--- _id: '9548' abstract: - lang: eng text: 'We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it.' acknowledgement: The authors acknowledge the support of the grant of the Russian Government N 075-15-2019-1926. article_processing_charge: No article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Igor full_name: Tsiutsiurupa, Igor last_name: Tsiutsiurupa citation: ama: Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4 apa: Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4 chicago: Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4. ieee: G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021. ista: Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric Analysis. 31, 11493–11528. mla: Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4. short: G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528. date_created: 2021-06-13T22:01:32Z date_published: 2021-05-31T00:00:00Z date_updated: 2023-08-08T14:04:49Z day: '31' department: - _id: UlWa doi: 10.1007/s12220-021-00691-4 external_id: arxiv: - '2008.09543' isi: - '000656507500001' intvolume: ' 31' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.09543 month: '05' oa: 1 oa_version: Preprint page: 11493-11528 publication: Journal of Geometric Analysis publication_identifier: eissn: - 1559-002X issn: - 1050-6926 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Functional Löwner ellipsoids type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 31 year: '2021' ... --- _id: '13080' abstract: - lang: eng text: "Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well." article_processing_charge: No author: - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia - first_name: Esteban full_name: Martinez, Esteban last_name: Martinez - first_name: Gerbold full_name: Menard, Gerbold last_name: Menard - first_name: Andreas full_name: Pöschl, Andreas last_name: Pöschl - first_name: Sergei full_name: Gronin, Sergei last_name: Gronin - first_name: Geoffrey full_name: Gardner, Geoffrey last_name: Gardner - first_name: Ray full_name: Kallaher, Ray last_name: Kallaher - first_name: Michael full_name: Manfra, Michael last_name: Manfra - first_name: Charles full_name: Marcus, Charles last_name: Marcus - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Lucas full_name: Casparis, Lucas last_name: Casparis citation: ama: Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435 apa: Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435 chicago: Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435. ieee: D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. ista: Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435. mla: Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435. short: D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021). date_created: 2023-05-23T17:11:28Z date_published: 2021-03-09T00:00:00Z date_updated: 2023-08-08T14:08:07Z day: '09' ddc: - '530' department: - _id: AnHi doi: 10.5281/ZENODO.4592435 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.4592460 month: '03' oa: 1 oa_version: Published Version publisher: Zenodo related_material: link: - relation: software url: https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3 record: - id: '9570' relation: used_in_publication status: public status: public title: Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9569' abstract: - lang: eng text: We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values. acknowledgement: The research is funded by Higher Education Commission (HEC) Pakistan under start-up research grant program (SRGP) Project no. 2454. article_processing_charge: No article_type: original author: - first_name: M. S. full_name: Dar, M. S. last_name: Dar - first_name: Khush Bakhat full_name: Akram, Khush Bakhat last_name: Akram - first_name: Ayesha full_name: Sohail, Ayesha last_name: Sohail - first_name: Fatima full_name: Arif, Fatima last_name: Arif - first_name: Fatemeh full_name: Zabihi, Fatemeh last_name: Zabihi - first_name: Shengyuan full_name: Yang, Shengyuan last_name: Yang - first_name: Shamsa full_name: Munir, Shamsa last_name: Munir - first_name: Meifang full_name: Zhu, Meifang last_name: Zhu - first_name: M. full_name: Abid, M. last_name: Abid - first_name: Muhammad full_name: Nauman, Muhammad id: 32c21954-2022-11eb-9d5f-af9f93c24e71 last_name: Nauman orcid: 0000-0002-2111-4846 citation: ama: Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 2021;11(35):21702-21715. doi:10.1039/d1ra03428f apa: Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman, M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/d1ra03428f chicago: Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi, Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1ra03428f. ieee: M. S. Dar et al., “Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling,” RSC Advances, vol. 11, no. 35. Royal Society of Chemistry, pp. 21702–21715, 2021. ista: Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 11(35), 21702–21715. mla: Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15, doi:10.1039/d1ra03428f. short: M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M. Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715. date_created: 2021-06-19T07:27:45Z date_published: 2021-06-18T00:00:00Z date_updated: 2023-08-08T14:23:21Z day: '18' ddc: - '540' department: - _id: KiMo doi: 10.1039/d1ra03428f external_id: isi: - '000665644000048' file: - access_level: open_access checksum: cd582d67ace7151078e46b3a896871a9 content_type: application/pdf creator: asandaue date_created: 2021-06-23T13:09:34Z date_updated: 2021-06-23T13:09:34Z file_id: '9596' file_name: 2021_RSCAdvances_Dar.pdf file_size: 2114557 relation: main_file success: 1 file_date_updated: 2021-06-23T13:09:34Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '35' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 21702-21715 publication: RSC Advances publication_identifier: eissn: - 2046-2069 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling 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: 11 year: '2021' ... --- _id: '9558' abstract: - lang: eng text: "We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n" acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster." article_number: '244502' article_processing_charge: No article_type: letter_note author: - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 citation: ama: Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502 apa: Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502 chicago: Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502. ieee: G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” Physical Review Letters, vol. 126, no. 24. American Physical Society, 2021. ista: Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502. mla: Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502. short: G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021). date_created: 2021-06-16T15:45:36Z date_published: 2021-06-18T00:00:00Z date_updated: 2023-08-08T14:08:36Z day: '18' department: - _id: GradSch - _id: BjHo doi: 10.1103/PhysRevLett.126.244502 external_id: arxiv: - '2007.02584' isi: - '000663310100008' intvolume: ' 126' isi: 1 issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.02584 month: '06' oa: 1 oa_version: Preprint project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/turbulent-flow-simplified/ status: public title: Coarse graining the state space of a turbulent flow using periodic orbits type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 126 year: '2021' ... --- _id: '9607' abstract: - lang: eng text: While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use. acknowledgement: This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands). article_processing_charge: No article_type: original author: - first_name: Anton full_name: Bespalov, Anton last_name: Bespalov - first_name: René full_name: Bernard, René last_name: Bernard - first_name: Anja full_name: Gilis, Anja last_name: Gilis - first_name: Björn full_name: Gerlach, Björn last_name: Gerlach - first_name: Javier full_name: Guillén, Javier last_name: Guillén - first_name: Vincent full_name: Castagné, Vincent last_name: Castagné - first_name: Isabel A. full_name: Lefevre, Isabel A. last_name: Lefevre - first_name: Fiona full_name: Ducrey, Fiona last_name: Ducrey - first_name: Lee full_name: Monk, Lee last_name: Monk - first_name: Sandrine full_name: Bongiovanni, Sandrine last_name: Bongiovanni - first_name: Bruce full_name: Altevogt, Bruce last_name: Altevogt - first_name: María full_name: Arroyo-Araujo, María last_name: Arroyo-Araujo - first_name: Lior full_name: Bikovski, Lior last_name: Bikovski - first_name: Natasja full_name: De Bruin, Natasja last_name: De Bruin - first_name: Esmeralda full_name: Castaños-Vélez, Esmeralda last_name: Castaños-Vélez - first_name: Alexander full_name: Dityatev, Alexander last_name: Dityatev - first_name: Christoph H. full_name: Emmerich, Christoph H. last_name: Emmerich - first_name: Raafat full_name: Fares, Raafat last_name: Fares - first_name: Chantelle full_name: Ferland-Beckham, Chantelle last_name: Ferland-Beckham - first_name: Christelle full_name: Froger-Colléaux, Christelle last_name: Froger-Colléaux - first_name: Valerie full_name: Gailus-Durner, Valerie last_name: Gailus-Durner - first_name: Sabine M. full_name: Hölter, Sabine M. last_name: Hölter - first_name: Martine Cj full_name: Hofmann, Martine Cj last_name: Hofmann - first_name: Patricia full_name: Kabitzke, Patricia last_name: Kabitzke - first_name: Martien Jh full_name: Kas, Martien Jh last_name: Kas - first_name: Claudia full_name: Kurreck, Claudia last_name: Kurreck - first_name: Paul full_name: Moser, Paul last_name: Moser - first_name: Malgorzata full_name: Pietraszek, Malgorzata last_name: Pietraszek - first_name: Piotr full_name: Popik, Piotr last_name: Popik - first_name: Heidrun full_name: Potschka, Heidrun last_name: Potschka - first_name: Ernesto full_name: Prado Montes De Oca, Ernesto last_name: Prado Montes De Oca - first_name: Leonardo full_name: Restivo, Leonardo last_name: Restivo - first_name: Gernot full_name: Riedel, Gernot last_name: Riedel - first_name: Merel full_name: Ritskes-Hoitinga, Merel last_name: Ritskes-Hoitinga - first_name: Janko full_name: Samardzic, Janko last_name: Samardzic - first_name: Michael full_name: Schunn, Michael id: 4272DB4A-F248-11E8-B48F-1D18A9856A87 last_name: Schunn orcid: 0000-0003-4326-5300 - first_name: Claudia full_name: Stöger, Claudia last_name: Stöger - first_name: Vootele full_name: Voikar, Vootele last_name: Voikar - first_name: Jan full_name: Vollert, Jan last_name: Vollert - first_name: Kimberley E. full_name: Wever, Kimberley E. last_name: Wever - first_name: Kathleen full_name: Wuyts, Kathleen last_name: Wuyts - first_name: Malcolm R. full_name: Macleod, Malcolm R. last_name: Macleod - first_name: Ulrich full_name: Dirnagl, Ulrich last_name: Dirnagl - first_name: Thomas full_name: Steckler, Thomas last_name: Steckler citation: ama: Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294 apa: Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294 chicago: Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294. ieee: A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10. mla: Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294. short: A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021). date_created: 2021-06-27T22:01:49Z date_published: 2021-05-24T00:00:00Z date_updated: 2023-08-10T13:36:50Z day: '24' ddc: - '570' department: - _id: PreCl doi: 10.7554/eLife.63294 external_id: isi: - '000661272000001' pmid: - '34028353' file: - access_level: open_access checksum: 885b746051a7a6b6e24e3d2781a48fde content_type: application/pdf creator: asandaue date_created: 2021-06-28T11:35:30Z date_updated: 2021-06-28T11:35:30Z file_id: '9609' file_name: 2021_ELife_Bespalov.pdf file_size: 2500720 relation: main_file success: 1 file_date_updated: 2021-06-28T11:35:30Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Introduction to the EQIPD quality system 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: '2021' ... --- _id: '9601' abstract: - lang: eng text: 'In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.' acknowledgement: The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334). article_number: '3804' article_processing_charge: No article_type: original author: - first_name: Laura full_name: Santini, Laura last_name: Santini - first_name: Florian full_name: Halbritter, Florian last_name: Halbritter - first_name: Fabian full_name: Titz-Teixeira, Fabian last_name: Titz-Teixeira - first_name: Toru full_name: Suzuki, Toru last_name: Suzuki - first_name: Maki full_name: Asami, Maki last_name: Asami - first_name: Xiaoyan full_name: Ma, Xiaoyan last_name: Ma - first_name: Julia full_name: Ramesmayer, Julia last_name: Ramesmayer - first_name: Andreas full_name: Lackner, Andreas last_name: Lackner - first_name: Nick full_name: Warr, Nick last_name: Warr - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Ernest full_name: Laue, Ernest last_name: Laue - first_name: Matthias full_name: Farlik, Matthias last_name: Farlik - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Andreas full_name: Beyer, Andreas last_name: Beyer - first_name: Anthony C.F. full_name: Perry, Anthony C.F. last_name: Perry - first_name: Martin full_name: Leeb, Martin last_name: Leeb citation: ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23510-4 apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4 chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4. ieee: L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804. mla: Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:10.1038/s41467-021-23510-4. short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021). date_created: 2021-06-27T22:01:46Z date_published: 2021-07-12T00:00:00Z date_updated: 2023-08-10T13:53:23Z day: '12' ddc: - '570' department: - _id: SiHi doi: 10.1038/s41467-021-23510-4 external_id: isi: - '000667248600005' file: - access_level: open_access checksum: 75dd89d09945185b2d14b2434a0bcb50 content_type: application/pdf creator: asandaue date_created: 2021-06-28T08:04:22Z date_updated: 2021-06-28T08:04:22Z file_id: '9608' file_name: 2021_NatureCommunications_Santini.pdf file_size: 2156554 relation: main_file success: 1 file_date_updated: 2021-06-28T08:04:22Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3 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: '2021' ... --- _id: '9602' abstract: - lang: eng text: "An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees." acknowledgement: We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926. 