j.apnum.2020.06.009 ec_funded: 1 external_id: isi: - '000564648400018' file: - access_level: open_access checksum: 87d81324a62c82baa925c009dfcb0200 content_type: application/pdf creator: dernst date_created: 2020-07-02T09:08:59Z date_updated: 2020-07-14T12:48:09Z file_id: '8078' file_name: 2020_AppliedNumericalMath_Shehu.pdf file_size: 2874203 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 157' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 315-337 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Applied Numerical Mathematics publication_identifier: issn: - 0168-9274 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 157 year: '2020' ... --- _id: '8039' abstract: - lang: eng text: In the present work, we report a solution-based strategy to produce crystallographically textured SnSe bulk nanomaterials and printed layers with optimized thermoelectric performance in the direction normal to the substrate. Our strategy is based on the formulation of a molecular precursor that can be continuously decomposed to produce a SnSe powder or printed into predefined patterns. The precursor formulation and decomposition conditions are optimized to produce pure phase 2D SnSe nanoplates. The printed layer and the bulk material obtained after hot press displays a clear preferential orientation of the crystallographic domains, resulting in an ultralow thermal conductivity of 0.55 W m–1 K–1 in the direction normal to the substrate. Such textured nanomaterials present highly anisotropic properties with the best thermoelectric performance in plane, i.e., in the directions parallel to the substrate, which coincide with the crystallographic bc plane of SnSe. This is an unfortunate characteristic because thermoelectric devices are designed to create/harvest temperature gradients in the direction normal to the substrate. We further demonstrate that this limitation can be overcome with the introduction of small amounts of tellurium in the precursor. The presence of tellurium allows one to reduce the band gap and increase both the charge carrier concentration and the mobility, especially the cross plane, with a minimal decrease of the Seebeck coefficient. These effects translate into record out of plane ZT values at 800 K. article_processing_charge: No article_type: original author: - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Congcong full_name: Xing, Congcong last_name: Xing - first_name: Ting full_name: Zhang, Ting last_name: Zhang - first_name: Mengyao full_name: Li, Mengyao last_name: Li - first_name: Mercè full_name: Pacios, Mercè last_name: Pacios - first_name: Xiaoting full_name: Yu, Xiaoting last_name: Yu - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Zhang Y, Liu Y, Xing C, et al. Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. 2020;12(24):27104-27111. doi:10.1021/acsami.0c04331 apa: Zhang, Y., Liu, Y., Xing, C., Zhang, T., Li, M., Pacios, M., … Cabot, A. (2020). Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.0c04331 chicago: Zhang, Yu, Yu Liu, Congcong Xing, Ting Zhang, Mengyao Li, Mercè Pacios, Xiaoting Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces. American Chemical Society, 2020. https://doi.org/10.1021/acsami.0c04331. ieee: Y. Zhang et al., “Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices,” ACS Applied Materials and Interfaces, vol. 12, no. 24. American Chemical Society, pp. 27104–27111, 2020. ista: Zhang Y, Liu Y, Xing C, Zhang T, Li M, Pacios M, Yu X, Arbiol J, Llorca J, Cadavid D, Ibáñez M, Cabot A. 2020. Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices. ACS Applied Materials and Interfaces. 12(24), 27104–27111. mla: Zhang, Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces, vol. 12, no. 24, American Chemical Society, 2020, pp. 27104–11, doi:10.1021/acsami.0c04331. short: Y. Zhang, Y. Liu, C. Xing, T. Zhang, M. Li, M. Pacios, X. Yu, J. Arbiol, J. Llorca, D. Cadavid, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 12 (2020) 27104–27111. date_created: 2020-06-29T07:59:35Z date_published: 2020-06-17T00:00:00Z date_updated: 2023-08-22T07:50:08Z day: '17' department: - _id: MaIb doi: 10.1021/acsami.0c04331 ec_funded: 1 external_id: isi: - '000542925300032' pmid: - '32437128' intvolume: ' 12' isi: 1 issue: '24' language: - iso: eng month: '06' oa_version: None page: 27104-27111 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: ACS Applied Materials and Interfaces publication_identifier: eissn: - '19448252' publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2020' ... --- _id: '8133' abstract: - lang: eng text: The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease. article_number: '60' article_processing_charge: No article_type: original author: - first_name: Robert F. full_name: Hillary, Robert F. last_name: Hillary - first_name: Daniel full_name: Trejo-Banos, Daniel last_name: Trejo-Banos - first_name: Athanasios full_name: Kousathanas, Athanasios last_name: Kousathanas - first_name: Daniel L. full_name: Mccartney, Daniel L. last_name: Mccartney - first_name: Sarah E. full_name: Harris, Sarah E. last_name: Harris - first_name: Anna J. full_name: Stevenson, Anna J. last_name: Stevenson - first_name: Marion full_name: Patxot, Marion last_name: Patxot - first_name: Sven Erik full_name: Ojavee, Sven Erik last_name: Ojavee - first_name: Qian full_name: Zhang, Qian last_name: Zhang - first_name: David C. full_name: Liewald, David C. last_name: Liewald - first_name: Craig W. full_name: Ritchie, Craig W. last_name: Ritchie - first_name: Kathryn L. full_name: Evans, Kathryn L. last_name: Evans - first_name: Elliot M. full_name: Tucker-Drob, Elliot M. last_name: Tucker-Drob - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Allan F. full_name: Mcrae, Allan F. last_name: Mcrae - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Ian J. full_name: Deary, Ian J. last_name: Deary - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Riccardo E. full_name: Marioni, Riccardo E. last_name: Marioni citation: ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 2020;12(1). doi:10.1186/s13073-020-00754-1 apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-020-00754-1 chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1. ieee: R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults,” Genome Medicine, vol. 12, no. 1. Springer Nature, 2020. ista: Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 12(1), 60. mla: Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine, vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1. short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020). date_created: 2020-07-19T22:00:58Z date_published: 2020-07-08T00:00:00Z date_updated: 2023-08-22T07:55:37Z day: '08' ddc: - '570' department: - _id: MaRo doi: 10.1186/s13073-020-00754-1 external_id: isi: - '000551778400001' pmid: - '32641083' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-07-22T06:27:38Z date_updated: 2020-07-22T06:27:38Z file_id: '8145' file_name: 2020_GenomeMedicine_Hillary.pdf file_size: 1136983 relation: main_file success: 1 file_date_updated: 2020-07-22T06:27:38Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Medicine publication_identifier: eissn: - 1756994X publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '9706' relation: research_data status: public scopus_import: '1' status: public title: Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2020' ... --- _id: '8127' abstract: - lang: eng text: Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics. acknowledgement: We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster. article_number: e56261 article_processing_charge: No article_type: original author: - first_name: Pedro J. full_name: Gonçalves, Pedro J. last_name: Gonçalves orcid: 0000-0002-6987-4836 - first_name: Jan-Matthis full_name: Lueckmann, Jan-Matthis last_name: Lueckmann orcid: 0000-0003-4320-4663 - first_name: Michael full_name: Deistler, Michael last_name: Deistler orcid: 0000-0002-3573-0404 - first_name: Marcel full_name: Nonnenmacher, Marcel last_name: Nonnenmacher orcid: 0000-0001-6044-6627 - first_name: Kaan full_name: Öcal, Kaan last_name: Öcal orcid: 0000-0002-8528-6858 - first_name: Giacomo full_name: Bassetto, Giacomo last_name: Bassetto - first_name: Chaitanya full_name: Chintaluri, Chaitanya id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E last_name: Chintaluri orcid: 0000-0003-4252-1608 - first_name: William F. full_name: Podlaski, William F. last_name: Podlaski orcid: 0000-0001-6619-7502 - first_name: Sara A. full_name: Haddad, Sara A. last_name: Haddad orcid: 0000-0003-0807-0823 - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: David S. full_name: Greenberg, David S. last_name: Greenberg - first_name: Jakob H. full_name: Macke, Jakob H. last_name: Macke orcid: 0000-0001-5154-8912 citation: ama: Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261 apa: Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261 chicago: Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261. ieee: P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261. mla: Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261. short: P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020). date_created: 2020-07-16T12:26:04Z date_published: 2020-09-17T00:00:00Z date_updated: 2023-08-22T07:54:52Z day: '17' ddc: - '570' department: - _id: TiVo doi: 10.7554/eLife.56261 ec_funded: 1 external_id: isi: - '000584989400001' pmid: - '32940606' file: - access_level: open_access checksum: c4300ddcd93ed03fc9c6cdf1f77890be content_type: application/pdf creator: cziletti date_created: 2020-10-27T11:37:32Z date_updated: 2020-10-27T11:37:32Z file_id: '8709' file_name: 2020_eLife_Gonçalves.pdf file_size: 17355867 relation: main_file success: 1 file_date_updated: 2020-10-27T11:37:32Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Training deep neural density estimators to identify mechanistic models of neural dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '8126' abstract: - lang: eng text: Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents. article_processing_charge: No article_type: original author: - first_name: Everton J. full_name: Agnes, Everton J. last_name: Agnes orcid: 0000-0001-7184-7311 - first_name: Andrea I. full_name: Luppi, Andrea I. last_name: Luppi - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020 apa: Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020 chicago: Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020. ieee: E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020. ista: Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649. mla: Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:10.1523/JNEUROSCI.0276-20.2020. short: E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649. date_created: 2020-07-16T12:25:04Z date_published: 2020-12-09T00:00:00Z date_updated: 2023-08-22T07:54:26Z day: '09' ddc: - '570' department: - _id: TiVo doi: 10.1523/JNEUROSCI.0276-20.2020 external_id: isi: - '000606706400009' pmid: - '33168622' file: - access_level: open_access checksum: 7977e4dd6b89357d1a5cc88babac56da content_type: application/pdf creator: dernst date_created: 2020-12-28T08:31:47Z date_updated: 2020-12-28T08:31:47Z file_id: '8977' file_name: 2020_JourNeuroscience_Agnes.pdf file_size: 2750920 relation: main_file success: 1 file_date_updated: 2020-12-28T08:31:47Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '50' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 9634-9649 pmid: 1 publication: The Journal of Neuroscience publication_identifier: eissn: - 1529-2401 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2020' ... --- _id: '8132' abstract: - lang: eng text: The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity. article_number: eabc3979 article_processing_charge: No article_type: original author: - first_name: Elisabeth full_name: Salzer, Elisabeth last_name: Salzer - first_name: Samaneh full_name: Zoghi, Samaneh last_name: Zoghi - first_name: Máté G. full_name: Kiss, Máté G. last_name: Kiss - first_name: Frieda full_name: Kage, Frieda last_name: Kage - first_name: Christina full_name: Rashkova, Christina last_name: Rashkova - first_name: Stephanie full_name: Stahnke, Stephanie last_name: Stahnke - first_name: Matthias full_name: Haimel, Matthias last_name: Haimel - first_name: René full_name: Platzer, René last_name: Platzer - first_name: Michael full_name: Caldera, Michael last_name: Caldera - first_name: Rico Chandra full_name: Ardy, Rico Chandra last_name: Ardy - first_name: Birgit full_name: Hoeger, Birgit last_name: Hoeger - first_name: Jana full_name: Block, Jana last_name: Block - first_name: David full_name: Medgyesi, David last_name: Medgyesi - first_name: Celine full_name: Sin, Celine last_name: Sin - first_name: Sepideh full_name: Shahkarami, Sepideh last_name: Shahkarami - first_name: Renate full_name: Kain, Renate last_name: Kain - first_name: Vahid full_name: Ziaee, Vahid last_name: Ziaee - first_name: Peter full_name: Hammerl, Peter last_name: Hammerl - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Jörg full_name: Menche, Jörg last_name: Menche - first_name: Loïc full_name: Dupré, Loïc last_name: Dupré - first_name: Johannes B. full_name: Huppa, Johannes B. last_name: Huppa - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Alexis full_name: Lomakin, Alexis last_name: Lomakin - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Christoph J. full_name: Binder, Christoph J. last_name: Binder - first_name: Theresia E.B. full_name: Stradal, Theresia E.B. last_name: Stradal - first_name: Nima full_name: Rezaei, Nima last_name: Rezaei - first_name: Kaan full_name: Boztug, Kaan last_name: Boztug citation: ama: Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 2020;5(49). doi:10.1126/sciimmunol.abc3979 apa: Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., … Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979 chicago: Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology. AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979. ieee: E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020. ista: Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A, Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 5(49), eabc3979. mla: Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979, AAAS, 2020, doi:10.1126/sciimmunol.abc3979. short: E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel, R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S. Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B. Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei, K. Boztug, Science Immunology 5 (2020). date_created: 2020-07-19T22:00:58Z date_published: 2020-07-10T00:00:00Z date_updated: 2023-08-22T07:56:04Z day: '10' department: - _id: MiSi doi: 10.1126/sciimmunol.abc3979 external_id: isi: - '000546994600004' pmid: - '32646852' intvolume: ' 5' isi: 1 issue: '49' language: - iso: eng month: '07' oa_version: None pmid: 1 publication: Science Immunology publication_identifier: eissn: - '24709468' publication_status: published publisher: AAAS quality_controlled: '1' scopus_import: '1' status: public title: The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2020' ... --- _id: '9706' abstract: - lang: eng text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).' article_processing_charge: No author: - first_name: Robert F. full_name: Hillary, Robert F. last_name: Hillary - first_name: Daniel full_name: Trejo-Banos, Daniel last_name: Trejo-Banos - first_name: Athanasios full_name: Kousathanas, Athanasios last_name: Kousathanas - first_name: Daniel L. full_name: McCartney, Daniel L. last_name: McCartney - first_name: Sarah E. full_name: Harris, Sarah E. last_name: Harris - first_name: Anna J. full_name: Stevenson, Anna J. last_name: Stevenson - first_name: Marion full_name: Patxot, Marion last_name: Patxot - first_name: Sven Erik full_name: Ojavee, Sven Erik last_name: Ojavee - first_name: Qian full_name: Zhang, Qian last_name: Zhang - first_name: David C. full_name: Liewald, David C. last_name: Liewald - first_name: Craig W. full_name: Ritchie, Craig W. last_name: Ritchie - first_name: Kathryn L. full_name: Evans, Kathryn L. last_name: Evans - first_name: Elliot M. full_name: Tucker-Drob, Elliot M. last_name: Tucker-Drob - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: 'Allan F. ' full_name: 'McRae, Allan F. ' last_name: McRae - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Ian J. full_name: Deary, Ian J. last_name: Deary - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: 'Riccardo E. ' full_name: 'Marioni, Riccardo E. ' last_name: Marioni citation: ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1 apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1 chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1. ieee: R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020. ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1. mla: Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1. short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020). date_created: 2021-07-23T08:59:15Z date_published: 2020-07-09T00:00:00Z date_updated: 2023-08-22T07:55:36Z day: '09' department: - _id: MaRo doi: 10.6084/m9.figshare.12629697.v1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.12629697.v1 month: '07' oa: 1 oa_version: Published Version other_data_license: CC0 + CC BY (4.0) publisher: Springer Nature related_material: record: - id: '8133' relation: used_in_publication status: public status: public title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '8134' abstract: - lang: eng text: We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion. article_number: '061901' article_processing_charge: No article_type: original author: - first_name: Simon full_name: Mayer, Simon id: 30C4630A-F248-11E8-B48F-1D18A9856A87 last_name: Mayer - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950 apa: Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0005950 chicago: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005950. ieee: S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no. 6. AIP Publishing, 2020. ista: Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901. mla: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950. short: S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020). date_created: 2020-07-19T22:00:59Z date_published: 2020-06-22T00:00:00Z date_updated: 2023-08-22T08:12:40Z day: '22' department: - _id: RoSe doi: 10.1063/5.0005950 ec_funded: 1 external_id: arxiv: - '2002.08281' isi: - '000544595100001' intvolume: ' 61' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.08281 month: '06' oa: 1 oa_version: Preprint project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Journal of Mathematical Physics publication_identifier: issn: - '00222488' publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: The free energy of the two-dimensional dilute Bose gas. II. Upper bound type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 61 year: '2020' ... --- _id: '8112' article_number: '20190530' article_processing_charge: No article_type: letter_note author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530' apa: 'Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530' chicago: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530.' ieee: 'N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.' mla: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530.' short: 'N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-13T03:41:39Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T07:53:52Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0530 external_id: isi: - '000552662100002' pmid: - '32654647' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng month: '07' oa_version: None pmid: 1 publication: 'Philosophical Transactions of the Royal Society. Series B: Biological Sciences' publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: On the completion of speciation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '8162' abstract: - lang: eng text: In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl acknowledgement: We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H. article_processing_charge: No article_type: original author: - first_name: Susanne full_name: Laukoter, Susanne id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87 last_name: Laukoter orcid: 0000-0002-7903-3010 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Thomas full_name: Penz, Thomas last_name: Penz - first_name: Christoph full_name: Bock, Christoph last_name: Bock orcid: 0000-0001-6091-3088 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031 apa: Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031 chicago: Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031. ieee: S. Laukoter et al., “Cell-type specificity of genomic imprinting in cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020. ista: Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9. mla: Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031. short: S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9. date_created: 2020-07-23T16:03:12Z date_published: 2020-09-23T00:00:00Z date_updated: 2023-08-22T08:20:11Z day: '23' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.neuron.2020.06.031 ec_funded: 1 external_id: isi: - '000579698700006' file: - access_level: open_access checksum: 7becdc16a6317304304631087ae7dd7f content_type: application/pdf creator: dernst date_created: 2020-12-02T09:26:46Z date_updated: 2020-12-02T09:26:46Z file_id: '8828' file_name: 2020_Neuron_Laukoter.pdf file_size: 8911830 relation: main_file success: 1 file_date_updated: 2020-12-02T09:26:46Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1160-1179.e9 project: - _id: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular Mechanisms of Radial Neuronal Migration - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T0101031 name: Role of Eed in neural stem cell lineage progression - _id: 264E56E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02416 name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex - _id: 25D92700-B435-11E9-9278-68D0E5697425 grant_number: LS13-002 name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain - _id: 25D7962E-B435-11E9-9278-68D0E5697425 grant_number: RGP0053/2014 name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/ scopus_import: '1' status: public title: Cell-type specificity of genomic imprinting in cerebral cortex tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2020' ... --- _id: '8138' abstract: - lang: eng text: Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration. acknowledgement: We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864). article_processing_charge: No article_type: original author: - first_name: J full_name: Zhang, J last_name: Zhang - first_name: E full_name: Mazur, E last_name: Mazur - first_name: J full_name: Balla, J last_name: Balla - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: P full_name: Kalousek, P last_name: Kalousek - first_name: Z full_name: Medveďová, Z last_name: Medveďová - first_name: Y full_name: Li, Y last_name: Li - first_name: Y full_name: Wang, Y last_name: Wang - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat - first_name: Mina K full_name: Vasileva, Mina K id: 3407EB18-F248-11E8-B48F-1D18A9856A87 last_name: Vasileva - first_name: V full_name: Reinöhl, V last_name: Reinöhl - first_name: S full_name: Procházka, S last_name: Procházka - first_name: R full_name: Halouzka, R last_name: Halouzka - first_name: P full_name: Tarkowski, P last_name: Tarkowski - first_name: C full_name: Luschnig, C last_name: Luschnig - first_name: PB full_name: Brewer, PB last_name: Brewer - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508. doi:10.1038/s41467-020-17252-y apa: Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y chicago: Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y. ieee: J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer Nature, p. 3508, 2020. ista: Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508. mla: Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y. short: J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508. date_created: 2020-07-21T08:58:07Z date_published: 2020-07-14T00:00:00Z date_updated: 2023-08-22T08:13:44Z day: '14' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-020-17252-y ec_funded: 1 external_id: isi: - '000550062200004' pmid: - '32665554' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-07-22T08:32:55Z date_updated: 2020-07-22T08:32:55Z file_id: '8148' file_name: 2020_NatureComm_Zhang.pdf file_size: 1759490 relation: main_file success: 1 file_date_updated: 2020-07-22T08:32:55Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '3508' pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11626' relation: dissertation_contains status: public scopus_import: '1' status: public title: Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8168' abstract: - lang: eng text: Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. article_number: '20190528' article_processing_charge: No article_type: original author: - first_name: Jonna full_name: Kulmuni, Jonna last_name: Kulmuni - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Kay full_name: Lucek, Kay last_name: Lucek - first_name: Vincent full_name: Savolainen, Vincent last_name: Savolainen - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528' apa: 'Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528' chicago: 'Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.' ieee: 'J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.' mla: 'Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.' short: 'J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-26T22:01:01Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T08:21:31Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0528 ec_funded: 1 external_id: isi: - '000552662100001' pmid: - '32654637' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rstb.2019.0528 month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: 'Philosophical Transactions of the Royal Society. Series B: Biological sciences' publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: 'Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '8167' abstract: - lang: eng text: The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. acknowledgement: Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript. article_number: '20190545' article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Zuzanna B. full_name: Zagrodzka, Zuzanna B. last_name: Zagrodzka - first_name: Isobel full_name: Eyres, Isobel last_name: Eyres - first_name: Thomas full_name: Broquet, Thomas last_name: Broquet - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545' apa: 'Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545' chicago: 'Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.' ieee: 'S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.' mla: 'Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.' short: 'S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-26T22:01:01Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T08:22:13Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0545 external_id: isi: - '000552662100014' pmid: - '32654639' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rstb.2019.0545 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: 'Philosophical Transactions of the Royal Society. Series B: Biological Sciences' publication_identifier: eissn: - 1471-2970 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: The evolution of strong reproductive isolation between sympatric intertidal snails type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '8170' abstract: - lang: eng text: "Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes." acknowledgement: "H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University." article_number: '013001' article_processing_charge: No article_type: original author: - first_name: Adam S. full_name: Chatterley, Adam S. last_name: Chatterley - first_name: Lars full_name: Christiansen, Lars last_name: Christiansen - first_name: Constant A. full_name: Schouder, Constant A. last_name: Schouder - first_name: Anders V. full_name: Jørgensen, Anders V. last_name: Jørgensen - first_name: Benjamin full_name: Shepperson, Benjamin last_name: Shepperson - first_name: Igor full_name: Cherepanov, Igor id: 339C7E5A-F248-11E8-B48F-1D18A9856A87 last_name: Cherepanov - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Robert E. full_name: Zillich, Robert E. last_name: Zillich - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Henrik full_name: Stapelfeldt, Henrik last_name: Stapelfeldt citation: ama: 'Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001' apa: 'Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001' chicago: 'Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.' ieee: 'A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical Review Letters, vol. 125, no. 1. American Physical Society, 2020.' ista: 'Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.' mla: 'Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.013001.' short: A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020). date_created: 2020-07-26T22:01:02Z date_published: 2020-07-03T00:00:00Z date_updated: 2023-08-22T08:22:43Z day: '03' department: - _id: MiLe doi: 10.1103/PhysRevLett.125.013001 ec_funded: 1 external_id: arxiv: - '2006.02694' isi: - '000544526900006' intvolume: ' 125' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2006.02694 month: '07' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Physical Review Letters publication_identifier: eissn: - '10797114' issn: - '00319007' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 125 year: '2020' ... --- _id: '8194' abstract: - lang: eng text: 'Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Marek full_name: Baranowski, Marek last_name: Baranowski - first_name: Shaobo full_name: He, Shaobo last_name: He - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Thanh Son full_name: Nguyen, Thanh Son last_name: Nguyen - first_name: Zvonimir full_name: Rakamarić, Zvonimir last_name: Rakamarić citation: ama: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31. doi:10.1007/978-3-030-51074-9_2' apa: 'Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2' chicago: Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning, 12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2. ieee: M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France, 2020, vol. 12166, pp. 13–31. ista: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.' mla: Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2. short: M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31. conference: end_date: 2020-07-04 location: Paris, France name: 'IJCAR: International Joint Conference on Automated Reasoning' start_date: 2020-07-01 date_created: 2020-08-02T22:00:59Z date_published: 2020-06-24T00:00:00Z date_updated: 2023-08-22T08:27:25Z day: '24' department: - _id: ToHe doi: 10.1007/978-3-030-51074-9_2 external_id: isi: - '000884318000002' intvolume: ' 12166' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-030-51074-9_2 month: '06' oa: 1 oa_version: Published Version page: 13-31 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Automated Reasoning publication_identifier: eissn: - '16113349' isbn: - '9783030510732' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: An SMT theory of fixed-point arithmetic type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12166 year: '2020' ... --- _id: '8169' abstract: - lang: eng text: Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation. acknowledgement: This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions. article_number: '20190544' article_processing_charge: No article_type: original author: - first_name: Huiying full_name: Shang, Huiying last_name: Shang - first_name: Jaqueline full_name: Hess, Jaqueline last_name: Hess - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Pär K. full_name: Ingvarsson, Pär K. last_name: Ingvarsson - first_name: Jianquan full_name: Liu, Jianquan last_name: Liu - first_name: Christian full_name: Lexer, Christian last_name: Lexer citation: ama: 'Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0544' apa: 'Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., & Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544' chicago: 'Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0544.' ieee: 'H. Shang et al., “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.' mla: 'Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544.' short: 'H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-26T22:01:02Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T08:23:24Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0544 external_id: isi: - '000552662100013' pmid: - '32654641' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng month: '07' oa_version: Published Version pmid: 1 publication: 'Philosophical Transactions of the Royal Society. Series B: Biological Sciences' publication_identifier: eissn: - '14712970' publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: 'Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '8189' abstract: - lang: eng text: Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface. acknowledgement: This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program. article_number: '105116' article_processing_charge: No article_type: original author: - first_name: Xiaoting full_name: Yu, Xiaoting last_name: Yu - first_name: Junfeng full_name: Liu, Junfeng last_name: Liu - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Zhishan full_name: Luo, Zhishan last_name: Luo - first_name: Yong full_name: Zuo, Yong last_name: Zuo - first_name: Congcong full_name: Xing, Congcong last_name: Xing - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Déspina full_name: Nasiou, Déspina last_name: Nasiou - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Kai full_name: Pan, Kai last_name: Pan - first_name: Tobias full_name: Kleinhanns, Tobias id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425 last_name: Kleinhanns - first_name: Ying full_name: Xie, Ying last_name: Xie - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 2020;77(11). doi:10.1016/j.nanoen.2020.105116 apa: Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2020.105116 chicago: Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy. Elsevier, 2020. https://doi.org/10.1016/j.nanoen.2020.105116. ieee: X. Yu et al., “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” Nano Energy, vol. 77, no. 11. Elsevier, 2020. ista: Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116. mla: Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” Nano Energy, vol. 77, no. 11, 105116, Elsevier, 2020, doi:10.1016/j.nanoen.2020.105116. short: X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020). date_created: 2020-08-02T22:00:57Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-08-22T08:24:05Z day: '01' department: - _id: MaIb doi: 10.1016/j.nanoen.2020.105116 external_id: isi: - '000581738300030' intvolume: ' 77' isi: 1 issue: '11' language: - iso: eng month: '11' oa_version: None publication: Nano Energy publication_identifier: issn: - 2211-2855 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 77 year: '2020' ... --- _id: '8220' abstract: - lang: eng text: Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings. acknowledgement: "We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z." article_processing_charge: No article_type: original author: - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 - first_name: Colinda L.G.J. full_name: Scheele, Colinda L.G.J. last_name: Scheele - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi - first_name: Saskia I.J. full_name: Ellenbroek, Saskia I.J. last_name: Ellenbroek - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons - first_name: Jacco full_name: Van Rheenen, Jacco last_name: Van Rheenen - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117 apa: Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117 chicago: Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117. ieee: B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020. ista: Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975. mla: Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117. short: B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975. date_created: 2020-08-09T22:00:52Z date_published: 2020-07-21T00:00:00Z date_updated: 2023-08-22T08:29:30Z day: '21' ddc: - '570' department: - _id: EdHa doi: 10.1073/pnas.1921205117 ec_funded: 1 external_id: isi: - '000553292900014' pmid: - '32611816' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-10T06:50:28Z date_updated: 2020-08-10T06:50:28Z file_id: '8223' file_name: 2020_PNAS_Corominas.pdf file_size: 1111604 relation: main_file success: 1 file_date_updated: 2020-08-10T06:50:28Z has_accepted_license: '1' intvolume: ' 117' isi: 1 issue: '29' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 16969-16975 pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - '10916490' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: press_release url: https://ist.ac.at/en/news/order-from-noise/ scopus_import: '1' status: public title: Stem cell lineage survival as a noisy competition for niche access tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 117 year: '2020' ... --- _id: '8199' abstract: - lang: eng text: We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist. acknowledgement: "N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft" article_number: '015' article_processing_charge: No article_type: original author: - first_name: Tobias full_name: Gulden, Tobias id: 1083E038-9F73-11E9-A4B5-532AE6697425 last_name: Gulden orcid: 0000-0001-6814-7541 - first_name: Erez full_name: Berg, Erez last_name: Berg - first_name: Mark Spencer full_name: Rudner, Mark Spencer last_name: Rudner - first_name: Netanel full_name: Lindner, Netanel last_name: Lindner citation: ama: Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9. doi:10.21468/scipostphys.9.1.015 apa: Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015 chicago: Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015. ieee: T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” SciPost Physics, vol. 9. SciPost Foundation, 2020. ista: Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015. mla: Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost Foundation, 2020, doi:10.21468/scipostphys.9.1.015. short: T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020). date_created: 2020-08-04T13:04:15Z date_published: 2020-07-29T00:00:00Z date_updated: 2023-08-22T08:28:24Z day: '29' ddc: - '530' department: - _id: MaSe doi: 10.21468/scipostphys.9.1.015 ec_funded: 1 external_id: isi: - '000557362300008' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-06T08:56:06Z date_updated: 2020-08-06T08:56:06Z file_id: '8202' file_name: 2020_SciPostPhys_Gulden.pdf file_size: 531137 relation: main_file success: 1 file_date_updated: 2020-08-06T08:56:06Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: SciPost Physics publication_identifier: issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' scopus_import: '1' status: public title: Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '8261' abstract: - lang: eng text: Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion. acknowledged_ssus: - _id: M-Shop - _id: ScienComp - _id: PreCl acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support. article_processing_charge: No article_type: original author: - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006 apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006 chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006. ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020. ista: Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225. mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006. short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225. date_created: 2020-08-14T09:36:05Z date_published: 2020-09-23T00:00:00Z date_updated: 2023-08-22T08:30:55Z day: '23' ddc: - '570' department: - _id: PeJo - _id: ScienComp doi: 10.1016/j.neuron.2020.07.006 ec_funded: 1 external_id: isi: - '000579698700009' pmid: - '32763145' file: - access_level: open_access checksum: 44a5960fc083a4cb3488d22224859fdc content_type: application/pdf creator: dernst date_created: 2020-12-04T09:29:21Z date_updated: 2020-12-04T09:29:21Z file_id: '8920' file_name: 2020_Neuron_Zhang.pdf file_size: 3011120 relation: main_file success: 1 file_date_updated: 2020-12-04T09:29:21Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1212-1225 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/ status: public title: Selective routing of spatial information flow from input to output in hippocampal granule cells tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2020' ... --- _id: '8268' abstract: - lang: eng text: 'Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.' acknowledgement: The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich. article_processing_charge: No article_type: original author: - first_name: Nezihe Merve full_name: Gurel, Nezihe Merve last_name: Gurel - first_name: Kaan full_name: Kara, Kaan last_name: Kara - first_name: Alen full_name: Stojanov, Alen last_name: Stojanov - first_name: Tyler full_name: Smith, Tyler last_name: Smith - first_name: Thomas full_name: Lemmin, Thomas last_name: Lemmin - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Markus full_name: Puschel, Markus last_name: Puschel - first_name: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355' apa: 'Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355' chicago: 'Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.' ieee: 'N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.' ista: 'Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.' mla: 'Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.' short: N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282. date_created: 2020-08-16T22:00:56Z date_published: 2020-07-20T00:00:00Z date_updated: 2023-08-22T08:40:08Z day: '20' department: - _id: DaAl doi: 10.1109/TSP.2020.3010355 external_id: arxiv: - '1802.04907' isi: - '000562044500001' intvolume: ' 68' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.04907 month: '07' oa: 1 oa_version: Preprint page: 4268-4282 publication: IEEE Transactions on Signal Processing publication_identifier: eissn: - '19410476' issn: - 1053587X publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 68 year: '2020' ... --- _id: '8271' acknowledgement: We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared. article_processing_charge: No article_type: original author: - first_name: Peng full_name: He, Peng last_name: He - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Guanghui full_name: Xiao, Guanghui last_name: Xiao citation: ama: He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006 apa: He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.07.006 chicago: He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.07.006. ieee: P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020. ista: He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240. mla: He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:10.1016/j.molp.2020.07.006. short: P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240. date_created: 2020-08-16T22:00:57Z date_published: 2020-09-07T00:00:00Z date_updated: 2023-08-22T08:40:35Z day: '07' department: - _id: JiFr doi: 10.1016/j.molp.2020.07.006 external_id: isi: - '000566895400007' pmid: - '32688032' intvolume: ' 13' isi: 1 issue: '9' language: - iso: eng month: '09' oa_version: None page: 1238-1240 pmid: 1 publication: Molecular Plant publication_identifier: eissn: - '17529867' issn: - '16742052' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Origin of a subgenome and genome evolution of allotetraploid cotton species type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2020' ... --- _id: '8101' abstract: - lang: eng text: By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature. acknowledgement: "We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411." article_number: '082602' article_processing_charge: Yes article_type: original author: - first_name: Galien M full_name: Grosjean, Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald - first_name: Juan Carlos A full_name: Sobarzo Ponce, Juan Carlos A id: 4B807D68-AE37-11E9-AC72-31CAE5697425 last_name: Sobarzo Ponce - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602 apa: Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602 chicago: Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602. ieee: G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020. ista: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602. mla: Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602. short: G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020). date_created: 2020-07-07T11:33:54Z date_published: 2020-08-17T00:00:00Z date_updated: 2023-08-22T08:41:32Z day: '17' ddc: - '530' department: - _id: ScWa doi: 10.1103/PhysRevMaterials.4.082602 ec_funded: 1 external_id: arxiv: - '2006.07120' isi: - '000561897000001' file: - access_level: open_access checksum: 288fef1eeb6540c6344bb8f7c8159dc9 content_type: application/pdf creator: ggrosjea date_created: 2020-08-17T15:54:20Z date_updated: 2020-08-17T15:54:20Z file_id: '8277' file_name: Grosjean2020.pdf file_size: 853753 relation: main_file success: 1 file_date_updated: 2020-08-17T15:54:20Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '8' keyword: - electric charge - tribocharging - soft matter - granular materials - polymers language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Materials publication_identifier: issn: - 2475-9953 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '12697' relation: popular_science status: public scopus_import: '1' status: public title: Quantitatively consistent scale-spanning model for same-material tribocharging tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 4 year: '2020' ... --- _id: '8325' abstract: - lang: eng text: "Let \U0001D439:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. " acknowledgement: We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers. article_processing_charge: No article_type: original author: - first_name: Nikita full_name: Kalinin, Nikita last_name: Kalinin - first_name: Mikhail full_name: Shkolnikov, Mikhail id: 35084A62-F248-11E8-B48F-1D18A9856A87 last_name: Shkolnikov orcid: 0000-0002-4310-178X citation: ama: Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8 apa: Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8 chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8. ieee: N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020. ista: Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675. mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8. short: N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675. date_created: 2020-08-30T22:01:13Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T09:00:03Z day: '01' department: - _id: TaHa doi: 10.1007/s00220-020-03828-8 ec_funded: 1 external_id: arxiv: - '1711.04285' isi: - '000560620600001' intvolume: ' 378' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.04285 month: '09' oa: 1 oa_version: Preprint page: 1649-1675 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Communications in Mathematical Physics publication_identifier: eissn: - '14320916' issn: - '00103616' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Sandpile solitons via smoothing of superharmonic functions type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 378 year: '2020' ... --- _id: '8318' abstract: - lang: eng text: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I. acknowledgement: This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster. article_number: '4135' article_processing_charge: No article_type: original author: - first_name: Javier full_name: Gutierrez-Fernandez, Javier id: 3D9511BA-F248-11E8-B48F-1D18A9856A87 last_name: Gutierrez-Fernandez - first_name: Karol full_name: Kaszuba, Karol id: 3FDF9472-F248-11E8-B48F-1D18A9856A87 last_name: Kaszuba - first_name: Gurdeep S. full_name: Minhas, Gurdeep S. last_name: Minhas - first_name: Rozbeh full_name: Baradaran, Rozbeh last_name: Baradaran - first_name: Margherita full_name: Tambalo, Margherita id: 4187dfe4-ec23-11ea-ae46-f08ab378313a last_name: Tambalo - first_name: David T. full_name: Gallagher, David T. last_name: Gallagher - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0 apa: Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0 chicago: Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0. ieee: J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020. ista: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135. mla: Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0. short: J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020). date_created: 2020-08-30T22:01:10Z date_published: 2020-08-18T00:00:00Z date_updated: 2023-08-22T09:03:00Z day: '18' ddc: - '570' department: - _id: LeSa doi: 10.1038/s41467-020-17957-0 external_id: isi: - '000607072900001' pmid: - '32811817' file: - access_level: open_access checksum: 52b96f41d7d0db9728064c08da00d030 content_type: application/pdf creator: cziletti date_created: 2020-08-31T13:40:00Z date_updated: 2020-08-31T13:40:00Z file_id: '8326' file_name: 2020_NatComm_Gutierrez-Fernandez.pdf file_size: 7527373 relation: main_file success: 1 file_date_updated: 2020-08-31T13:40:00Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/ scopus_import: '1' status: public title: Key role of quinone in the mechanism of respiratory complex I tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8320' abstract: - lang: eng text: The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. acknowledgement: We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay. article_processing_charge: No article_type: original author: - first_name: S. A. full_name: Mukba, S. A. last_name: Mukba - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: P. M. full_name: Kolosov, P. M. last_name: Kolosov - first_name: E. Y. full_name: Shuvalova, E. Y. last_name: Shuvalova - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111' apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111' chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.' ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.' ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.' mla: 'Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.' short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484. date_created: 2020-08-30T22:01:11Z date_published: 2020-08-19T00:00:00Z date_updated: 2023-08-22T09:01:03Z day: '19' department: - _id: FyKo doi: 10.1134/S0026893320040111 external_id: isi: - '000562110300001' intvolume: ' 54' isi: 1 issue: '4' language: - iso: eng month: '08' oa_version: None page: 475-484 publication: Molecular Biology publication_identifier: eissn: - '16083245' issn: - '00268933' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8321' relation: original status: public scopus_import: '1' status: public title: 'Expanding the genetic code: Unnatural base pairs in biological systems' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 54 year: '2020' ... --- _id: '8321' abstract: - lang: eng text: The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. article_processing_charge: No article_type: original author: - first_name: S. A. full_name: Mukba, S. A. last_name: Mukba - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: P. M. full_name: Kolosov, P. M. last_name: Kolosov - first_name: E. Y. full_name: Shuvalova, E. Y. last_name: Shuvalova - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126' apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126' chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.' ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.' ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.' mla: 'Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.' short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541. date_created: 2020-08-30T22:01:11Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T09:01:02Z day: '01' department: - _id: FyKo doi: 10.31857/S0026898420040126 external_id: pmid: - '32799218' intvolume: ' 54' issue: '4' language: - iso: rus month: '07' oa_version: None page: 531-541 pmid: 1 publication: Molekuliarnaia biologiia publication_identifier: issn: - '00268984' publication_status: published publisher: Russian Academy of Sciences quality_controlled: '1' related_material: record: - id: '8320' relation: translation status: public scopus_import: '1' status: public title: 'Expanding the genetic code: Unnatural base pairs in biological systems' type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 54 year: '2020' ... --- _id: '8323' article_processing_charge: No article_type: letter_note author: - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach citation: ama: Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5 apa: Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5 chicago: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5. ieee: J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020. ista: Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574. mla: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5. short: J. Pach, Discrete and Computational Geometry 64 (2020) 571–574. date_created: 2020-08-30T22:01:12Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T09:05:04Z day: '01' department: - _id: HeEd doi: 10.1007/s00454-020-00237-5 external_id: isi: - '000561483500001' intvolume: ' 64' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00454-020-00237-5 month: '10' oa: 1 oa_version: None page: 571-574 publication: Discrete and Computational Geometry publication_identifier: eissn: - '14320444' issn: - '01795376' publication_status: published publisher: Springer Nature scopus_import: '1' status: public title: A farewell to Ricky Pollack type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 64 year: '2020' ... --- _id: '8336' abstract: - lang: eng text: Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.). article_number: '4285' article_processing_charge: No article_type: original author: - first_name: Karolina full_name: Kubiasova, Karolina id: 946011F4-3E71-11EA-860B-C7A73DDC885E last_name: Kubiasova orcid: 0000-0001-5630-9419 - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Olga full_name: Šamajová, Olga last_name: Šamajová - first_name: Jaroslav full_name: Nisler, Jaroslav last_name: Nisler - first_name: Václav full_name: Mik, Václav last_name: Mik - first_name: Hana full_name: Semeradova, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semeradova - first_name: Lucie full_name: Plíhalová, Lucie last_name: Plíhalová - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Peter full_name: Marhavý, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavý orcid: 0000-0001-5227-5741 - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: David full_name: Zalabák, David last_name: Zalabák - first_name: Karel full_name: Berka, Karel last_name: Berka - first_name: Karel full_name: Doležal, Karel last_name: Doležal - first_name: Petr full_name: Galuszka, Petr last_name: Galuszka - first_name: Jozef full_name: Šamaj, Jozef last_name: Šamaj - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ondřej full_name: Plíhal, Ondřej last_name: Plíhal - first_name: Lukáš full_name: Spíchal, Lukáš last_name: Spíchal citation: ama: Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0 apa: Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0 chicago: Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0. ieee: K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285. mla: Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0. short: K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020). date_created: 2020-09-06T22:01:12Z date_published: 2020-08-27T00:00:00Z date_updated: 2023-08-22T09:09:06Z day: '27' ddc: - '580' department: - _id: EvBe doi: 10.1038/s41467-020-17949-0 ec_funded: 1 external_id: isi: - '000567931000002' pmid: - '32855390' file: - access_level: open_access checksum: 7494b7665b3d2bf2d8edb13e4f12b92d content_type: application/pdf creator: dernst date_created: 2020-09-10T08:05:19Z date_updated: 