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Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-07-24T00:00:00Z","page":"119","citation":{"ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020.","ama":"Avvakumov S. 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We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 2","status":"public","title":" The local density approximation in density functional theory","_id":"14891","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","page":"35-73","article_type":"original","citation":{"mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:10.2140/paa.2020.2.35.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.","chicago":"Lewin, Mathieu, Elliott H. 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Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord."}],"type":"journal_article","date_published":"2020-12-01T00:00:00Z","publication":"Neuroscience","citation":{"apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2020.08.011","ieee":"A. Salamatina et al., “Differential loss of spinal interneurons in a mouse model of ALS,” Neuroscience, vol. 450. 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Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. 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Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097"},"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.15479/AT:ISTA:8097","date_published":"2020-07-15T00:00:00Z","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"article_processing_charge":"No","has_accepted_license":"1","month":"07","day":"15","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"status":"public","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","_id":"8097","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_created":"2020-07-06T20:38:27Z","date_updated":"2020-07-14T12:48:09Z","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","relation":"main_file","file_id":"8098","content_type":"application/zip","file_size":255770756,"creator":"bkavcic","file_name":"natComm_2020_scripts.zip","access_level":"open_access"}],"date_updated":"2024-02-21T12:40:51Z","date_created":"2020-07-06T20:40:19Z","contributor":[{"first_name":"Gašper","last_name":"Tkačik","contributor_type":"research_group","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","last_name":"Bollenbach","first_name":"Tobias"}],"author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor"}],"type":"research_data","file_date_updated":"2020-07-14T12:48:09Z","abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology.","lang":"eng"}]},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8280","date_updated":"2020-08-18T08:03:23Z","date_created":"2020-08-18T08:03:23Z","checksum":"4f1382ed4384751b6013398c11557bf6","success":1,"file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access","file_size":5778420,"content_type":"application/x-zip-compressed","creator":"dernst"}],"date_created":"2020-08-12T12:49:23Z","date_updated":"2024-02-21T12:41:09Z","contributor":[{"first_name":"Louise S","last_name":"Arathoon","contributor_type":"data_collector","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Parvathy","last_name":"Surendranadh","contributor_type":"project_member","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","contributor_type":"project_member","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","contributor_type":"project_member","last_name":"Field"},{"contributor_type":"project_member","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carina","contributor_type":"project_member","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11321","status":"public","relation":"later_version"},{"relation":"later_version","status":"public","id":"9192"}]},"author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"status":"public","ddc":["576"],"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8254","year":"2020","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"file_date_updated":"2020-08-18T08:03:23Z","type":"research_data","date_published":"2020-08-18T00:00:00Z","doi":"10.15479/AT:ISTA:8254","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","short":"L.S. Arathoon, (2020).","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254."},"has_accepted_license":"1","article_processing_charge":"No","month":"08","day":"18"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7541","intvolume":" 32","ddc":["530"],"status":"public","title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","file":[{"file_id":"8782","relation":"main_file","success":1,"checksum":"c622737dc295972065782558337124a2","date_updated":"2020-11-20T10:11:35Z","date_created":"2020-11-20T10:11:35Z","access_level":"open_access","file_name":"2020_AdvancedMaterials_Gao.pdf","creator":"dernst","file_size":5242880,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"16","abstract":[{"text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon.","lang":"eng"}],"citation":{"short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020).","mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523, Wiley, 2020, doi:10.1002/adma.201906523.","chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16). doi:10.1002/adma.201906523","apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523","ieee":"F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley, 2020.","ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523."},"publication":"Advanced Materials","article_type":"original","date_published":"2020-04-23T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"23","year":"2020","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","department":[{"_id":"GeKa"}],"publisher":"Wiley","publication_status":"published","related_material":{"record":[{"id":"7996","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"9222"}]},"author":[{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"first_name":"Jian-Huan","last_name":"Wang","full_name":"Wang, Jian-Huan"},{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"full_name":"Hu, Hao","first_name":"Hao","last_name":"Hu"},{"last_name":"Rančić","first_name":"Marko J.","full_name":"Rančić, Marko J."},{"last_name":"Zhang","first_name":"Jie-Yin","full_name":"Zhang, Jie-Yin"},{"last_name":"Wang","first_name":"Ting","full_name":"Wang, Ting"},{"first_name":"Yuan","last_name":"Yao","full_name":"Yao, Yuan"},{"last_name":"Wang","first_name":"Gui-Lei","full_name":"Wang, Gui-Lei"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"first_name":"Lada","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada"},{"full_name":"Kloeffel, Christoph","first_name":"Christoph","last_name":"Kloeffel"},{"full_name":"Loss, Daniel","first_name":"Daniel","last_name":"Loss"},{"first_name":"Feng","last_name":"Liu","full_name":"Liu, Feng"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"},{"full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun","last_name":"Zhang"}],"volume":32,"date_created":"2020-02-28T09:47:00Z","date_updated":"2024-02-21T12:42:12Z","article_number":"1906523","ec_funded":1,"file_date_updated":"2020-11-20T10:11:35Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000516660900001"]},"project":[{"grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"},{"grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices","call_identifier":"FWF"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"quality_controlled":"1","doi":"10.1002/adma.201906523","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication_identifier":{"issn":["0935-9648"]},"month":"04"},{"type":"research_data","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"file_date_updated":"2020-12-09T15:00:19Z","_id":"8930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"ddc":["570"],"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8997"}]},"contributor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","contributor_type":"supervisor","last_name":"Tkačik"},{"last_name":"Bollenbach","contributor_type":"supervisor","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor"}],"file":[{"relation":"main_file","file_id":"8932","date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","success":1,"file_name":"PLoSCompBiol2020_datarep.zip","access_level":"open_access","file_size":315494370,"content_type":"application/zip","creator":"bkavcic"}],"oa_version":"Published Version","date_created":"2020-12-09T15:04:02Z","date_updated":"2024-02-21T12:41:42Z","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"10","citation":{"short":"B. Kavcic, (2020).","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:8930","date_published":"2020-12-10T00:00:00Z"},{"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","status":"public","ddc":["570"],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","_id":"8951","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:41:57Z","date_created":"2020-12-20T10:00:26Z","file":[{"file_size":523,"content_type":"text/plain","creator":"bkavcic","access_level":"open_access","file_name":"readme.txt","checksum":"f57862aeee1690c7effd2b1117d40ed1","success":1,"date_updated":"2020-12-20T09:52:52Z","date_created":"2020-12-20T09:52:52Z","relation":"main_file","file_id":"8952"},{"creator":"bkavcic","content_type":"application/octet-stream","file_size":379228,"access_level":"open_access","file_name":"GRNs Research depository.gb","success":1,"checksum":"f2c6d5232ec6d551b6993991e8689e9f","date_created":"2020-12-20T22:01:44Z","date_updated":"2020-12-20T22:01:44Z","file_id":"8954","relation":"main_file"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","first_name":"Anna A","full_name":"Nagy-Staron, Anna A"}],"related_material":{"record":[{"id":"9283","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","contributor_type":"project_member","last_name":"Nagy-Staron"},{"contributor_type":"project_member","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Caruso Carter","contributor_type":"project_member","first_name":"Caroline"},{"first_name":"Elisabeth","last_name":"Sonnleitner","contributor_type":"project_member"},{"last_name":"Kavcic","contributor_type":"project_member","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","last_name":"Paixão","contributor_type":"project_member"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","contributor_type":"project_manager","first_name":"Calin C"}],"type":"research_data","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"file_date_updated":"2020-12-20T22:01:44Z","citation":{"apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020).","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8951","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"day":"21","month":"12","has_accepted_license":"1","article_processing_charge":"No"},{"date_published":"2020-01-28T00:00:00Z","doi":"10.15479/AT:ISTA:7383","oa":1,"citation":{"chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","short":"R. Grah, (2020).","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383"},"day":"28","month":"01","article_processing_charge":"No","has_accepted_license":"1","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"date_updated":"2024-02-21T12:42:31Z","date_created":"2020-01-28T10:41:49Z","oa_version":"Published