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: István full_name: Tomon, István last_name: Tomon citation: ama: Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004 apa: Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004 chicago: Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004. ieee: J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021. ista: Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37. mla: Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp. 21–37, doi:10.1016/j.jctb.2021.05.004. short: J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37. date_created: 2021-06-27T22:01:47Z date_published: 2021-06-09T00:00:00Z date_updated: 2023-08-10T13:38:00Z day: '09' ddc: - '510' department: - _id: HeEd doi: 10.1016/j.jctb.2021.05.004 external_id: isi: - '000702280800002' file: - access_level: open_access checksum: 15fbc9064cd9d1c777ac0043b78c8f12 content_type: application/pdf creator: asandaue date_created: 2021-06-28T13:33:23Z date_updated: 2021-06-28T13:33:23Z file_id: '9612' file_name: 2021_JournalOfCombinatorialTheory_Pach.pdf file_size: 418168 relation: main_file success: 1 file_date_updated: 2021-06-28T13:33:23Z has_accepted_license: '1' intvolume: ' 151' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 21-37 project: - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize publication: Journal of Combinatorial Theory. Series B publication_identifier: issn: - 0095-8956 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Erdős-Hajnal-type results for monotone paths 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: 151 year: '2021' ... --- _id: '9606' abstract: - lang: eng text: Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results. acknowledgement: "G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata." article_number: L061303 article_processing_charge: No article_type: letter_note author: - first_name: A. full_name: Tononi, A. last_name: Tononi - first_name: Alberto full_name: Cappellaro, Alberto id: 9d13b3cb-30a2-11eb-80dc-f772505e8660 last_name: Cappellaro orcid: 0000-0001-6110-2359 - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: L. full_name: Salasnich, L. last_name: Salasnich citation: ama: Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6). doi:10.1103/PhysRevA.103.L061303 apa: Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303 chicago: Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303. ieee: A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” Physical Review A, vol. 103, no. 6. American Physical Society, 2021. ista: Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303. mla: Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303. short: A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021). date_created: 2021-06-27T22:01:49Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-10T13:37:25Z day: '01' department: - _id: MiLe doi: 10.1103/PhysRevA.103.L061303 external_id: arxiv: - '2009.06491' isi: - '000662296700014' intvolume: ' 103' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2009.06491 month: '06' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - '24699934' issn: - '24699926' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Propagation of first and second sound in a two-dimensional Fermi superfluid type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 103 year: '2021' ... --- _id: '9642' abstract: - lang: eng text: Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain. acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.). article_number: '109313' article_processing_charge: No article_type: original author: - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Rouven full_name: Schulz, Rouven id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87 last_name: Schulz orcid: 0000-0001-5297-733X - first_name: Héctor full_name: De Jesús-Cortés, Héctor last_name: De Jesús-Cortés - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Balint full_name: Nagy, Balint id: 93C65ECC-A6F2-11E9-8DF9-9712E6697425 last_name: Nagy - first_name: Francis full_name: Reilly-Andújar, Francis last_name: Reilly-Andújar - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Florianne E full_name: Schoot Uiterkamp, Florianne E id: 3526230C-F248-11E8-B48F-1D18A9856A87 last_name: Schoot Uiterkamp - first_name: Mark F. full_name: Bear, Mark F. last_name: Bear - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313 apa: Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313 chicago: Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier, 2021. https://doi.org/10.1016/j.celrep.2021.109313. ieee: A. Venturino et al., “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” Cell Reports, vol. 36, no. 1. Elsevier, 2021. ista: Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313. mla: Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313. short: A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021). date_created: 2021-07-11T22:01:16Z date_published: 2021-07-06T00:00:00Z date_updated: 2023-08-10T14:09:39Z day: '06' ddc: - '570' department: - _id: SaSi doi: 10.1016/j.celrep.2021.109313 ec_funded: 1 external_id: isi: - '000670188500004' pmid: - '34233180' file: - access_level: open_access checksum: f056255f6d01fd9a86b5387635928173 content_type: application/pdf creator: cziletti date_created: 2021-07-19T13:32:17Z date_updated: 2021-07-19T13:32:17Z file_id: '9693' file_name: 2021_CellReports_Venturino.pdf file_size: 56388540 relation: main_file success: 1 file_date_updated: 2021-07-19T13:32:17Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25D4A630-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715571' name: Microglia action towards neuronal circuit formation and function in health and disease publication: Cell Reports publication_identifier: eissn: - '22111247' 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/the-twinkle-and-the-brain/ scopus_import: '1' status: public title: Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain 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: 36 year: '2021' ... --- _id: '9603' abstract: - lang: eng text: Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl acknowledgement: We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H. article_number: '109274' article_processing_charge: No article_type: original author: - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Amarbayasgalan full_name: Davaatseren, Amarbayasgalan id: 70ADC922-B424-11E9-99E3-BA18E6697425 last_name: Davaatseren - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Johanna full_name: Sonntag, Johanna id: 32FE7D7C-F248-11E8-B48F-1D18A9856A87 last_name: Sonntag - first_name: Lill full_name: Andersen, Lill last_name: Andersen - first_name: Tina full_name: Bernthaler, Tina last_name: Bernthaler - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Anna-Magdalena full_name: Heger, Anna-Magdalena id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87 last_name: Heger - first_name: Randy L. full_name: Johnson, Randy L. last_name: Johnson - first_name: Lindsay A. full_name: Schwarz, Lindsay A. last_name: Schwarz - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Thomas full_name: Rülicke, Thomas last_name: Rülicke - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274 apa: Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274 chicago: Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274. ieee: X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021. ista: Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274. mla: Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274. short: X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021). date_created: 2021-06-27T22:01:48Z date_published: 2021-06-22T00:00:00Z date_updated: 2023-08-10T13:55:00Z day: '22' ddc: - '570' department: - _id: SiHi - _id: LoSw - _id: PreCl doi: 10.1016/j.celrep.2021.109274 ec_funded: 1 external_id: isi: - '000664463600016' file: - access_level: open_access checksum: d49520fdcbbb5c2f883bddb67cee5d77 content_type: application/pdf creator: asandaue date_created: 2021-06-28T14:06:24Z date_updated: 2021-06-28T14:06:24Z file_id: '9613' file_name: 2021_CellReports_Contreras.pdf file_size: 7653149 relation: main_file success: 1 file_date_updated: 2021-06-28T14:06:24Z has_accepted_license: '1' intvolume: ' 35' isi: 1 issue: '12' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular Mechanisms of Radial Neuronal Migration - _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: Cell Reports publication_identifier: eissn: - '22111247' publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/ scopus_import: '1' status: public title: A genome-wide library of MADM mice for single-cell genetic mosaic analysis 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: 35 year: '2021' ...