--- _id: '687' abstract: - lang: eng text: Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs. author: - first_name: Ben full_name: Davison, Ben id: 4634AB1E-F248-11E8-B48F-1D18A9856A87 last_name: Davison orcid: 0000-0002-8944-4390 citation: ama: Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053 apa: Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053 chicago: Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053. ieee: B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017. ista: Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703. mla: Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053. short: B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:24Z day: '01' department: - _id: TaHa doi: 10.1093/qmath/haw053 ec_funded: 1 intvolume: ' 68' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.7172 month: '06' oa: 1 oa_version: Submitted Version page: 635 - 703 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Quarterly Journal of Mathematics publication_identifier: issn: - '00335606' publication_status: published publisher: Oxford University Press publist_id: '7022' quality_controlled: '1' scopus_import: 1 status: public title: The critical CoHA of a quiver with potential type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2017' ... --- _id: '686' abstract: - lang: eng text: Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology. author: - 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 citation: ama: 'Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006' apa: 'Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006' chicago: 'Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006.' ieee: 'C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.' ista: 'Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.' mla: 'Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.' short: C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:23Z day: '01' department: - _id: CaHe doi: 10.1016/j.mod.2017.03.006 intvolume: ' 145' language: - iso: eng month: '06' oa_version: None page: 32 - 37 publication: Mechanisms of Development publication_identifier: issn: - '09254773' publication_status: published publisher: Elsevier publist_id: '7024' quality_controlled: '1' scopus_import: 1 status: public title: 'D''Arcy Thompson''s ‘on growth and form’: From soap bubbles to tissue self organization' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2017' ... --- _id: '689' abstract: - lang: eng text: Rett syndrome modeling in monkey mirrors the human disorder. article_number: eaan8196 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196 apa: Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196 chicago: Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196. ieee: G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196. mla: Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:47:56Z date_published: 2017-06-07T00:00:00Z date_updated: 2021-01-12T08:09:29Z day: '07' department: - _id: GaNo doi: 10.1126/scitranslmed.aan8196 intvolume: ' 9' issue: '393' language: - iso: eng month: '06' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '7019' quality_controlled: '1' scopus_import: 1 status: public title: Rett syndrome modeling goes simian type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '693' abstract: - lang: eng text: 'Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ' article_processing_charge: Yes (in subscription journal) author: - first_name: Takafumi full_name: Miki, Takafumi last_name: Miki - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Gerardo full_name: Malagon, Gerardo last_name: Malagon - first_name: Laura full_name: Gomez, Laura last_name: Gomez - first_name: Katsuhiko full_name: Tabuchi, Katsuhiko last_name: Tabuchi - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Alain full_name: Marty, Alain last_name: Marty citation: ama: Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114 apa: Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114 chicago: Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114. ieee: T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017. ista: Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255. mla: Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114. short: T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255. date_created: 2018-12-11T11:47:57Z date_published: 2017-06-27T00:00:00Z date_updated: 2023-02-23T12:54:57Z day: '27' ddc: - '570' department: - _id: EM-Fac - _id: RySh doi: 10.1073/pnas.1704470114 external_id: pmid: - '28607047' file: - access_level: open_access checksum: 2ab75d554f3df4a34d20fa8040589b7e content_type: application/pdf creator: kschuh date_created: 2020-01-03T13:27:29Z date_updated: 2020-07-14T12:47:44Z file_id: '7223' file_name: 2017_PNAS_Miki.pdf file_size: 2721544 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 114' issue: '26' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: E5246 - E5255 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7013' quality_controlled: '1' scopus_import: 1 status: public title: Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '694' abstract: - lang: eng text: A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells. article_type: original author: - first_name: Astrid full_name: Veß, Astrid last_name: Veß - first_name: Ulrich full_name: Blache, Ulrich last_name: Blache - first_name: Laura full_name: Leitner, Laura last_name: Leitner - first_name: Angela full_name: Kurz, Angela last_name: Kurz - first_name: Anja full_name: Ehrenpfordt, Anja last_name: Ehrenpfordt - 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: Guido full_name: Posern, Guido last_name: Posern citation: ama: Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899 apa: Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899 chicago: Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899. ieee: A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017. ista: Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184. mla: Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899. short: A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184. date_created: 2018-12-11T11:47:58Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:09:41Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1242/jcs.200899 external_id: pmid: - '28515231' file: - access_level: open_access checksum: 42c81a0a4fc3128883b391c3af3f74bc content_type: application/pdf creator: dernst date_created: 2019-10-24T09:43:56Z date_updated: 2020-07-14T12:47:45Z file_id: '6966' file_name: 2017_CellScience_Vess.pdf file_size: 10847596 relation: main_file file_date_updated: 2020-07-14T12:47:45Z has_accepted_license: '1' intvolume: ' 130' issue: '13' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2172 - 2184 pmid: 1 publication: Journal of Cell Science publication_identifier: issn: - '00219533' publication_status: published publisher: Company of Biologists publist_id: '7008' quality_controlled: '1' scopus_import: 1 status: public title: A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2017' ... --- _id: '697' abstract: - lang: eng text: 'De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. ' alternative_title: - LIPIcs article_number: '39' author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39' apa: 'Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39' chicago: Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39. ieee: 'K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.' ista: 'Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.' mla: Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39. short: K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-07-14 location: Warsaw, Poland name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2017-07-10 date_created: 2018-12-11T11:47:59Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:11:15Z day: '01' ddc: - '005' department: - _id: KrPi doi: 10.4230/LIPIcs.ICALP.2017.39 ec_funded: 1 file: - access_level: open_access checksum: e95618a001692f1af2d68f5fde43bc1f content_type: application/pdf creator: system date_created: 2018-12-12T10:08:40Z date_updated: 2020-07-14T12:47:46Z file_id: '4701' file_name: IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf file_size: 601004 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 80' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7003' pubrep_id: '893' quality_controlled: '1' scopus_import: 1 status: public title: Non uniform attacks against pseudoentropy 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2017' ... --- _id: '698' abstract: - lang: eng text: 'Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. ' author: - first_name: Yejun full_name: Wang, Yejun last_name: Wang - first_name: Mallika full_name: Nagarajan, Mallika last_name: Nagarajan - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Gv full_name: Shivashankar, Gv last_name: Shivashankar citation: ama: Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825 apa: Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825 chicago: Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825. ieee: Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017. ista: Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009. mla: Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825. short: Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009. date_created: 2018-12-11T11:47:59Z date_published: 2017-07-07T00:00:00Z date_updated: 2021-01-12T08:11:17Z day: '07' ddc: - '519' department: - _id: CaUh doi: 10.1091/mbc.E16-12-0825 file: - access_level: open_access checksum: de01dac9e30970cfa6ae902480a4e04d content_type: application/pdf creator: system date_created: 2018-12-12T10:10:53Z date_updated: 2020-07-14T12:47:46Z file_id: '4844' file_name: IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf file_size: 1086097 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 28' issue: '14' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version page: 1997 - 2009 project: - _id: 2530CA10-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 903-N35 name: 'Gaussian Graphical Models: Theory and Applications' publication: Molecular Biology of the Cell publication_identifier: issn: - '10591524' publication_status: published publisher: American Society for Cell Biology publist_id: '7001' pubrep_id: '892' quality_controlled: '1' scopus_import: 1 status: public title: Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2017' ... --- _id: '699' abstract: - lang: eng text: 'In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ' author: - first_name: Carl full_name: Veller, Carl last_name: Veller - first_name: Laura full_name: Hayward, Laura last_name: Hayward - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X citation: ama: Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114 apa: Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114 chicago: Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114. ieee: C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017. ista: Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405. mla: Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114. short: C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405. date_created: 2018-12-11T11:48:00Z date_published: 2017-07-03T00:00:00Z date_updated: 2021-01-12T08:11:21Z day: '03' department: - _id: KrCh doi: 10.1073/pnas.1702020114 external_id: pmid: - '28630336' intvolume: ' 114' issue: '27' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/ month: '07' oa: 1 oa_version: Submitted Version page: E5396 - E5405 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7002' quality_controlled: '1' scopus_import: 1 status: public title: The red queen and king in finite populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '700' abstract: - lang: eng text: Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs. article_number: '012404' author: - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Vahid full_name: Salari, Vahid last_name: Salari - first_name: Jack full_name: Tuszynski, Jack last_name: Tuszynski - first_name: Michal full_name: Cifra, Michal last_name: Cifra - first_name: Christoph full_name: Simon, Christoph last_name: Simon citation: ama: Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404 apa: Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404 chicago: Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404. ieee: S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017. ista: Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404. mla: Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404. short: S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017). date_created: 2018-12-11T11:48:00Z date_published: 2017-07-12T00:00:00Z date_updated: 2023-02-23T12:56:35Z day: '12' department: - _id: JoFi doi: 10.1103/PhysRevE.96.012404 ec_funded: 1 intvolume: ' 96' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/pdf/1612.07061.pdf month: '07' oa: 1 oa_version: Submitted Version project: - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics' publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics ' publication_identifier: issn: - '24700045' publication_status: published publisher: American Institute of Physics publist_id: '6997' quality_controlled: '1' scopus_import: 1 status: public title: Optomechanical proposal for monitoring microtubule mechanical vibrations type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ... --- _id: '701' abstract: - lang: eng text: A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2. author: - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 citation: ama: Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44. apa: Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press. chicago: Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017. ieee: J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017. ista: Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44. mla: Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44. short: J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44. date_created: 2018-12-11T11:48:00Z date_published: 2017-07-14T00:00:00Z date_updated: 2021-01-12T08:11:28Z day: '14' ddc: - '500' department: - _id: UlWa file: - access_level: open_access checksum: a431e573e31df13bc0f66de3061006ec content_type: application/pdf creator: system date_created: 2018-12-12T10:14:25Z date_updated: 2020-07-14T12:47:47Z file_id: '5077' file_name: IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf file_size: 544042 relation: main_file file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' intvolume: ' 24' issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 1-44 publication: The Electronic Journal of Combinatorics publication_identifier: issn: - '10778926' publication_status: published publisher: International Press publist_id: '6996' pubrep_id: '984' quality_controlled: '1' status: public title: On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2017' ...