Version","file":[{"file_name":"Scripts.zip","access_level":"open_access","creator":"rgrah","content_type":"application/zip","file_size":73363365,"file_id":"7384","relation":"main_file","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:40Z","checksum":"9d292cf5207b3829225f44c044cdb3fd"},{"creator":"rgrah","file_size":962,"content_type":"text/plain","file_name":"READ_ME_MAIN.txt","access_level":"open_access","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:30Z","checksum":"4076ceab32ef588cc233802bab24c1ab","file_id":"7385","relation":"main_file"}],"author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok"}],"contributor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","contributor_type":"project_leader","last_name":"Guet"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7652"}]},"title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2020","_id":"7383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"file_date_updated":"2020-07-14T12:47:57Z","type":"research_data"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"status":"public","ddc":["530"],"title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","_id":"9222","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":13317557,"content_type":"application/x-zip-compressed","creator":"gkatsaro","file_name":"DOI_SiteControlledHWs.zip","access_level":"open_access","date_created":"2021-03-05T17:50:45Z","date_updated":"2021-03-05T17:50:45Z","checksum":"41b66e195ed3dbd73077feee77b05652","relation":"main_file","file_id":"9223"},{"date_created":"2021-03-10T07:31:50Z","date_updated":"2021-03-10T07:31:50Z","checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","success":1,"relation":"main_file","file_id":"9233","content_type":"text/plain","file_size":3515,"creator":"dernst","file_name":"Readme.txt","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:42:13Z","date_created":"2021-03-05T18:00:47Z","related_material":{"record":[{"id":"7541","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","contributor_type":"research_group","first_name":"Georgios"}],"author":[{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"type":"research_data","file_date_updated":"2021-03-10T07:31:50Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"G. Katsaros, (2020).","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222."},"oa":1,"doi":"10.15479/AT:ISTA:9222","date_published":"2020-03-16T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"16","month":"03"},{"keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"day":"21","article_processing_charge":"No","has_accepted_license":"1","page":"118","citation":{"chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366.","mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366"},"date_published":"2020-09-21T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop."}],"title":"Computational design of curved thin shells: From glass façades to programmable matter","ddc":["000"],"status":"public","_id":"8366","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"rguseino","content_type":"application/pdf","file_size":70950442,"access_level":"open_access","file_name":"thesis_rguseinov.pdf","success":1,"checksum":"f8da89553da36037296b0a80f14ebf50","date_created":"2020-09-10T16:11:49Z","date_updated":"2020-09-10T16:11:49Z","file_id":"8367","relation":"main_file"},{"checksum":"e8fd944c960c20e0e27e6548af69121d","date_created":"2020-09-11T09:39:48Z","date_updated":"2020-09-16T15:11:01Z","relation":"source_file","file_id":"8374","file_size":76207597,"content_type":"application/x-zip-compressed","creator":"rguseino","access_level":"closed","file_name":"thesis_source.zip"}],"oa_version":"Published Version","month":"09","publication_identifier":{"isbn":["978-3-99078-010-7"],"issn":["2663-337X"]},"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"oa":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"degree_awarded":"PhD","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8366","file_date_updated":"2020-09-16T15:11:01Z","ec_funded":1,"publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","year":"2020","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","date_updated":"2024-02-21T12:44:29Z","date_created":"2020-09-10T16:19:55Z","author":[{"full_name":"Guseinov, Ruslan","first_name":"Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077"}],"related_material":{"record":[{"relation":"research_data","status":"deleted","id":"7151"},{"relation":"part_of_dissertation","status":"public","id":"7262"},{"id":"8562","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1001"},{"relation":"research_data","status":"public","id":"8375"}]}},{"article_type":"original","publication":"ACM Transactions on Graphics","citation":{"ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","ieee":"K. Gavriil et al., “Computational design of cold bent glass façades,” ACM Transactions on Graphics, vol. 39, no. 6. Association for Computing Machinery, 2020.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3414685.3417843","ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. ACM Transactions on Graphics. 2020;39(6). doi:10.1145/3414685.3417843","chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3414685.3417843.","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:10.1145/3414685.3417843.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020)."},"date_published":"2020-11-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["000"],"title":"Computational design of cold bent glass façades","intvolume":" 39","_id":"8562","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"13084","date_updated":"2023-05-23T20:54:43Z","date_created":"2023-05-23T20:54:43Z","checksum":"c7f67717ad74e670b7daeae732abe151","success":1,"file_name":"coldglass.pdf","access_level":"open_access","file_size":28964641,"content_type":"application/pdf","creator":"bbickel"}],"type":"journal_article","abstract":[{"text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface.","lang":"eng"}],"issue":"6","quality_controlled":"1","isi":1,"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"external_id":{"isi":["000595589100048"],"arxiv":["2009.03667"]},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3414685.3417843","month":"11","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"year":"2020","acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","date_updated":"2024-02-21T12:43:21Z","date_created":"2020-09-23T11:30:02Z","volume":39,"author":[{"full_name":"Gavriil, Konstantinos","first_name":"Konstantinos","last_name":"Gavriil"},{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","last_name":"Guseinov","full_name":"Guseinov, Ruslan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez","full_name":"Perez Rodriguez, Jesus"},{"first_name":"Davide","last_name":"Pellis","full_name":"Pellis, Davide"},{"last_name":"Henderson","first_name":"Paul M","orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M"},{"full_name":"Rist, Florian","first_name":"Florian","last_name":"Rist"},{"full_name":"Pottmann, Helmut","first_name":"Helmut","last_name":"Pottmann"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8366"},{"id":"8761","relation":"research_data","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/bend-dont-break/"}]},"article_number":"208","file_date_updated":"2023-05-23T20:54:43Z","ec_funded":1},{"doi":"10.1021/acs.nanolett.0c01466","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000548893200066"],"pmid":["32479090"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Towards scalable hut wire quantum devices","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"month":"06","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"author":[{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"},{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","first_name":"Lada","full_name":"Vukušić, Lada"},{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"full_name":"Wang, Ting","last_name":"Wang","first_name":"Ting","orcid":"0000-0002-4619-9575"},{"last_name":"Zhang","first_name":"Jian-Jun","full_name":"Zhang, Jian-Jun"},{"full_name":"Held, Karsten","last_name":"Held","first_name":"Karsten"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"7689"}]},"date_created":"2020-08-06T09:25:04Z","date_updated":"2024-02-21T12:44:01Z","volume":20,"year":"2020","acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","pmid":1,"publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"American Chemical Society","file_date_updated":"2020-08-06T09:35:37Z","ec_funded":1,"date_published":"2020-06-01T00:00:00Z","publication":"Nano Letters","citation":{"apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01466","ieee":"G. Katsaros et al., “Zero field splitting of heavy-hole states in quantum dots,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 2020;20(7):5201-5206. doi:10.1021/acs.nanolett.0c01466","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01466.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:10.1021/acs.nanolett.0c01466."},"article_type":"original","page":"5201-5206","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","file":[{"success":1,"date_created":"2020-08-06T09:35:37Z","date_updated":"2020-08-06T09:35:37Z","file_id":"8204","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":3308906,"access_level":"open_access","file_name":"2020_NanoLetters_Katsaros.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8203","status":"public","ddc":["530"],"title":"Zero field splitting of heavy-hole states in quantum dots","intvolume":" 20","abstract":[{"lang":"eng","text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits."}],"issue":"7","type":"journal_article"},{"month":"10","publication_identifier":{"eissn":["2050084X"]},"isi":1,"quality_controlled":"1","project":[{"name":"Interneuron plasticity during spatial learning","call_identifier":"FWF","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27"},{"call_identifier":"FWF","name":"Interneuro Plasticity During Spatial Learning","grant_number":"I03713","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000584369000001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.61106","article_number":"61106","file_date_updated":"2020-11-09T09:17:40Z","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"JoCs"}],"acknowledgement":"We thank Michele Nardin and Federico Stella for comments on an earlier version of the manuscript. K Deisseroth for providing the pAAV-CaMKIIα::eNpHR3.0-YFP plasmid through Addgene. E Boyden for providing AAV2/1.CaMKII::ArchT.GFP.WPRE.SV40 plasmid through Penn Vector Core. This work was supported by the Austrian Science Fund (I02072 and I03713) and a Swiss National Science Foundation grant to PS. The authors declare no conflicts of interest.","year":"2020","date_updated":"2024-02-21T12:43:40Z","date_created":"2020-11-08T23:01:25Z","volume":9,"author":[{"full_name":"Gridchyn, Igor","last_name":"Gridchyn","first_name":"Igor","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schönenberger, Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Schönenberger"},{"full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill"},{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"8563"}]},"scopus_import":"1","day":"05","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"eLife","citation":{"ieee":"I. Gridchyn, P. 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Light application and associated firing alteration of pyramidal and interneuron populations led to lasting changes in pyramidal-interneuron connection weights as indicated by spike transmission changes. Spike transmission alterations were predicted by the light-mediated changes in the number of pre- and postsynaptic spike pairing events and by firing rate changes of interneurons but not pyramidal cells. This work demonstrates the presence of activity-dependent associative and non-associative reorganization of pyramidal-interneuron connections triggered by the optogenetic modification of the firing rate and spike synchrony of cells.","lang":"eng"}],"ddc":["570"],"status":"public","title":"Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior","intvolume":" 9","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8740","oa_version":"Published Version","file":[{"checksum":"6a7b0543c440f4c000a1864e69377d95","success":1,"date_created":"2020-11-09T09:17:40Z","date_updated":"2020-11-09T09:17:40Z","relation":"main_file","file_id":"8749","content_type":"application/pdf","file_size":447669,"creator":"dernst","access_level":"open_access","file_name":"2020_eLife_Gridchyn.pdf"}]},{"day":"21","month":"09","article_processing_charge":"No","has_accepted_license":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Guseinov R. 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All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. 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Schönenberger, (2020).","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8563.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","ieee":"J. L. Csicsvari, I. Gridchyn, and P. 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Elife.","lang":"eng"}]},{"article_type":"original","citation":{"short":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, B. Bickel, Nature Communications 11 (2020).","mla":"Guseinov, Ruslan, et al. “Programming Temporal Morphing of Self-Actuated Shells.” Nature Communications, vol. 11, 237, Springer Nature, 2020, doi:10.1038/s41467-019-14015-2.","chicago":"Guseinov, Ruslan, Connor McMahan, Jesus Perez Rodriguez, Chiara Daraio, and Bernd Bickel. “Programming Temporal Morphing of Self-Actuated Shells.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-019-14015-2.","ama":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. Programming temporal morphing of self-actuated shells. Nature Communications. 2020;11. doi:10.1038/s41467-019-14015-2","ieee":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, and B. Bickel, “Programming temporal morphing of self-actuated shells,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Guseinov, R., McMahan, C., Perez Rodriguez, J., Daraio, C., & Bickel, B. (2020). Programming temporal morphing of self-actuated shells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-14015-2","ista":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. 2020. Programming temporal morphing of self-actuated shells. Nature Communications. 11, 237."},"publication":"Nature Communications","date_published":"2020-01-13T00:00:00Z","keyword":["Design","Synthesis and processing","Mechanical engineering","Polymers"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"13","intvolume":" 11","title":"Programming temporal morphing of self-actuated shells","ddc":["000"],"status":"public","_id":"7262","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"7336","checksum":"7db23fef2f4cda712f17f1004116ddff","date_created":"2020-01-15T14:35:34Z","date_updated":"2020-07-14T12:47:55Z","access_level":"open_access","file_name":"2020_NatureComm_Guseinov.pdf","file_size":1315270,"content_type":"application/pdf","creator":"rguseino"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Advances in shape-morphing materials, such as hydrogels, shape-memory polymers and light-responsive polymers have enabled prescribing self-directed deformations of initially flat geometries. However, most proposed solutions evolve towards a target geometry without considering time-dependent actuation paths. To achieve more complex geometries and avoid self-collisions, it is critical to encode a spatial and temporal shape evolution within the initially flat shell. Recent realizations of time-dependent morphing are limited to the actuation of few, discrete hinges and cannot form doubly curved surfaces. Here, we demonstrate a method for encoding temporal shape evolution in architected shells that assume complex shapes and doubly curved geometries. The shells are non-periodic tessellations of pre-stressed contractile unit cells that soften in water at rates prescribed locally by mesostructure geometry. The ensuing midplane contraction is coupled to the formation of encoded curvatures. We propose an inverse design tool based on a data-driven model for unit cells’ temporal responses."}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000511916800015"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-14015-2","publication_identifier":{"issn":["2041-1723"]},"month":"01","publisher":"Springer Nature","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2020","volume":11,"date_created":"2020-01-13T16:54:26Z","date_updated":"2024-02-21T12:45:02Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/geometry-meets-time/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"8366","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"research_data","id":"7154"}]},"author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","last_name":"Guseinov","full_name":"Guseinov, Ruslan"},{"full_name":"McMahan, Connor","first_name":"Connor","last_name":"McMahan"},{"full_name":"Perez Rodriguez, Jesus","first_name":"Jesus","last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Daraio, Chiara","first_name":"Chiara","last_name":"Daraio"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"article_number":"237","ec_funded":1,"file_date_updated":"2020-07-14T12:47:55Z"},{"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","short":"F.K. Schur, (2020)."},"article_processing_charge":"No","has_accepted_license":"1","day":"01","month":"12","file":[{"content_type":"application/zip","file_size":49297,"creator":"fschur","file_name":"3Dprint-files_download_v2.zip","access_level":"open_access","date_updated":"2023-11-22T14:58:44Z","date_created":"2023-11-22T14:58:44Z","checksum":"0108616e2a59e51879ea51299a29b091","success":1,"relation":"main_file","file_id":"14593"},{"content_type":"text/plain","file_size":641,"creator":"cchlebak","file_name":"readme.txt","access_level":"open_access","date_updated":"2023-12-01T10:39:59Z","date_created":"2023-12-01T10:39:59Z","checksum":"4c66ddedee4d01c1c4a7978208350cfc","success":1,"relation":"main_file","file_id":"14637"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:44:48Z","date_created":"2023-11-22T15:00:57Z","contributor":[{"contributor_type":"researcher","last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bettina","contributor_type":"researcher","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","contributor_type":"researcher","last_name":"Hauschild"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","contributor_type":"researcher","first_name":"Florian KM"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"8586"}]},"author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"ddc":["570"],"status":"public","title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","year":"2020","_id":"14592","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-12-01T10:39:59Z","abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"type":"research_data"},{"oa":1,"external_id":{"isi":["000843927300003"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.1007/978-3-030-36687-2_3","conference":{"end_date":"2019-12-12","location":"Lisbon, Portugal","start_date":"2019-12-10","name":"COMPLEX: International Conference on Complex Networks and their Applications"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030366865"],"eissn":["18609503"],"issn":["1860949X"]},"month":"01","year":"2020","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"publication_status":"published","author":[{"first_name":"Sumit","last_name":"Bhatia","full_name":"Bhatia, Sumit"},{"full_name":"Chatterjee, Bapi","last_name":"Chatterjee","first_name":"Bapi","orcid":"0000-0002-2742-4028","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nathani","first_name":"Deepak","full_name":"Nathani, Deepak"},{"full_name":"Kaul, Manohar","last_name":"Kaul","first_name":"Manohar"}],"volume":881,"date_updated":"2024-02-22T13:16:06Z","date_created":"2019-12-29T23:00:45Z","ec_funded":1,"file_date_updated":"2020-10-08T08:16:48Z","citation":{"chicago":"Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent Homology Perspective to the Link Prediction Problem.” In Complex Networks and Their Applications VIII, 881:27–39. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36687-2_3.","mla":"Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction Problem.” Complex Networks and Their Applications VIII, vol. 881, Springer Nature, 2020, pp. 27–39, doi:10.1007/978-3-030-36687-2_3.","short":"S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and Their Applications VIII, Springer Nature, 2020, pp. 27–39.","ista":"Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective to the link prediction problem. Complex Networks and their applications VIII. COMPLEX: International Conference on Complex Networks and their Applications, SCI, vol. 881, 27–39.","apa":"Bhatia, S., Chatterjee, B., Nathani, D., & Kaul, M. (2020). A persistent homology perspective to the link prediction problem. In Complex Networks and their applications VIII (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-36687-2_3","ieee":"S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology perspective to the link prediction problem,” in Complex Networks and their applications VIII, Lisbon, Portugal, 2020, vol. 881, pp. 27–39.","ama":"Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective to the link prediction problem. In: Complex Networks and Their Applications VIII. Vol 881. Springer Nature; 2020:27-39. doi:10.1007/978-3-030-36687-2_3"},"publication":"Complex Networks and their applications VIII","page":"27-39","date_published":"2020-01-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","_id":"7213","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 881","ddc":["004"],"title":"A persistent homology perspective to the link prediction problem","status":"public","oa_version":"Submitted Version","file":[{"file_id":"8625","relation":"main_file","date_created":"2020-10-08T08:16:48Z","date_updated":"2020-10-08T08:16:48Z","success":1,"checksum":"8951f094c8c7dae9ff8db885199bc296","file_name":"main.pdf","access_level":"open_access","creator":"bchatter","file_size":310598,"content_type":"application/pdf"}],"type":"conference","alternative_title":["SCI"],"abstract":[{"text":"Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture the topological properties of data succinctly at different spatial resolutions. For graphical data, the shape, and structure of the neighborhood of individual data items (nodes) are an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology-based methods for network analysis.","lang":"eng"}]},{"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ElKo"}],"year":"2020","acknowledgement":"We would like to thank Ittai Abraham for the discussions and guidance during the initial conception of the project, especially for HAVSS. Furthermore, we would like to thank the anonymous reviewers for pointing out the relevance of this work to MPC protocols.","date_created":"2021-12-16T13:23:27Z","date_updated":"2024-02-22T13:10:45Z","author":[{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Malkhi","first_name":"Dahlia","full_name":"Malkhi, Dahlia"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"month":"10","publication_identifier":{"isbn":["978-1-4503-7089-9"]},"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2019/1015","open_access":"1"}],"oa":1,"external_id":{"isi":["000768470400104"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2020-11-13","location":"Virtual, United States","start_date":"2020-11-09","name":"CCS: Computer and Communications Security"},"doi":"10.1145/3372297.3423364","type":"conference","abstract":[{"lang":"eng","text":"In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364","apa":"Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. https://doi.org/10.1145/3372297.3423364","ieee":"E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures,” in Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Virtual, United States, 2020, pp. 1751–1767.","ista":"Kokoris Kogias E, Malkhi D, Spiegelman A. 2020. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. CCS: Computer and Communications Security, 1751–1767.","short":"E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767.","mla":"Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364.","chicago":"Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, 1751–1767. Association for Computing Machinery, 2020. https://doi.org/10.1145/3372297.3423364."},"date_published":"2020-10-30T00:00:00Z"},{"date_published":"2020-12-01T00:00:00Z","publication":"2020 IEEE Real-Time Systems Symposium","citation":{"chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” In 2020 IEEE Real-Time Systems Symposium, 244–56. IEEE, 2020. https://doi.org/10.1109/RTSS49844.2020.00031.","short":"M. Garcia Soto, P. Prabhakar, in:, 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–256.","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–56, doi:10.1109/RTSS49844.2020.00031.","ieee":"M. Garcia Soto and P. Prabhakar, “Hybridization for stability verification of nonlinear switched systems,” in 2020 IEEE Real-Time Systems Symposium, Houston, TX, USA , 2020, pp. 244–256.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Hybridization for stability verification of nonlinear switched systems. In 2020 IEEE Real-Time Systems Symposium (pp. 244–256). Houston, TX, USA : IEEE. https://doi.org/10.1109/RTSS49844.2020.00031","ista":"Garcia Soto M, Prabhakar P. 2020. Hybridization for stability verification of nonlinear switched systems. 2020 IEEE Real-Time Systems Symposium. RTTS: Real-Time Systems Symposium, 244–256.","ama":"Garcia Soto M, Prabhakar P. Hybridization for stability verification of nonlinear switched systems. In: 2020 IEEE Real-Time Systems Symposium. IEEE; 2020:244-256. doi:10.1109/RTSS49844.2020.00031"},"page":"244-256","day":"01","has_accepted_license":"1","article_processing_charge":"No","file":[{"file_name":"main.pdf","access_level":"open_access","creator":"mgarcias","file_size":1125794,"content_type":"application/pdf","file_id":"9203","relation":"main_file","date_created":"2021-02-26T16:38:14Z","date_updated":"2021-02-26T16:38:14Z","checksum":"8f97f229316c3b3a6f0cf99297aa0941"}],"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"9202","title":"Hybridization for stability verification of nonlinear switched systems","ddc":["000"],"status":"public","abstract":[{"lang":"eng","text":"We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function."}],"type":"conference","conference":{"name":"RTTS: Real-Time Systems Symposium","end_date":"2020-12-04","location":"Houston, TX, USA ","start_date":"2020-12-01"},"doi":"10.1109/RTSS49844.2020.00031","language":[{"iso":"eng"}],"external_id":{"isi":["000680435100021"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"month":"12","publication_identifier":{"eissn":["2576-3172"],"eisbn":["9781728183244"]},"author":[{"full_name":"Garcia Soto, Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2936-5719","first_name":"Miriam","last_name":"Garcia Soto"},{"full_name":"Prabhakar, Pavithra","last_name":"Prabhakar","first_name":"Pavithra"}],"date_created":"2021-02-26T16:38:24Z","date_updated":"2024-02-22T13:25:19Z","year":"2020","acknowledgement":"Miriam Garc´ıa Soto was partially supported by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Pavithra Prabhakar was partially supported by NSF CAREER Award No. 1552668, NSF Award No. 2008957 and ONR YIP Award No. N000141712577.","publication_status":"published","publisher":"IEEE","department":[{"_id":"ToHe"}],"file_date_updated":"2021-02-26T16:38:14Z"},{"date_published":"2020-06-01T00:00:00Z","publication":"Communications in Mathematical Physics","citation":{"chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics. Springer, 2020. https://doi.org/10.1007/s00220-019-03555-9.","mla":"Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics, vol. 376, Springer, 2020, pp. 1311–95, doi:10.1007/s00220-019-03555-9.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical Physics 376 (2020) 1311–1395.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 376, 1311–1395.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-019-03555-9","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime,” Communications in Mathematical Physics, vol. 376. Springer, pp. 1311–1395, 2020.","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 2020;376:1311-1395. doi:10.1007/s00220-019-03555-9"},"article_type":"original","page":"1311-1395","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"6906","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime","status":"public","intvolume":" 376","abstract":[{"text":"We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime. We show that low-energy states exhibit complete Bose–Einstein condensation with an optimal bound on the number of orthogonal excitations. This extends recent results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing the assumption of small interaction potential.","lang":"eng"}],"type":"journal_article","doi":"10.1007/s00220-019-03555-9","language":[{"iso":"eng"}],"external_id":{"arxiv":["1812.03086"],"isi":["000536053300012"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.03086"}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"month":"06","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"author":[{"first_name":"Chiara","last_name":"Boccato","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara"},{"full_name":"Brennecke, Christian","first_name":"Christian","last_name":"Brennecke"},{"full_name":"Cenatiempo, Serena","last_name":"Cenatiempo","first_name":"Serena"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"}],"date_updated":"2024-02-22T13:33:02Z","date_created":"2019-09-24T17:30:59Z","volume":376,"year":"2020","acknowledgement":"We would like to thank P. T. Nam and R. Seiringer for several useful discussions and\r\nfor suggesting us to use the localization techniques from [9]. C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges support from the NCCR SwissMAP and from the Swiss National Foundation of Science (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties of Bose–Einstein condensates”.","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"ec_funded":1},{"author":[{"last_name":"Sun","first_name":"Rémy","full_name":"Sun, Rémy"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6482"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11263-019-01262-5"}]},"date_updated":"2024-02-22T14:57:30Z","date_created":"2019-10-14T09:14:28Z","volume":128,"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:45Z","ec_funded":1,"doi":"10.1007/s11263-019-01232-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000494406800001"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"month":"04","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_IJCV_Sun.pdf","file_size":1715072,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7110","checksum":"155e63edf664dcacb3bdc1c2223e606f","date_created":"2019-11-26T10:30:02Z","date_updated":"2020-07-14T12:47:45Z"}],"_id":"6944","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications","status":"public","intvolume":" 128","abstract":[{"text":"We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2020-04-01T00:00:00Z","publication":"International Journal of Computer Vision","citation":{"ama":"Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 2020;128(4):970-995. doi:10.1007/s11263-019-01232-x","ista":"Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995.","apa":"Sun, R., & Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01232-x","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” International Journal of Computer Vision, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.","mla":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:10.1007/s11263-019-01232-x.","short":"R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995.","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01232-x."},"article_type":"original","page":"970-995","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"issue":"POPL","type":"conference","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_ACM_POPL_Wang.pdf","file_size":564151,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"8328","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","success":1,"date_updated":"2020-09-01T11:12:58Z","date_created":"2020-09-01T11:12:58Z"}],"status":"public","title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","ddc":["004"],"intvolume":" 4","_id":"8324","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","publication":"Proceedings of the ACM on Programming Languages","citation":{"ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093."},"file_date_updated":"2020-09-01T11:12:58Z","article_number":"25","date_created":"2020-08-30T22:01:12Z","date_updated":"2024-02-22T15:16:45Z","volume":4,"author":[{"last_name":"Wang","first_name":"Peixin","full_name":"Wang, Peixin"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Deng","first_name":"Yuxin","full_name":"Deng, Yuxin"},{"full_name":"Xu, Ming","last_name":"Xu","first_name":"Ming"}],"related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.3533633","relation":"software"}]},"publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"year":"2020","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","month":"01","publication_identifier":{"eissn":["2475-1421"]},"language":[{"iso":"eng"}],"doi":"10.1145/3371093","quality_controlled":"1","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1902.04744"]},"oa":1},{"issue":"2","abstract":[{"lang":"eng","text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 48","title":"Correlated random matrices: Band rigidity and edge universality","status":"public","_id":"6184","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-03-01T00:00:00Z","page":"963-1001","article_type":"original","citation":{"ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” Annals of Probability, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020.","apa":"Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379","ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379.","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379.","short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001."},"publication":"Annals of Probability","ec_funded":1,"volume":48,"date_updated":"2024-02-22T14:34:33Z","date_created":"2019-03-28T09:20:08Z","related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"6179"}]},"author":[{"full_name":"Alt, Johannes","last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2020","publication_identifier":{"issn":["0091-1798"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1214/19-AOP1379","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.07744","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1804.07744"],"isi":["000528269100013"]}},{"type":"journal_article","abstract":[{"lang":"eng","text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants."}],"issue":"5","status":"public","ddc":["580"],"title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15037","oa_version":"Published Version","file":[{"file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3089212,"file_id":"15038","relation":"main_file","date_created":"2024-02-28T12:39:56Z","date_updated":"2024-02-28T12:39:56Z","success":1,"checksum":"c538a5008f7827f62d17d40a3bfabe65"}],"keyword":["Plant Science","Molecular Biology"],"day":"04","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"717-731","publication":"Molecular Plant","citation":{"mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020."},"date_published":"2020-05-04T00:00:00Z","file_date_updated":"2024-02-28T12:39:56Z","publication_status":"published","publisher":"Elsevier","department":[{"_id":"EvBe"}],"year":"2020","pmid":1,"date_created":"2024-02-28T08:55:56Z","date_updated":"2024-02-28T12:41:52Z","volume":13,"author":[{"full_name":"Moulinier-Anzola, Jeanette","first_name":"Jeanette","last_name":"Moulinier-Anzola"},{"first_name":"Maximilian","last_name":"Schwihla","full_name":"Schwihla, Maximilian"},{"last_name":"De-Araújo","first_name":"Lucinda","full_name":"De-Araújo, Lucinda"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina"},{"first_name":"Lisa","last_name":"Jörg","full_name":"Jörg, Lisa"},{"full_name":"Konstantinova, Nataliia","last_name":"Konstantinova","first_name":"Nataliia"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"last_name":"Korbei","first_name":"Barbara","full_name":"Korbei, Barbara"}],"month":"05","publication_identifier":{"issn":["1674-2052"]},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32087370"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2020.02.012"},{"article_type":"original","page":"5784-5801","publication":"Journal of Molecular Biology","citation":{"chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001"},"date_published":"2020-10-02T00:00:00Z","keyword":["Molecular Biology","Structural Biology"],"day":"02","article_processing_charge":"No","title":"Molecular recognition at septin interfaces: The switches hold the key","status":"public","intvolume":" 432","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15036","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"issue":"21","quality_controlled":"1","external_id":{"pmid":["32910969"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.jmb.2020.09.001","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2020.09.001","month":"10","publication_identifier":{"issn":["0022-2836"]},"publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Elsevier","year":"2020","pmid":1,"date_updated":"2024-02-28T12:37:54Z","date_created":"2024-02-28T08:50:34Z","volume":432,"author":[{"full_name":"Rosa, Higor Vinícius Dias","first_name":"Higor Vinícius Dias","last_name":"Rosa"},{"first_name":"Diego Antonio","last_name":"Leonardo","full_name":"Leonardo, Diego Antonio"},{"first_name":"Gabriel","last_name":"Brognara","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","full_name":"Brognara, Gabriel"},{"full_name":"Brandão-Neto, José","last_name":"Brandão-Neto","first_name":"José"},{"last_name":"D'Muniz Pereira","first_name":"Humberto","full_name":"D'Muniz Pereira, Humberto"},{"last_name":"Araújo","first_name":"Ana Paula Ulian","full_name":"Araújo, Ana Paula Ulian"},{"full_name":"Garratt, Richard Charles","last_name":"Garratt","first_name":"Richard Charles"}]},{"date_published":"2020-07-08T00:00:00Z","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392405.","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405."},"day":"08","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"file_size":14935529,"content_type":"application/pdf","creator":"dernst","file_name":"2020_soapfilm_submitted.pdf","access_level":"open_access","date_updated":"2020-11-23T09:03:19Z","date_created":"2020-11-23T09:03:19Z","checksum":"813831ca91319d794d9748c276b24578","success":1,"relation":"main_file","file_id":"8795"}],"oa_version":"Submitted Version","title":"A model for soap film dynamics with evolving thickness","ddc":["000"],"status":"public","intvolume":" 39","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8384","abstract":[{"text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.","lang":"eng"}],"issue":"4","type":"journal_article","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3386569.3392405","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392405","open_access":"1"}],"oa":1,"external_id":{"isi":["000583700300004"]},"month":"07","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"date_created":"2020-09-13T22:01:18Z","date_updated":"2024-02-28T12:57:31Z","volume":39,"author":[{"last_name":"Ishida","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige"},{"id":"331776E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Synak","full_name":"Synak, Peter"},{"first_name":"Fumiya","last_name":"Narita","full_name":"Narita, Fumiya"},{"full_name":"Hachisuka, Toshiya","first_name":"Toshiya","last_name":"Hachisuka"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","year":"2020","file_date_updated":"2020-11-23T09:03:19Z","ec_funded":1,"article_number":"31"},{"ec_funded":1,"author":[{"orcid":"0000-0002-5646-9524","first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"full_name":"Davies, Peter","first_name":"Peter","last_name":"Davies","id":"11396234-BB50-11E9-B24C-90FCE5697425","orcid":"0000-0002-5646-9524"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"related_material":{"record":[{"id":"9541","status":"public","relation":"later_version"}]},"date_created":"2020-05-06T08:53:34Z","date_updated":"2024-02-28T12:53:09Z","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"month":"07","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2020-07-15","location":"Virtual Event, United States","end_date":"2020-07-17"},"doi":"10.1145/3350755.3400282","language":[{"iso":"eng"}],"external_id":{"arxiv":["1912.05390"],"isi":["000744436200015"]},"main_file_link":[{"url":"https://arxiv.org/abs/1912.05390","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"abstract":[{"lang":"eng","text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17]."}],"issue":"7","type":"conference","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7802","title":"Graph sparsification for derandomizing massively parallel computation with low space","status":"public","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-01T00:00:00Z","publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282.","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185.","ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282"},"page":"175-185"},{"page":"276-291","citation":{"short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91, doi:10.1145/3332466.3374542.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542.","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:276-291. doi:10.1145/3332466.3374542","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 276–291.","apa":"Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291."},"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","date_published":"2020-02-19T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"19","title":"Non-blocking interpolation search trees with doubly-logarithmic running time","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7636","oa_version":"Published Version","type":"conference","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000564476500020"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3332466.3374542","conference":{"location":"San Diego, CA, United States","start_date":"2020-02-22","end_date":"2020-02-26","name":"PPOPP: Principles and Practice of Parallel Programming"},"publication_identifier":{"isbn":["9781450368186"]},"month":"02","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","year":"2020","date_created":"2020-04-05T22:00:49Z","date_updated":"2024-02-28T12:55:14Z","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"first_name":"Aleksandar","last_name":"Prokopec","full_name":"Prokopec, Aleksandar"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"ec_funded":1},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392412","open_access":"1"}],"external_id":{"isi":["000583700300021"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"doi":"10.1145/3386569.3392412","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"author":[{"full_name":"Sperl, Georg","first_name":"Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narain, Rahul","last_name":"Narain","first_name":"Rahul"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"related_material":{"record":[{"id":"12358","status":"public","relation":"dissertation_contains"}]},"date_created":"2020-09-13T22:01:18Z","date_updated":"2024-02-28T12:57:47Z","volume":39,"article_number":"48","file_date_updated":"2020-11-23T09:01:22Z","ec_funded":1,"publication":"ACM Transactions on Graphics","citation":{"ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","apa":"Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392412","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392412.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412."},"article_type":"original","date_published":"2020-07-08T00:00:00Z","scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No","_id":"8385","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Homogenized yarn-level cloth","ddc":["000"],"intvolume":" 39","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":38922662,"creator":"dernst","access_level":"open_access","file_name":"2020_hylc_submitted.pdf","checksum":"cf4c1d361c3196c4bd424520a5588205","success":1,"date_created":"2020-11-23T09:01:22Z","date_updated":"2020-11-23T09:01:22Z","relation":"main_file","file_id":"8794"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"issue":"4"},{"issue":"20","abstract":[{"lang":"eng","text":"When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles."}],"type":"journal_article","oa_version":"Published Version","_id":"7956","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 152","title":"Shear-induced ordering in systems with competing interactions: A machine learning study","status":"public","article_processing_charge":"No","day":"29","scopus_import":"1","date_published":"2020-05-29T00:00:00Z","citation":{"short":"J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical Physics 152 (2020).","mla":"Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no. 20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194.","chicago":"Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194.","ama":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 2020;152(20). doi:10.1063/5.0005194","apa":"Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194","ieee":"J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering in systems with competing interactions: A machine learning study,” The Journal of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.","ista":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 152(20), 204905."},"publication":"The Journal of chemical physics","article_type":"original","ec_funded":1,"article_number":"204905","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10759"}]},"author":[{"first_name":"J.","last_name":"Pȩkalski","full_name":"Pȩkalski, J."},{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","first_name":"Wojciech","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech"},{"first_name":"A. Z.","last_name":"Panagiotopoulos","full_name":"Panagiotopoulos, A. Z."}],"volume":152,"date_created":"2020-06-14T22:00:49Z","date_updated":"2024-02-28T13:00:28Z","year":"2020","publisher":"AIP Publishing","department":[{"_id":"MiLe"}],"publication_status":"published","publication_identifier":{"eissn":["10897690"]},"month":"05","doi":"10.1063/5.0005194","language":[{"iso":"eng"}],"external_id":{"isi":["000537900300001"],"arxiv":["2002.07294"]},"main_file_link":[{"url":"https://doi.org/10.1063/5.0005194","open_access":"1"}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"quality_controlled":"1"},{"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02860087/document","open_access":"1"}],"citation":{"ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived snapshots with polylogarithmic amortized step complexity,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 31–40.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2020). Long-lived snapshots with polylogarithmic amortized step complexity. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 31–40). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3406005","ista":"Baig MA, Hendler D, Milani A, Travers C. 2020. Long-lived snapshots with polylogarithmic amortized step complexity. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 31–40.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived snapshots with polylogarithmic amortized step complexity. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:31-40. doi:10.1145/3382734.3406005","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 31–40. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3406005.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40.","mla":"Baig, Mirza Ahad, et al. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40, doi:10.1145/3382734.3406005."},"oa":1,"publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","page":"31-40","quality_controlled":"1","date_published":"2020-07-31T00:00:00Z","doi":"10.1145/3382734.3406005","conference":{"location":"Virtual, Italy","start_date":"2020-08-03","end_date":"2020-08-07","name":"PODC: Principles of Distributed Computing"},"language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9781450375825"]},"month":"07","day":"31","year":"2020","_id":"8382","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","title":"Long-lived snapshots with polylogarithmic amortized step complexity","status":"public","publication_status":"published","author":[{"full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig"},{"full_name":"Hendler, Danny","last_name":"Hendler","first_name":"Danny"},{"full_name":"Milani, Alessia","first_name":"Alessia","last_name":"Milani"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"oa_version":"Preprint","date_updated":"2024-02-28T12:54:30Z","date_created":"2020-09-13T22:01:17Z","type":"conference","abstract":[{"text":"We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest.","lang":"eng"}]},{"article_number":"020504","year":"2020","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"full_name":"Lopes, P. L.S.","first_name":"P. L.S.","last_name":"Lopes"},{"full_name":"Hosur, Pavan","last_name":"Hosur","first_name":"Pavan"},{"last_name":"Gilbert","first_name":"Matthew J.","full_name":"Gilbert, Matthew J."},{"first_name":"Pouyan","last_name":"Ghaemi","full_name":"Ghaemi, Pouyan"}],"volume":101,"date_updated":"2024-02-28T13:11:13Z","date_created":"2020-02-02T23:01:01Z","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"oa":1,"external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevB.101.020504","language":[{"iso":"eng"}],"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7428","intvolume":" 101","status":"public","title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"13","citation":{"ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504","ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” Physical Review B, vol. 101, no. 2. American Physical Society, 2020.","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.020504."},"publication":"Physical Review B","article_type":"original","date_published":"2020-01-13T00:00:00Z"},{"doi":"10.1103/PhysRevA.102.012224","language":[{"iso":"eng"}],"external_id":{"isi":["000555104200011"],"arxiv":["1912.08334"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1912.08334","open_access":"1"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"month":"07","author":[{"full_name":"Wu, Yunfan","first_name":"Yunfan","last_name":"Wu"},{"full_name":"Krishnakumar, Rajiv","first_name":"Rajiv","last_name":"Krishnakumar"},{"last_name":"Martínez-Rincón","first_name":"Julián","full_name":"Martínez-Rincón, Julián"},{"full_name":"Malia, Benjamin K.","last_name":"Malia","first_name":"Benjamin K."},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten","full_name":"Hosten, Onur"},{"last_name":"Kasevich","first_name":"Mark A.","full_name":"Kasevich, Mark A."}],"volume":102,"date_updated":"2024-02-28T13:11:28Z","date_created":"2020-08-30T22:01:10Z","year":"2020","acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","department":[{"_id":"OnHo"}],"publisher":"American Physical Society","publication_status":"published","article_number":"012224","date_published":"2020-07-30T00:00:00Z","citation":{"ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224."},"publication":"Physical Review A","article_type":"original","article_processing_charge":"No","day":"30","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8319","intvolume":" 102","status":"public","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","issue":"1","abstract":[{"text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.","lang":"eng"}],"type":"journal_article"},{"author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Novotný","first_name":"Petr","full_name":"Novotný, Petr"},{"full_name":"Vahala, Jiří","last_name":"Vahala","first_name":"Jiří"}],"volume":34,"date_updated":"2024-03-04T08:30:16Z","date_created":"2024-03-04T08:07:22Z","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y.","year":"2020","department":[{"_id":"KrCh"}],"publisher":"Association for the Advancement of Artificial Intelligence","publication_status":"published","publication_identifier":{"issn":["2374-3468"]},"month":"04","doi":"10.1609/aaai.v34i06.6531","conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2020-02-07","location":"New York, NY, United States","end_date":"2020-02-12"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2002.12086","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2002.12086"]},"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"quality_controlled":"1","issue":"06","abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states."}],"type":"journal_article","oa_version":"Preprint","_id":"15055","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 34","status":"public","title":"Reinforcement learning of risk-constrained policies in Markov decision processes","article_processing_charge":"No","day":"03","keyword":["General Medicine"],"date_published":"2020-04-03T00:00:00Z","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531.","apa":"Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.","ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531"},"publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","page":"9794-9801","article_type":"original"},{"doi":"10.1126/sciadv.aaw7824","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["2375-2548"]},"month":"07","author":[{"full_name":"Park, Sangsoon","first_name":"Sangsoon","last_name":"Park"},{"full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","first_name":"Murat","last_name":"Artan"},{"first_name":"Seung Hyun","last_name":"Han","full_name":"Han, Seung Hyun"},{"first_name":"Hae-Eun H.","last_name":"Park","full_name":"Park, Hae-Eun H."},{"full_name":"Jung, Yoonji","last_name":"Jung","first_name":"Yoonji"},{"full_name":"Hwang, Ara B.","first_name":"Ara B.","last_name":"Hwang"},{"last_name":"Shin","first_name":"Won Sik","full_name":"Shin, Won Sik"},{"full_name":"Kim, Kyong-Tai","first_name":"Kyong-Tai","last_name":"Kim"},{"full_name":"Lee, Seung-Jae V.","last_name":"Lee","first_name":"Seung-Jae V."}],"volume":6,"date_updated":"2024-03-04T09:52:09Z","date_created":"2024-03-04T09:41:57Z","year":"2020","acknowledgement":"This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366 funded by the Korean Government (MSIT) through the National Research Foundation (NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440) funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. ","publisher":"American Association for the Advancement of Science","department":[{"_id":"MaDe"}],"publication_status":"published","file_date_updated":"2024-03-04T09:46:41Z","article_number":"aaw7824","date_published":"2020-07-01T00:00:00Z","citation":{"ista":"Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 6(27), aaw7824.","apa":"Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., … Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw7824","ieee":"S. Park et al., “VRK-1 extends life span by activation of AMPK via phosphorylation,” Science Advances, vol. 6, no. 27. American Association for the Advancement of Science, 2020.","ama":"Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824","chicago":"Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung, Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824.","mla":"Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824.","short":"S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin, K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020)."},"publication":"Science Advances","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01","file":[{"access_level":"open_access","file_name":"2020_ScienceAdvances_Park.pdf","file_size":1864415,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"15058","checksum":"a37157cd0de709dce5fe03f4a31cd0b6","success":1,"date_created":"2024-03-04T09:46:41Z","date_updated":"2024-03-04T09:46:41Z"}],"oa_version":"Published Version","_id":"15057","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","title":"VRK-1 extends life span by activation of AMPK via phosphorylation","ddc":["570"],"status":"public","issue":"27","abstract":[{"text":"Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans.","lang":"eng"}],"type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15061","title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","status":"public","intvolume":" 117","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.","lang":"eng"}],"issue":"36","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112.","ieee":"N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117","mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.","short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117."},"article_type":"original","page":"22101-22112","date_published":"2020-09-08T00:00:00Z","day":"08","article_processing_charge":"No","year":"2020","acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. ","pmid":1,"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"CaBe"}],"author":[{"full_name":"Pinotsis, Nikos","last_name":"Pinotsis","first_name":"Nikos"},{"full_name":"Zielinska, Karolina","first_name":"Karolina","last_name":"Zielinska"},{"last_name":"Babuta","first_name":"Mrigya","full_name":"Babuta, Mrigya"},{"full_name":"Arolas, Joan L.","last_name":"Arolas","first_name":"Joan L."},{"full_name":"Kostan, Julius","first_name":"Julius","last_name":"Kostan"},{"first_name":"Muhammad Bashir","last_name":"Khan","full_name":"Khan, Muhammad Bashir"},{"last_name":"Schreiner","first_name":"Claudia","full_name":"Schreiner, Claudia"},{"first_name":"Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P"},{"full_name":"Ciccarelli, Luciano","last_name":"Ciccarelli","first_name":"Luciano"},{"first_name":"Martin","last_name":"Puchinger","full_name":"Puchinger, Martin"},{"full_name":"Gkougkoulia, Eirini A.","first_name":"Eirini A.","last_name":"Gkougkoulia"},{"full_name":"Ribeiro, Euripedes de Almeida","first_name":"Euripedes de Almeida","last_name":"Ribeiro"},{"last_name":"Marlovits","first_name":"Thomas C.","full_name":"Marlovits, Thomas C."},{"last_name":"Bhattacharya","first_name":"Alok","full_name":"Bhattacharya, Alok"},{"full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina","last_name":"Djinovic-Carugo"}],"date_created":"2024-03-04T10:03:52Z","date_updated":"2024-03-04T10:14:44Z","volume":117,"oa":1,"external_id":{"pmid":["32848067"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.191726911"}],"quality_controlled":"1","doi":"10.1073/pnas.1917269117","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]}},{"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","page":"455-480","article_type":"original","citation":{"ama":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8","ista":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 4(4), 455–480.","apa":"Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8","ieee":"U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient flow and homology inference for self-maps,” Journal of Applied and Computational Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020.","mla":"Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology, vol. 4, no. 4, Springer Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8.","short":"U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480.","chicago":"Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8."},"publication":"Journal of Applied and Computational Topology","date_published":"2020-12-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems."}],"intvolume":" 4","ddc":["500"],"title":"Čech-Delaunay gradient flow and homology inference for self-maps","status":"public","_id":"15064","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2020_JourApplCompTopology_Bauer.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":851190,"file_id":"15065","relation":"main_file","date_created":"2024-03-04T10:52:42Z","date_updated":"2024-03-04T10:52:42Z","success":1,"checksum":"eed1168b6e66cd55272c19bb7fca8a1c"}],"oa_version":"Published Version","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"month":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s41468-020-00058-8","file_date_updated":"2024-03-04T10:52:42Z","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2020","acknowledgement":"This research has been supported by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding provided by Projekt DEAL.","volume":4,"date_updated":"2024-03-04T10:54:04Z","date_created":"2024-03-04T10:47:49Z","author":[{"first_name":"U.","last_name":"Bauer","full_name":"Bauer, U."},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jablonski, Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866","first_name":"Grzegorz","last_name":"Jablonski"},{"first_name":"M.","last_name":"Mrozek","full_name":"Mrozek, M."}]},{"scopus_import":"1","keyword":["General Medicine"],"day":"16","article_processing_charge":"No","publication":"Probability and Mathematical Physics","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 2020;1(1):101-146. doi:10.2140/pmp.2020.1.101","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2020). Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2020.1.101","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least singular value of the shifted Ginibre ensemble,” Probability and Mathematical Physics, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2020. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 1(1), 101–146.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics 1 (2020) 101–146.","mla":"Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics, vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:10.2140/pmp.2020.1.101.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/pmp.2020.1.101."},"article_type":"original","page":"101-146","date_published":"2020-11-16T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395)."}],"issue":"1","_id":"15063","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Optimal lower bound on the least singular value of the shifted Ginibre ensemble","status":"public","intvolume":" 1","oa_version":"Preprint","month":"11","publication_identifier":{"issn":["2690-1005","2690-0998"]},"external_id":{"arxiv":["1908.01653"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1908.01653","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.2140/pmp.2020.1.101","language":[{"iso":"eng"}],"ec_funded":1,"year":"2020","acknowledgement":"Partially supported by ERC Advanced Grant No. 338804. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 66538","publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"LaEr"}],"author":[{"last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-03-04T10:27:57Z","date_updated":"2024-03-04T10:33:15Z","volume":1},{"oa_version":"Published Version","file":[{"success":1,"checksum":"23e2d9321aef53092dc1e24a8ab82d72","date_created":"2024-03-05T07:08:27Z","date_updated":"2024-03-05T07:08:27Z","file_id":"15075","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":303529,"access_level":"open_access","file_name":"2020_LIPIcs_Brandt.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15074","status":"public","ddc":["000"],"title":"Brief announcement: Efficient load-balancing through distributed token dropping","intvolume":" 179","abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds."}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2020-10-07T00:00:00Z","publication":"34th International Symposium on Distributed Computing","citation":{"mla":"Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” 34th International Symposium on Distributed Computing, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In 34th International Symposium on Distributed Computing, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40.","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: 34th International Symposium on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement: Efficient load-balancing through distributed token dropping. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 179, 40.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In 34th International Symposium on Distributed Computing (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in 34th International Symposium on Distributed Computing, Virtual, 2020, vol. 179."},"day":"07","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Sebastian","last_name":"Brandt","full_name":"Brandt, Sebastian"},{"first_name":"Barbara","last_name":"Keller","full_name":"Keller, Barbara"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel","full_name":"Rybicki, Joel"},{"last_name":"Suomela","first_name":"Jukka","full_name":"Suomela, Jukka"},{"full_name":"Uitto, Jara","first_name":"Jara","last_name":"Uitto"}],"related_material":{"record":[{"id":"9678","relation":"later_version","status":"public"}]},"date_updated":"2024-03-05T07:13:13Z","date_created":"2024-03-05T07:09:12Z","volume":179,"year":"2020","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2024-03-05T07:08:27Z","license":"https://creativecommons.org/licenses/by/3.0/","article_number":"40","conference":{"name":"DISC: Symposium on Distributed Computing","location":"Virtual","start_date":"2020-10-12","end_date":"2020-10-16"},"doi":"10.4230/LIPIcs.DISC.2020.40","language":[{"iso":"eng"}],"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2005.07761"]},"oa":1,"quality_controlled":"1","month":"10"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29","citation":{"ista":"Alistarh D-A, Nadiradze G, Sabour A. 2020. Dynamic averaging load balancing on cycles. 47th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 168, 7.","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2020). Dynamic averaging load balancing on cycles. In 47th International Colloquium on Automata, Languages, and Programming (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2020.7","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” in 47th International Colloquium on Automata, Languages, and Programming, Saarbrücken, Germany, Virtual, 2020, vol. 168.","ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. In: 47th International Colloquium on Automata, Languages, and Programming. Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ICALP.2020.7","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” In 47th International Colloquium on Automata, Languages, and Programming, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ICALP.2020.7.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” 47th International Colloquium on Automata, Languages, and Programming, vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ICALP.2020.7.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020."},"publication":"47th International Colloquium on Automata, Languages, and Programming","date_published":"2020-06-29T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor.","lang":"eng"}],"intvolume":" 168","title":"Dynamic averaging load balancing on cycles","ddc":["000"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15077","oa_version":"Published Version","file":[{"creator":"dernst","file_size":782987,"content_type":"application/pdf","file_name":"2020_LIPIcs_Alistarh.pdf","access_level":"open_access","date_created":"2024-03-05T07:25:15Z","date_updated":"2024-03-05T07:25:15Z","success":1,"checksum":"e5eb16199f4ccfd77a321977eb3f026f","file_id":"15078","relation":"main_file"}],"month":"06","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2003.09297"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2020.7","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2020-07-08","location":"Saarbrücken, Germany, Virtual","end_date":"2020-07-11"},"article_number":"7","ec_funded":1,"file_date_updated":"2024-03-05T07:25:15Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2020","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier\r\nversions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments.\r\nFunding: European Research Council funding award PR1042ERC01","volume":168,"date_created":"2024-03-05T07:25:37Z","date_updated":"2024-03-05T07:35:53Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"8286"}]},"author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Nadiradze, Giorgi","first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731"},{"id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba","last_name":"Sabour","full_name":"Sabour, Amirmojtaba"}]},{"article_processing_charge":"No","month":"04","day":"01","date_published":"2020-04-01T00:00:00Z","conference":{"name":"EuroCG: European Workshop on Computational Geometry","end_date":"2020-03-18","start_date":"2020-03-16","location":"Würzburg, Germany, Virtual"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf"}],"oa":1,"citation":{"chicago":"Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec. “Disjoint Tree-Compatible Plane Perfect Matchings.” In 36th European Workshop on Computational Geometry, 2020.","short":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European Workshop on Computational Geometry, 2020.","mla":"Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.” 36th European Workshop on Computational Geometry, 56, 2020.","ieee":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, and J. Tkadlec, “Disjoint tree-compatible plane perfect matchings,” in 36th European Workshop on Computational Geometry, Würzburg, Germany, Virtual, 2020.","apa":"Aichholzer, O., Obmann, J., Patak, P., Perz, D., & Tkadlec, J. (2020). Disjoint tree-compatible plane perfect matchings. In 36th European Workshop on Computational Geometry. Würzburg, Germany, Virtual.","ista":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. 2020. Disjoint tree-compatible plane perfect matchings. 36th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 56.","ama":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible plane perfect matchings. In: 36th European Workshop on Computational Geometry. ; 2020."},"publication":"36th European Workshop on Computational Geometry","quality_controlled":"1","abstract":[{"lang":"eng","text":"Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2.\r\nWe show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter\r\nof this graph is either 4 or 5, independent of n."}],"type":"conference","article_number":"56","author":[{"last_name":"Aichholzer","first_name":"Oswin","full_name":"Aichholzer, Oswin"},{"full_name":"Obmann, Julia","last_name":"Obmann","first_name":"Julia"},{"id":"B593B804-1035-11EA-B4F1-947645A5BB83","last_name":"Patak","first_name":"Pavel","full_name":"Patak, Pavel"},{"full_name":"Perz, Daniel","first_name":"Daniel","last_name":"Perz"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"}],"oa_version":"Published Version","date_created":"2024-03-05T08:57:17Z","date_updated":"2024-03-05T09:00:07Z","_id":"15082","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Research on this work was initiated at the 6th Austrian-Japanese-Mexican-Spanish Workshop on Discrete Geometry and continued during the 16th European Geometric Graph-Week, both held near Strobl, Austria. We are grateful to the participants for the inspiring atmosphere. We especially thank Alexander Pilz for bringing this class of problems to our attention and Birgit Vogtenhuber for inspiring discussions. D.P. is partially supported by the FWF grant I 3340-N35 (Collaborative DACH project Arrangements and Drawings). The research stay of P.P. at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734922.","department":[{"_id":"KrCh"},{"_id":"UlWa"}],"title":"Disjoint tree-compatible plane perfect matchings","publication_status":"published","status":"public"},{"date_published":"2020-12-11T00:00:00Z","citation":{"ama":"Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 2020;48(6):3619-3642. doi:10.1214/20-AOS1945","ista":"Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.","ieee":"A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural network via displacement convexity,” Annals of Statistics, vol. 48, no. 6. Institute of Mathematical Statistics, pp. 3619–3642, 2020.","apa":"Javanmard, A., Mondelli, M., & Montanari, A. (2020). Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/20-AOS1945","mla":"Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics, vol. 48, no. 6, Institute of Mathematical Statistics, 2020, pp. 3619–42, doi:10.1214/20-AOS1945.","short":"A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.","chicago":"Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-AOS1945."},"publication":"Annals of Statistics","page":"3619-3642","article_type":"original","article_processing_charge":"No","day":"11","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6748","intvolume":" 48","status":"public","title":"Analysis of a two-layer neural network via displacement convexity","issue":"6","abstract":[{"lang":"eng","text":"Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.\r\nHere we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge."}],"type":"journal_article","doi":"10.1214/20-AOS1945","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1901.01375","open_access":"1"}],"external_id":{"arxiv":["1901.01375"],"isi":["000598369200021"]},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1932-6157"],"eissn":["1941-7330"]},"month":"12","author":[{"first_name":"Adel","last_name":"Javanmard","full_name":"Javanmard, Adel"},{"full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020"},{"full_name":"Montanari, Andrea","first_name":"Andrea","last_name":"Montanari"}],"volume":48,"date_updated":"2024-03-06T08:28:50Z","date_created":"2019-07-31T09:39:42Z","year":"2020","publisher":"Institute of Mathematical Statistics","department":[{"_id":"MaMo"}],"publication_status":"published"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-06-01T00:00:00Z","citation":{"ama":"Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599","ieee":"A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal Society, 2020.","apa":"Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.200599","ista":"Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 7(6), 200599.","short":"A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020).","mla":"Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020, doi:10.1098/rsos.200599.","chicago":"Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F. Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science. The Royal Society, 2020. https://doi.org/10.1098/rsos.200599."},"publication":"Royal Society Open Science","article_type":"original","issue":"6","abstract":[{"lang":"eng","text":"In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions\r\non the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of\r\nthese qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"8748","relation":"main_file","success":1,"checksum":"5505c445de373bfd836eb4d3b48b1f37","date_updated":"2020-11-09T09:07:11Z","date_created":"2020-11-09T09:07:11Z","access_level":"open_access","file_name":"2020_RoyalSocOpenScience_Klose.pdf","creator":"dernst","file_size":1611485,"content_type":"application/pdf"}],"_id":"8741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","ddc":["530","550"],"title":"Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements","status":"public","publication_identifier":{"eissn":["20545703"]},"month":"06","doi":"10.1098/rsos.200599","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000545625200001"],"arxiv":["1910.12042"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-11-09T09:07:11Z","article_number":"200599","author":[{"full_name":"Klose, Ann Kristin","first_name":"Ann Kristin","last_name":"Klose"},{"full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle","first_name":"Volker"},{"full_name":"Winkelmann, Ricarda","first_name":"Ricarda","last_name":"Winkelmann"},{"full_name":"Donges, Jonathan F.","last_name":"Donges","first_name":"Jonathan F."}],"volume":7,"date_created":"2020-11-08T23:01:25Z","date_updated":"2024-03-12T12:31:30Z","acknowledgement":"V.K. thanks the German National Academic Foundation (Studienstiftung des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork (PB.net), the Earth League’s EarthDoc program and the European Research Council Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements. This work has been performed in the context of the copan collaboration and the FutureLab on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments by N. Wunderling, J. Heitzig and M. Wiedermann.","year":"2020","publisher":"The Royal Society","department":[{"_id":"MiLe"}],"publication_status":"published"},{"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","citation":{"ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59.","ieee":"D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020.","apa":"Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491","ama":"Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491","chicago":"Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491.","mla":"Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491.","short":"D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59."},"article_type":"original","page":"46-59","date_published":"2020-04-28T00:00:00Z","scopus_import":"1","day":"28","has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7687","status":"public","ddc":["020"],"title":"(Core Trust) Seal your repository!","intvolume":" 73","popular_science":"1","file":[{"file_name":"2020_VOEB_Ernst.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":579291,"file_id":"7970","relation":"main_file","date_updated":"2024-03-12T10:12:33Z","date_created":"2020-06-17T10:50:13Z","checksum":"fee784f15a489deb7def6ccf8c5bf8c3"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested."},{"lang":"ger","text":" Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich."}],"issue":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.31263/voebm.v73i1.3491","language":[{"iso":"ger"}],"month":"04","publication_identifier":{"issn":["1022-2588"]},"year":"2020","publication_status":"published","department":[{"_id":"E-Lib"}],"publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","author":[{"last_name":"Ernst","first_name":"Doris","orcid":"0000-0002-2354-0195","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","full_name":"Ernst, Doris"},{"first_name":"Gertraud","last_name":"Novotny","full_name":"Novotny, Gertraud"},{"full_name":"Schönher, Eva Maria","first_name":"Eva Maria","last_name":"Schönher"}],"date_created":"2020-04-28T08:37:38Z","date_updated":"2024-03-12T10:12:33Z","volume":73,"file_date_updated":"2024-03-12T10:12:33Z"},{"abstract":[{"text":"A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism.","lang":"eng"}],"type":"conference","file":[{"checksum":"d1914af7811a21a4b2744eb51b5834e3","success":1,"date_created":"2024-03-20T08:05:46Z","date_updated":"2024-03-20T08:05:46Z","relation":"main_file","file_id":"15127","content_type":"application/pdf","file_size":595543,"creator":"dernst","access_level":"open_access","file_name":"2020_ECM_Oshurkova.pdf"}],"oa_version":"Published Version","_id":"15071","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T","article_processing_charge":"Yes","has_accepted_license":"1","day":"02","date_published":"2020-11-02T00:00:00Z","citation":{"ieee":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic Conference on Microbiology, Virtual, 2020.","apa":"Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., & Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116","ista":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology. ECM: Electronic Conference on Microbiology.","ama":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: Proceedings of 1st International Electronic Conference on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116","chicago":"Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of 1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116.","short":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020.","mla":"Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116."},"publication":"Proceedings of 1st International Electronic Conference on Microbiology","file_date_updated":"2024-03-20T08:05:46Z","author":[{"full_name":"Oshurkova, Viktoriia","last_name":"Oshurkova","first_name":"Viktoriia"},{"full_name":"Troshina, Olga","first_name":"Olga","last_name":"Troshina"},{"full_name":"Trubitsyn, Vladimir","first_name":"Vladimir","last_name":"Trubitsyn"},{"full_name":"Ryzhmanova, Yana","last_name":"Ryzhmanova","first_name":"Yana"},{"last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"full_name":"Shcherbakova, Viktoria","last_name":"Shcherbakova","first_name":"Viktoria"}],"date_updated":"2024-03-20T08:06:22Z","date_created":"2024-03-04T11:41:31Z","acknowledgement":"The work was supported by of Russian Foundation of Basic Research: grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334 for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST, Austria) for their help in obtaining the genomic sequence of strain JL01. ","year":"2020","publisher":"MDPI","department":[{"_id":"FyKo"}],"publication_status":"published","month":"11","doi":"10.3390/ecm2020-07116","conference":{"name":"ECM: Electronic Conference on Microbiology","location":"Virtual","start_date":"2020-11-02","end_date":"2020-11-30"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1"}]