2020-09-10T08:05:19Z file_id: '8357' file_name: 2020_NatureComm_Kubiasova.pdf file_size: 3455704 relation: main_file success: 1 file_date_updated: 2020-09-10T08:05:19Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis. - _id: 253E54C8-B435-11E9-9278-68D0E5697425 grant_number: ALTF710-2016 name: Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8337' abstract: - lang: eng text: Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses. acknowledged_ssus: - _id: Bio acknowledgement: 'We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.' article_number: '4284' article_processing_charge: No article_type: original author: - first_name: Ioanna full_name: Antoniadi, Ioanna last_name: Antoniadi - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Ondřej full_name: Plíhal, Ondřej last_name: Plíhal - first_name: Radim full_name: Simerský, Radim last_name: Simerský - first_name: Václav full_name: Mik, Václav last_name: Mik - first_name: Thomas full_name: Vain, Thomas last_name: Vain - first_name: Eduardo full_name: Mateo-Bonmatí, Eduardo last_name: Mateo-Bonmatí - first_name: Michal full_name: Karady, Michal last_name: Karady - first_name: Markéta full_name: Pernisová, Markéta last_name: Pernisová - first_name: Lenka full_name: Plačková, Lenka last_name: Plačková - first_name: Korawit full_name: Opassathian, Korawit last_name: Opassathian - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Karel full_name: Doležal, Karel last_name: Doležal - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Colin full_name: Turnbull, Colin last_name: Turnbull citation: ama: Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9 apa: Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9 chicago: Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9. ieee: I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284. mla: Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9. short: I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020). date_created: 2020-09-06T22:01:13Z date_published: 2020-08-27T00:00:00Z date_updated: 2023-08-22T09:10:32Z day: '27' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-020-17700-9 ec_funded: 1 external_id: isi: - '000567931000001' file: - access_level: open_access checksum: 5b96f39b598de7510cfefefb819b9a6d content_type: application/pdf creator: dernst date_created: 2020-12-10T12:23:56Z date_updated: 2020-12-10T12:23:56Z file_id: '8936' file_name: 2020_NatureComm_Antoniadi.pdf file_size: 3526415 relation: main_file success: 1 file_date_updated: 2020-12-10T12:23:56Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cell-surface receptors enable perception of extracellular cytokinins tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8067' abstract: - lang: eng text: "With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7." alternative_title: - IST Austria Technical Report article_processing_charge: No author: - first_name: Alberto full_name: Varzi, Alberto last_name: Varzi - first_name: Katharina full_name: Thanner, Katharina last_name: Thanner - first_name: Roberto full_name: Scipioni, Roberto last_name: Scipioni - first_name: Daniele full_name: Di Lecce, Daniele last_name: Di Lecce - first_name: Jusef full_name: Hassoun, Jusef last_name: Hassoun - first_name: Susanne full_name: Dörfler, Susanne last_name: Dörfler - first_name: Holger full_name: Altheus, Holger last_name: Altheus - first_name: Stefan full_name: Kaskel, Stefan last_name: Kaskel - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067 apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067 chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067. ieee: A. Varzi et al., Current status and future perspectives of Lithium metal batteries. IST Austria. ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives of Lithium metal batteries, IST Austria, 63p. mla: Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067. short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives of Lithium Metal Batteries, IST Austria, n.d. date_created: 2020-06-30T07:37:39Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T09:20:36Z day: '01' ddc: - '540' department: - _id: StFr doi: 10.15479/AT:ISTA:8067 file: - access_level: open_access checksum: d183ca1465a1cbb4f8db27875cd156f7 content_type: application/pdf creator: dernst date_created: 2020-07-02T07:36:04Z date_updated: 2020-07-14T12:48:08Z file_id: '8076' file_name: 20200612_JPS_review_Li_metal_submitted.pdf file_size: 2612498 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' keyword: - Battery - Lithium metal - Lithium-sulphur - Lithium-air - All-solid-state language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '63' publication_identifier: issn: - 2664-1690 publication_status: submitted publisher: IST Austria related_material: record: - id: '8361' relation: later_version status: public status: public title: Current status and future perspectives of Lithium metal batteries type: technical_report user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8361' abstract: - lang: eng text: With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7. acknowledgement: A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria. article_number: '228803' article_processing_charge: No article_type: original author: - first_name: Alberto full_name: Varzi, Alberto last_name: Varzi orcid: 0000-0001-5069-0589 - first_name: Katharina full_name: Thanner, Katharina last_name: Thanner orcid: 0000-0001-5394-2323 - first_name: Roberto full_name: Scipioni, Roberto last_name: Scipioni orcid: 0000-0003-1926-421X - first_name: Daniele full_name: Di Lecce, Daniele last_name: Di Lecce - first_name: Jusef full_name: Hassoun, Jusef last_name: Hassoun - first_name: Susanne full_name: Dörfler, Susanne last_name: Dörfler - first_name: Holger full_name: Altheus, Holger last_name: Altheus - first_name: Stefan full_name: Kaskel, Stefan last_name: Kaskel - first_name: Christian full_name: Prehal, Christian last_name: Prehal orcid: 0000-0003-0654-0940 - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803 apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803 chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803. ieee: A. Varzi et al., “Current status and future perspectives of lithium metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier, 2020. ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803. mla: Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier, 2020, doi:10.1016/j.jpowsour.2020.228803. short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020). date_created: 2020-09-10T10:48:40Z date_published: 2020-12-31T00:00:00Z date_updated: 2023-08-22T09:20:37Z day: '31' department: - _id: StFr doi: 10.1016/j.jpowsour.2020.228803 external_id: isi: - '000593857300001' intvolume: ' 480' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jpowsour.2020.228803 month: '12' oa: 1 oa_version: Published Version publication: Journal of Power Sources publication_identifier: issn: - 0378-7753 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '8067' relation: earlier_version status: public status: public title: Current status and future perspectives of lithium metal batteries type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 480 year: '2020' ... --- _id: '14028' abstract: - lang: eng text: 'The present review addresses the technical advances and the theoretical developments to realize and rationalize attosecond-science experiments that reveal a new dynamical time scale (10−15-10−18 s), with a particular emphasis on molecular systems and the implications of attosecond processes for chemical dynamics. After a brief outline of the theoretical framework for treating non-perturbative phenomena in Section 2, we introduce the physical mechanisms underlying high-harmonic generation and attosecond technology. The relevant technological developments and experimental schemes are covered in Section 3. Throughout the remainder of the chapter, we report on selected applications in molecular attosecond physics, thereby addressing specific phenomena mediated by purely electronic dynamics: charge localization in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic spectroscopy, and delays in molecular photoionization.' article_processing_charge: No author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. doi:10.48550/arXiv.2002.02111 apa: Baykusheva, D. R., & Wörner, H. J. (n.d.). Attosecond molecular spectroscopy and dynamics. https://doi.org/10.48550/arXiv.2002.02111 chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Spectroscopy and Dynamics,” n.d. https://doi.org/10.48550/arXiv.2002.02111. ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond molecular spectroscopy and dynamics.” . ista: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. 10.48550/arXiv.2002.02111. mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. Attosecond Molecular Spectroscopy and Dynamics. doi:10.48550/arXiv.2002.02111. short: D.R. Baykusheva, H.J. Wörner, (n.d.). date_created: 2023-08-10T06:47:45Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-22T09:17:34Z day: '01' doi: 10.48550/arXiv.2002.02111 extern: '1' external_id: arxiv: - '2002.02111' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2002.02111 month: '02' oa: 1 oa_version: Preprint page: '2002.02111' publication_status: submitted status: public title: Attosecond molecular spectroscopy and dynamics type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8529' abstract: - lang: eng text: Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform. acknowledged_ssus: - _id: NanoFab acknowledgement: We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET). article_number: '4460' article_processing_charge: No article_type: original author: - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 2020;11. doi:10.1038/s41467-020-18269-z apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18269-z chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z. ieee: G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460. mla: Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460, Springer Nature, 2020, doi:10.1038/s41467-020-18269-z. short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020). date_created: 2020-09-18T10:56:20Z date_published: 2020-09-08T00:00:00Z date_updated: 2023-08-22T09:27:12Z day: '08' ddc: - '530' department: - _id: JoFi doi: 10.1038/s41467-020-18269-z ec_funded: 1 external_id: isi: - '000577280200001' file: - access_level: open_access checksum: 88f92544889eb18bb38e25629a422a86 content_type: application/pdf creator: dernst date_created: 2020-09-18T13:02:37Z date_updated: 2020-09-18T13:02:37Z file_id: '8530' file_name: 2020_NatureComm_Arnold.pdf file_size: 1002818 relation: main_file success: 1 file_date_updated: 2020-09-18T13:02:37Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: 2671EB66-B435-11E9-9278-68D0E5697425 name: Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-020-18912-9 - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/ record: - id: '13056' relation: research_data status: public status: public title: Converting microwave and telecom photons with a silicon photonic nanomechanical interface tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8535' abstract: - lang: eng text: We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation. acknowledged_ssus: - _id: ScienComp acknowledgement: We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385. article_number: '65' article_processing_charge: No article_type: original author: - first_name: Tomas full_name: Skrivan, Tomas id: 486A5A46-F248-11E8-B48F-1D18A9856A87 last_name: Skrivan - first_name: Andreas full_name: Soderstrom, Andreas last_name: Soderstrom - first_name: John full_name: Johansson, John last_name: Johansson - first_name: Christoph full_name: Sprenger, Christoph last_name: Sprenger - first_name: Ken full_name: Museth, Ken last_name: Museth - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466' apa: 'Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., & Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392466' chicago: 'Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.' ieee: 'T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.' ista: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.' mla: 'Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.' short: T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020). date_created: 2020-09-20T22:01:37Z date_published: 2020-07-08T00:00:00Z date_updated: 2023-08-22T09:28:27Z day: '08' ddc: - '000' department: - _id: ChWo doi: 10.1145/3386569.3392466 ec_funded: 1 external_id: isi: - '000583700300038' file: - access_level: open_access checksum: c3a680893f01cc4a9e961ff0a4cfa12f content_type: application/pdf creator: dernst date_created: 2020-09-21T07:51:44Z date_updated: 2020-09-21T07:51:44Z file_id: '8541' file_name: 2020_ACM_Skrivan.pdf file_size: 20223953 relation: main_file success: 1 file_date_updated: 2020-09-21T07:51:44Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 39 year: '2020' ... --- _id: '8539' abstract: - lang: eng text: Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions. - lang: fre text: "Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. " article_processing_charge: No article_type: original author: - first_name: C. full_name: Su, C. last_name: Su - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao - first_name: C. full_name: Zhong, C. last_name: Zhong citation: ama: Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671. doi:10.24033/asens.2431 apa: Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France. https://doi.org/10.24033/asens.2431 chicago: Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431. ieee: C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020. ista: Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671. mla: Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:10.24033/asens.2431. short: C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671. date_created: 2020-09-20T22:01:38Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-08-22T09:27:57Z day: '01' department: - _id: TaHa doi: 10.24033/asens.2431 external_id: arxiv: - '1708.08013' isi: - '000592182600004' intvolume: ' 53' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.08013 month: '06' oa: 1 oa_version: Preprint page: 663-671 publication: Annales Scientifiques de l'Ecole Normale Superieure publication_identifier: issn: - 0012-9593 publication_status: published publisher: Société Mathématique de France quality_controlled: '1' scopus_import: '1' status: public title: On the K-theory stable bases of the springer resolution type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 53 year: '2020' ... --- _id: '14000' abstract: - lang: eng text: This chapter presents an overview of the state of the art in attosecond time-resolved spectroscopy. The theoretical foundations of strong-field light–matter interaction and attosecond pulse generation are described. The enabling laser technologies are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization to the generation and characterization of attosecond pulses. The applications of attosecond pulses and pulse trains in electron- or ion-imaging experiments are presented, followed by attosecond electron spectroscopy in larger molecules. After this, high-harmonic spectroscopy and its applications to probing charge migration on attosecond time scales is reviewed. The rapidly evolving field of molecular photoionization delays is discussed. Finally, the applications of attosecond transient absorption to probing molecular dynamics are presented. article_processing_charge: No author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: 'Baykusheva DR, Wörner HJ. Attosecond Molecular Dynamics and Spectroscopy. In: Marquardt R, Quack M, eds. Molecular Spectroscopy and Quantum Dynamics. 1st ed. Elsevier; 2020:113-161. doi:10.1016/b978-0-12-817234-6.00009-x' apa: Baykusheva, D. R., & Wörner, H. J. (2020). Attosecond Molecular Dynamics and Spectroscopy. In R. Marquardt & M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics (1st ed., pp. 113–161). Elsevier. https://doi.org/10.1016/b978-0-12-817234-6.00009-x chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” In Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., 113–61. Elsevier, 2020. https://doi.org/10.1016/b978-0-12-817234-6.00009-x. ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond Molecular Dynamics and Spectroscopy,” in Molecular Spectroscopy and Quantum Dynamics, 1st ed., R. Marquardt and M. Quack, Eds. Elsevier, 2020, pp. 113–161. ista: 'Baykusheva DR, Wörner HJ. 2020.Attosecond Molecular Dynamics and Spectroscopy. In: Molecular Spectroscopy and Quantum Dynamics. , 113–161.' mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., Elsevier, 2020, pp. 113–61, doi:10.1016/b978-0-12-817234-6.00009-x. short: D.R. Baykusheva, H.J. Wörner, in:, R. Marquardt, M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics, 1st ed., Elsevier, 2020, pp. 113–161. date_created: 2023-08-09T13:10:23Z date_published: 2020-09-25T00:00:00Z date_updated: 2023-08-22T09:25:07Z day: '25' doi: 10.1016/b978-0-12-817234-6.00009-x edition: '1' editor: - first_name: Roberto full_name: Marquardt, Roberto last_name: Marquardt - first_name: Martin full_name: Quack, Martin last_name: Quack extern: '1' language: - iso: eng month: '09' oa_version: None page: 113-161 publication: Molecular Spectroscopy and Quantum Dynamics publication_identifier: eisbn: - '0128172355' isbn: - '9780128172353' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Attosecond Molecular Dynamics and Spectroscopy type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13056' abstract: - lang: eng text: This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request. article_processing_charge: No author: - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561 apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561 chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561. ieee: G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020. ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561. mla: Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561. short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020). date_created: 2023-05-23T13:37:41Z date_published: 2020-07-27T00:00:00Z date_updated: 2023-08-22T09:27:11Z day: '27' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.3961561 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.3961562 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '8529' relation: used_in_publication status: public status: public title: Converting microwave and telecom photons with a silicon photonic nanomechanical interface tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8579' abstract: - lang: eng text: Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells. article_number: '242' article_processing_charge: No article_type: original author: - first_name: Andreea full_name: Andrei, Andreea last_name: Andrei - first_name: Yavuz full_name: Öztürk, Yavuz last_name: Öztürk - first_name: Bahia full_name: Khalfaoui-Hassani, Bahia last_name: Khalfaoui-Hassani - first_name: Juna full_name: Rauch, Juna last_name: Rauch - first_name: Dorian full_name: Marckmann, Dorian last_name: Marckmann - first_name: Petru Iulian full_name: Trasnea, Petru Iulian id: D560034C-10C4-11EA-ABF4-A4B43DDC885E last_name: Trasnea - first_name: Fevzi full_name: Daldal, Fevzi last_name: Daldal - first_name: Hans-Georg full_name: Koch, Hans-Georg last_name: Koch citation: ama: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242' apa: 'Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes. MDPI. https://doi.org/10.3390/membranes10090242' chicago: 'Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.' ieee: 'A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,” Membranes, vol. 10, no. 9. MDPI, 2020.' ista: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.' mla: 'Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes, vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242.' short: A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020). date_created: 2020-09-28T08:59:26Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T09:34:06Z day: '01' ddc: - '570' department: - _id: LeSa doi: 10.3390/membranes10090242 external_id: isi: - '000581446000001' file: - access_level: open_access checksum: ceb43d7554e712dea6f36f9287271737 content_type: application/pdf creator: dernst date_created: 2020-09-28T11:36:50Z date_updated: 2020-09-28T11:36:50Z file_id: '8583' file_name: 2020_Membranes_Andrei.pdf file_size: 4612258 relation: main_file success: 1 file_date_updated: 2020-09-28T11:36:50Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Membranes publication_identifier: eissn: - '20770375' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: 'Cu homeostasis in bacteria: The ins and outs' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '8581' abstract: - lang: eng text: The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine. acknowledged_ssus: - _id: EM-Fac - _id: ScienComp acknowledgement: We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission. article_processing_charge: No article_type: original author: - first_name: Gergely full_name: Pinke, Gergely id: 4D5303E6-F248-11E8-B48F-1D18A9856A87 last_name: Pinke - first_name: Long full_name: Zhou, Long id: 3E751364-F248-11E8-B48F-1D18A9856A87 last_name: Zhou orcid: 0000-0002-1864-8951 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085. doi:10.1038/s41594-020-0503-8 apa: Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-020-0503-8 chicago: Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8. ieee: G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020. ista: Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085. mla: Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8. short: G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085. date_created: 2020-09-28T08:59:27Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-08-22T09:33:09Z day: '01' department: - _id: LeSa doi: 10.1038/s41594-020-0503-8 external_id: isi: - '000569299400004' pmid: - '32929284' intvolume: ' 27' isi: 1 issue: '11' language: - iso: eng month: '11' oa_version: None page: 1077-1085 pmid: 1 publication: Nature Structural and Molecular Biology publication_identifier: eissn: - '15459985' issn: - '15459993' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/structure-of-atpase-solved/ scopus_import: '1' status: public title: Cryo-EM structure of the entire mammalian F-type ATP synthase type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2020' ... --- _id: '8580' abstract: - lang: eng text: We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients. article_number: '9158054' article_processing_charge: No author: - first_name: Grzegorz full_name: Graff, Grzegorz last_name: Graff - first_name: Beata full_name: Graff, Beata last_name: Graff - first_name: Grzegorz full_name: Jablonski, Grzegorz id: 4483EF78-F248-11E8-B48F-1D18A9856A87 last_name: Jablonski orcid: 0000-0002-3536-9866 - first_name: Krzysztof full_name: Narkiewicz, Krzysztof last_name: Narkiewicz citation: ama: 'Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054' apa: 'Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054' chicago: 'Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.' ieee: 'G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020.' ista: 'Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054.' mla: 'Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.' short: 'G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020.' conference: end_date: 2020-07-15 location: Pisa, Italy name: 'ESGCO: European Study Group on Cardiovascular Oscillations' start_date: 2020-07-15 date_created: 2020-09-28T08:59:27Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-08-22T09:33:34Z day: '01' department: - _id: HeEd doi: 10.1109/ESGCO49734.2020.9158054 external_id: isi: - '000621172600045' isi: 1 language: - iso: eng month: '08' oa_version: None publication: '11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ' publication_identifier: isbn: - '9781728157511' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: The application of persistent homology in the analysis of heart rate variability type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '8592' abstract: - lang: eng text: Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma. acknowledgement: The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation. article_number: '2001724' article_processing_charge: No article_type: original author: - first_name: Anhao full_name: Tian, Anhao last_name: Tian - first_name: Bo full_name: Kang, Bo last_name: Kang - first_name: Baizhou full_name: Li, Baizhou last_name: Li - first_name: Biying full_name: Qiu, Biying last_name: Qiu - first_name: Wenhong full_name: Jiang, Wenhong last_name: Jiang - first_name: Fangjie full_name: Shao, Fangjie last_name: Shao - first_name: Qingqing full_name: Gao, Qingqing last_name: Gao - first_name: Rui full_name: Liu, Rui last_name: Liu - first_name: Chengwei full_name: Cai, Chengwei last_name: Cai - first_name: Rui full_name: Jing, Rui last_name: Jing - first_name: Wei full_name: Wang, Wei last_name: Wang - first_name: Pengxiang full_name: Chen, Pengxiang last_name: Chen - first_name: Qinghui full_name: Liang, Qinghui last_name: Liang - first_name: Lili full_name: Bao, Lili last_name: Bao - first_name: Jianghong full_name: Man, Jianghong last_name: Man - first_name: Yan full_name: Wang, Yan last_name: Wang - first_name: Yu full_name: Shi, Yu last_name: Shi - first_name: Jin full_name: Li, Jin last_name: Li - first_name: Minmin full_name: Yang, Minmin last_name: Yang - first_name: Lisha full_name: Wang, Lisha last_name: Wang - first_name: Jianmin full_name: Zhang, Jianmin last_name: Zhang - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Junming full_name: Zhu, Junming last_name: Zhu - first_name: Xiuwu full_name: Bian, Xiuwu last_name: Bian - first_name: Ying‐Jie full_name: Wang, Ying‐Jie last_name: Wang - first_name: Chong full_name: Liu, Chong last_name: Liu citation: ama: Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724 apa: Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. Wiley. https://doi.org/10.1002/advs.202001724 chicago: Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724. ieee: A. Tian et al., “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020. ista: Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724. mla: Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724. short: A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020). date_created: 2020-10-01T09:44:13Z date_published: 2020-11-04T00:00:00Z date_updated: 2023-08-22T09:53:01Z day: '04' ddc: - '570' department: - _id: SiHi doi: 10.1002/advs.202001724 ec_funded: 1 external_id: isi: - '000573860700001' file: - access_level: open_access checksum: 92818c23ecc70e35acfa671f3cfb9909 content_type: application/pdf creator: dernst date_created: 2020-12-10T14:07:24Z date_updated: 2020-12-10T14:07:24Z file_id: '8938' file_name: 2020_AdvScience_Tian.pdf file_size: 7835833 relation: main_file success: 1 file_date_updated: 2020-12-10T14:07:24Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '21' keyword: - General Engineering - General Physics and Astronomy - General Materials Science - Medicine (miscellaneous) - General Chemical Engineering - Biochemistry - Genetics and Molecular Biology (miscellaneous) language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Advanced Science publication_identifier: issn: - 2198-3844 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 year: '2020' ... --- _id: '8568' abstract: - lang: eng text: Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries. article_number: '4838' article_processing_charge: No article_type: original author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Harald full_name: Fitzek, Harald last_name: Fitzek - first_name: Gerald full_name: Kothleitner, Gerald last_name: Kothleitner - first_name: Volker full_name: Presser, Volker last_name: Presser - first_name: Bernhard full_name: Gollas, Bernhard last_name: Gollas - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Qamar full_name: Abbas, Qamar last_name: Abbas citation: ama: Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 2020;11. doi:10.1038/s41467-020-18610-6 apa: Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6 chicago: Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6. ieee: C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838. mla: Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer Nature, 2020, doi:10.1038/s41467-020-18610-6. short: C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020). date_created: 2020-09-25T07:23:13Z date_published: 2020-09-24T00:00:00Z date_updated: 2023-08-22T09:37:24Z day: '24' ddc: - '530' department: - _id: StFr doi: 10.1038/s41467-020-18610-6 external_id: isi: - '000573756600004' file: - access_level: open_access checksum: eada7bc8dd16a49390137cff882ef328 content_type: application/pdf creator: dernst date_created: 2020-09-28T13:16:15Z date_updated: 2020-09-28T13:16:15Z file_id: '8585' file_name: 2020_NatureComm_Prehal.pdf file_size: 1822469 relation: main_file success: 1 file_date_updated: 2020-09-28T13:16:15Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-020-19720-x status: public title: Persistent and reversible solid iodine electrodeposition in nanoporous carbons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8643' abstract: - lang: eng text: The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors. acknowledgement: 'We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).' article_number: '16220' article_processing_charge: No article_type: original author: - first_name: Alfonso full_name: Deichler, Alfonso last_name: Deichler - first_name: Denisse full_name: Carrasco, Denisse last_name: Carrasco - first_name: Luciana full_name: Lopez-Jury, Luciana last_name: Lopez-Jury - first_name: Tomas A full_name: Vega Zuniga, Tomas A id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87 last_name: Vega Zuniga - first_name: Natalia full_name: Marquez, Natalia last_name: Marquez - first_name: Jorge full_name: Mpodozis, Jorge last_name: Mpodozis - first_name: Gonzalo full_name: Marin, Gonzalo last_name: Marin citation: ama: Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0 apa: Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0 chicago: Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0. ieee: A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020. ista: Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220. mla: Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0. short: A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020). date_created: 2020-10-11T22:01:14Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T09:58:21Z day: '01' ddc: - '570' department: - _id: MaJö doi: 10.1038/s41598-020-72848-0 external_id: isi: - '000577142600032' file: - access_level: open_access checksum: f6dd99954f1c0ffb4da5a1d2d739bf31 content_type: application/pdf creator: dernst date_created: 2020-10-12T12:39:10Z date_updated: 2020-10-12T12:39:10Z file_id: '8651' file_name: 2020_ScientificReport_Deichler.pdf file_size: 3906744 relation: main_file success: 1 file_date_updated: 2020-10-12T12:39:10Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '8645' abstract: - lang: eng text: 'Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.' acknowledgement: 'This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ' article_processing_charge: No article_type: original author: - first_name: Laura A full_name: Esteban, Laura A last_name: Esteban - first_name: Lyubov R full_name: Lonishin, Lyubov R last_name: Lonishin - first_name: Daniil M full_name: Bobrovskiy, Daniil M last_name: Bobrovskiy - first_name: Gregory full_name: Leleytner, Gregory last_name: Leleytner - first_name: Natalya S full_name: Bogatyreva, Natalya S last_name: Bogatyreva - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: 'Dmitry N ' full_name: 'Ivankov, Dmitry N ' last_name: Ivankov citation: ama: 'Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841' apa: 'Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841' chicago: 'Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.' ieee: 'L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.' ista: 'Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.' mla: 'Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.' short: L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962. date_created: 2020-10-11T22:01:14Z date_published: 2020-03-15T00:00:00Z date_updated: 2023-08-22T09:57:29Z day: '15' ddc: - '000' - '570' department: - _id: FyKo doi: 10.1093/bioinformatics/btz841 ec_funded: 1 external_id: isi: - '000538696800054' pmid: - '31742320' file: - access_level: open_access checksum: 21d6f71839deb3b83e4a356193f72767 content_type: application/pdf creator: dernst date_created: 2020-10-12T12:02:09Z date_updated: 2020-10-12T12:02:09Z file_id: '8649' file_name: 2020_Bioinformatics_Esteban.pdf file_size: 308341 relation: main_file success: 1 file_date_updated: 2020-10-12T12:02:09Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1960-1962 pmid: 1 project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Bioinformatics publication_identifier: eissn: - 1460-2059 issn: - 1367-4803 publication_status: published publisher: Oxford Academic quality_controlled: '1' scopus_import: '1' status: public title: 'HypercubeME: Two hundred million combinatorially complete datasets from a single experiment' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 36 year: '2020' ... --- _id: '8597' abstract: - lang: eng text: Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy. acknowledgement: I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions. article_number: '065005' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 citation: ama: Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db apa: Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abb2db chicago: Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing, 2020. https://doi.org/10.1088/1478-3975/abb2db. ieee: J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP Publishing, 2020. ista: Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005. mla: Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db. short: J. Merrin, Physical Biology 17 (2020). date_created: 2020-10-04T22:01:35Z date_published: 2020-09-23T00:00:00Z date_updated: 2023-08-22T09:53:29Z day: '23' ddc: - '510' - '570' department: - _id: NanoFab doi: 10.1088/1478-3975/abb2db external_id: isi: - '000575539700001' file: - access_level: open_access checksum: fec9bdd355ed349f09990faab20838a7 content_type: application/pdf creator: dernst date_created: 2020-10-05T13:53:59Z date_updated: 2020-10-05T13:53:59Z file_id: '8609' file_name: 2020_PhysBio_Merrin.pdf file_size: 1667111 relation: main_file success: 1 file_date_updated: 2020-10-05T13:53:59Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Physical Biology publication_identifier: eissn: - '14783975' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2020' ... --- _id: '8674' abstract: - lang: eng text: 'Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections.' acknowledgement: We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.). article_processing_charge: No article_type: original author: - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Lucie full_name: Bard, Lucie last_name: Bard - first_name: Aude full_name: Panatier, Aude last_name: Panatier - first_name: James P. full_name: Reynolds, James P. last_name: Reynolds - first_name: Olga full_name: Kopach, Olga last_name: Kopach - first_name: Nikolay I. full_name: Medvedev, Nikolay I. last_name: Medvedev - first_name: Daniel full_name: Minge, Daniel last_name: Minge - first_name: Michel K. full_name: Herde, Michel K. last_name: Herde - first_name: Stefanie full_name: Anders, Stefanie last_name: Anders - first_name: Igor full_name: Kraev, Igor last_name: Kraev - first_name: Janosch P. full_name: Heller, Janosch P. last_name: Heller - first_name: Sylvain full_name: Rama, Sylvain last_name: Rama - first_name: Kaiyu full_name: Zheng, Kaiyu last_name: Zheng - first_name: Thomas P. full_name: Jensen, Thomas P. last_name: Jensen - first_name: Inmaculada full_name: Sanchez-Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez-Romero - first_name: Colin J. full_name: Jackson, Colin J. last_name: Jackson - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Ole Petter full_name: Ottersen, Ole Petter last_name: Ottersen - first_name: Erlend Arnulf full_name: Nagelhus, Erlend Arnulf last_name: Nagelhus - first_name: Stephane H.R. full_name: Oliet, Stephane H.R. last_name: Oliet - first_name: Michael G. full_name: Stewart, Michael G. last_name: Stewart - first_name: U. VAlentin full_name: Nägerl, U. VAlentin last_name: Nägerl - first_name: 'Dmitri A. ' full_name: 'Rusakov, Dmitri A. ' last_name: Rusakov citation: ama: Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030 apa: Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030 chicago: Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030. ieee: C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020. ista: Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11. mla: Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030. short: C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11. date_created: 2020-10-18T22:01:38Z date_published: 2020-12-09T00:00:00Z date_updated: 2023-08-22T09:59:29Z day: '09' ddc: - '570' department: - _id: HaJa doi: 10.1016/j.neuron.2020.08.030 external_id: isi: - '000603428000010' pmid: - '32976770' file: - access_level: open_access checksum: 054562bb50165ef9a1f46631c1c5e36b content_type: application/pdf creator: dernst date_created: 2020-12-10T14:42:09Z date_updated: 2020-12-10T14:42:09Z file_id: '8939' file_name: 2020_Neuron_Henneberger.pdf file_size: 7518960 relation: main_file success: 1 file_date_updated: 2020-12-10T14:42:09Z has_accepted_license: '1' intvolume: ' 108' isi: 1 issue: '5' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: P919-936.E11 pmid: 1 publication: Neuron publication_identifier: eissn: - '10974199' issn: - '08966273' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 108 year: '2020' ... --- _id: '8652' abstract: - lang: eng text: Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules. acknowledgement: "This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON)." article_number: '178' article_processing_charge: Yes article_type: original author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8 apa: Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8 chicago: Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8. ieee: A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020. ista: Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178. mla: Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8. short: A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020). date_created: 2020-10-13T09:48:59Z date_published: 2020-10-09T00:00:00Z date_updated: 2023-08-22T09:58:46Z day: '09' ddc: - '530' department: - _id: MiLe doi: 10.1038/s42005-020-00445-8 ec_funded: 1 external_id: isi: - '000581681000001' file: - access_level: open_access checksum: 60cd35b99f0780acffc7b6060e49ec8b content_type: application/pdf creator: dernst date_created: 2020-10-14T15:16:28Z date_updated: 2020-10-14T15:16:28Z file_id: '8662' file_name: 2020_CommPhysics_Ghazaryan.pdf file_size: 1462934 relation: main_file success: 1 file_date_updated: 2020-10-14T15:16:28Z has_accepted_license: '1' intvolume: ' 3' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Communications Physics publication_identifier: issn: - 2399-3650 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Filtering spins by scattering from a lattice of point magnets tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 3 year: '2020' ... --- _id: '8669' abstract: - lang: eng text: Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development. article_number: '5037' article_processing_charge: No article_type: original author: - first_name: Magdalena K. full_name: Sznurkowska, Magdalena K. last_name: Sznurkowska - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Roberta full_name: Azzarelli, Roberta last_name: Azzarelli - first_name: Lemonia full_name: Chatzeli, Lemonia last_name: Chatzeli - first_name: Tatsuro full_name: Ikeda, Tatsuro last_name: Ikeda - first_name: Shosei full_name: Yoshida, Shosei last_name: Yoshida - first_name: Anna full_name: Philpott, Anna last_name: Philpott - first_name: Benjamin D full_name: Simons, Benjamin D last_name: Simons citation: ama: Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3 apa: Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3 chicago: Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3. ieee: M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037. mla: Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3. short: M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020). date_created: 2020-10-18T22:01:35Z date_published: 2020-10-07T00:00:00Z date_updated: 2023-08-22T10:18:17Z day: '07' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41467-020-18837-3 external_id: isi: - '000577244600003' pmid: - '33028844' file: - access_level: open_access checksum: 0ecc0eab72d2d50694852579611a6624 content_type: application/pdf creator: dernst date_created: 2020-10-19T11:27:46Z date_updated: 2020-10-19T11:27:46Z file_id: '8677' file_name: 2020_NatureComm_Sznurkowska.pdf file_size: 5540540 relation: main_file success: 1 file_date_updated: 2020-10-19T11:27:46Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Tracing the cellular basis of islet specification in mouse pancreas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8672' abstract: - lang: eng text: Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions. acknowledgement: This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015). article_processing_charge: No article_type: original author: - first_name: Agathe full_name: Chaigne, Agathe last_name: Chaigne - first_name: Céline full_name: Labouesse, Céline last_name: Labouesse - first_name: Ian J. full_name: White, Ian J. last_name: White - first_name: Meghan full_name: Agnew, Meghan last_name: Agnew - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Kevin J. full_name: Chalut, Kevin J. last_name: Chalut - first_name: Ewa K. full_name: Paluch, Ewa K. last_name: Paluch citation: ama: Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001 apa: Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001 chicago: Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001. ieee: A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020. ista: Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208. mla: Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001. short: A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208. date_created: 2020-10-18T22:01:37Z date_published: 2020-10-26T00:00:00Z date_updated: 2023-08-22T10:16:58Z day: '26' ddc: - '570' department: - _id: EdHa doi: 10.1016/j.devcel.2020.09.001 external_id: isi: - '000582501100012' pmid: - '32979313' file: - access_level: open_access checksum: 88e1a031a61689165d19a19c2f16d795 content_type: application/pdf creator: dernst date_created: 2021-02-04T10:20:02Z date_updated: 2021-02-04T10:20:02Z file_id: '9086' file_name: 2020_DevelopmCell_Chaigne.pdf file_size: 6929686 relation: main_file success: 1 file_date_updated: 2021-02-04T10:20:02Z has_accepted_license: '1' intvolume: ' 55' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 195-208 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - '18781551' issn: - '15345807' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Abscission couples cell division to embryonic stem cell fate tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 55 year: '2020' ... --- _id: '8697' abstract: - lang: eng text: In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Michael full_name: Kniely, Michael id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87 last_name: Kniely orcid: 0000-0001-5645-4333 citation: ama: Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728 apa: Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728 chicago: Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728. ieee: J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020. ista: Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772. mla: Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728. short: J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772. date_created: 2020-10-25T23:01:16Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-08-22T10:38:38Z day: '01' ddc: - '510' department: - _id: JuFi doi: 10.1088/1361-6544/ab9728 external_id: arxiv: - '1906.12245' isi: - '000576492700001' file: - access_level: open_access checksum: ed90bc6eb5f32ee6157fef7f3aabc057 content_type: application/pdf creator: cziletti date_created: 2020-10-27T12:09:57Z date_updated: 2020-10-27T12:09:57Z file_id: '8710' file_name: 2020_Nonlinearity_Fischer.pdf file_size: 1223899 relation: main_file success: 1 file_date_updated: 2020-10-27T12:09:57Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '11' oa: 1 oa_version: Published Version page: 5733-5772 publication: Nonlinearity publication_identifier: eissn: - '13616544' issn: - '09517715' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2020' ... --- _id: '8680' abstract: - lang: eng text: Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning. acknowledgement: "We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.)." article_processing_charge: No article_type: original author: - first_name: Tony Y.-C. full_name: Tsai, Tony Y.-C. last_name: Tsai - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Peng full_name: Xia, Peng id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87 last_name: Xia orcid: 0000-0002-5419-7756 - first_name: Tugba full_name: Colak-Champollion, Tugba last_name: Colak-Champollion - first_name: Holger full_name: Knaut, Holger last_name: Knaut - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Sean G. full_name: Megason, Sean G. last_name: Megason citation: ama: Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637 apa: Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637 chicago: Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637. ieee: T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020. ista: Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116. mla: Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637. short: T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116. date_created: 2020-10-19T14:09:38Z date_published: 2020-10-02T00:00:00Z date_updated: 2023-08-22T10:36:35Z day: '02' department: - _id: CaHe doi: 10.1126/science.aba6637 ec_funded: 1 external_id: isi: - '000579169000053' intvolume: ' 370' isi: 1 issue: '6512' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/803635v1 month: '10' oa: 1 oa_version: Preprint page: 113-116 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/sticking-together/ scopus_import: '1' status: public title: An adhesion code ensures robust pattern formation during tissue morphogenesis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 370 year: '2020' ... --- _id: '8707' abstract: - lang: eng text: Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data. acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.' article_processing_charge: No article_type: original author: - first_name: Silvia full_name: ' Galan, Silvia' last_name: ' Galan' - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik orcid: 0000-0001-6617-9742 - first_name: Kai full_name: Kruse, Kai last_name: Kruse - first_name: Noelia full_name: Díaz, Noelia last_name: Díaz - first_name: Marc A full_name: Marti-Renom, Marc A last_name: Marti-Renom - first_name: Juan M full_name: Vaquerizas, Juan M last_name: Vaquerizas citation: ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y. ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020. ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255. mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y. short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255. date_created: 2020-10-25T23:01:20Z date_published: 2020-10-19T00:00:00Z date_updated: 2023-08-22T10:37:10Z day: '19' department: - _id: FyKo doi: 10.1038/s41588-020-00712-y external_id: isi: - '000579693500004' pmid: - '33077914' intvolume: ' 52' isi: 1 language: - iso: eng month: '10' oa_version: None page: 1247-1255 pmid: 1 publication: Nature Genetics publication_identifier: eissn: - '15461718' issn: - '10614036' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2020' ... --- _id: '8679' abstract: - lang: eng text: A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system. article_processing_charge: No article_type: original author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Daniela full_name: Rus, Daniela last_name: Rus - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652. doi:10.1038/s42256-020-00237-3 apa: Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3 chicago: Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3. ieee: M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” Nature Machine Intelligence, vol. 2. Springer Nature, pp. 642–652, 2020. ista: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652. mla: Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52, doi:10.1038/s42256-020-00237-3. short: M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652. date_created: 2020-10-19T13:46:06Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T10:36:06Z day: '01' department: - _id: ToHe doi: 10.1038/s42256-020-00237-3 external_id: isi: - '000583337200011' intvolume: ' 2' isi: 1 language: - iso: eng month: '10' oa_version: None page: 642-652 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Nature Machine Intelligence publication_identifier: eissn: - 2522-5839 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-deep-learning-models/ scopus_import: '1' status: public title: Neural circuit policies enabling auditable autonomy type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 2 year: '2020' ... --- _id: '8670' abstract: - lang: eng text: The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)]. acknowledgement: This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments. article_number: '102201' article_processing_charge: No article_type: original author: - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787 apa: Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787 chicago: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787. ieee: H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020. ista: Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201. mla: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787. short: H. Zhang, Journal of Mathematical Physics 61 (2020). date_created: 2020-10-18T22:01:36Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T10:32:29Z day: '01' department: - _id: JaMa doi: 10.1063/5.0022787 ec_funded: 1 external_id: arxiv: - '2007.06644' isi: - '000578529200001' intvolume: ' 61' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.06644 month: '10' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Mathematical Physics publication_identifier: issn: - '00222488' publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Equality conditions of data processing inequality for α-z Rényi relative entropies type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 61 year: '2020' ... --- _id: '8698' abstract: - lang: eng text: The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation. acknowledgement: We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.). article_processing_charge: No article_type: original author: - first_name: Ori full_name: Maoz, Ori last_name: Maoz - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Mohamad Saleh full_name: Esteki, Mohamad Saleh last_name: Esteki - first_name: Roozbeh full_name: Kiani, Roozbeh last_name: Kiani - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman citation: ama: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117 apa: Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117 chicago: Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117. ieee: O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020. ista: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073. mla: Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117. short: O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073. date_created: 2020-10-25T23:01:16Z date_published: 2020-10-06T00:00:00Z date_updated: 2023-08-22T12:11:23Z day: '06' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.1912804117 external_id: isi: - '000579045200012' pmid: - '32948691' file: - access_level: open_access checksum: c6a24fdecf3f28faf447078e7a274a88 content_type: application/pdf creator: cziletti date_created: 2020-10-27T14:57:50Z date_updated: 2020-10-27T14:57:50Z file_id: '8713' file_name: 2020_PNAS_Maoz.pdf file_size: 1755359 relation: main_file success: 1 file_date_updated: 2020-10-27T14:57:50Z has_accepted_license: '1' intvolume: ' 117' isi: 1 issue: '40' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 25066-25073 pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Learning probabilistic neural representations with randomly connected circuits tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 117 year: '2020' ... --- _id: '8704' abstract: - lang: eng text: Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E. acknowledgement: M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company. alternative_title: - ICRA article_processing_charge: No author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Daniela full_name: Rus, Daniela last_name: Rus - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: Proceedings - IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452. doi:10.1109/ICRA40945.2020.9196608' apa: 'Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In Proceedings - IEEE International Conference on Robotics and Automation (pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608' chicago: Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In Proceedings - IEEE International Conference on Robotics and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608. ieee: M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in Proceedings - IEEE International Conference on Robotics and Automation, Paris, France, 2020, pp. 5446–5452. ista: 'Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452.' mla: Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608. short: M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452. conference: end_date: 2020-08-31 location: Paris, France name: 'ICRA: International Conference on Robotics and Automation' start_date: 2020-05-31 date_created: 2020-10-25T23:01:19Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-22T10:40:15Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/ICRA40945.2020.9196608 external_id: isi: - '000712319503110' file: - access_level: open_access checksum: fccf7b986ac78046918a298cc6849a50 content_type: application/pdf creator: dernst date_created: 2020-11-06T10:58:49Z date_updated: 2020-11-06T10:58:49Z file_id: '8733' file_name: 2020_ICRA_Lechner.pdf file_size: 1070010 relation: main_file success: 1 file_date_updated: 2020-11-06T10:58:49Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 5446-5452 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings - IEEE International Conference on Robotics and Automation publication_identifier: isbn: - '9781728173955' issn: - '10504729' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '8700' abstract: - lang: eng text: Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency. acknowledgement: We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work. article_processing_charge: No article_type: original author: - first_name: E. E. full_name: Sokolova, E. E. last_name: Sokolova - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: A. V. full_name: Shuvalov, A. V. last_name: Shuvalov - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088 apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320050088 chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320050088. ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020. ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748. mla: Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088. short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748. date_created: 2020-10-25T23:01:17Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T10:39:38Z day: '01' department: - _id: FyKo doi: 10.1134/S0026893320050088 external_id: isi: - '000579441200009' intvolume: ' 54' isi: 1 issue: '5' language: - iso: eng month: '09' oa_version: None page: 739-748 publication: Molecular Biology publication_identifier: eissn: - '16083245' issn: - '00268933' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8701' relation: original status: public scopus_import: '1' status: public title: The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 54 year: '2020' ... --- _id: '8701' abstract: - lang: eng text: Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency. article_processing_charge: No article_type: original author: - first_name: E. E. full_name: Sokolova, E. E. last_name: Sokolova - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: A. V. full_name: Shuvalov, A. V. last_name: Shuvalov - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080 apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420050080 chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080. ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020. ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848. mla: Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:10.31857/S0026898420050080. short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848. date_created: 2020-10-25T23:01:17Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T10:39:37Z day: '01' department: - _id: FyKo doi: 10.31857/S0026898420050080 external_id: pmid: - '33009793' intvolume: ' 54' issue: '5' language: - iso: rus month: '09' oa_version: None page: 837-848 pmid: 1 publication: Molekuliarnaia biologiia publication_identifier: issn: - '00268984' publication_status: published publisher: Russian Academy of Sciences quality_controlled: '1' related_material: record: - id: '8700' relation: translation status: public scopus_import: '1' status: public title: The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 54 year: '2020' ... --- _id: '14096' abstract: - lang: eng text: A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources. article_number: '2011.06630' article_processing_charge: No author: - first_name: Jamie A. P. Law-Smith full_name: Jamie A. P. Law-Smith, Jamie A. P. Law-Smith last_name: Jamie A. P. Law-Smith - first_name: Rosa Wallace full_name: Everson, Rosa Wallace last_name: Everson - first_name: Enrico Ramirez-Ruiz full_name: Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz last_name: Enrico Ramirez-Ruiz - first_name: Selma E. de full_name: Mink, Selma E. de last_name: Mink - first_name: Lieke A. C. van full_name: Son, Lieke A. C. van last_name: Son - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: Stefan full_name: Zellmann, Stefan last_name: Zellmann - first_name: Alejandro Vigna-Gómez full_name: Alejandro Vigna-Gómez, Alejandro Vigna-Gómez last_name: Alejandro Vigna-Gómez - first_name: Mathieu full_name: Renzo, Mathieu last_name: Renzo - first_name: Samantha full_name: Wu, Samantha last_name: Wu - first_name: Sophie L. full_name: Schrøder, Sophie L. last_name: Schrøder - first_name: Ryan J. full_name: Foley, Ryan J. last_name: Foley - first_name: Tenley Hutchinson-Smith full_name: Tenley Hutchinson-Smith, Tenley Hutchinson-Smith last_name: Tenley Hutchinson-Smith citation: ama: Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, et al. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. doi:10.48550/arXiv.2011.06630 apa: Jamie A. P. Law-Smith, J. A. P. L.-S., Everson, R. W., Enrico Ramirez-Ruiz, E. R.-R., Mink, S. E. de, Son, L. A. C. van, Götberg, Y. L. L., … Tenley Hutchinson-Smith, T. H.-S. (n.d.). Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. https://doi.org/10.48550/arXiv.2011.06630 chicago: Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, Rosa Wallace Everson, Enrico Ramirez-Ruiz Enrico Ramirez-Ruiz, Selma E. de Mink, Lieke A. C. van Son, Ylva Louise Linsdotter Götberg, Stefan Zellmann, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2011.06630. ieee: J. A. P. L.-S. Jamie A. P. Law-Smith et al., “Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics,” arXiv. . ista: Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, Mink SE de, Son LAC van, Götberg YLL, Zellmann S, Alejandro Vigna-Gómez AV-G, Renzo M, Wu S, Schrøder SL, Foley RJ, Tenley Hutchinson-Smith TH-S. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv, 2011.06630. mla: Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, 2011.06630, doi:10.48550/arXiv.2011.06630. short: J.A.P.L.-S. Jamie A. P. Law-Smith, R.W. Everson, E.R.-R. Enrico Ramirez-Ruiz, S.E. de Mink, L.A.C. van Son, Y.L.L. Götberg, S. Zellmann, A.V.-G. Alejandro Vigna-Gómez, M. Renzo, S. Wu, S.L. Schrøder, R.J. Foley, T.H.-S. Tenley Hutchinson-Smith, ArXiv (n.d.). date_created: 2023-08-21T10:10:41Z date_published: 2020-11-12T00:00:00Z date_updated: 2023-08-22T11:03:00Z day: '12' doi: 10.48550/arXiv.2011.06630 external_id: arxiv: - '2011.06630' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2011.06630 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8699' abstract: - lang: eng text: In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling. acknowledgement: 'We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.' article_processing_charge: No article_type: original author: - first_name: Eugenio full_name: Paris, Eugenio last_name: Paris - first_name: Yi full_name: Tseng, Yi last_name: Tseng - first_name: Ekaterina full_name: Paerschke, Ekaterina id: 8275014E-6063-11E9-9B7F-6338E6697425 last_name: Paerschke orcid: 0000-0003-0853-8182 - first_name: Wenliang full_name: Zhang, Wenliang last_name: Zhang - first_name: Mary H full_name: Upton, Mary H last_name: Upton - first_name: Anna full_name: Efimenko, Anna last_name: Efimenko - first_name: Katharina full_name: Rolfs, Katharina last_name: Rolfs - first_name: Daniel E full_name: McNally, Daniel E last_name: McNally - first_name: Laura full_name: Maurel, Laura last_name: Maurel - first_name: Muntaser full_name: Naamneh, Muntaser last_name: Naamneh - first_name: Marco full_name: Caputo, Marco last_name: Caputo - first_name: Vladimir N full_name: Strocov, Vladimir N last_name: Strocov - first_name: Zhiming full_name: Wang, Zhiming last_name: Wang - first_name: Diego full_name: Casa, Diego last_name: Casa - first_name: Christof W full_name: Schneider, Christof W last_name: Schneider - first_name: Ekaterina full_name: Pomjakushina, Ekaterina last_name: Pomjakushina - first_name: Krzysztof full_name: Wohlfeld, Krzysztof last_name: Wohlfeld - first_name: Milan full_name: Radovic, Milan last_name: Radovic - first_name: Thorsten full_name: Schmitt, Thorsten last_name: Schmitt citation: ama: Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117 apa: Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117 chicago: Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117. ieee: E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020. ista: Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770. mla: Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117. short: E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770. date_created: 2020-10-25T23:01:17Z date_published: 2020-10-06T00:00:00Z date_updated: 2023-08-22T12:11:52Z day: '06' ddc: - '530' department: - _id: MiLe doi: 10.1073/pnas.2012043117 ec_funded: 1 external_id: arxiv: - '2009.12262' isi: - '000579059100029' pmid: - '32958669' file: - access_level: open_access checksum: 1638fa36b442e2868576c6dd7d6dc505 content_type: application/pdf creator: cziletti date_created: 2020-10-28T11:53:12Z date_updated: 2020-10-28T11:53:12Z file_id: '8715' file_name: 2020_PNAS_Paris.pdf file_size: 1176522 relation: main_file success: 1 file_date_updated: 2020-10-28T11:53:12Z has_accepted_license: '1' intvolume: ' 117' isi: 1 issue: '40' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 24764-24770 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Strain engineering of the charge and spin-orbital interactions in Sr2IrO4 tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 117 year: '2020' ... --- _id: '8737' abstract: - lang: eng text: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions. acknowledged_ssus: - _id: LifeSc - _id: EM-Fac acknowledgement: We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385 article_number: eabc4209 article_processing_charge: No article_type: original author: - first_name: Domen full_name: Kampjut, Domen id: 37233050-F248-11E8-B48F-1D18A9856A87 last_name: Kampjut - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516). doi:10.1126/science.abc4209 apa: Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abc4209 chicago: Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.abc4209. ieee: D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, 2020. ista: Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209. mla: Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209. short: D. Kampjut, L.A. Sazanov, Science 370 (2020). date_created: 2020-11-08T23:01:23Z date_published: 2020-10-30T00:00:00Z date_updated: 2023-08-22T12:35:38Z day: '30' ddc: - '572' department: - _id: LeSa doi: 10.1126/science.abc4209 ec_funded: 1 external_id: isi: - '000583031800004' pmid: - '32972993' file: - access_level: open_access checksum: 658ba90979ca9528a2efdfac8547047a content_type: application/pdf creator: lsazanov date_created: 2020-11-26T18:47:58Z date_updated: 2020-11-26T18:47:58Z file_id: '8820' file_name: Full_manuscript_with_SI_opt_red.pdf file_size: 7618987 relation: main_file success: 1 file_date_updated: 2020-11-26T18:47:58Z has_accepted_license: '1' intvolume: ' 370' isi: 1 issue: '6516' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Science publication_identifier: eissn: - '10959203' publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: The coupling mechanism of mammalian respiratory complex I type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 370 year: '2020' ... --- _id: '8722' abstract: - lang: eng text: "Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy." article_processing_charge: No author: - first_name: Shigang full_name: Li, Shigang last_name: Li - first_name: Tal Ben-Nun full_name: Tal Ben-Nun, Tal Ben-Nun last_name: Tal Ben-Nun - first_name: Salvatore Di full_name: Girolamo, Salvatore Di last_name: Girolamo - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Torsten full_name: Hoefler, Torsten last_name: Hoefler citation: ama: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528' apa: 'Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528' chicago: Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 45–61. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528. ieee: S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 45–61. ista: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61.' mla: Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528. short: S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61. conference: end_date: 2020-02-26 location: San Diego, CA, United States name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming' start_date: 2020-02-22 date_created: 2020-11-05T15:25:30Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-22T12:13:48Z day: '01' department: - _id: DaAl doi: 10.1145/3332466.3374528 ec_funded: 1 external_id: arxiv: - '1908.04207' isi: - '000564476500004' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.04207 month: '02' oa: 1 oa_version: Preprint page: 45-61 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: Taming unbalanced training workloads in deep learning with partial collective operations type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '8744' abstract: - lang: eng text: Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding. acknowledgement: 'We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.' article_number: '5569' article_processing_charge: No article_type: original author: - first_name: Linda full_name: Schulte, Linda last_name: Schulte - first_name: Jiafei full_name: Mao, Jiafei last_name: Mao - first_name: Julian full_name: Reitz, Julian last_name: Reitz - first_name: Sridhar full_name: Sreeramulu, Sridhar last_name: Sreeramulu - first_name: Denis full_name: Kudlinzki, Denis last_name: Kudlinzki - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Jakob full_name: Meier-Credo, Jakob last_name: Meier-Credo - first_name: Krishna full_name: Saxena, Krishna last_name: Saxena - first_name: Florian full_name: Buhr, Florian last_name: Buhr - first_name: Julian D. full_name: Langer, Julian D. last_name: Langer - first_name: Martin full_name: Blackledge, Martin last_name: Blackledge - first_name: Achilleas S. full_name: Frangakis, Achilleas S. last_name: Frangakis - first_name: Clemens full_name: Glaubitz, Clemens last_name: Glaubitz - first_name: Harald full_name: Schwalbe, Harald last_name: Schwalbe citation: ama: Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x apa: Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x chicago: Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x. ieee: L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569. mla: Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x. short: L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020). date_created: 2020-11-09T07:49:36Z date_published: 2020-11-04T00:00:00Z date_updated: 2023-08-22T12:36:07Z day: '04' ddc: - '570' department: - _id: EM-Fac doi: 10.1038/s41467-020-19372-x external_id: isi: - '000592028600001' file: - access_level: open_access checksum: b2688f0347e69e6629bba582077278c5 content_type: application/pdf creator: dernst date_created: 2020-11-09T07:56:24Z date_updated: 2020-11-09T07:56:24Z file_id: '8745' file_name: 2020_NatureComm_Schulte.pdf file_size: 1670898 relation: main_file success: 1 file_date_updated: 2020-11-09T07:56:24Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cysteine oxidation and disulfide formation in the ribosomal exit tunnel tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8747' abstract: - lang: eng text: "Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites\r\nproduced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3." acknowledgement: "This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economı´a y\r\nCompetitividad through the project SEHTOP (ENE2016-77798-C4-3-R). Y. Z. and X. H., thank the China Scholarship Council for scholarship support. M. C. has received funding from the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M. I. acknowledges financial support from IST Austria. Y. L. acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement no. 754411. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat \r\nAuto`noma de Barcelona Materials Science PhD program." article_processing_charge: No article_type: original author: - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mariano full_name: Calcabrini, Mariano last_name: Calcabrini - first_name: Congcong full_name: Xing, Congcong last_name: Xing - first_name: Xu full_name: Han, Xu last_name: Han - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Zhang Y, Liu Y, Calcabrini M, et al. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 2020;8(40):14092-14099. doi:10.1039/D0TC02182B apa: Zhang, Y., Liu, Y., Calcabrini, M., Xing, C., Han, X., Arbiol, J., … Cabot, A. (2020). Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/D0TC02182B chicago: Zhang, Yu, Yu Liu, Mariano Calcabrini, Congcong Xing, Xu Han, Jordi Arbiol, Doris Cadavid, Maria Ibáñez, and Andreu Cabot. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2020. https://doi.org/10.1039/D0TC02182B. ieee: Y. Zhang et al., “Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks,” Journal of Materials Chemistry C, vol. 8, no. 40. Royal Society of Chemistry, pp. 14092–14099, 2020. ista: Zhang Y, Liu Y, Calcabrini M, Xing C, Han X, Arbiol J, Cadavid D, Ibáñez M, Cabot A. 2020. Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks. Journal of Materials Chemistry C. 8(40), 14092–14099. mla: Zhang, Yu, et al. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured Building Blocks.” Journal of Materials Chemistry C, vol. 8, no. 40, Royal Society of Chemistry, 2020, pp. 14092–99, doi:10.1039/D0TC02182B. short: Y. Zhang, Y. Liu, M. Calcabrini, C. Xing, X. Han, J. Arbiol, D. Cadavid, M. Ibáñez, A. Cabot, Journal of Materials Chemistry C 8 (2020) 14092–14099. date_created: 2020-11-09T08:37:51Z date_published: 2020-10-28T00:00:00Z date_updated: 2023-08-22T12:41:05Z day: '28' department: - _id: MaIb doi: 10.1039/D0TC02182B ec_funded: 1 external_id: isi: - '000581559100015' intvolume: ' 8' isi: 1 issue: '40' language: - iso: eng month: '10' oa_version: None page: 14092-14099 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Materials Chemistry C publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2020' ... --- _id: '14095' abstract: - lang: eng text: 'The Habitable Exoplanet Observatory, or HabEx, has been designed to be the Great Observatory of the 2030s. For the first time in human history, technologies have matured sufficiently to enable an affordable space-based telescope mission capable of discovering and characterizing Earthlike planets orbiting nearby bright sunlike stars in order to search for signs of habitability and biosignatures. Such a mission can also be equipped with instrumentation that will enable broad and exciting general astrophysics and planetary science not possible from current or planned facilities. HabEx is a space telescope with unique imaging and multi-object spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR. These capabilities allow for a broad suite of compelling science that cuts across the entire NASA astrophysics portfolio. HabEx has three primary science goals: (1) Seek out nearby worlds and explore their habitability; (2) Map out nearby planetary systems and understand the diversity of the worlds they contain; (3) Enable new explorations of astrophysical systems from our own solar system to external galaxies by extending our reach in the UV through near-IR. This Great Observatory science will be selected through a competed GO program, and will account for about 50% of the HabEx primary mission. The preferred HabEx architecture is a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph and a starshade, each with their own dedicated instrument.' article_number: '2001.06683' article_processing_charge: No author: - first_name: B. Scott full_name: Gaudi, B. Scott last_name: Gaudi - first_name: Sara full_name: Seager, Sara last_name: Seager - first_name: Bertrand full_name: Mennesson, Bertrand last_name: Mennesson - first_name: Alina full_name: Kiessling, Alina last_name: Kiessling - first_name: Keith full_name: Warfield, Keith last_name: Warfield - first_name: Kerri full_name: Cahoy, Kerri last_name: Cahoy - first_name: John T. full_name: Clarke, John T. last_name: Clarke - first_name: Shawn Domagal-Goldman full_name: Shawn Domagal-Goldman, Shawn Domagal-Goldman last_name: Shawn Domagal-Goldman - first_name: Lee full_name: Feinberg, Lee last_name: Feinberg - first_name: Olivier full_name: Guyon, Olivier last_name: Guyon - first_name: Jeremy full_name: Kasdin, Jeremy last_name: Kasdin - first_name: Dimitri full_name: Mawet, Dimitri last_name: Mawet - first_name: Peter full_name: Plavchan, Peter last_name: Plavchan - first_name: Tyler full_name: Robinson, Tyler last_name: Robinson - first_name: Leslie full_name: Rogers, Leslie last_name: Rogers - first_name: Paul full_name: Scowen, Paul last_name: Scowen - first_name: Rachel full_name: Somerville, Rachel last_name: Somerville - first_name: Karl full_name: Stapelfeldt, Karl last_name: Stapelfeldt - first_name: Christopher full_name: Stark, Christopher last_name: Stark - first_name: Daniel full_name: Stern, Daniel last_name: Stern - first_name: Margaret full_name: Turnbull, Margaret last_name: Turnbull - first_name: Rashied full_name: Amini, Rashied last_name: Amini - first_name: Gary full_name: Kuan, Gary last_name: Kuan - first_name: Stefan full_name: Martin, Stefan last_name: Martin - first_name: Rhonda full_name: Morgan, Rhonda last_name: Morgan - first_name: David full_name: Redding, David last_name: Redding - first_name: H. Philip full_name: Stahl, H. Philip last_name: Stahl - first_name: Ryan full_name: Webb, Ryan last_name: Webb - first_name: Oscar Alvarez-Salazar full_name: Oscar Alvarez-Salazar, Oscar Alvarez-Salazar last_name: Oscar Alvarez-Salazar - first_name: William L. full_name: Arnold, William L. last_name: Arnold - first_name: Manan full_name: Arya, Manan last_name: Arya - first_name: Bala full_name: Balasubramanian, Bala last_name: Balasubramanian - first_name: Mike full_name: Baysinger, Mike last_name: Baysinger - first_name: Ray full_name: Bell, Ray last_name: Bell - first_name: Chris full_name: Below, Chris last_name: Below - first_name: Jonathan full_name: Benson, Jonathan last_name: Benson - first_name: Lindsey full_name: Blais, Lindsey last_name: Blais - first_name: Jeff full_name: Booth, Jeff last_name: Booth - first_name: Robert full_name: Bourgeois, Robert last_name: Bourgeois - first_name: Case full_name: Bradford, Case last_name: Bradford - first_name: Alden full_name: Brewer, Alden last_name: Brewer - first_name: Thomas full_name: Brooks, Thomas last_name: Brooks - first_name: Eric full_name: Cady, Eric last_name: Cady - first_name: Mary full_name: Caldwell, Mary last_name: Caldwell - first_name: Rob full_name: Calvet, Rob last_name: Calvet - first_name: Steven full_name: Carr, Steven last_name: Carr - first_name: Derek full_name: Chan, Derek last_name: Chan - first_name: Velibor full_name: Cormarkovic, Velibor last_name: Cormarkovic - first_name: Keith full_name: Coste, Keith last_name: Coste - first_name: Charlie full_name: Cox, Charlie last_name: Cox - first_name: Rolf full_name: Danner, Rolf last_name: Danner - first_name: Jacqueline full_name: Davis, Jacqueline last_name: Davis - first_name: Larry full_name: Dewell, Larry last_name: Dewell - first_name: Lisa full_name: Dorsett, Lisa last_name: Dorsett - first_name: Daniel full_name: Dunn, Daniel last_name: Dunn - first_name: Matthew full_name: East, Matthew last_name: East - first_name: Michael full_name: Effinger, Michael last_name: Effinger - first_name: Ron full_name: Eng, Ron last_name: Eng - first_name: Greg full_name: Freebury, Greg last_name: Freebury - first_name: Jay full_name: Garcia, Jay last_name: Garcia - first_name: Jonathan full_name: Gaskin, Jonathan last_name: Gaskin - first_name: Suzan full_name: Greene, Suzan last_name: Greene - first_name: John full_name: Hennessy, John last_name: Hennessy - first_name: Evan full_name: Hilgemann, Evan last_name: Hilgemann - first_name: Brad full_name: Hood, Brad last_name: Hood - first_name: Wolfgang full_name: Holota, Wolfgang last_name: Holota - first_name: Scott full_name: Howe, Scott last_name: Howe - first_name: Pei full_name: Huang, Pei last_name: Huang - first_name: Tony full_name: Hull, Tony last_name: Hull - first_name: Ron full_name: Hunt, Ron last_name: Hunt - first_name: Kevin full_name: Hurd, Kevin last_name: Hurd - first_name: Sandra full_name: Johnson, Sandra last_name: Johnson - first_name: Andrew full_name: Kissil, Andrew last_name: Kissil - first_name: Brent full_name: Knight, Brent last_name: Knight - first_name: Daniel full_name: Kolenz, Daniel last_name: Kolenz - first_name: Oliver full_name: Kraus, Oliver last_name: Kraus - first_name: John full_name: Krist, John last_name: Krist - first_name: Mary full_name: Li, Mary last_name: Li - first_name: Doug full_name: Lisman, Doug last_name: Lisman - first_name: Milan full_name: Mandic, Milan last_name: Mandic - first_name: John full_name: Mann, John last_name: Mann - first_name: Luis full_name: Marchen, Luis last_name: Marchen - first_name: Colleen Marrese-Reading full_name: Colleen Marrese-Reading, Colleen Marrese-Reading last_name: Colleen Marrese-Reading - first_name: Jonathan full_name: McCready, Jonathan last_name: McCready - first_name: Jim full_name: McGown, Jim last_name: McGown - first_name: Jessica full_name: Missun, Jessica last_name: Missun - first_name: Andrew full_name: Miyaguchi, Andrew last_name: Miyaguchi - first_name: Bradley full_name: Moore, Bradley last_name: Moore - first_name: Bijan full_name: Nemati, Bijan last_name: Nemati - first_name: Shouleh full_name: Nikzad, Shouleh last_name: Nikzad - first_name: Joel full_name: Nissen, Joel last_name: Nissen - first_name: Megan full_name: Novicki, Megan last_name: Novicki - first_name: Todd full_name: Perrine, Todd last_name: Perrine - first_name: Claudia full_name: Pineda, Claudia last_name: Pineda - first_name: Otto full_name: Polanco, Otto last_name: Polanco - first_name: Dustin full_name: Putnam, Dustin last_name: Putnam - first_name: Atif full_name: Qureshi, Atif last_name: Qureshi - first_name: Michael full_name: Richards, Michael last_name: Richards - first_name: A. J. Eldorado full_name: Riggs, A. J. Eldorado last_name: Riggs - first_name: Michael full_name: Rodgers, Michael last_name: Rodgers - first_name: Mike full_name: Rud, Mike last_name: Rud - first_name: Navtej full_name: Saini, Navtej last_name: Saini - first_name: Dan full_name: Scalisi, Dan last_name: Scalisi - first_name: Dan full_name: Scharf, Dan last_name: Scharf - first_name: Kevin full_name: Schulz, Kevin last_name: Schulz - first_name: Gene full_name: Serabyn, Gene last_name: Serabyn - first_name: Norbert full_name: Sigrist, Norbert last_name: Sigrist - first_name: Glory full_name: Sikkia, Glory last_name: Sikkia - first_name: Andrew full_name: Singleton, Andrew last_name: Singleton - first_name: Stuart full_name: Shaklan, Stuart last_name: Shaklan - first_name: Scott full_name: Smith, Scott last_name: Smith - first_name: Bart full_name: Southerd, Bart last_name: Southerd - first_name: Mark full_name: Stahl, Mark last_name: Stahl - first_name: John full_name: Steeves, John last_name: Steeves - first_name: Brian full_name: Sturges, Brian last_name: Sturges - first_name: Chris full_name: Sullivan, Chris last_name: Sullivan - first_name: Hao full_name: Tang, Hao last_name: Tang - first_name: Neil full_name: Taras, Neil last_name: Taras - first_name: Jonathan full_name: Tesch, Jonathan last_name: Tesch - first_name: Melissa full_name: Therrell, Melissa last_name: Therrell - first_name: Howard full_name: Tseng, Howard last_name: Tseng - first_name: Marty full_name: Valente, Marty last_name: Valente - first_name: David Van full_name: Buren, David Van last_name: Buren - first_name: Juan full_name: Villalvazo, Juan last_name: Villalvazo - first_name: Steve full_name: Warwick, Steve last_name: Warwick - first_name: David full_name: Webb, David last_name: Webb - first_name: Thomas full_name: Westerhoff, Thomas last_name: Westerhoff - first_name: Rush full_name: Wofford, Rush last_name: Wofford - first_name: Gordon full_name: Wu, Gordon last_name: Wu - first_name: Jahning full_name: Woo, Jahning last_name: Woo - first_name: Milana full_name: Wood, Milana last_name: Wood - first_name: John full_name: Ziemer, John last_name: Ziemer - first_name: Giada full_name: Arney, Giada last_name: Arney - first_name: Jay full_name: Anderson, Jay last_name: Anderson - first_name: Jesús Maíz-Apellániz full_name: Jesús Maíz-Apellániz, Jesús Maíz-Apellániz last_name: Jesús Maíz-Apellániz - first_name: James full_name: Bartlett, James last_name: Bartlett - first_name: Ruslan full_name: Belikov, Ruslan last_name: Belikov - first_name: Eduardo full_name: Bendek, Eduardo last_name: Bendek - first_name: Brad full_name: Cenko, Brad last_name: Cenko - first_name: Ewan full_name: Douglas, Ewan last_name: Douglas - first_name: Shannon full_name: Dulz, Shannon last_name: Dulz - first_name: Chris full_name: Evans, Chris last_name: Evans - first_name: Virginie full_name: Faramaz, Virginie last_name: Faramaz - first_name: Y. Katherina full_name: Feng, Y. Katherina last_name: Feng - first_name: Harry full_name: Ferguson, Harry last_name: Ferguson - first_name: Kate full_name: Follette, Kate last_name: Follette - first_name: Saavik full_name: Ford, Saavik last_name: Ford - first_name: Miriam full_name: García, Miriam last_name: García - first_name: Marla full_name: Geha, Marla last_name: Geha - first_name: Dawn full_name: Gelino, Dawn last_name: Gelino - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: Sergi full_name: Hildebrandt, Sergi last_name: Hildebrandt - first_name: Renyu full_name: Hu, Renyu last_name: Hu - first_name: Knud full_name: Jahnke, Knud last_name: Jahnke - first_name: Grant full_name: Kennedy, Grant last_name: Kennedy - first_name: Laura full_name: Kreidberg, Laura last_name: Kreidberg - first_name: Andrea full_name: Isella, Andrea last_name: Isella - first_name: Eric full_name: Lopez, Eric last_name: Lopez - first_name: Franck full_name: Marchis, Franck last_name: Marchis - first_name: Lucas full_name: Macri, Lucas last_name: Macri - first_name: Mark full_name: Marley, Mark last_name: Marley - first_name: William full_name: Matzko, William last_name: Matzko - first_name: Johan full_name: Mazoyer, Johan last_name: Mazoyer - first_name: Stephan full_name: McCandliss, Stephan last_name: McCandliss - first_name: Tiffany full_name: Meshkat, Tiffany last_name: Meshkat - first_name: Christoph full_name: Mordasini, Christoph last_name: Mordasini - first_name: Patrick full_name: Morris, Patrick last_name: Morris - first_name: Eric full_name: Nielsen, Eric last_name: Nielsen - first_name: Patrick full_name: Newman, Patrick last_name: Newman - first_name: Erik full_name: Petigura, Erik last_name: Petigura - first_name: Marc full_name: Postman, Marc last_name: Postman - first_name: Amy full_name: Reines, Amy last_name: Reines - first_name: Aki full_name: Roberge, Aki last_name: Roberge - first_name: Ian full_name: Roederer, Ian last_name: Roederer - first_name: Garreth full_name: Ruane, Garreth last_name: Ruane - first_name: Edouard full_name: Schwieterman, Edouard last_name: Schwieterman - first_name: Dan full_name: Sirbu, Dan last_name: Sirbu - first_name: Christopher full_name: Spalding, Christopher last_name: Spalding - first_name: Harry full_name: Teplitz, Harry last_name: Teplitz - first_name: Jason full_name: Tumlinson, Jason last_name: Tumlinson - first_name: Neal full_name: Turner, Neal last_name: Turner - first_name: Jessica full_name: Werk, Jessica last_name: Werk - first_name: Aida full_name: Wofford, Aida last_name: Wofford - first_name: Mark full_name: Wyatt, Mark last_name: Wyatt - first_name: Amber full_name: Young, Amber last_name: Young - first_name: Rob full_name: Zellem, Rob last_name: Zellem citation: ama: Gaudi BS, Seager S, Mennesson B, et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. doi:10.48550/arXiv.2001.06683 apa: Gaudi, B. S., Seager, S., Mennesson, B., Kiessling, A., Warfield, K., Cahoy, K., … Zellem, R. (n.d.). The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. https://doi.org/10.48550/arXiv.2001.06683 chicago: Gaudi, B. Scott, Sara Seager, Bertrand Mennesson, Alina Kiessling, Keith Warfield, Kerri Cahoy, John T. Clarke, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2001.06683. ieee: B. S. Gaudi et al., “The habitable exoplanet observatory (HabEx) mission concept study final report,” arXiv. . ista: Gaudi BS et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv, 2001.06683. mla: Gaudi, B. Scott, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, 2001.06683, doi:10.48550/arXiv.2001.06683. short: B.S. Gaudi, S. Seager, B. Mennesson, A. Kiessling, K. Warfield, K. Cahoy, J.T. Clarke, S.D.-G. Shawn Domagal-Goldman, L. Feinberg, O. Guyon, J. Kasdin, D. Mawet, P. Plavchan, T. Robinson, L. Rogers, P. Scowen, R. Somerville, K. Stapelfeldt, C. Stark, D. Stern, M. Turnbull, R. Amini, G. Kuan, S. Martin, R. Morgan, D. Redding, H.P. Stahl, R. Webb, O.A.-S. Oscar Alvarez-Salazar, W.L. Arnold, M. Arya, B. Balasubramanian, M. Baysinger, R. Bell, C. Below, J. Benson, L. Blais, J. Booth, R. Bourgeois, C. Bradford, A. Brewer, T. Brooks, E. Cady, M. Caldwell, R. Calvet, S. Carr, D. Chan, V. Cormarkovic, K. Coste, C. Cox, R. Danner, J. Davis, L. Dewell, L. Dorsett, D. Dunn, M. East, M. Effinger, R. Eng, G. Freebury, J. Garcia, J. Gaskin, S. Greene, J. Hennessy, E. Hilgemann, B. Hood, W. Holota, S. Howe, P. Huang, T. Hull, R. Hunt, K. Hurd, S. Johnson, A. Kissil, B. Knight, D. Kolenz, O. Kraus, J. Krist, M. Li, D. Lisman, M. Mandic, J. Mann, L. Marchen, C.M.-R. Colleen Marrese-Reading, J. McCready, J. McGown, J. Missun, A. Miyaguchi, B. Moore, B. Nemati, S. Nikzad, J. Nissen, M. Novicki, T. Perrine, C. Pineda, O. Polanco, D. Putnam, A. Qureshi, M. Richards, A.J.E. Riggs, M. Rodgers, M. Rud, N. Saini, D. Scalisi, D. Scharf, K. Schulz, G. Serabyn, N. Sigrist, G. Sikkia, A. Singleton, S. Shaklan, S. Smith, B. Southerd, M. Stahl, J. Steeves, B. Sturges, C. Sullivan, H. Tang, N. Taras, J. Tesch, M. Therrell, H. Tseng, M. Valente, D.V. Buren, J. Villalvazo, S. Warwick, D. Webb, T. Westerhoff, R. Wofford, G. Wu, J. Woo, M. Wood, J. Ziemer, G. Arney, J. Anderson, J.M.-A. Jesús Maíz-Apellániz, J. Bartlett, R. Belikov, E. Bendek, B. Cenko, E. Douglas, S. Dulz, C. Evans, V. Faramaz, Y.K. Feng, H. Ferguson, K. Follette, S. Ford, M. García, M. Geha, D. Gelino, Y.L.L. Götberg, S. Hildebrandt, R. Hu, K. Jahnke, G. Kennedy, L. Kreidberg, A. Isella, E. Lopez, F. Marchis, L. Macri, M. Marley, W. Matzko, J. Mazoyer, S. McCandliss, T. Meshkat, C. Mordasini, P. Morris, E. Nielsen, P. Newman, E. Petigura, M. Postman, A. Reines, A. Roberge, I. Roederer, G. Ruane, E. Schwieterman, D. Sirbu, C. Spalding, H. Teplitz, J. Tumlinson, N. Turner, J. Werk, A. Wofford, M. Wyatt, A. Young, R. Zellem, ArXiv (n.d.). date_created: 2023-08-21T10:10:21Z date_published: 2020-01-18T00:00:00Z date_updated: 2023-08-22T13:13:18Z day: '18' doi: 10.48550/arXiv.2001.06683 extern: '1' external_id: arxiv: - '2001.06683' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2001.06683' month: '01' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: The habitable exoplanet observatory (HabEx) mission concept study final report type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8767' abstract: - lang: eng text: Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring. acknowledgement: 'We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.' article_number: e1008402 article_processing_charge: No article_type: original author: - first_name: Kamran full_name: Kaveh, Kamran last_name: Kaveh - first_name: Alex full_name: McAvoy, Alex last_name: McAvoy - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402 apa: Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402 chicago: Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402. ieee: K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020. ista: Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402. mla: Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402. short: K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020). date_created: 2020-11-18T07:20:23Z date_published: 2020-11-05T00:00:00Z date_updated: 2023-08-22T12:49:18Z day: '05' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pcbi.1008402 external_id: isi: - '000591317200004' file: - access_level: open_access checksum: 555456dd0e47bcf9e0994bcb95577e88 content_type: application/pdf creator: dernst date_created: 2020-11-18T07:26:10Z date_updated: 2020-11-18T07:26:10Z file_id: '8768' file_name: 2020_PlosCompBio_Kaveh.pdf file_size: 2498594 relation: main_file success: 1 file_date_updated: 2020-11-18T07:26:10Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '11' keyword: - Ecology - Modelling and Simulation - Computational Theory and Mathematics - Genetics - Ecology - Evolution - Behavior and Systematics - Molecular Biology - Cellular and Molecular Neuroscience language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: PLOS Computational Biology publication_identifier: eissn: - 1553-7358 issn: - 1553-734X publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: The Moran process on 2-chromatic graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2020' ... --- _id: '8750' abstract: - lang: eng text: "Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost." article_number: '9314994' article_processing_charge: No author: - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Daniel full_name: Freire, Daniel last_name: Freire - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994' apa: 'Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994' chicago: Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994. ieee: M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions,” in 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, Virtual Conference, 2020. ista: 'Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994.' mla: Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, 9314994, IEEE, 2020, doi:10.1109/MEMOCODE51338.2020.9314994. short: M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020. conference: end_date: 2020-12-04 location: Virtual Conference name: 'MEMOCODE: Conference on Formal Methods and Models for System Design' start_date: 2020-12-02 date_created: 2020-11-10T07:04:57Z date_published: 2020-12-04T00:00:00Z date_updated: 2023-08-22T12:48:18Z day: '04' department: - _id: ToHe doi: 10.1109/MEMOCODE51338.2020.9314994 ec_funded: 1 external_id: arxiv: - '2006.12325' isi: - '000661920400013' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2006.12325 month: '12' oa: 1 oa_version: Preprint project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design publication_identifier: isbn: - '9781728191485' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ...