--- _id: '818' abstract: - lang: eng text: 'Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ' acknowledgement: 'First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch citation: ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862 apa: Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862 chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862. ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017. ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. mla: Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862. short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:40Z date_published: 2017-09-27T00:00:00Z date_updated: 2023-09-07T12:00:26Z day: '27' ddc: - '571' - '579' degree_awarded: PhD department: - _id: ToBo doi: 10.15479/AT:ISTA:th_862 file: - access_level: closed checksum: da3993c5f90f59a8e8623cc31ad501dd content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:48:51Z date_updated: 2020-07-14T12:48:09Z file_id: '6210' file_name: Thesis_KarinMitosch.docx file_size: 6331071 relation: source_file - access_level: open_access checksum: 24c3d9e51992f1b721f3df55aa13fcb8 content_type: application/pdf creator: dernst date_created: 2019-04-05T08:48:51Z date_updated: 2020-07-14T12:48:09Z file_id: '6211' file_name: Thesis_KarinMitosch.pdf file_size: 9289852 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '113' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6831' pubrep_id: '862' related_material: record: - id: '2001' relation: part_of_dissertation status: public - id: '666' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X title: Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '666' abstract: - lang: eng text: Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors. article_processing_charge: Yes (in subscription journal) author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001 apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001 chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001. ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017. ista: Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403. mla: Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001. short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403. date_created: 2018-12-11T11:47:48Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-07T12:00:25Z day: '26' ddc: - '576' - '610' department: - _id: ToBo - _id: GaTk doi: 10.1016/j.cels.2017.03.001 ec_funded: 1 file: - access_level: open_access checksum: 04ff20011c3d9a601c514aa999a5fe1a content_type: application/pdf creator: system date_created: 2018-12-12T10:13:54Z date_updated: 2020-07-14T12:47:35Z file_id: '5041' file_name: IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf file_size: 2438660 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 4' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 393 - 403 project: - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Cell Systems publication_identifier: issn: - '24054712' publication_status: published publisher: Cell Press publist_id: '7061' pubrep_id: '901' quality_controlled: '1' related_material: record: - id: '818' relation: dissertation_contains status: public scopus_import: 1 status: public title: Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2017' ... --- _id: '821' abstract: - lang: eng text: "This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games." acknowledgement: "First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, \ Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854 apa: Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854 chicago: Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854. ieee: A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017. ista: Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. mla: Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854. short: A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:41Z date_published: 2017-08-09T00:00:00Z date_updated: 2023-09-07T12:01:59Z day: '09' ddc: - '000' degree_awarded: PhD department: - _id: KrCh doi: 10.15479/AT:ISTA:th_854 ec_funded: 1 file: - access_level: open_access checksum: 3a3ec003f6ee73f41f82a544d63dfc77 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:44Z date_updated: 2020-07-14T12:48:10Z file_id: '4900' file_name: IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf file_size: 4103115 relation: main_file - access_level: closed checksum: bd2facc45ff8a2e20c5ed313c2ccaa83 content_type: application/zip creator: dernst date_created: 2019-04-05T07:59:31Z date_updated: 2020-07-14T12:48:10Z file_id: '6201' file_name: 2017_thesis_Pavlogiannis.zip file_size: 14744374 relation: source_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '08' oa: 1 oa_version: Published Version page: '418' project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6828' pubrep_id: '854' related_material: record: - id: '1071' relation: part_of_dissertation status: public - id: '1437' relation: part_of_dissertation status: public - id: '1602' relation: part_of_dissertation status: public - id: '1604' relation: part_of_dissertation status: public - id: '1607' relation: part_of_dissertation status: public - id: '1714' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Algorithmic advances in program analysis and their applications tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '820' abstract: - lang: eng text: "The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background." acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Fabienne full_name: Jesse, Fabienne id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87 last_name: Jesse citation: ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857 apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857 chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857. ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017. ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria. mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857. short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:41Z date_published: 2017-08-25T00:00:00Z date_updated: 2023-09-07T12:01:21Z day: '25' ddc: - '576' - '577' - '579' degree_awarded: PhD department: - _id: JoBo doi: 10.15479/AT:ISTA:th_857 ec_funded: 1 file: - access_level: open_access checksum: c62257a7bff0c5f39e1abffc6bfcca5c content_type: application/pdf creator: system date_created: 2018-12-12T10:17:00Z date_updated: 2020-07-14T12:48:10Z file_id: '5252' file_name: IST-2017-857-v1+1_thesis_fabienne.pdf file_size: 3417773 relation: main_file - access_level: closed checksum: fc87d7d72fce52824a3ae7dcad0413a8 content_type: application/x-tex creator: dernst date_created: 2019-04-05T08:51:59Z date_updated: 2020-07-14T12:48:10Z file_id: '6212' file_name: 2017_thesis_Jesse_source.tex file_size: 215899 relation: source_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '87' project: - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6829' pubrep_id: '857' status: public supervisor: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 title: The lac operon in the wild tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '838' abstract: - lang: eng text: 'In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828 apa: Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828 chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828. ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017. ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria. mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828. short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:46Z date_published: 2017-06-26T00:00:00Z date_updated: 2023-09-07T12:02:28Z day: '26' ddc: - '000' degree_awarded: PhD department: - _id: KrPi doi: 10.15479/AT:ISTA:th_828 file: - access_level: open_access checksum: ff8639ec4bded6186f44c7bd3ee26804 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:13Z date_updated: 2020-07-14T12:48:12Z file_id: '4799' file_name: IST-2017-828-v1+3_2017_Rybar_thesis.pdf file_size: 847400 relation: main_file - access_level: closed checksum: 3462101745ce8ad199c2d0f75dae4a7e content_type: application/zip creator: dernst date_created: 2019-04-05T08:24:11Z date_updated: 2020-07-14T12:48:12Z file_id: '6202' file_name: 2017_Thesis_Rybar_source.zip file_size: 26054879 relation: source_file file_date_updated: 2020-07-14T12:48:12Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '86' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6810' pubrep_id: '828' related_material: record: - id: '2082' relation: part_of_dissertation status: public - id: '6196' relation: part_of_dissertation status: public status: public title: (The exact security of) Message authentication codes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6196' abstract: - lang: eng text: PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem. author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161 apa: Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC. IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161 chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum, 2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161. ieee: P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017. ista: Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161. mla: Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161. short: P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161. date_created: 2019-04-04T13:48:23Z date_published: 2017-02-03T00:00:00Z date_updated: 2023-09-07T12:02:27Z day: '03' ddc: - '000' department: - _id: KrPi doi: 10.13154/TOSC.V2016.I2.145-161 ec_funded: 1 file: - access_level: open_access checksum: f23161d685dd957ae8d7274132999684 content_type: application/pdf creator: dernst date_created: 2019-04-04T13:53:58Z date_updated: 2020-07-14T12:47:24Z file_id: '6197' file_name: 2017_IACR_Gazi.pdf file_size: 597335 relation: main_file file_date_updated: 2020-07-14T12:47:24Z has_accepted_license: '1' intvolume: ' 2016' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 145-161 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: IACR Transactions on Symmetric Cryptology publication_identifier: eissn: - 2519-173X publication_status: published publisher: Ruhr University Bochum quality_controlled: '1' related_material: record: - id: '838' relation: dissertation_contains status: public status: public title: The exact security of PMAC tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016 year: '2017' ... --- _id: '837' abstract: - lang: eng text: 'The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ' acknowledgement: 'I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Haibing full_name: Xu, Haibing id: 310349D0-F248-11E8-B48F-1D18A9856A87 last_name: Xu citation: ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858 apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858 chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858. ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017. ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858. short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:46Z date_published: 2017-08-23T00:00:00Z date_updated: 2023-09-07T12:06:38Z day: '23' ddc: - '571' degree_awarded: PhD department: - _id: JoCs doi: 10.15479/AT:ISTA:th_858 file: - access_level: closed checksum: f11925fbbce31e495124b6bc4f10573c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:59:51Z date_updated: 2020-07-14T12:48:12Z file_id: '6213' file_name: 2017_Xu_Haibing_Thesis_Source.docx file_size: 3589490 relation: source_file - access_level: open_access checksum: ffb10749a537d615fab1ef0937ccb157 content_type: application/pdf creator: dernst date_created: 2019-04-05T08:59:51Z date_updated: 2020-07-14T12:48:12Z file_id: '6214' file_name: 2017_Xu_Thesis_IST.pdf file_size: 11668613 relation: main_file file_date_updated: 2020-07-14T12:48:12Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '93' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6811' pubrep_id: '858' related_material: record: - id: '5828' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '938' abstract: - lang: eng text: The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 citation: ama: Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842 apa: Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842 chicago: Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842. ieee: M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017. ista: Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. mla: Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842. short: M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:49:18Z date_published: 2017-06-02T00:00:00Z date_updated: 2023-09-07T12:06:09Z day: '02' ddc: - '581' - '583' - '580' degree_awarded: PhD department: - _id: JiFr doi: 10.15479/AT:ISTA:th_842 file: - access_level: closed checksum: 193425764d9aaaed3ac57062a867b315 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:03:20Z date_updated: 2020-07-14T12:48:15Z file_id: '6215' file_name: 2017_Adamowski-Thesis_Source.docx file_size: 46903863 relation: source_file - access_level: open_access checksum: df5ab01be81f821e1b958596a1ec8d21 content_type: application/pdf creator: dernst date_created: 2019-04-05T09:03:19Z date_updated: 2020-07-14T12:48:15Z file_id: '6216' file_name: 2017_Adamowski-Thesis.pdf file_size: 8698888 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '117' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6483' pubrep_id: '842' related_material: record: - id: '1591' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '992' abstract: - lang: eng text: "An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language)." acknowledgement: FP7/2007-2013/ERC grant agreement no 616160 alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815 apa: Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815 chicago: Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815. ieee: M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017. ista: Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria. mla: Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815. short: M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:49:35Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-09-07T12:05:41Z day: '01' ddc: - '004' degree_awarded: PhD department: - _id: VlKo doi: 10.15479/AT:ISTA:th_815 ec_funded: 1 file: - access_level: open_access checksum: 81761fb939acb7585c36629f765b4373 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:55Z date_updated: 2020-07-14T12:48:18Z file_id: '4654' file_name: IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf file_size: 786145 relation: main_file - access_level: closed checksum: 2b2d7e1d6c1c79a9795a7aa0f860baf3 content_type: application/zip creator: dernst date_created: 2019-04-05T08:43:24Z date_updated: 2020-07-14T12:48:18Z file_id: '6208' file_name: 2017_Thesis_Rolinek_source.zip file_size: 5936337 relation: source_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '97' project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6407' pubrep_id: '815' status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov title: Complexity of constraint satisfaction type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '718' abstract: - lang: eng text: Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 - first_name: Matthias full_name: Reitzner, Matthias last_name: Reitzner citation: ama: Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 2017;49(3):745-767. doi:10.1017/apr.2017.20 apa: Edelsbrunner, H., Nikitenko, A., & Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. Cambridge University Press. https://doi.org/10.1017/apr.2017.20 chicago: Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability. Cambridge University Press, 2017. https://doi.org/10.1017/apr.2017.20. ieee: H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” Advances in Applied Probability, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017. ista: Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767. mla: Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:10.1017/apr.2017.20. short: H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767. date_created: 2018-12-11T11:48:07Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-07T12:07:12Z day: '01' department: - _id: HeEd doi: 10.1017/apr.2017.20 ec_funded: 1 external_id: arxiv: - '1607.05915' intvolume: ' 49' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.05915 month: '09' oa: 1 oa_version: Preprint page: 745 - 767 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Advances in Applied Probability publication_identifier: issn: - '00018678' publication_status: published publisher: Cambridge University Press publist_id: '6962' quality_controlled: '1' related_material: record: - id: '6287' relation: dissertation_contains status: public scopus_import: 1 status: public title: Expected sizes of poisson Delaunay mosaics and their discrete Morse functions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2017' ... --- _id: '559' abstract: - lang: eng text: 'Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).' alternative_title: - LNCS author: - first_name: Hamza M full_name: Abusalah, Hamza M id: 40297222-F248-11E8-B48F-1D18A9856A87 last_name: Abusalah - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Bram full_name: Cohen, Bram last_name: Cohen - first_name: Danylo full_name: Khilko, Danylo last_name: Khilko - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Leonid full_name: Reyzin, Leonid last_name: Reyzin citation: ama: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer; 2017:357-379. doi:10.1007/978-3-319-70697-9_13' apa: 'Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., & Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China: Springer. https://doi.org/10.1007/978-3-319-70697-9_13' chicago: Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13. ieee: 'H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L. Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.' ista: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625, 357–379.' mla: Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13. short: H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379. conference: end_date: 2017-12-07 location: Hong Kong, China name: 'ASIACRYPT: Theory and Applications of Cryptology and Information Security' start_date: 2017-12-03 date_created: 2018-12-11T11:47:10Z date_published: 2017-11-18T00:00:00Z date_updated: 2023-09-07T12:30:22Z day: '18' department: - _id: KrPi doi: 10.1007/978-3-319-70697-9_13 ec_funded: 1 intvolume: ' 10625' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/893.pdf month: '11' oa: 1 oa_version: Submitted Version page: 357 - 379 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331970696-2 publication_status: published publisher: Springer publist_id: '7257' quality_controlled: '1' related_material: record: - id: '83' relation: dissertation_contains status: public scopus_import: 1 status: public title: Beyond Hellman’s time-memory trade-offs with applications to proofs of space type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10625 year: '2017' ... --- _id: '550' abstract: - lang: eng text: For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities. article_number: '63' author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt citation: ama: Alt J. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 2017;22. doi:10.1214/17-ECP97 apa: Alt, J. (2017). Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-ECP97 chicago: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-ECP97. ieee: J. Alt, “Singularities of the density of states of random Gram matrices,” Electronic Communications in Probability, vol. 22. Institute of Mathematical Statistics, 2017. ista: Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63. mla: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability, vol. 22, 63, Institute of Mathematical Statistics, 2017, doi:10.1214/17-ECP97. short: J. Alt, Electronic Communications in Probability 22 (2017). date_created: 2018-12-11T11:47:07Z date_published: 2017-11-21T00:00:00Z date_updated: 2023-09-07T12:38:08Z day: '21' ddc: - '539' department: - _id: LaEr doi: 10.1214/17-ECP97 ec_funded: 1 file: - access_level: open_access checksum: 0ec05303a0de190de145654237984c79 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:04Z date_updated: 2020-07-14T12:47:00Z file_id: '4663' file_name: IST-2018-926-v1+1_euclid.ecp.1511233247.pdf file_size: 470876 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Communications in Probability publication_identifier: issn: - 1083589X publication_status: published publisher: Institute of Mathematical Statistics publist_id: '7265' pubrep_id: '926' quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: 1 status: public title: Singularities of the density of states of random Gram matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2017' ... --- _id: '647' abstract: - lang: eng text: Despite researchers’ efforts in the last couple of decades, reachability analysis is still a challenging problem even for linear hybrid systems. Among the existing approaches, the most practical ones are mainly based on bounded-time reachable set over-approximations. For the purpose of unbounded-time analysis, one important strategy is to abstract the original system and find an invariant for the abstraction. In this paper, we propose an approach to constructing a new kind of abstraction called conic abstraction for affine hybrid systems, and to computing reachable sets based on this abstraction. The essential feature of a conic abstraction is that it partitions the state space of a system into a set of convex polyhedral cones which is derived from a uniform conic partition of the derivative space. Such a set of polyhedral cones is able to cut all trajectories of the system into almost straight segments so that every segment of a reach pipe in a polyhedral cone tends to be straight as well, and hence can be over-approximated tightly by polyhedra using similar techniques as HyTech or PHAVer. In particular, for diagonalizable affine systems, our approach can guarantee to find an invariant for unbounded reachable sets, which is beyond the capability of bounded-time reachability analysis tools. We implemented the approach in a tool and experiments on benchmarks show that our approach is more powerful than SpaceEx and PHAVer in dealing with diagonalizable systems. alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 citation: ama: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7' apa: 'Bogomolov, S., Giacobbe, M., Henzinger, T. A., & Kong, H. (2017). Conic abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_7' chicago: Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_7. ieee: 'S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.' ista: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 116–132.' mla: Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol. 10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7. short: S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132. conference: end_date: 2017-09-07 location: Berlin, Germany name: 'FORMATS: Formal Modelling and Analysis of Timed Systems' start_date: 2017-09-05 date_created: 2018-12-11T11:47:41Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-07T12:53:00Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-319-65765-3_7 file: - access_level: open_access checksum: faf546914ba29bcf9974ee36b6b16750 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:38Z date_updated: 2020-07-14T12:47:31Z file_id: '4956' file_name: IST-2017-831-v1+1_main.pdf file_size: 3806864 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 116 - 132 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-331965764-6 publication_status: published publisher: Springer publist_id: '7129' pubrep_id: '831' quality_controlled: '1' related_material: record: - id: '6894' relation: dissertation_contains status: public scopus_import: 1 status: public title: Conic abstractions for hybrid systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: '10419 ' year: '2017' ... --- _id: '631' abstract: - lang: eng text: Template polyhedra generalize intervals and octagons to polyhedra whose facets are orthogonal to a given set of arbitrary directions. They have been employed in the abstract interpretation of programs and, with particular success, in the reachability analysis of hybrid automata. While previously, the choice of directions has been left to the user or a heuristic, we present a method for the automatic discovery of directions that generalize and eliminate spurious counterexamples. We show that for the class of convex hybrid automata, i.e., hybrid automata with (possibly nonlinear) convex constraints on derivatives, such directions always exist and can be found using convex optimization. We embed our method inside a CEGAR loop, thus enabling the time-unbounded reachability analysis of an important and richer class of hybrid automata than was previously possible. We evaluate our method on several benchmarks, demonstrating also its superior efficiency for the special case of linear hybrid automata. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), by the European Commission under grant 643921 (UnCoVerCPS), and by the ARC project DP140104219 (Robust AI Planning for Hybrid Systems). alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. Counterexample guided refinement of template polyhedra. In: Vol 10205. Springer; 2017:589-606. doi:10.1007/978-3-662-54577-5_34' apa: 'Bogomolov, S., Frehse, G., Giacobbe, M., & Henzinger, T. A. (2017). Counterexample guided refinement of template polyhedra (Vol. 10205, pp. 589–606). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_34' chicago: Bogomolov, Sergiy, Goran Frehse, Mirco Giacobbe, and Thomas A Henzinger. “Counterexample Guided Refinement of Template Polyhedra,” 10205:589–606. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_34. ieee: 'S. Bogomolov, G. Frehse, M. Giacobbe, and T. A. Henzinger, “Counterexample guided refinement of template polyhedra,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 589–606.' ista: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. 2017. Counterexample guided refinement of template polyhedra. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 589–606.' mla: Bogomolov, Sergiy, et al. Counterexample Guided Refinement of Template Polyhedra. Vol. 10205, Springer, 2017, pp. 589–606, doi:10.1007/978-3-662-54577-5_34. short: S. Bogomolov, G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2017, pp. 589–606. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2017-04-22 date_created: 2018-12-11T11:47:36Z date_published: 2017-03-31T00:00:00Z date_updated: 2023-09-07T12:53:00Z day: '31' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-662-54577-5_34 file: - access_level: open_access checksum: f395d0d20102b89aeaad8b4ef4f18f4f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:41Z date_updated: 2020-07-14T12:47:27Z file_id: '4897' file_name: IST-2017-741-v1+1_main.pdf file_size: 569863 relation: main_file - access_level: open_access checksum: f416ee1ae4497b23ecdf28b1f18bb8df content_type: application/pdf creator: system date_created: 2018-12-12T10:11:42Z date_updated: 2020-07-14T12:47:27Z file_id: '4898' file_name: IST-2018-741-v2+2_main.pdf file_size: 563276 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' intvolume: ' 10205' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 589 - 606 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-366254576-8 publication_status: published publisher: Springer publist_id: '7162' pubrep_id: '966' quality_controlled: '1' related_material: record: - id: '6894' relation: dissertation_contains status: public scopus_import: 1 status: public title: Counterexample guided refinement of template polyhedra type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10205 year: '2017' ... --- _id: '1144' abstract: - lang: eng text: We show that matrix elements of functions of N × N Wigner matrices fluctuate on a scale of order N−1/2 and we identify the limiting fluctuation. Our result holds for any function f of the matrix that has bounded variation thus considerably relaxing the regularity requirement imposed in [7, 11]. acknowledgement: Partially supported by the IST Austria Excellence Scholarship. article_number: '86' author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Erdös L, Schröder DJ. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 2017;21. doi:10.1214/16-ECP38 apa: Erdös, L., & Schröder, D. J. (2017). Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-ECP38 chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-ECP38. ieee: L. Erdös and D. J. Schröder, “Fluctuations of functions of Wigner matrices,” Electronic Communications in Probability, vol. 21. Institute of Mathematical Statistics, 2017. ista: Erdös L, Schröder DJ. 2017. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 21, 86. mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability, vol. 21, 86, Institute of Mathematical Statistics, 2017, doi:10.1214/16-ECP38. short: L. Erdös, D.J. Schröder, Electronic Communications in Probability 21 (2017). date_created: 2018-12-11T11:50:23Z date_published: 2017-01-02T00:00:00Z date_updated: 2023-09-07T12:54:12Z day: '02' ddc: - '510' department: - _id: LaEr doi: 10.1214/16-ECP38 ec_funded: 1 file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:18:10Z date_updated: 2018-12-12T10:18:10Z file_id: '5329' file_name: IST-2017-747-v1+1_euclid.ecp.1483347665.pdf file_size: 440770 relation: main_file file_date_updated: 2018-12-12T10:18:10Z has_accepted_license: '1' intvolume: ' 21' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Communications in Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6214' pubrep_id: '747' quality_controlled: '1' related_material: record: - id: '6179' relation: dissertation_contains status: public scopus_import: 1 status: public title: Fluctuations of functions of Wigner matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2017' ... --- _id: '486' abstract: - lang: eng text: Color texture reproduction in 3D printing commonly ignores volumetric light transport (cross-talk) between surface points on a 3D print. Such light diffusion leads to significant blur of details and color bleeding, and is particularly severe for highly translucent resin-based print materials. Given their widely varying scattering properties, this cross-talk between surface points strongly depends on the internal structure of the volume surrounding each surface point. Existing scattering-aware methods use simplified models for light diffusion, and often accept the visual blur as an immutable property of the print medium. In contrast, our work counteracts heterogeneous scattering to obtain the impression of a crisp albedo texture on top of the 3D print, by optimizing for a fully volumetric material distribution that preserves the target appearance. Our method employs an efficient numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous scattering, supported by a practical calibration procedure to obtain scattering parameters from a given set of printer materials. Despite the inherent translucency of the medium, we reproduce detailed surface textures on 3D prints. We evaluate our system using a commercial, five-tone 3D print process and compare against the printer’s native color texturing mode, demonstrating that our method preserves high-frequency features well without having to compromise on color gamut. article_number: '241' article_processing_charge: No article_type: original author: - first_name: Oskar full_name: Elek, Oskar last_name: Elek - first_name: Denis full_name: Sumin, Denis last_name: Sumin - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Alexander full_name: Wilkie, Alexander last_name: Wilkie - first_name: Jaroslav full_name: Krivanek, Jaroslav last_name: Krivanek citation: ama: Elek O, Sumin D, Zhang R, et al. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 2017;36(6). doi:10.1145/3130800.3130890 apa: Elek, O., Sumin, D., Zhang, R., Weyrich, T., Myszkowski, K., Bickel, B., … Krivanek, J. (2017). Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3130800.3130890 chicago: Elek, Oskar, Denis Sumin, Ran Zhang, Tim Weyrich, Karol Myszkowski, Bernd Bickel, Alexander Wilkie, and Jaroslav Krivanek. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3130800.3130890. ieee: O. Elek et al., “Scattering-aware texture reproduction for 3D printing,” ACM Transactions on Graphics, vol. 36, no. 6. ACM, 2017. ista: Elek O, Sumin D, Zhang R, Weyrich T, Myszkowski K, Bickel B, Wilkie A, Krivanek J. 2017. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 36(6), 241. mla: Elek, Oskar, et al. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics, vol. 36, no. 6, 241, ACM, 2017, doi:10.1145/3130800.3130890. short: O. Elek, D. Sumin, R. Zhang, T. Weyrich, K. Myszkowski, B. Bickel, A. Wilkie, J. Krivanek, ACM Transactions on Graphics 36 (2017). date_created: 2018-12-11T11:46:44Z date_published: 2017-11-20T00:00:00Z date_updated: 2023-09-07T13:11:15Z day: '20' ddc: - '003' - '000' - '005' department: - _id: BeBi doi: 10.1145/3130800.3130890 ec_funded: 1 file: - access_level: open_access checksum: 48386fa6956c3645fc89594dc898b147 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:46Z date_updated: 2020-07-14T12:46:35Z file_id: '4836' file_name: IST-2018-1052-v1+1_ElekSumin2017SGA.pdf file_size: 107349827 relation: main_file - access_level: open_access checksum: 21c89c28fb8d70f6602f752bf997aa0f content_type: application/pdf creator: bbickel date_created: 2019-12-16T14:48:57Z date_updated: 2020-07-14T12:46:35Z file_id: '7189' file_name: ElekSumin2017SGA_reduced_file_size.pdf file_size: 4683145 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 36' issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ACM Transactions on Graphics publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '7334' pubrep_id: '1052' quality_controlled: '1' related_material: record: - id: '8386' relation: dissertation_contains status: public scopus_import: 1 status: public title: Scattering-aware texture reproduction for 3D printing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ... --- _id: '637' abstract: - lang: eng text: For many cryptographic primitives, it is relatively easy to achieve selective security (where the adversary commits a-priori to some of the choices to be made later in the attack) but appears difficult to achieve the more natural notion of adaptive security (where the adversary can make all choices on the go as the attack progresses). A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption (Panjwani, TCC ’07 and Fuchsbauer et al., CRYPTO ’15), constrained PRFs (Fuchsbauer et al., ASIACRYPT ’14), and Yao garbled circuits (Jafargholi and Wichs, TCC ’16b). Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework that connects all of these works and allows us to present them in a unified and simplified fashion. Moreover, we use the framework to derive a new result for adaptively secure secret sharing over access structures defined via monotone circuits. We envision that further applications will follow in the future. Underlying our framework is the following simple idea. It is well known that selective security, where the adversary commits to n-bits of information about his future choices, automatically implies adaptive security at the cost of amplifying the adversary’s advantage by a factor of up to 2n. However, in some cases the proof of selective security proceeds via a sequence of hybrids, where each pair of adjacent hybrids locally only requires some smaller partial information consisting of m ≪ n bits. The partial information needed might be completely different between different pairs of hybrids, and if we look across all the hybrids we might rely on the entire n-bit commitment. Nevertheless, the above is sufficient to prove adaptive security, at the cost of amplifying the adversary’s advantage by a factor of only 2m ≪ 2n. In all of our examples using the above framework, the different hybrids are captured by some sort of a graph pebbling game and the amount of information that the adversary needs to commit to in each pair of hybrids is bounded by the maximum number of pebbles in play at any point in time. Therefore, coming up with better strategies for proving adaptive security translates to various pebbling strategies for different types of graphs. alternative_title: - LNCS author: - first_name: Zahra full_name: Jafargholi, Zahra last_name: Jafargholi - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Ilan full_name: Komargodski, Ilan last_name: Komargodski - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. Be adaptive avoid overcommitting. In: Katz J, Shacham H, eds. Vol 10401. Springer; 2017:133-163. doi:10.1007/978-3-319-63688-7_5' apa: 'Jafargholi, Z., Kamath Hosdurg, C., Klein, K., Komargodski, I., Pietrzak, K. Z., & Wichs, D. (2017). Be adaptive avoid overcommitting. In J. Katz & H. Shacham (Eds.) (Vol. 10401, pp. 133–163). Presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-319-63688-7_5' chicago: Jafargholi, Zahra, Chethan Kamath Hosdurg, Karen Klein, Ilan Komargodski, Krzysztof Z Pietrzak, and Daniel Wichs. “Be Adaptive Avoid Overcommitting.” edited by Jonathan Katz and Hovav Shacham, 10401:133–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63688-7_5. ieee: 'Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K. Z. Pietrzak, and D. Wichs, “Be adaptive avoid overcommitting,” presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States, 2017, vol. 10401, pp. 133–163.' ista: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. 2017. Be adaptive avoid overcommitting. CRYPTO: Cryptology, LNCS, vol. 10401, 133–163.' mla: Jafargholi, Zahra, et al. Be Adaptive Avoid Overcommitting. Edited by Jonathan Katz and Hovav Shacham, vol. 10401, Springer, 2017, pp. 133–63, doi:10.1007/978-3-319-63688-7_5. short: Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K.Z. Pietrzak, D. Wichs, in:, J. Katz, H. Shacham (Eds.), Springer, 2017, pp. 133–163. conference: end_date: 2017-07-24 location: Santa Barbara, CA, United States name: 'CRYPTO: Cryptology' start_date: 2017-07-20 date_created: 2018-12-11T11:47:38Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-07T13:32:11Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-63688-7_5 ec_funded: 1 editor: - first_name: Jonathan full_name: Katz, Jonathan last_name: Katz - first_name: Hovav full_name: Shacham, Hovav last_name: Shacham intvolume: ' 10401' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/515 month: '01' oa: 1 oa_version: Submitted Version page: 133 - 163 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331963687-0 publication_status: published publisher: Springer publist_id: '7151' quality_controlled: '1' related_material: record: - id: '10035' relation: dissertation_contains status: public scopus_import: 1 status: public title: Be adaptive avoid overcommitting type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10401 year: '2017' ... --- _id: '9842' abstract: - lang: eng text: Mathematica notebooks used to generate figures. article_processing_charge: No author: - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1' apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1' chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.' ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.' ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.' mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.' short: A. Etheridge, N.H. Barton, (2017). date_created: 2021-08-09T13:18:55Z date_published: 2017-12-29T00:00:00Z date_updated: 2023-09-11T13:41:21Z day: '29' department: - _id: NiBa doi: 10.17632/nw68fxzjpm.1 main_file_link: - open_access: '1' url: https://doi.org/10.17632/nw68fxzjpm.1 month: '12' oa: 1 oa_version: Published Version publisher: Mendeley Data related_material: record: - id: '564' relation: used_in_publication status: public status: public title: 'Data for: Establishment in a new habitat by polygenic adaptation' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '202' abstract: - lang: eng text: 'Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.' acknowledgement: "During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 citation: ama: Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:10.15479/AT:ISTA:th_916 apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916 chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916. ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017. ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916. short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:45:10Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-15T12:04:56Z day: '01' ddc: - '576' - '579' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:th_916 file: - access_level: open_access checksum: 33cfb59674e91f82e3738396d3fb3776 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:48Z date_updated: 2020-07-14T12:45:24Z file_id: '4710' file_name: IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf file_size: 18569590 relation: main_file - access_level: closed checksum: dcc239968decb233e7f98cf1083d8c26 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:33:14Z date_updated: 2020-07-14T12:45:24Z file_id: '6204' file_name: 2017_Pleska_Maros_Thesis.docx file_size: 2801649 relation: source_file file_date_updated: 2020-07-14T12:45:24Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '126' project: - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7711' pubrep_id: '916' related_material: record: - id: '1243' relation: part_of_dissertation status: public - id: '561' relation: part_of_dissertation status: public - id: '457' relation: part_of_dissertation status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Biology of restriction-modification systems at the single-cell and population level tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6287' abstract: - lang: eng text: The main objects considered in the present work are simplicial and CW-complexes with vertices forming a random point cloud. In particular, we consider a Poisson point process in R^n and study Delaunay and Voronoi complexes of the first and higher orders and weighted Delaunay complexes obtained as sections of Delaunay complexes, as well as the Čech complex. Further, we examine theDelaunay complex of a Poisson point process on the sphere S^n, as well as of a uniform point cloud, which is equivalent to the convex hull, providing a connection to the theory of random polytopes. Each of the complexes in question can be endowed with a radius function, which maps its cells to the radii of appropriately chosen circumspheres, called the radius of the cell. Applying and developing discrete Morse theory for these functions, joining it together with probabilistic and sometimes analytic machinery, and developing several integral geometric tools, we aim at getting the distributions of circumradii of typical cells. For all considered complexes, we are able to generalize and obtain up to constants the distribution of radii of typical intervals of all types. In low dimensions the constants can be computed explicitly, thus providing the explicit expressions for the expected numbers of cells. In particular, it allows to find the expected density of simplices of every dimension for a Poisson point process in R^4, whereas the result for R^3 was known already in 1970's. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873 apa: Nikitenko, A. (2017). Discrete Morse theory for random complexes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_873 chicago: Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_873. ieee: A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017. ista: Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria. mla: Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873. short: A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017. date_created: 2019-04-09T15:04:32Z date_published: 2017-10-27T00:00:00Z date_updated: 2023-09-15T12:10:34Z day: '27' ddc: - '514' - '516' - '519' degree_awarded: PhD department: - _id: HeEd doi: 10.15479/AT:ISTA:th_873 file: - access_level: open_access checksum: ece7e598a2f060b263c2febf7f3fe7f9 content_type: application/pdf creator: dernst date_created: 2019-04-09T14:54:51Z date_updated: 2020-07-14T12:47:26Z file_id: '6289' file_name: 2017_Thesis_Nikitenko.pdf file_size: 2324870 relation: main_file - access_level: closed checksum: 99b7ad76e317efd447af60f91e29b49b content_type: application/zip creator: dernst date_created: 2019-04-09T14:54:51Z date_updated: 2020-07-14T12:47:26Z file_id: '6290' file_name: 2017_Thesis_Nikitenko_source.zip file_size: 2863219 relation: source_file file_date_updated: 2020-07-14T12:47:26Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '86' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria pubrep_id: '873' related_material: record: - id: '718' relation: part_of_dissertation status: public - id: '5678' relation: part_of_dissertation status: public - id: '87' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: 'Discrete Morse theory for random complexes ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '1127' abstract: - lang: eng text: "Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms controlling plant development. Auxin itself could change localization of PINs and\r\nthereby control direction of its own flow. We performed an expression profiling experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally\r\nregulated by auxin signalling. We identified several novel regulators and performed a detailed\r\ncharacterization of the transcription factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin transport processes such as gravitropism and leaf vascular pattern\r\nformation were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct targets of WRKY23, we performed consequential expression\r\nprofiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits transcriptional behaviour, subcellular localization. Based on global expression data, we\r\ntried to identify ligand responsible for mechanism of signalling and suggest signalling partner\r\nand interactors. Additionally, we described role of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this\r\nfield.\r\nOur results provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork and characterised its mediatory role in plant development. We identified direct\r\neffectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and\r\nPIN-dependent auxin transport processes." acknowledgement: I would like to first acknowledge my supervisor Jiří Friml for support, kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg forever. I would like to thank all past and present lab members for the friendship and friendly and scientific environment in the groups. It was so nice to cooperate with you, guys. There was always someone who helped me with experiments, troubleshoot issues coming from our work etc. At this place, I would like to thank especially to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became my tutor and guide through my PhD. From no one else during my entire professional career, I’ve learned that much. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat citation: ama: Prat T. Identification of novel regulators of PIN polarity and development of novel auxin sensor. 2017. apa: Prat, T. (2017). Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria. chicago: Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017. ieee: T. Prat, “Identification of novel regulators of PIN polarity and development of novel auxin sensor,” Institute of Science and Technology Austria, 2017. ista: Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria. mla: Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017. short: T. Prat, Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:50:17Z date_published: 2017-01-12T00:00:00Z date_updated: 2023-09-19T10:39:33Z day: '12' ddc: - '580' degree_awarded: PhD department: - _id: JiFr file: - access_level: closed checksum: d192c7c6c5ea32c8432437286dc4909e content_type: application/pdf creator: dernst date_created: 2019-04-05T08:45:14Z date_updated: 2019-04-05T08:45:14Z file_id: '6209' file_name: IST_Austria_Thesis_Tomáš_Prát.pdf file_size: 10285946 relation: main_file - access_level: open_access checksum: bab18b52cf98145926042d8ed99fdb3b content_type: application/pdf creator: dernst date_created: 2021-02-22T11:52:56Z date_updated: 2021-02-22T11:52:56Z file_id: '9185' file_name: 2017_Thesis_Prat.pdf file_size: 9802991 relation: main_file success: 1 file_date_updated: 2021-02-22T11:52:56Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '131' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6233' related_material: record: - id: '449' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Identification of novel regulators of PIN polarity and development of novel auxin sensor type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '2016' abstract: - lang: eng text: The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane. article_processing_charge: No author: - first_name: Abraham full_name: Martin Del Campo Sanchez, Abraham last_name: Martin Del Campo Sanchez - first_name: Sarah A full_name: Cepeda Humerez, Sarah A id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87 last_name: Cepeda Humerez - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306. doi:10.1111/sjos.12251 apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251 chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251. ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” Scandinavian Journal of Statistics, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017. ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306. mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:10.1111/sjos.12251. short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306. date_created: 2018-12-11T11:55:13Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-19T15:13:27Z day: '01' department: - _id: GaTk doi: 10.1111/sjos.12251 external_id: arxiv: - '1410.1242' isi: - '000400985000001' intvolume: ' 44' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.1242 month: '06' oa: 1 oa_version: Preprint page: 285 - 306 publication: Scandinavian Journal of Statistics publication_identifier: issn: - '03036898' publication_status: published publisher: Wiley-Blackwell publist_id: '5060' quality_controlled: '1' related_material: record: - id: '6473' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Exact goodness-of-fit testing for the Ising model type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 44 year: '2017' ... --- _id: '1528' abstract: - lang: eng text: 'We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized.' acknowledgement: "Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Bao Z, Erdös L. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 2017;167(3-4):673-776. doi:10.1007/s00440-015-0692-y apa: Bao, Z., & Erdös, L. (2017). Delocalization for a class of random block band matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-015-0692-y chicago: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” Probability Theory and Related Fields. Springer, 2017. https://doi.org/10.1007/s00440-015-0692-y. ieee: Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” Probability Theory and Related Fields, vol. 167, no. 3–4. Springer, pp. 673–776, 2017. ista: Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776. mla: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” Probability Theory and Related Fields, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:10.1007/s00440-015-0692-y. short: Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776. date_created: 2018-12-11T11:52:32Z date_published: 2017-04-01T00:00:00Z date_updated: 2023-09-20T09:42:12Z day: '01' ddc: - '530' department: - _id: LaEr doi: 10.1007/s00440-015-0692-y ec_funded: 1 external_id: isi: - '000398842700004' file: - access_level: open_access checksum: 67afa85ff1e220cbc1f9f477a828513c content_type: application/pdf creator: system date_created: 2018-12-12T10:08:05Z date_updated: 2020-07-14T12:45:00Z file_id: '4665' file_name: IST-2016-489-v1+1_s00440-015-0692-y.pdf file_size: 1615755 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 167' isi: 1 issue: 3-4 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 673 - 776 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Probability Theory and Related Fields publication_identifier: issn: - '01788051' publication_status: published publisher: Springer publist_id: '5644' pubrep_id: '489' quality_controlled: '1' scopus_import: '1' status: public title: Delocalization for a class of random block band matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 167 year: '2017' ... --- _id: '1433' abstract: - lang: eng text: Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology. article_processing_charge: No article_type: original author: - first_name: Ulrich full_name: Bauer, Ulrich last_name: Bauer - first_name: Michael full_name: Kerber, Michael last_name: Kerber - first_name: Jan full_name: Reininghaus, Jan last_name: Reininghaus - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008 apa: Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. Academic Press. https://doi.org/10.1016/j.jsc.2016.03.008 chicago: Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation. Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008. ieee: U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic Press, pp. 76–90, 2017. ista: Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90. mla: Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008. short: U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90. date_created: 2018-12-11T11:51:59Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T09:42:40Z day: '01' department: - _id: HeEd doi: 10.1016/j.jsc.2016.03.008 ec_funded: 1 external_id: isi: - '000384396000005' intvolume: ' 78' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jsc.2016.03.008 month: '01' oa: 1 oa_version: Published Version page: 76 - 90 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Journal of Symbolic Computation publication_identifier: issn: - ' 07477171' publication_status: published publisher: Academic Press publist_id: '5765' quality_controlled: '1' related_material: record: - id: '10894' relation: earlier_version status: public scopus_import: '1' status: public title: Phat - Persistent homology algorithms toolbox type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 78 year: '2017' ... --- _id: '1407' abstract: - lang: eng text: We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study. article_processing_charge: No author: - first_name: Mária full_name: Svoreňová, Mária last_name: Svoreňová - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ivana full_name: Cěrná, Ivana last_name: Cěrná - first_name: Cǎlin full_name: Belta, Cǎlin last_name: Belta citation: ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006' apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006' chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.' ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.' ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.' mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.' short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.' date_created: 2018-12-11T11:51:50Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T09:43:09Z day: '01' department: - _id: ToHe - _id: KrCh doi: 10.1016/j.nahs.2016.04.006 ec_funded: 1 external_id: arxiv: - '1410.5387' isi: - '000390637000014' intvolume: ' 23' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.5387 month: '02' oa: 1 oa_version: Preprint page: 230 - 253 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: 'Nonlinear Analysis: Hybrid Systems' publication_status: published publisher: Elsevier publist_id: '5800' quality_controlled: '1' related_material: record: - id: '1689' relation: earlier_version status: public scopus_import: '1' status: public title: Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2017' ... --- _id: '1367' abstract: - lang: eng text: One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids. acknowledgement: This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209). article_processing_charge: No author: - first_name: Pierre full_name: Manteaux, Pierre last_name: Manteaux - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Rahul full_name: Narain, Rahul last_name: Narain - first_name: Stéphane full_name: Redon, Stéphane last_name: Redon - first_name: François full_name: Faure, François last_name: Faure - first_name: Marie full_name: Cani, Marie last_name: Cani citation: ama: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically based models in computer graphics. Computer Graphics Forum. 2017;36(6):312-337. doi:10.1111/cgf.12941 apa: Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M. (2017). Adaptive physically based models in computer graphics. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941 chicago: Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941. ieee: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” Computer Graphics Forum, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017. ista: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337. mla: Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:10.1111/cgf.12941. short: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337. date_created: 2018-12-11T11:51:37Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-20T11:05:36Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12941 external_id: isi: - '000408634200019' file: - access_level: open_access checksum: 7676e9a9ead6d58c3000988c97deb2ef content_type: application/pdf creator: system date_created: 2018-12-12T10:16:21Z date_updated: 2020-07-14T12:44:47Z file_id: '5208' file_name: IST-2016-634-v1+1_starAdaptivity-cgf.pdf file_size: 1434439 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 312 - 337 publication: Computer Graphics Forum publication_identifier: issn: - '01677055' publication_status: published publisher: Wiley-Blackwell publist_id: '5873' pubrep_id: '634' quality_controlled: '1' scopus_import: '1' status: public title: Adaptive physically based models in computer graphics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 36 year: '2017' ... --- _id: '1338' abstract: - lang: eng text: We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively. article_processing_charge: No author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Edmund full_name: Clarke, Edmund last_name: Clarke - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Leonid full_name: Ryzhyk, Leonid last_name: Ryzhyk - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Thorsten full_name: Tarrach, Thorsten id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87 last_name: Tarrach orcid: 0000-0003-4409-8487 citation: ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 2017;50(2-3):97-139. doi:10.1007/s10703-016-0256-5 apa: Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-016-0256-5 chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Formal Methods in System Design. Springer, 2017. https://doi.org/10.1007/s10703-016-0256-5. ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” Formal Methods in System Design, vol. 50, no. 2–3. Springer, pp. 97–139, 2017. ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139. mla: Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Formal Methods in System Design, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:10.1007/s10703-016-0256-5. short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139. date_created: 2018-12-11T11:51:27Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:13:51Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/s10703-016-0256-5 ec_funded: 1 external_id: isi: - '000399888900001' file: - access_level: open_access checksum: 1163dfd997e8212c789525d4178b1653 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:05Z date_updated: 2020-07-14T12:44:44Z file_id: '4985' file_name: IST-2016-656-v1+1_s10703-016-0256-5.pdf file_size: 1416170 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 50' isi: 1 issue: 2-3 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 97 - 139 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '5929' pubrep_id: '656' quality_controlled: '1' related_material: record: - id: '1729' relation: earlier_version status: public scopus_import: '1' status: public title: From non-preemptive to preemptive scheduling using synchronization synthesis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 50 year: '2017' ... --- _id: '1351' abstract: - lang: eng text: The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights. article_processing_charge: No author: - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x. ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017. ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787. mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x. short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787. date_created: 2018-12-11T11:51:32Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-20T11:06:03Z day: '01' ddc: - '006' - '576' department: - _id: ToHe - _id: CaGu - _id: NiBa doi: 10.1007/s00236-016-0278-x ec_funded: 1 external_id: isi: - '000414343200003' file: - access_level: open_access checksum: 4e661d9135d7f8c342e8e258dee76f3e content_type: application/pdf creator: dernst date_created: 2019-01-17T15:57:29Z date_updated: 2020-07-14T12:44:46Z file_id: '5841' file_name: 2017_ActaInformatica_Giacobbe.pdf file_size: 755241 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 54' isi: 1 issue: '8' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 765 - 787 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Acta Informatica publication_identifier: issn: - '00015903' publication_status: published publisher: Springer publist_id: '5898' pubrep_id: '649' quality_controlled: '1' related_material: record: - id: '1835' relation: earlier_version status: public scopus_import: '1' status: public title: Model checking the evolution of gene regulatory networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 54 year: '2017' ... --- _id: '1336' abstract: - lang: eng text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient. article_processing_charge: No author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Jorge full_name: Pérez Heredia, Jorge last_name: Pérez Heredia - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1 apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer. https://doi.org/10.1007/s00453-016-0212-1 chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1. ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2. Springer, pp. 681–713, 2017. ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713. mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1. short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713. date_created: 2018-12-11T11:51:27Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:14:42Z day: '01' ddc: - '576' department: - _id: NiBa - _id: CaGu doi: 10.1007/s00453-016-0212-1 ec_funded: 1 external_id: isi: - '000400379500013' file: - access_level: open_access checksum: 7873f665a0c598ac747c908f34cb14b9 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:19Z date_updated: 2020-07-14T12:44:44Z file_id: '4805' file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf file_size: 710206 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 78' isi: 1 issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 681 - 713 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Algorithmica publication_identifier: issn: - '01784617' publication_status: published publisher: Springer publist_id: '5931' pubrep_id: '658' quality_controlled: '1' scopus_import: '1' status: public title: Towards a runtime comparison of natural and artificial evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 78 year: '2017' ... --- _id: '1337' abstract: - lang: eng text: We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes. acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). ' article_processing_charge: Yes (via OA deal) author: - first_name: Oskari H full_name: Ajanki, Oskari H id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87 last_name: Ajanki - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 2017;169(3-4):667-727. doi:10.1007/s00440-016-0740-2 apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2017). Universality for general Wigner-type matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-016-0740-2 chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” Probability Theory and Related Fields. Springer, 2017. https://doi.org/10.1007/s00440-016-0740-2. ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” Probability Theory and Related Fields, vol. 169, no. 3–4. Springer, pp. 667–727, 2017. ista: Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727. mla: Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” Probability Theory and Related Fields, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:10.1007/s00440-016-0740-2. short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727. date_created: 2018-12-11T11:51:27Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-20T11:14:17Z day: '01' ddc: - '510' - '530' department: - _id: LaEr doi: 10.1007/s00440-016-0740-2 ec_funded: 1 external_id: isi: - '000414358400002' file: - access_level: open_access checksum: 29f5a72c3f91e408aeb9e78344973803 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:25Z date_updated: 2020-07-14T12:44:44Z file_id: '4686' file_name: IST-2017-657-v1+2_s00440-016-0740-2.pdf file_size: 988843 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 169' isi: 1 issue: 3-4 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 667 - 727 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Probability Theory and Related Fields publication_identifier: issn: - '01788051' publication_status: published publisher: Springer publist_id: '5930' pubrep_id: '657' quality_controlled: '1' scopus_import: '1' status: public title: Universality for general Wigner-type matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 169 year: '2017' ... --- _id: '1294' abstract: - lang: eng text: We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints. article_processing_charge: No author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera citation: ama: Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 2017;84:144-170. doi:10.1016/j.jcss.2016.09.009 apa: Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2017). Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.09.009 chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” Journal of Computer and System Sciences. Elsevier, 2017. https://doi.org/10.1016/j.jcss.2016.09.009. ieee: T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” Journal of Computer and System Sciences, vol. 84. Elsevier, pp. 144–170, 2017. ista: Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170. mla: Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” Journal of Computer and System Sciences, vol. 84, Elsevier, 2017, pp. 144–70, doi:10.1016/j.jcss.2016.09.009. short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170. date_created: 2018-12-11T11:51:12Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-20T11:15:31Z day: '01' ddc: - '004' - '006' department: - _id: KrCh doi: 10.1016/j.jcss.2016.09.009 ec_funded: 1 external_id: isi: - '000388430000011' file: - access_level: open_access checksum: 91271b23cf884d7c06d33bef0cd623b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:30Z date_updated: 2020-07-14T12:44:42Z file_id: '4885' file_name: IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf file_size: 708657 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 84' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 144 - 170 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Computer and System Sciences publication_status: published publisher: Elsevier publist_id: '6009' pubrep_id: '717' quality_controlled: '1' related_material: record: - id: '2305' relation: earlier_version status: public scopus_import: '1' status: public title: Trading performance for stability in Markov decision processes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 84 year: '2017' ... --- _id: '1228' abstract: - lang: eng text: Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD. acknowledgement: This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W. article_processing_charge: No article_type: review author: - first_name: Ulrich full_name: Sauerzopf, Ulrich last_name: Sauerzopf - first_name: Roberto full_name: Sacco, Roberto id: 42C9F57E-F248-11E8-B48F-1D18A9856A87 last_name: Sacco - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Marco full_name: Niello, Marco last_name: Niello - first_name: Ana full_name: Weidenauer, Ana last_name: Weidenauer - first_name: Nicole full_name: Praschak Rieder, Nicole last_name: Praschak Rieder - first_name: Harald full_name: Sitte, Harald last_name: Sitte - first_name: Matthaeus full_name: Willeit, Matthaeus last_name: Willeit citation: ama: Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 2017;45(1):45-57. doi:10.1111/ejn.13418 apa: Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.13418 chicago: Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1111/ejn.13418. ieee: U. Sauerzopf et al., “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” European Journal of Neuroscience, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017. ista: Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57. mla: Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” European Journal of Neuroscience, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:10.1111/ejn.13418. short: U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57. date_created: 2018-12-11T11:50:50Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:16:01Z day: '01' ddc: - '616' department: - _id: GaNo doi: 10.1111/ejn.13418 external_id: isi: - '000392487100005' pmid: - '27690184' file: - access_level: open_access checksum: c572cf02be8fbb7020cfcfb892182e4c content_type: application/pdf creator: system date_created: 2018-12-12T10:10:48Z date_updated: 2020-07-14T12:44:39Z file_id: '4838' file_name: IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf file_size: 169145 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 45' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 45 - 57 pmid: 1 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '6106' pubrep_id: '738' quality_controlled: '1' scopus_import: '1' status: public title: Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 45 year: '2017' ... --- _id: '1213' abstract: - lang: eng text: Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin. acknowledged_ssus: - _id: Bio acknowledgement: Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell). alternative_title: - Methods in Cell Biology article_processing_charge: No author: - first_name: Natalia full_name: Baranova, Natalia id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: 'Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. Cytokinesis. Vol 137. Academic Press; 2017:355-370. doi:10.1016/bs.mcb.2016.03.036' apa: Baranova, N. S., & Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), Cytokinesis (Vol. 137, pp. 355–370). Academic Press. https://doi.org/10.1016/bs.mcb.2016.03.036 chicago: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In Cytokinesis, edited by Arnaud Echard, 137:355–70. Academic Press, 2017. https://doi.org/10.1016/bs.mcb.2016.03.036. ieee: N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in Cytokinesis, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370. ista: 'Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370.' mla: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” Cytokinesis, edited by Arnaud Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:10.1016/bs.mcb.2016.03.036. short: N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370. date_created: 2018-12-11T11:50:45Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-20T11:16:30Z day: '01' department: - _id: MaLo doi: 10.1016/bs.mcb.2016.03.036 ec_funded: 1 editor: - first_name: 'Arnaud ' full_name: 'Echard, Arnaud ' last_name: Echard external_id: isi: - '000403542900022' intvolume: ' 137' isi: 1 language: - iso: eng month: '12' oa_version: None page: 355 - 370 project: - _id: 2596EAB6-B435-11E9-9278-68D0E5697425 grant_number: ALTF 2015-1163 name: Synthesis of bacterial cell wall - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Cytokinesis publication_identifier: issn: - 0091679X publication_status: published publisher: Academic Press publist_id: '6134' quality_controlled: '1' scopus_import: '1' status: public title: Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 137 year: '2017' ... --- _id: '1198' abstract: - lang: eng text: We consider a model of fermions interacting via point interactions, defined via a certain weighted Dirichlet form. While for two particles the interaction corresponds to infinite scattering length, the presence of further particles effectively decreases the interaction strength. We show that the model becomes trivial in the thermodynamic limit, in the sense that the free energy density at any given particle density and temperature agrees with the corresponding expression for non-interacting particles. acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). ' article_processing_charge: Yes (via OA deal) author: - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Moser T, Seiringer R. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 2017;107(3):533-552. doi:10.1007/s11005-016-0915-x apa: Moser, T., & Seiringer, R. (2017). Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0915-x chicago: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s11005-016-0915-x. ieee: T. Moser and R. Seiringer, “Triviality of a model of particles with point interactions in the thermodynamic limit,” Letters in Mathematical Physics, vol. 107, no. 3. Springer, pp. 533–552, 2017. ista: Moser T, Seiringer R. 2017. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3), 533–552. mla: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics, vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:10.1007/s11005-016-0915-x. short: T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552. date_created: 2018-12-11T11:50:40Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-20T11:18:13Z day: '01' ddc: - '510' - '539' department: - _id: RoSe doi: 10.1007/s11005-016-0915-x external_id: isi: - '000394280200007' file: - access_level: open_access checksum: c0c835def162c1bc52f978fad26e3c2f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:40Z date_updated: 2020-07-14T12:44:38Z file_id: '5296' file_name: IST-2016-723-v1+1_s11005-016-0915-x.pdf file_size: 587207 relation: main_file file_date_updated: 2020-07-14T12:44:38Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: ' 533 - 552' project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Letters in Mathematical Physics publication_identifier: issn: - '03779017' publication_status: published publisher: Springer publist_id: '6152' pubrep_id: '723' quality_controlled: '1' related_material: record: - id: '52' relation: dissertation_contains status: public scopus_import: '1' status: public title: Triviality of a model of particles with point interactions in the thermodynamic limit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 107 year: '2017' ... --- _id: '1207' abstract: - lang: eng text: The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix. article_processing_charge: Yes (via OA deal) author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 2017;349(3):947-990. doi:10.1007/s00220-016-2805-6 apa: Bao, Z., Erdös, L., & Schnelli, K. (2017). Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2805-6 chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition of Random Matrices on Optimal Scale.” Communications in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s00220-016-2805-6. ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices on optimal scale,” Communications in Mathematical Physics, vol. 349, no. 3. Springer, pp. 947–990, 2017. ista: Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 349(3), 947–990. mla: Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.” Communications in Mathematical Physics, vol. 349, no. 3, Springer, 2017, pp. 947–90, doi:10.1007/s00220-016-2805-6. short: Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349 (2017) 947–990. date_created: 2018-12-11T11:50:43Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:16:57Z day: '01' ddc: - '530' department: - _id: LaEr doi: 10.1007/s00220-016-2805-6 ec_funded: 1 external_id: isi: - '000393696700005' file: - access_level: open_access checksum: ddff79154c3daf27237de5383b1264a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:47Z date_updated: 2020-07-14T12:44:39Z file_id: '5102' file_name: IST-2016-722-v1+1_s00220-016-2805-6.pdf file_size: 1033743 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 349' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 947 - 990 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Communications in Mathematical Physics publication_identifier: issn: - '00103616' publication_status: published publisher: Springer publist_id: '6141' pubrep_id: '722' quality_controlled: '1' scopus_import: '1' status: public title: Local law of addition of random matrices on optimal scale tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 349 year: '2017' ... --- _id: '1196' abstract: - lang: eng text: 'We define the . model-measuring problem: given a model . M and specification . ϕ, what is the maximal distance . ρ such that all models . M'' within distance . ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes a distance function on models. We concentrate on . automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification; robustness problems that measure how much a model can be perturbed without violating the specification; and parameter synthesis for hybrid systems. We show that for automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular branching-time, and (c) hybrid specifications, the model-measuring problem can be solved.We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for word, tree, and hybrid automata by the . optimal-value question for the weighted versions of these automata. For automata over words and trees, we consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. For hybrid automata, we consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete) weighted automata.We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications. Further, we propose the modeling framework for model measuring to ease the specification and reduce the likelihood of errors in modeling.Finally, we present a variant of the model-measuring problem, called the . model-repair problem. The model-repair problem applies to models that do not satisfy the specification; it can be used to derive restrictions, under which the model satisfies the specification, i.e., to repair the model.' acknowledgement: "This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this article is available via: https://repository.ist.ac.at/171/" article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: 'Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 2017;23:166-190. doi:10.1016/j.nahs.2016.09.001' apa: 'Henzinger, T. A., & Otop, J. (2017). Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.09.001' chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.09.001.' ieee: 'T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,” Nonlinear Analysis: Hybrid Systems, vol. 23. Elsevier, pp. 166–190, 2017.' ista: 'Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 23, 166–190.' mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” Nonlinear Analysis: Hybrid Systems, vol. 23, Elsevier, 2017, pp. 166–90, doi:10.1016/j.nahs.2016.09.001.' short: 'T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190.' date_created: 2018-12-11T11:50:39Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:18:50Z day: '01' department: - _id: ToHe doi: 10.1016/j.nahs.2016.09.001 ec_funded: 1 external_id: isi: - '000390637000011' intvolume: ' 23' isi: 1 language: - iso: eng month: '02' oa_version: None page: 166 - 190 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 'Nonlinear Analysis: Hybrid Systems' publication_status: published publisher: Elsevier publist_id: '6154' quality_controlled: '1' scopus_import: '1' status: public title: Model measuring for discrete and hybrid systems type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2017' ... --- _id: '1199' abstract: - lang: eng text: Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects. article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. How does epistasis influence the response to selection? Heredity. 2017;118:96-109. doi:10.1038/hdy.2016.109 apa: Barton, N. H. (2017). How does epistasis influence the response to selection? Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109 chicago: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109. ieee: N. H. Barton, “How does epistasis influence the response to selection?,” Heredity, vol. 118. Nature Publishing Group, pp. 96–109, 2017. ista: Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109. mla: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109. short: N.H. Barton, Heredity 118 (2017) 96–109. date_created: 2018-12-11T11:50:40Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:17:47Z day: '01' department: - _id: NiBa doi: 10.1038/hdy.2016.109 ec_funded: 1 external_id: isi: - '000392229100011' intvolume: ' 118' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/ month: '01' oa: 1 oa_version: Submitted Version page: 96 - 109 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Heredity publication_status: published publisher: Nature Publishing Group publist_id: '6151' quality_controlled: '1' related_material: record: - id: '9710' relation: research_data status: public scopus_import: '1' status: public title: How does epistasis influence the response to selection? type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1208' abstract: - lang: eng text: We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd. article_processing_charge: No author: - first_name: Piotr full_name: Zwiernik, Piotr last_name: Zwiernik - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Donald full_name: Richards, Donald last_name: Richards citation: ama: 'Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society Series B: Statistical Methodology. 2017;79(4):1269-1292. doi:10.1111/rssb.12217' apa: 'Zwiernik, P., Uhler, C., & Richards, D. (2017). Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. Wiley-Blackwell. https://doi.org/10.1111/rssb.12217' chicago: 'Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical Methodology. Wiley-Blackwell, 2017. https://doi.org/10.1111/rssb.12217.' ieee: 'P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for linear Gaussian covariance models,” Journal of the Royal Statistical Society. Series B: Statistical Methodology, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292, 2017.' ista: 'Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. 79(4), 1269–1292.' mla: 'Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical Methodology, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:10.1111/rssb.12217.' short: 'P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society. Series B: Statistical Methodology 79 (2017) 1269–1292.' date_created: 2018-12-11T11:50:43Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-20T11:17:21Z day: '01' department: - _id: CaUh doi: 10.1111/rssb.12217 external_id: isi: - '000411712300012' intvolume: ' 79' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.5604 month: '09' oa: 1 oa_version: Submitted Version page: 1269 - 1292 project: - _id: 2530CA10-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 903-N35 name: 'Gaussian Graphical Models: Theory and Applications' publication: 'Journal of the Royal Statistical Society. Series B: Statistical Methodology' publication_identifier: issn: - '13697412' publication_status: published publisher: Wiley-Blackwell publist_id: '6142' quality_controlled: '1' scopus_import: '1' status: public title: Maximum likelihood estimation for linear Gaussian covariance models type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 79 year: '2017' ... --- _id: '1174' abstract: - lang: eng text: Security of cryptographic applications is typically defined by security games. The adversary, within certain resources, cannot win with probability much better than 0 (for unpredictability applications, like one-way functions) or much better than 1/2 (indistinguishability applications for instance encryption schemes). In so called squared-friendly applications the winning probability of the adversary, for different values of the application secret randomness, is not only close to 0 or 1/2 on average, but also concentrated in the sense that its second central moment is small. The class of squared-friendly applications, which contains all unpredictability applications and many indistinguishability applications, is particularly important for key derivation. Barak et al. observed that for square-friendly applications one can beat the "RT-bound", extracting secure keys with significantly smaller entropy loss. In turn Dodis and Yu showed that in squared-friendly applications one can directly use a "weak" key, which has only high entropy, as a secure key. In this paper we give sharp lower bounds on square security assuming security for "weak" keys. We show that any application which is either (a) secure with weak keys or (b) allows for entropy savings for keys derived by universal hashing, must be square-friendly. Quantitatively, our lower bounds match the positive results of Dodis and Yu and Barak et al. (TCC\'13, CRYPTO\'11) Hence, they can be understood as a general characterization of squared-friendly applications. While the positive results on squared-friendly applications where derived by one clever application of the Cauchy-Schwarz Inequality, for tight lower bounds we need more machinery. In our approach we use convex optimization techniques and some theory of circular matrices. alternative_title: - LIPIcs article_number: '57' article_processing_charge: No author: - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Skórski M. Lower bounds on key derivation for square-friendly applications. In: Vol 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.STACS.2017.57' apa: 'Skórski, M. (2017). Lower bounds on key derivation for square-friendly applications (Vol. 66). Presented at the STACS: Symposium on Theoretical Aspects of Computer Science, Hannover, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2017.57' chicago: Skórski, Maciej. “Lower Bounds on Key Derivation for Square-Friendly Applications,” Vol. 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.STACS.2017.57. ieee: 'M. Skórski, “Lower bounds on key derivation for square-friendly applications,” presented at the STACS: Symposium on Theoretical Aspects of Computer Science, Hannover, Germany, 2017, vol. 66.' ista: 'Skórski M. 2017. Lower bounds on key derivation for square-friendly applications. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 66, 57.' mla: Skórski, Maciej. Lower Bounds on Key Derivation for Square-Friendly Applications. Vol. 66, 57, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.STACS.2017.57. short: M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-03-11 location: Hannover, Germany name: 'STACS: Symposium on Theoretical Aspects of Computer Science' start_date: 2017-03-08 date_created: 2018-12-11T11:50:32Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-20T11:23:15Z day: '01' department: - _id: KrPi doi: 10.4230/LIPIcs.STACS.2017.57 ec_funded: 1 external_id: isi: - '000521077300057' intvolume: ' 66' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://drops.dagstuhl.de/opus/volltexte/2017/6976 month: '03' oa: 1 oa_version: Submitted Version project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6180' quality_controlled: '1' scopus_import: '1' status: public title: Lower bounds on key derivation for square-friendly applications type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2017' ... --- _id: '1176' abstract: - lang: eng text: The algorithm Argon2i-B of Biryukov, Dinu and Khovratovich is currently being considered by the IRTF (Internet Research Task Force) as a new de-facto standard for password hashing. An older version (Argon2i-A) of the same algorithm was chosen as the winner of the recent Password Hashing Competition. An important competitor to Argon2i-B is the recently introduced Balloon Hashing (BH) algorithm of Corrigan-Gibs, Boneh and Schechter. A key security desiderata for any such algorithm is that evaluating it (even using a custom device) requires a large amount of memory amortized across multiple instances. Alwen and Blocki (CRYPTO 2016) introduced a class of theoretical attacks against Argon2i-A and BH. While these attacks yield large asymptotic reductions in the amount of memory, it was not, a priori, clear if (1) they can be extended to the newer Argon2i-B, (2) the attacks are effective on any algorithm for practical parameter ranges (e.g., 1GB of memory) and (3) if they can be effectively instantiated against any algorithm under realistic hardware constrains. In this work we answer all three of these questions in the affirmative for all three algorithms. This is also the first work to analyze the security of Argon2i-B. In more detail, we extend the theoretical attacks of Alwen and Blocki (CRYPTO 2016) to the recent Argon2i-B proposal demonstrating severe asymptotic deficiencies in its security. Next we introduce several novel heuristics for improving the attack's concrete memory efficiency even when on-chip memory bandwidth is bounded. We then simulate our attacks on randomly sampled Argon2i-A, Argon2i-B and BH instances and measure the resulting memory consumption for various practical parameter ranges and for a variety of upperbounds on the amount of parallelism available to the attacker. Finally we describe, implement, and test a new heuristic for applying the Alwen-Blocki attack to functions employing a technique developed by Corrigan-Gibs et al. for improving concrete security of memory-hard functions. We analyze the collected data and show the effects various parameters have on the memory consumption of the attack. In particular, we can draw several interesting conclusions about the level of security provided by these functions. · For the Alwen-Blocki attack to fail against practical memory parameters, Argon2i-B must be instantiated with more than 10 passes on memory - beyond the "paranoid" parameter setting in the current IRTF proposal. · The technique of Corrigan-Gibs for improving security can also be overcome by the Alwen-Blocki attack under realistic hardware constraints. · On a positive note, both the asymptotic and concrete security of Argon2i-B seem to improve on that of Argon2i-A. article_number: '7961977' article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Jeremiah full_name: Blocki, Jeremiah last_name: Blocki citation: ama: 'Alwen JF, Blocki J. Towards practical attacks on Argon2i and balloon hashing. In: IEEE; 2017. doi:10.1109/EuroSP.2017.47' apa: 'Alwen, J. F., & Blocki, J. (2017). Towards practical attacks on Argon2i and balloon hashing. Presented at the EuroS&P: European Symposium on Security and Privacy, Paris, France: IEEE. https://doi.org/10.1109/EuroSP.2017.47' chicago: Alwen, Joel F, and Jeremiah Blocki. “Towards Practical Attacks on Argon2i and Balloon Hashing.” IEEE, 2017. https://doi.org/10.1109/EuroSP.2017.47. ieee: 'J. F. Alwen and J. Blocki, “Towards practical attacks on Argon2i and balloon hashing,” presented at the EuroS&P: European Symposium on Security and Privacy, Paris, France, 2017.' ista: 'Alwen JF, Blocki J. 2017. Towards practical attacks on Argon2i and balloon hashing. EuroS&P: European Symposium on Security and Privacy, 7961977.' mla: Alwen, Joel F., and Jeremiah Blocki. Towards Practical Attacks on Argon2i and Balloon Hashing. 7961977, IEEE, 2017, doi:10.1109/EuroSP.2017.47. short: J.F. Alwen, J. Blocki, in:, IEEE, 2017. conference: end_date: 2017-04-28 location: Paris, France name: 'EuroS&P: European Symposium on Security and Privacy' start_date: 2017-04-26 date_created: 2018-12-11T11:50:33Z date_published: 2017-07-03T00:00:00Z date_updated: 2023-09-20T11:22:25Z day: '03' department: - _id: KrPi doi: 10.1109/EuroSP.2017.47 external_id: isi: - '000424197300011' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/759 month: '07' oa: 1 oa_version: Submitted Version publication_identifier: isbn: - 978-150905761-0 publication_status: published publisher: IEEE publist_id: '6178' quality_controlled: '1' scopus_import: '1' status: public title: Towards practical attacks on Argon2i and balloon hashing type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '1187' abstract: - lang: eng text: We construct efficient authentication protocols and message authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work—starting with the (Formula presented.) protocol of Hopper and Blum in 2001—until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle attacks. A MAC implies such a (two-round) protocol. article_processing_charge: No article_type: original author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniele full_name: Venturi, Daniele last_name: Venturi - first_name: David full_name: Cash, David last_name: Cash - first_name: Abhishek full_name: Jain, Abhishek last_name: Jain citation: ama: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. Efficient authentication from hard learning problems. Journal of Cryptology. 2017;30(4):1238-1275. doi:10.1007/s00145-016-9247-3 apa: Kiltz, E., Pietrzak, K. Z., Venturi, D., Cash, D., & Jain, A. (2017). Efficient authentication from hard learning problems. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-016-9247-3 chicago: Kiltz, Eike, Krzysztof Z Pietrzak, Daniele Venturi, David Cash, and Abhishek Jain. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology. Springer, 2017. https://doi.org/10.1007/s00145-016-9247-3. ieee: E. Kiltz, K. Z. Pietrzak, D. Venturi, D. Cash, and A. Jain, “Efficient authentication from hard learning problems,” Journal of Cryptology, vol. 30, no. 4. Springer, pp. 1238–1275, 2017. ista: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. 2017. Efficient authentication from hard learning problems. Journal of Cryptology. 30(4), 1238–1275. mla: Kiltz, Eike, et al. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology, vol. 30, no. 4, Springer, 2017, pp. 1238–75, doi:10.1007/s00145-016-9247-3. short: E. Kiltz, K.Z. Pietrzak, D. Venturi, D. Cash, A. Jain, Journal of Cryptology 30 (2017) 1238–1275. date_created: 2018-12-11T11:50:37Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-20T11:20:58Z day: '01' ddc: - '000' department: - _id: KrPi doi: 10.1007/s00145-016-9247-3 ec_funded: 1 external_id: isi: - '000410788600007' file: - access_level: open_access checksum: c647520d115b772a1682fc06fa273eb1 content_type: application/pdf creator: dernst date_created: 2020-05-14T16:30:17Z date_updated: 2020-07-14T12:44:37Z file_id: '7843' file_name: 2017_JournalCrypto_Kiltz.pdf file_size: 516959 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 1238 - 1275 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Journal of Cryptology publication_status: published publisher: Springer publist_id: '6166' quality_controlled: '1' related_material: record: - id: '3238' relation: earlier_version status: public scopus_import: '1' status: public title: Efficient authentication from hard learning problems type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2017' ... --- _id: '1192' abstract: - lang: eng text: The main result of this paper is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even Δ-matroid constraints allows us to extend the tractability result to a larger class of Δ-matroids that includes many classes that were known to be tractable before, namely co-independent, compact, local and binary. article_processing_charge: No author: - first_name: Alexandr full_name: Kazda, Alexandr id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87 last_name: Kazda - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: 'Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar Boolean CSPs. In: SIAM; 2017:307-326. doi:10.1137/1.9781611974782.20' apa: 'Kazda, A., Kolmogorov, V., & Rolinek, M. (2017). Even delta-matroids and the complexity of planar Boolean CSPs (pp. 307–326). Presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain: SIAM. https://doi.org/10.1137/1.9781611974782.20' chicago: Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs,” 307–26. SIAM, 2017. https://doi.org/10.1137/1.9781611974782.20. ieee: 'A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar Boolean CSPs,” presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain, 2017, pp. 307–326.' ista: 'Kazda A, Kolmogorov V, Rolinek M. 2017. Even delta-matroids and the complexity of planar Boolean CSPs. SODA: Symposium on Discrete Algorithms, 307–326.' mla: Kazda, Alexandr, et al. Even Delta-Matroids and the Complexity of Planar Boolean CSPs. SIAM, 2017, pp. 307–26, doi:10.1137/1.9781611974782.20. short: A. Kazda, V. Kolmogorov, M. Rolinek, in:, SIAM, 2017, pp. 307–326. conference: end_date: 2017-01019 location: Barcelona, Spain name: 'SODA: Symposium on Discrete Algorithms' start_date: 2017-01-16 date_created: 2018-12-11T11:50:38Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:20:26Z day: '01' department: - _id: VlKo doi: 10.1137/1.9781611974782.20 ec_funded: 1 external_id: isi: - '000426965800020' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.03124 month: '01' oa: 1 oa_version: Submitted Version page: 307 - 326 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: isbn: - 978-161197478-2 publication_status: published publisher: SIAM publist_id: '6159' quality_controlled: '1' related_material: record: - id: '6032' relation: later_version status: public status: public title: Even delta-matroids and the complexity of planar Boolean CSPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '1180' abstract: - lang: eng text: In this article we define an algebraic vertex of a generalized polyhedron and show that the set of algebraic vertices is the smallest set of points needed to define the polyhedron. We prove that the indicator function of a generalized polytope P is a linear combination of indicator functions of simplices whose vertices are algebraic vertices of P. We also show that the indicator function of any generalized polyhedron is a linear combination, with integer coefficients, of indicator functions of cones with apices at algebraic vertices and line-cones. The concept of an algebraic vertex is closely related to the Fourier–Laplace transform. We show that a point v is an algebraic vertex of a generalized polyhedron P if and only if the tangent cone of P, at v, has non-zero Fourier–Laplace transform. article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Imre full_name: Bárány, Imre last_name: Bárány - first_name: Sinai full_name: Robins, Sinai last_name: Robins citation: ama: Akopyan A, Bárány I, Robins S. Algebraic vertices of non-convex polyhedra. Advances in Mathematics. 2017;308:627-644. doi:10.1016/j.aim.2016.12.026 apa: Akopyan, A., Bárány, I., & Robins, S. (2017). Algebraic vertices of non-convex polyhedra. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2016.12.026 chicago: Akopyan, Arseniy, Imre Bárány, and Sinai Robins. “Algebraic Vertices of Non-Convex Polyhedra.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2016.12.026. ieee: A. Akopyan, I. Bárány, and S. Robins, “Algebraic vertices of non-convex polyhedra,” Advances in Mathematics, vol. 308. Academic Press, pp. 627–644, 2017. ista: Akopyan A, Bárány I, Robins S. 2017. Algebraic vertices of non-convex polyhedra. Advances in Mathematics. 308, 627–644. mla: Akopyan, Arseniy, et al. “Algebraic Vertices of Non-Convex Polyhedra.” Advances in Mathematics, vol. 308, Academic Press, 2017, pp. 627–44, doi:10.1016/j.aim.2016.12.026. short: A. Akopyan, I. Bárány, S. Robins, Advances in Mathematics 308 (2017) 627–644. date_created: 2018-12-11T11:50:34Z date_published: 2017-02-21T00:00:00Z date_updated: 2023-09-20T11:21:27Z day: '21' department: - _id: HeEd doi: 10.1016/j.aim.2016.12.026 ec_funded: 1 external_id: isi: - '000409292900015' intvolume: ' 308' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.07594 month: '02' oa: 1 oa_version: Submitted Version page: 627 - 644 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Advances in Mathematics publication_identifier: issn: - '00018708' publication_status: published publisher: Academic Press publist_id: '6173' quality_controlled: '1' scopus_import: '1' status: public title: Algebraic vertices of non-convex polyhedra type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 308 year: '2017' ... --- _id: '1159' abstract: - lang: eng text: Auxin steers numerous physiological processes in plants, making the tight control of its endogenous levels and spatiotemporal distribution a necessity. This regulation is achieved by different mechanisms, including auxin biosynthesis, metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic acid (c-CA) as a novel and unique addition to a small group of endogenous molecules affecting in planta auxin concentrations. c-CA is the photo-isomerization product of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes characteristic for high auxin levels, including inhibition of primary root growth, induction of root hairs, and promotion of adventitious and lateral rooting. By molecular docking and receptor binding assays, we showed that c-CA itself is neither an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux. Auxin signaling reporters detected changes in spatiotemporal distribution of the auxin response along the root of c-CA-treated plants, and long-distance auxin transport assays showed no inhibition of rootward auxin transport. Overall, these results suggest that the phenotypes of c-CA-treated plants are the consequence of a local change in auxin accumulation, induced by the inhibition of auxin efflux. This work reveals a novel mechanism how plants may regulate auxin levels and adds a novel, naturally occurring molecule to the chemical toolbox for the studies of auxin homeostasis. article_processing_charge: No article_type: original author: - first_name: Ward full_name: Steenackers, Ward last_name: Steenackers - first_name: Petr full_name: Klíma, Petr last_name: Klíma - first_name: Mussa full_name: Quareshy, Mussa last_name: Quareshy - first_name: Igor full_name: Cesarino, Igor last_name: Cesarino - first_name: Robert full_name: Kumpf, Robert last_name: Kumpf - first_name: Sander full_name: Corneillie, Sander last_name: Corneillie - first_name: Pedro full_name: Araújo, Pedro last_name: Araújo - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Geert full_name: Goeminne, Geert last_name: Goeminne - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Joshua full_name: Blakeslee, Joshua last_name: Blakeslee - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Richard full_name: Napier, Richard last_name: Napier - first_name: Wout full_name: Boerjan, Wout last_name: Boerjan - first_name: Bartel full_name: Vanholme, Bartel last_name: Vanholme citation: ama: Steenackers W, Klíma P, Quareshy M, et al. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 2017;173(1):552-565. doi:10.1104/pp.16.00943 apa: Steenackers, W., Klíma, P., Quareshy, M., Cesarino, I., Kumpf, R., Corneillie, S., … Vanholme, B. (2017). Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00943 chicago: Steenackers, Ward, Petr Klíma, Mussa Quareshy, Igor Cesarino, Robert Kumpf, Sander Corneillie, Pedro Araújo, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.00943. ieee: W. Steenackers et al., “Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation,” Plant Physiology, vol. 173, no. 1. American Society of Plant Biologists, pp. 552–565, 2017. ista: Steenackers W, Klíma P, Quareshy M, Cesarino I, Kumpf R, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack M, Ljung K, Friml J, Blakeslee J, Novák O, Zažímalová E, Napier R, Boerjan W, Vanholme B. 2017. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 173(1), 552–565. mla: Steenackers, Ward, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology, vol. 173, no. 1, American Society of Plant Biologists, 2017, pp. 552–65, doi:10.1104/pp.16.00943. short: W. Steenackers, P. Klíma, M. Quareshy, I. Cesarino, R. Kumpf, S. Corneillie, P. Araújo, T. Viaene, G. Goeminne, M. Nowack, K. Ljung, J. Friml, J. Blakeslee, O. Novák, E. Zažímalová, R. Napier, W. Boerjan, B. Vanholme, Plant Physiology 173 (2017) 552–565. date_created: 2018-12-11T11:50:28Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:29:17Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1104/pp.16.00943 ec_funded: 1 external_id: isi: - '000394135800041' pmid: - '27837086' file: - access_level: open_access checksum: fd4d1cfe7ed70e54bb12ae3881f3fb91 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:12:25Z date_updated: 2020-07-14T12:44:36Z file_id: '7040' file_name: 2016_PlantPhysi_Steenackers.pdf file_size: 4109142 relation: main_file file_date_updated: 2020-07-14T12:44:36Z has_accepted_license: '1' intvolume: ' 173' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 552 - 565 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant Physiology publication_identifier: issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists publist_id: '6199' quality_controlled: '1' scopus_import: '1' status: public title: Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 173 year: '2017' ... --- _id: '1169' abstract: - lang: eng text: Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies. article_processing_charge: No author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak orcid: 0000-0002-2519-824X - first_name: Richard full_name: Kollár, Richard last_name: Kollár citation: ama: Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946 apa: Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946 chicago: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193946. ieee: S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017. ista: Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374. mla: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:10.1534/genetics.116.193946. short: S. Novak, R. Kollár, Genetics 205 (2017) 367–374. date_created: 2018-12-11T11:50:31Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:24:21Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1534/genetics.116.193946 ec_funded: 1 external_id: isi: - '000393677300025' file: - access_level: open_access checksum: 7c8ab79cda1f92760bbbbe0f53175bfc content_type: application/pdf creator: system date_created: 2018-12-12T10:10:43Z date_updated: 2020-07-14T12:44:37Z file_id: '4833' file_name: IST-2016-727-v1+1_SFC_Genetics_final.pdf file_size: 361500 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 205' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 367 - 374 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_identifier: issn: - '00166731' publication_status: published publisher: Genetics Society of America publist_id: '6188' pubrep_id: '727' quality_controlled: '1' scopus_import: '1' status: public title: Spatial gene frequency waves under genotype dependent dispersal type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 205 year: '2017' ... --- _id: '1160' abstract: - lang: eng text: 'We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined be-tween two concentric independently rotating cylinders - consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying out systematic bifurcation analysis. Without magnetic field, we find steady flow patterns, previously observed with a simple fluid, such as those containing normal one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states. However, when a symmetry-breaking transverse magnetic field is present, all flow states exhibit stimulated, finite two-fold mode. Various bifurcations between steady and unsteady states can occur, corresponding to the transitions between the two-cell and one-cell states. While unsteady, axially oscillating flow states can arise, we also detect the emergence of new unsteady flow states. In particular, we uncover two new states: one contains only the azimuthally oscillating solution in the configuration of the twin-cell flow state, and an-other a rotating flow state. Topologically, these flow states are a limit cycle and a quasiperiodic solution on a two-torus, respectively. Emergence of new flow states in addition to observed ones with classical fluid, indicates that richer but potentially more controllable dynamics in ferrofluidic flows, as such flow states depend on the external magnetic field.' article_number: '40012' article_processing_charge: No author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Ying full_name: Lai, Ying last_name: Lai citation: ama: Altmeyer S, Do Y, Lai Y. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. 2017;7. doi:10.1038/srep40012 apa: Altmeyer, S., Do, Y., & Lai, Y. (2017). Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep40012 chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep40012. ieee: S. Altmeyer, Y. Do, and Y. Lai, “Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio,” Scientific Reports, vol. 7. Nature Publishing Group, 2017. ista: Altmeyer S, Do Y, Lai Y. 2017. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. 7, 40012. mla: Altmeyer, Sebastian, et al. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports, vol. 7, 40012, Nature Publishing Group, 2017, doi:10.1038/srep40012. short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 7 (2017). date_created: 2018-12-11T11:50:28Z date_published: 2017-01-06T00:00:00Z date_updated: 2023-09-20T11:28:49Z day: '06' ddc: - '532' department: - _id: BjHo doi: 10.1038/srep40012 external_id: isi: - '000391269700001' file: - access_level: open_access checksum: 694aa70399444570825099c1a7ec91f2 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:16Z date_updated: 2020-07-14T12:44:36Z file_id: '4802' file_name: IST-2017-743-v1+1_srep40012.pdf file_size: 4546835 relation: main_file file_date_updated: 2020-07-14T12:44:36Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: issn: - '20452322' publication_status: published publisher: Nature Publishing Group publist_id: '6198' pubrep_id: '743' quality_controlled: '1' scopus_import: '1' status: public title: Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1162' abstract: - lang: eng text: Selected universal experimental properties of high-temperature superconducting (HTS) cuprates have been singled out in the last decade. One of the pivotal challenges in this field is the designation of a consistent interpretation framework within which we can describe quantitatively the universal features of those systems. Here we analyze in a detailed manner the principal experimental data and compare them quantitatively with the approach based on a single-band model of strongly correlated electrons supplemented with strong antiferromagnetic (super)exchange interaction (the so-called t−J−U model). The model rationale is provided by estimating its microscopic parameters on the basis of the three-band approach for the Cu-O plane. We use our original full Gutzwiller wave-function solution by going beyond the renormalized mean-field theory (RMFT) in a systematic manner. Our approach reproduces very well the observed hole doping (δ) dependence of the kinetic-energy gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer features of the cuprates. The calculated Fermi velocity in the nodal direction is practically δ-independent and its universal value agrees very well with that determined experimentally. Also, a weak doping dependence of the Fermi wave vector leads to an almost constant value of the effective mass in a pure superconducting phase which is both observed in experiment and reproduced within our approach. An assessment of the currently used models (t−J, Hubbard) is carried out and the results of the canonical RMFT as a zeroth-order solution are provided for comparison to illustrate the necessity of the introduced higher-order contributions. article_number: '024506' article_processing_charge: No author: - first_name: Jozef full_name: Spałek, Jozef last_name: Spałek - first_name: Michał full_name: Zegrodnik, Michał last_name: Zegrodnik - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 citation: ama: Spałek J, Zegrodnik M, Kaczmarczyk J. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. 2017;95(2). doi:10.1103/PhysRevB.95.024506 apa: Spałek, J., Zegrodnik, M., & Kaczmarczyk, J. (2017). Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.95.024506 chicago: Spałek, Jozef, Michał Zegrodnik, and Jan Kaczmarczyk. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.024506. ieee: J. Spałek, M. Zegrodnik, and J. Kaczmarczyk, “Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment,” Physical Review B - Condensed Matter and Materials Physics, vol. 95, no. 2. American Physical Society, 2017. ista: Spałek J, Zegrodnik M, Kaczmarczyk J. 2017. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. 95(2), 024506. mla: Spałek, Jozef, et al. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter and Materials Physics, vol. 95, no. 2, 024506, American Physical Society, 2017, doi:10.1103/PhysRevB.95.024506. short: J. Spałek, M. Zegrodnik, J. Kaczmarczyk, Physical Review B - Condensed Matter and Materials Physics 95 (2017). date_created: 2018-12-11T11:50:29Z date_published: 2017-01-13T00:00:00Z date_updated: 2023-09-20T11:25:56Z day: '13' department: - _id: MiLe doi: 10.1103/PhysRevB.95.024506 ec_funded: 1 external_id: isi: - '000391852800006' intvolume: ' 95' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.03247 month: '01' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - '24699950' publication_status: published publisher: American Physical Society publist_id: '6195' quality_controlled: '1' scopus_import: '1' status: public title: Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 95 year: '2017' ... --- _id: '1152' abstract: - lang: eng text: We propose a new memetic strategy that can solve the multi-physics, complex inverse problems, formulated as the multi-objective optimization ones, in which objectives are misfits between the measured and simulated states of various governing processes. The multi-deme structure of the strategy allows for both, intensive, relatively cheap exploration with a moderate accuracy and more accurate search many regions of Pareto set in parallel. The special type of selection operator prefers the coherent alternative solutions, eliminating artifacts appearing in the particular processes. The additional accuracy increment is obtained by the parallel convex searches applied to the local scalarizations of the misfit vector. The strategy is dedicated for solving ill-conditioned problems, for which inverting the single physical process can lead to the ambiguous results. The skill of the selection in artifact elimination is shown on the benchmark problem, while the whole strategy was applied for identification of oil deposits, where the misfits are related to various frequencies of the magnetic and electric waves of the magnetotelluric measurements. 2016 Elsevier B.V. article_processing_charge: No author: - first_name: Ewa P full_name: Gajda-Zagorska, Ewa P id: 47794CF0-F248-11E8-B48F-1D18A9856A87 last_name: Gajda-Zagorska - first_name: Robert full_name: Schaefer, Robert last_name: Schaefer - first_name: Maciej full_name: Smołka, Maciej last_name: Smołka - first_name: David full_name: Pardo, David last_name: Pardo - first_name: Julen full_name: Alvarez Aramberri, Julen last_name: Alvarez Aramberri citation: ama: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. 2017;18:85-94. doi:10.1016/j.jocs.2016.06.007 apa: Gajda-Zagorska, E. P., Schaefer, R., Smołka, M., Pardo, D., & Alvarez Aramberri, J. (2017). A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.06.007 chicago: Gajda-Zagorska, Ewa P, Robert Schaefer, Maciej Smołka, David Pardo, and Julen Alvarez Aramberri. “A Multi Objective Memetic Inverse Solver Reinforced by Local Optimization Methods.” Journal of Computational Science. Elsevier, 2017. https://doi.org/10.1016/j.jocs.2016.06.007. ieee: E. P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, and J. Alvarez Aramberri, “A multi objective memetic inverse solver reinforced by local optimization methods,” Journal of Computational Science, vol. 18. Elsevier, pp. 85–94, 2017. ista: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. 2017. A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. 18, 85–94. mla: Gajda-Zagorska, Ewa P., et al. “A Multi Objective Memetic Inverse Solver Reinforced by Local Optimization Methods.” Journal of Computational Science, vol. 18, Elsevier, 2017, pp. 85–94, doi:10.1016/j.jocs.2016.06.007. short: E.P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, J. Alvarez Aramberri, Journal of Computational Science 18 (2017) 85–94. date_created: 2018-12-11T11:50:26Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:29:44Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1016/j.jocs.2016.06.007 external_id: isi: - '000393528700009' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-01-18T08:43:16Z date_updated: 2019-01-18T08:43:16Z file_id: '5842' file_name: 2016_jocs_ewa.pdf file_size: 1083911 relation: main_file success: 1 file_date_updated: 2019-01-18T08:43:16Z has_accepted_license: '1' intvolume: ' 18' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 85 - 94 publication: Journal of Computational Science publication_identifier: issn: - '18777503' publication_status: published publisher: Elsevier publist_id: '6206' quality_controlled: '1' scopus_import: '1' status: public title: A multi objective memetic inverse solver reinforced by local optimization methods type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 18 year: '2017' ... --- _id: '1168' abstract: - lang: eng text: Optimum experimental design theory has recently been extended for parameter estimation in copula models. The use of these models allows one to gain in flexibility by considering the model parameter set split into marginal and dependence parameters. However, this separation also leads to the natural issue of estimating only a subset of all model parameters. In this work, we treat this problem with the application of the (Formula presented.)-optimality to copula models. First, we provide an extension of the corresponding equivalence theory. Then, we analyze a wide range of flexible copula models to highlight the usefulness of (Formula presented.)-optimality in many possible scenarios. Finally, we discuss how the usage of the introduced design criterion also relates to the more general issue of copula selection and optimal design for model discrimination. acknowledgement: 'This work has been supported by the project ANR-2011-IS01-001-01 “DESIRE” and Austrian Science Fund (FWF) I833-N18. Open access funding is provided by the Austrian Science Fund (FWF). ' article_processing_charge: No author: - first_name: Elisa full_name: Perrone, Elisa id: 2A5F8724-F248-11E8-B48F-1D18A9856A87 last_name: Perrone orcid: 0000-0003-0370-9835 - first_name: Andreas full_name: Rappold, Andreas last_name: Rappold - first_name: Werner full_name: Müller, Werner last_name: Müller citation: ama: Perrone E, Rappold A, Müller W. D inf s optimality in copula models. Statistical Methods and Applications. 2017;26(3):403-418. doi:10.1007/s10260-016-0375-6 apa: Perrone, E., Rappold, A., & Müller, W. (2017). D inf s optimality in copula models. Statistical Methods and Applications. Springer. https://doi.org/10.1007/s10260-016-0375-6 chicago: Perrone, Elisa, Andreas Rappold, and Werner Müller. “D Inf s Optimality in Copula Models.” Statistical Methods and Applications. Springer, 2017. https://doi.org/10.1007/s10260-016-0375-6. ieee: E. Perrone, A. Rappold, and W. Müller, “D inf s optimality in copula models,” Statistical Methods and Applications, vol. 26, no. 3. Springer, pp. 403–418, 2017. ista: Perrone E, Rappold A, Müller W. 2017. D inf s optimality in copula models. Statistical Methods and Applications. 26(3), 403–418. mla: Perrone, Elisa, et al. “D Inf s Optimality in Copula Models.” Statistical Methods and Applications, vol. 26, no. 3, Springer, 2017, pp. 403–18, doi:10.1007/s10260-016-0375-6. short: E. Perrone, A. Rappold, W. Müller, Statistical Methods and Applications 26 (2017) 403–418. date_created: 2018-12-11T11:50:31Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-09-20T11:25:09Z day: '01' ddc: - '519' department: - _id: CaUh doi: 10.1007/s10260-016-0375-6 external_id: isi: - '000407973200004' file: - access_level: open_access checksum: 0b2d1b647ca96e9ef13a14b8b6775e0f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:13Z date_updated: 2020-07-14T12:44:37Z file_id: '5199' file_name: IST-2017-739-v1+2_10260_2016_375_MOESM1_ESM.pdf file_size: 56664 relation: main_file - access_level: open_access checksum: 3321ef34e02e28acfc427f77cf32812a content_type: application/pdf creator: system date_created: 2018-12-12T10:16:14Z date_updated: 2020-07-14T12:44:37Z file_id: '5200' file_name: IST-2017-739-v1+3_s10260-016-0375-6.pdf file_size: 688953 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 403 - 418 publication: Statistical Methods and Applications publication_status: published publisher: Springer publist_id: '6189' pubrep_id: '739' quality_controlled: '1' scopus_import: '1' status: public title: D inf s optimality in copula models tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 26 year: '2017' ... --- _id: '1163' abstract: - lang: eng text: 'We investigate the effect of the electron-hole (e-h) symmetry breaking on d-wave superconductivity induced by non-local effects of correlations in the generalized Hubbard model. The symmetry breaking is introduced in a two-fold manner: by the next-to-nearest neighbor hopping of electrons and by the charge-bond interaction - the off-diagonal term of the Coulomb potential. Both terms lead to a pronounced asymmetry of the superconducting order parameter. The next-to-nearest neighbor hopping enhances superconductivity for h-doping, while diminishes it for e-doping. The charge-bond interaction alone leads to the opposite effect and, additionally, to the kinetic-energy gain upon condensation in the underdoped regime. With both terms included, with similar amplitudes, the height of the superconducting dome and the critical doping remain in favor of h-doping. The influence of the charge-bond interaction on deviations from symmetry of the shape of the gap at the Fermi surface in the momentum space is briefly discussed.' article_number: '085604' article_processing_charge: No author: - first_name: Marcin full_name: Wysokiński, Marcin last_name: Wysokiński - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 citation: ama: 'Wysokiński M, Kaczmarczyk J. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. 2017;29(8). doi:10.1088/1361-648X/aa532f' apa: 'Wysokiński, M., & Kaczmarczyk, J. (2017). Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/1361-648X/aa532f' chicago: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2017. https://doi.org/10.1088/1361-648X/aa532f.' ieee: 'M. Wysokiński and J. Kaczmarczyk, “Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms,” Journal of Physics: Condensed Matter, vol. 29, no. 8. IOP Publishing Ltd., 2017.' ista: 'Wysokiński M, Kaczmarczyk J. 2017. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. 29(8), 085604.' mla: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal of Physics: Condensed Matter, vol. 29, no. 8, 085604, IOP Publishing Ltd., 2017, doi:10.1088/1361-648X/aa532f.' short: 'M. Wysokiński, J. Kaczmarczyk, Journal of Physics: Condensed Matter 29 (2017).' date_created: 2018-12-11T11:50:29Z date_published: 2017-01-16T00:00:00Z date_updated: 2023-09-20T11:25:32Z day: '16' department: - _id: MiLe doi: 10.1088/1361-648X/aa532f ec_funded: 1 external_id: isi: - '000393955500001' intvolume: ' 29' isi: 1 issue: '8' language: - iso: eng month: '01' oa_version: None project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Journal of Physics: Condensed Matter' publication_identifier: issn: - '09538984' publication_status: published publisher: IOP Publishing Ltd. publist_id: '6194' quality_controlled: '1' scopus_import: '1' status: public title: Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 29 year: '2017' ... --- _id: '1173' abstract: - lang: eng text: We introduce the Voronoi functional of a triangulation of a finite set of points in the Euclidean plane and prove that among all geometric triangulations of the point set, the Delaunay triangulation maximizes the functional. This result neither extends to topological triangulations in the plane nor to geometric triangulations in three and higher dimensions. acknowledgement: This research is partially supported by the Russian Government under the Mega Project 11.G34.31.0053, by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by RFBR grant 11-01-00735, and by NSF grants DMS-1101688, DMS-1400876. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Alexey full_name: Glazyrin, Alexey last_name: Glazyrin - first_name: Oleg full_name: Musin, Oleg last_name: Musin - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Edelsbrunner H, Glazyrin A, Musin O, Nikitenko A. The Voronoi functional is maximized by the Delaunay triangulation in the plane. Combinatorica. 2017;37(5):887-910. doi:10.1007/s00493-016-3308-y apa: Edelsbrunner, H., Glazyrin, A., Musin, O., & Nikitenko, A. (2017). The Voronoi functional is maximized by the Delaunay triangulation in the plane. Combinatorica. Springer. https://doi.org/10.1007/s00493-016-3308-y chicago: Edelsbrunner, Herbert, Alexey Glazyrin, Oleg Musin, and Anton Nikitenko. “The Voronoi Functional Is Maximized by the Delaunay Triangulation in the Plane.” Combinatorica. Springer, 2017. https://doi.org/10.1007/s00493-016-3308-y. ieee: H. Edelsbrunner, A. Glazyrin, O. Musin, and A. Nikitenko, “The Voronoi functional is maximized by the Delaunay triangulation in the plane,” Combinatorica, vol. 37, no. 5. Springer, pp. 887–910, 2017. ista: Edelsbrunner H, Glazyrin A, Musin O, Nikitenko A. 2017. The Voronoi functional is maximized by the Delaunay triangulation in the plane. Combinatorica. 37(5), 887–910. mla: Edelsbrunner, Herbert, et al. “The Voronoi Functional Is Maximized by the Delaunay Triangulation in the Plane.” Combinatorica, vol. 37, no. 5, Springer, 2017, pp. 887–910, doi:10.1007/s00493-016-3308-y. short: H. Edelsbrunner, A. Glazyrin, O. Musin, A. Nikitenko, Combinatorica 37 (2017) 887–910. date_created: 2018-12-11T11:50:32Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-20T11:23:53Z day: '01' department: - _id: HeEd doi: 10.1007/s00493-016-3308-y ec_funded: 1 external_id: isi: - '000418056000005' intvolume: ' 37' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1411.6337 month: '10' oa: 1 oa_version: Submitted Version page: 887 - 910 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Combinatorica publication_identifier: issn: - '02099683' publication_status: published publisher: Springer publist_id: '6182' quality_controlled: '1' scopus_import: '1' status: public title: The Voronoi functional is maximized by the Delaunay triangulation in the plane type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2017' ... --- _id: '1161' abstract: - lang: eng text: Coordinated changes of cell shape are often the result of the excitable, wave-like dynamics of the actin cytoskeleton. New work shows that, in migrating cells, protrusion waves arise from mechanochemical crosstalk between adhesion sites, membrane tension and the actin protrusive machinery. article_processing_charge: No author: - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Müller J, Sixt MK. Cell migration: Making the waves. Current Biology. 2017;27(1):R24-R25. doi:10.1016/j.cub.2016.11.035' apa: 'Müller, J., & Sixt, M. K. (2017). Cell migration: Making the waves. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2016.11.035' chicago: 'Müller, Jan, and Michael K Sixt. “Cell Migration: Making the Waves.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2016.11.035.' ieee: 'J. Müller and M. K. Sixt, “Cell migration: Making the waves,” Current Biology, vol. 27, no. 1. Cell Press, pp. R24–R25, 2017.' ista: 'Müller J, Sixt MK. 2017. Cell migration: Making the waves. Current Biology. 27(1), R24–R25.' mla: 'Müller, Jan, and Michael K. Sixt. “Cell Migration: Making the Waves.” Current Biology, vol. 27, no. 1, Cell Press, 2017, pp. R24–25, doi:10.1016/j.cub.2016.11.035.' short: J. Müller, M.K. Sixt, Current Biology 27 (2017) R24–R25. date_created: 2018-12-11T11:50:29Z date_published: 2017-01-09T00:00:00Z date_updated: 2023-09-20T11:28:19Z day: '09' department: - _id: MiSi doi: 10.1016/j.cub.2016.11.035 external_id: isi: - '000391902500010' intvolume: ' 27' isi: 1 issue: '1' language: - iso: eng month: '01' oa_version: None page: R24 - R25 publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press publist_id: '6197' quality_controlled: '1' scopus_import: '1' status: public title: 'Cell migration: Making the waves' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 27 year: '2017' ... --- _id: '1116' abstract: - lang: eng text: "Time-triggered switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. Due to the criticality of the applications running over them, developers need to ensure that end-to-end communication is dependable and predictable. Traditional approaches assume static networks that are not flexible to changes caused by reconfigurations or, more importantly, faults, which are dealt with in the application using redundancy. We adopt the concept of handling faults in the switches from non-real-time networks while maintaining the required predictability. \r\n\r\nWe study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. We study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. For a given network with a forwarding scheme and a constant ℓ, we compute the {\\em score} of the scheme, namely the probability (induced by faults) that at least ℓ messages arrive on time. We reduce the scoring problem to a reachability problem on a Markov chain with a "product-like" structure. Its special structure allows us to reason about it symbolically, and reduce the scoring problem to #SAT. Our solution is generic and can be adapted to different networks and other contexts. Also, we show the computational complexity of the scoring problem is #P-complete, and we study methods to estimate the score. We evaluate the effectiveness of our techniques with an implementation. " alternative_title: - LNCS article_processing_charge: No author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Shubham full_name: Goel, Shubham last_name: Goel - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Guillermo full_name: Rodríguez Navas, Guillermo last_name: Rodríguez Navas citation: ama: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. Computing scores of forwarding schemes in switched networks with probabilistic faults. In: Vol 10206. Springer; 2017:169-187. doi:10.1007/978-3-662-54580-5_10' apa: 'Avni, G., Goel, S., Henzinger, T. A., & Rodríguez Navas, G. (2017). Computing scores of forwarding schemes in switched networks with probabilistic faults (Vol. 10206, pp. 169–187). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54580-5_10' chicago: Avni, Guy, Shubham Goel, Thomas A Henzinger, and Guillermo Rodríguez Navas. “Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults,” 10206:169–87. Springer, 2017. https://doi.org/10.1007/978-3-662-54580-5_10. ieee: 'G. Avni, S. Goel, T. A. Henzinger, and G. Rodríguez Navas, “Computing scores of forwarding schemes in switched networks with probabilistic faults,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10206, pp. 169–187.' ista: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. 2017. Computing scores of forwarding schemes in switched networks with probabilistic faults. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10206, 169–187.' mla: Avni, Guy, et al. Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults. Vol. 10206, Springer, 2017, pp. 169–87, doi:10.1007/978-3-662-54580-5_10. short: G. Avni, S. Goel, T.A. Henzinger, G. Rodríguez Navas, in:, Springer, 2017, pp. 169–187. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2017-04-22 date_created: 2018-12-11T11:50:14Z date_published: 2017-03-31T00:00:00Z date_updated: 2023-09-20T11:32:43Z day: '31' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-662-54580-5_10 external_id: isi: - '000440733400010' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:08:37Z date_updated: 2018-12-12T10:08:37Z file_id: '4698' file_name: IST-2017-758-v1+1_tacas-cr.pdf file_size: 321800 relation: main_file file_date_updated: 2018-12-12T10:08:37Z has_accepted_license: '1' intvolume: ' 10206' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 169 - 187 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6246' pubrep_id: '758' quality_controlled: '1' scopus_import: '1' status: public title: Computing scores of forwarding schemes in switched networks with probabilistic faults type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10206 year: '2017' ... --- _id: '1118' abstract: - lang: eng text: Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation during non-rapid eye movement sleep, immobility, and consummatory behavior. However, whether temporally modulated synaptic excitation or inhibition underlies the ripples is controversial. To address this question, we performed simultaneous recordings of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs, inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5. Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition, but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo. acknowledged_ssus: - _id: M-Shop - _id: ScienComp - _id: PreCl article_processing_charge: No author: - first_name: Jian full_name: Gan, Jian id: 3614E438-F248-11E8-B48F-1D18A9856A87 last_name: Gan - first_name: Shih-Ming full_name: Weng, Shih-Ming id: 2F9C5AC8-F248-11E8-B48F-1D18A9856A87 last_name: Weng - first_name: Alejandro full_name: Pernia-Andrade, Alejandro id: 36963E98-F248-11E8-B48F-1D18A9856A87 last_name: Pernia-Andrade - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. 2017;93(2):308-314. doi:10.1016/j.neuron.2016.12.018 apa: Gan, J., Weng, S.-M., Pernia-Andrade, A., Csicsvari, J. L., & Jonas, P. M. (2017). Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.12.018 chicago: Gan, Jian, Shih-Ming Weng, Alejandro Pernia-Andrade, Jozsef L Csicsvari, and Peter M Jonas. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2016.12.018. ieee: J. Gan, S.-M. Weng, A. Pernia-Andrade, J. L. Csicsvari, and P. M. Jonas, “Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo,” Neuron, vol. 93, no. 2. Elsevier, pp. 308–314, 2017. ista: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. 2017. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. 93(2), 308–314. mla: Gan, Jian, et al. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” Neuron, vol. 93, no. 2, Elsevier, 2017, pp. 308–14, doi:10.1016/j.neuron.2016.12.018. short: J. Gan, S.-M. Weng, A. Pernia-Andrade, J.L. Csicsvari, P.M. Jonas, Neuron 93 (2017) 308–314. date_created: 2018-12-11T11:50:15Z date_published: 2017-01-18T00:00:00Z date_updated: 2023-09-20T11:31:48Z day: '18' ddc: - '571' department: - _id: PeJo - _id: JoCs doi: 10.1016/j.neuron.2016.12.018 ec_funded: 1 external_id: isi: - '000396428200010' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:08:56Z date_updated: 2018-12-12T10:08:56Z file_id: '4719' file_name: IST-2017-752-v1+1_1-s2.0-S0896627316309606-main.pdf file_size: 2738950 relation: main_file file_date_updated: 2018-12-12T10:08:56Z has_accepted_license: '1' intvolume: ' 93' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 308 - 314 project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: Neuron publication_status: published publisher: Elsevier publist_id: '6244' pubrep_id: '752' quality_controlled: '1' scopus_import: '1' status: public title: Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 93 year: '2017' ... --- _id: '1117' abstract: - lang: eng text: 'GABAergic synapses in brain circuits generate inhibitory output signals with submillisecond latency and temporal precision. Whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Here, we examined the Ca^2+ sensor of exocytosis at GABAergic basket cell (BC) to Purkinje cell (PC) synapses in cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ∼10%, identifying Syt2 as the major Ca^2+ sensor at BC-PC synapses. Differential adenovirus-mediated rescue revealed that Syt2 triggered release with shorter latency and higher temporal precision and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as release sensor at BC-PC synapses ensures fast and efficient feedforward inhibition in cerebellar microcircuits. #bioimagingfacility-author' acknowledged_ssus: - _id: Bio - _id: PreCl article_processing_charge: No author: - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Itaru full_name: Arai, Itaru id: 32A73F6C-F248-11E8-B48F-1D18A9856A87 last_name: Arai - first_name: Rachel full_name: Satterield, Rachel last_name: Satterield - first_name: Samuel full_name: Young, Samuel last_name: Young - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 2017;18(3):723-736. doi:10.1016/j.celrep.2016.12.067 apa: Chen, C., Arai, itaru, Satterield, R., Young, S., & Jonas, P. M. (2017). Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.12.067 chicago: Chen, Chong, itaru Arai, Rachel Satterield, Samuel Young, and Peter M Jonas. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2016.12.067. ieee: C. Chen, itaru Arai, R. Satterield, S. Young, and P. M. Jonas, “Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse,” Cell Reports, vol. 18, no. 3. Cell Press, pp. 723–736, 2017. ista: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. 2017. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 18(3), 723–736. mla: Chen, Chong, et al. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell Reports, vol. 18, no. 3, Cell Press, 2017, pp. 723–36, doi:10.1016/j.celrep.2016.12.067. short: C. Chen, itaru Arai, R. Satterield, S. Young, P.M. Jonas, Cell Reports 18 (2017) 723–736. date_created: 2018-12-11T11:50:14Z date_published: 2017-01-17T00:00:00Z date_updated: 2023-09-20T11:32:15Z day: '17' ddc: - '571' department: - _id: PeJo doi: 10.1016/j.celrep.2016.12.067 ec_funded: 1 external_id: isi: - '000396470600013' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:09Z date_updated: 2018-12-12T10:16:09Z file_id: '5195' file_name: IST-2017-751-v1+1_1-s2.0-S2211124716317740-main.pdf file_size: 4427591 relation: main_file file_date_updated: 2018-12-12T10:16:09Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '3' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 723 - 736 project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: Cell Reports publication_identifier: issn: - '22111247' publication_status: published publisher: Cell Press publist_id: '6245' pubrep_id: '751' quality_controlled: '1' related_material: record: - id: '324' relation: dissertation_contains status: public scopus_import: '1' status: public title: Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 18 year: '2017' ... --- _id: '1132' abstract: - lang: eng text: The hippocampus is thought to initiate systems-wide mnemonic processes through the reactivation of previously acquired spatial and episodic memory traces, which can recruit the entorhinal cortex as a first stage of memory redistribution to other brain areas. Hippocampal reactivation occurs during sharp wave-ripples, in which synchronous network firing encodes sequences of places.We investigated the coordination of this replay by recording assembly activity simultaneously in the CA1 region of the hippocampus and superficial layers of the medial entorhinal cortex. We found that entorhinal cell assemblies can replay trajectories independently of the hippocampus and sharp wave-ripples. This suggests that the hippocampus is not the sole initiator of spatial and episodic memory trace reactivation. Memory systems involved in these processes may include nonhierarchical, parallel components. article_processing_charge: No author: - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Charlotte full_name: Boccara, Charlotte id: 3FC06552-F248-11E8-B48F-1D18A9856A87 last_name: Boccara orcid: 0000-0001-7237-5109 - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: O’Neill J, Boccara CN, Stella F, Schönenberger P, Csicsvari JL. Superficial layers of the medial entorhinal cortex replay independently of the hippocampus. Science. 2017;355(6321):184-188. doi:10.1126/science.aag2787 apa: O’Neill, J., Boccara, C. N., Stella, F., Schönenberger, P., & Csicsvari, J. L. (2017). Superficial layers of the medial entorhinal cortex replay independently of the hippocampus. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag2787 chicago: O’Neill, Joseph, Charlotte N. Boccara, Federico Stella, Philipp Schönenberger, and Jozsef L Csicsvari. “Superficial Layers of the Medial Entorhinal Cortex Replay Independently of the Hippocampus.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aag2787. ieee: J. O’Neill, C. N. Boccara, F. Stella, P. Schönenberger, and J. L. Csicsvari, “Superficial layers of the medial entorhinal cortex replay independently of the hippocampus,” Science, vol. 355, no. 6321. American Association for the Advancement of Science, pp. 184–188, 2017. ista: O’Neill J, Boccara CN, Stella F, Schönenberger P, Csicsvari JL. 2017. Superficial layers of the medial entorhinal cortex replay independently of the hippocampus. Science. 355(6321), 184–188. mla: O’Neill, Joseph, et al. “Superficial Layers of the Medial Entorhinal Cortex Replay Independently of the Hippocampus.” Science, vol. 355, no. 6321, American Association for the Advancement of Science, 2017, pp. 184–88, doi:10.1126/science.aag2787. short: J. O’Neill, C.N. Boccara, F. Stella, P. Schönenberger, J.L. Csicsvari, Science 355 (2017) 184–188. date_created: 2018-12-11T11:50:19Z date_published: 2017-01-13T00:00:00Z date_updated: 2023-09-20T11:30:35Z day: '13' ddc: - '571' department: - _id: JoCs doi: 10.1126/science.aag2787 ec_funded: 1 external_id: isi: - '000391743700044' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:10:22Z date_updated: 2018-12-12T10:10:22Z file_id: '4809' file_name: IST-2018-976-v1+1_2017Preprint_ONeill_Superficial_layers.pdf file_size: 3761201 relation: main_file file_date_updated: 2018-12-12T10:10:22Z has_accepted_license: '1' intvolume: ' 355' isi: 1 issue: '6321' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 184 - 188 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex publication: Science publication_identifier: issn: - '00368075' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6226' pubrep_id: '976' quality_controlled: '1' scopus_import: '1' status: public title: Superficial layers of the medial entorhinal cortex replay independently of the hippocampus type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 355 year: '2017' ... --- _id: '1120' abstract: - lang: eng text: 'The existence of a self-localization transition in the polaron problem has been under an active debate ever since Landau suggested it 83 years ago. Here we reveal the self-localization transition for the rotational analogue of the polaron -- the angulon quasiparticle. We show that, unlike for the polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of the symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. The predicted effects can potentially be addressed in experiments on cold molecules trapped in superfluid helium droplets and ultracold quantum gases, as well as on electronic excitations in solids and Bose-Einstein condensates. ' article_number: '033608' article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Li X, Seiringer R, Lemeshko M. Angular self-localization of impurities rotating in a bosonic bath. Physical Review A. 2017;95(3). doi:10.1103/PhysRevA.95.033608 apa: Li, X., Seiringer, R., & Lemeshko, M. (2017). Angular self-localization of impurities rotating in a bosonic bath. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.95.033608 chicago: Li, Xiang, Robert Seiringer, and Mikhail Lemeshko. “Angular Self-Localization of Impurities Rotating in a Bosonic Bath.” Physical Review A. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.033608. ieee: X. Li, R. Seiringer, and M. Lemeshko, “Angular self-localization of impurities rotating in a bosonic bath,” Physical Review A, vol. 95, no. 3. American Physical Society, 2017. ista: Li X, Seiringer R, Lemeshko M. 2017. Angular self-localization of impurities rotating in a bosonic bath. Physical Review A. 95(3), 033608. mla: Li, Xiang, et al. “Angular Self-Localization of Impurities Rotating in a Bosonic Bath.” Physical Review A, vol. 95, no. 3, 033608, American Physical Society, 2017, doi:10.1103/PhysRevA.95.033608. short: X. Li, R. Seiringer, M. Lemeshko, Physical Review A 95 (2017). date_created: 2018-12-11T11:50:15Z date_published: 2017-03-06T00:00:00Z date_updated: 2023-09-20T11:30:58Z day: '06' department: - _id: MiLe - _id: RoSe doi: 10.1103/PhysRevA.95.033608 ec_funded: 1 external_id: isi: - '000395981900009' intvolume: ' 95' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.04908 month: '03' oa: 1 oa_version: Published Version project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review A publication_identifier: issn: - '24699926' publication_status: published publisher: American Physical Society publist_id: '6242' quality_controlled: '1' related_material: record: - id: '8958' relation: dissertation_contains status: public scopus_import: '1' status: public title: Angular self-localization of impurities rotating in a bosonic bath type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 95 year: '2017' ... --- _id: '1133' abstract: - lang: eng text: 'It is a common knowledge that an effective interaction of a quantum impurity with an electromagnetic field can be screened by surrounding charge carriers, whether mobile or static. Here we demonstrate that very strong, "anomalous" screening can take place in the presence of a neutral, weakly polarizable environment, due to an exchange of orbital angular momentum between the impurity and the bath. Furthermore, we show that it is possible to generalize all phenomena related to isolated impurities in an external field to the case when a many-body environment is present, by casting the problem in terms of the angulon quasiparticle. As a result, the relevant observables such as the effective Rabi frequency, geometric phase, and impurity spatial alignment are straightforward to evaluate in terms of a single parameter: the angular-momentum-dependent screening factor.' article_number: '085302' article_processing_charge: No author: - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Yakaboylu E, Lemeshko M. Anomalous screening of quantum impurities by a neutral environment. Physical Review Letters. 2017;118(8). doi:10.1103/PhysRevLett.118.085302 apa: Yakaboylu, E., & Lemeshko, M. (2017). Anomalous screening of quantum impurities by a neutral environment. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.085302 chicago: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anomalous Screening of Quantum Impurities by a Neutral Environment.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.085302. ieee: E. Yakaboylu and M. Lemeshko, “Anomalous screening of quantum impurities by a neutral environment,” Physical Review Letters, vol. 118, no. 8. American Physical Society, 2017. ista: Yakaboylu E, Lemeshko M. 2017. Anomalous screening of quantum impurities by a neutral environment. Physical Review Letters. 118(8), 085302. mla: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anomalous Screening of Quantum Impurities by a Neutral Environment.” Physical Review Letters, vol. 118, no. 8, 085302, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.085302. short: E. Yakaboylu, M. Lemeshko, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:50:19Z date_published: 2017-02-22T00:00:00Z date_updated: 2023-09-20T11:30:08Z day: '22' department: - _id: MiLe doi: 10.1103/PhysRevLett.118.085302 ec_funded: 1 external_id: isi: - '000394667600003' intvolume: ' 118' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.02820 month: '02' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_identifier: issn: - '00319007' publication_status: published publisher: American Physical Society publist_id: '6225' quality_controlled: '1' scopus_import: '1' status: public title: Anomalous screening of quantum impurities by a neutral environment type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1119' abstract: - lang: eng text: Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently-predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)]. Most importantly, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle. article_number: '095301' article_processing_charge: No author: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Lemeshko M. Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. 2017;118(9). doi:10.1103/PhysRevLett.118.095301 apa: Lemeshko, M. (2017). Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.095301 chicago: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum Solvents.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.095301. ieee: M. Lemeshko, “Quasiparticle approach to molecules interacting with quantum solvents,” Physical Review Letters, vol. 118, no. 9. American Physical Society, 2017. ista: Lemeshko M. 2017. Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. 118(9), 095301. mla: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum Solvents.” Physical Review Letters, vol. 118, no. 9, 095301, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.095301. short: M. Lemeshko, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:50:15Z date_published: 2017-02-27T00:00:00Z date_updated: 2023-09-20T11:31:22Z day: '27' department: - _id: MiLe doi: 10.1103/PhysRevLett.118.095301 external_id: isi: - '000404769200006' intvolume: ' 118' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.01604 month: '02' oa: 1 oa_version: Submitted Version project: - _id: 25636330-B435-11E9-9278-68D0E5697425 grant_number: 11-NSF-1070 name: ROOTS Genome-wide Analysis of Root Traits publication: Physical Review Letters publication_identifier: issn: - '00319007' publication_status: published publisher: American Physical Society publist_id: '6243' quality_controlled: '1' status: public title: Quasiparticle approach to molecules interacting with quantum solvents type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1110' abstract: - lang: eng text: The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium. acknowledgement: European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S) [JF]. article_number: '41906' article_processing_charge: No author: - first_name: Benjamin full_name: Kuhn, Benjamin last_name: Kuhn - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Sanae full_name: Errafi, Sanae last_name: Errafi - first_name: Rahel full_name: Bucher, Rahel last_name: Bucher - first_name: Shibu full_name: Gupta, Shibu last_name: Gupta - first_name: Bibek full_name: Aryal, Bibek last_name: Aryal - first_name: Petre full_name: Dobrev, Petre last_name: Dobrev - first_name: Laurent full_name: Bigler, Laurent last_name: Bigler - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Christoph full_name: Ringli, Christoph last_name: Ringli citation: ama: Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 2017;7. doi:10.1038/srep41906 apa: Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli, C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906 chicago: Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta, Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906. ieee: B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,” Scientific Reports, vol. 7. Nature Publishing Group, 2017. ista: Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 7, 41906. mla: Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906. short: B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev, L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports 7 (2017). date_created: 2018-12-11T11:50:12Z date_published: 2017-02-06T00:00:00Z date_updated: 2023-09-20T11:35:35Z day: '06' ddc: - '581' department: - _id: JiFr doi: 10.1038/srep41906 ec_funded: 1 external_id: isi: - '000393367600001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:18:09Z date_updated: 2018-12-12T10:18:09Z file_id: '5328' file_name: IST-2017-803-v1+1_srep41906.pdf file_size: 1654496 relation: main_file file_date_updated: 2018-12-12T10:18:09Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Scientific Reports publication_identifier: issn: - '20452322' publication_status: published publisher: Nature Publishing Group publist_id: '6258' pubrep_id: '803' quality_controlled: '1' scopus_import: '1' status: public title: Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1104' abstract: - lang: eng text: In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems. article_number: '1964' article_processing_charge: No author: - first_name: Stephane full_name: Deny, Stephane last_name: Deny - first_name: Ulisse full_name: Ferrari, Ulisse last_name: Ferrari - first_name: Emilie full_name: Mace, Emilie last_name: Mace - first_name: Pierre full_name: Yger, Pierre last_name: Yger - first_name: Romain full_name: Caplette, Romain last_name: Caplette - first_name: Serge full_name: Picaud, Serge last_name: Picaud - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Olivier full_name: Marre, Olivier last_name: Marre citation: ama: Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y apa: Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y chicago: Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-02159-y. ieee: S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964. mla: Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y. short: S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:10Z date_published: 2017-12-06T00:00:00Z date_updated: 2023-09-20T11:41:19Z day: '06' ddc: - '571' department: - _id: GaTk doi: 10.1038/s41467-017-02159-y ec_funded: 1 external_id: isi: - '000417241200004' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:06Z date_updated: 2018-12-12T10:16:06Z file_id: '5191' file_name: IST-2018-921-v1+1_s41467-017-02159-y.pdf file_size: 2872887 relation: main_file file_date_updated: 2018-12-12T10:16:06Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25CD3DD2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '604102' name: Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6266' pubrep_id: '921' quality_controlled: '1' scopus_import: '1' status: public title: Multiplexed computations in retinal ganglion cells of a single type tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '1114' abstract: - lang: eng text: Nonequilibrium phase transitions exist in damped-driven open quantum systems when the continuous tuning of an external parameter leads to a transition between two robust steady states. In second-order transitions this change is abrupt at a critical point, whereas in first-order transitions the two phases can coexist in a critical hysteresis domain. Here, we report the observation of a first-order dissipative quantum phase transition in a driven circuit quantum electrodynamics system. It takes place when the photon blockade of the driven cavity-atom system is broken by increasing the drive power. The observed experimental signature is a bimodal phase space distribution with varying weights controlled by the drive strength. Our measurements show an improved stabilization of the classical attractors up to the millisecond range when the size of the quantum system is increased from one to three artificial atoms. The formation of such robust pointer states could be used for new quantum measurement schemes or to investigate multiphoton phases of finite-size, nonlinear, open quantum systems. article_number: '011012' article_processing_charge: Yes author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: András full_name: Dombi, András last_name: Dombi - first_name: András full_name: Vukics, András last_name: Vukics - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Peter full_name: Domokos, Peter last_name: Domokos citation: ama: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. Observation of the photon blockade breakdown phase transition. Physical Review X. 2017;7(1). doi:10.1103/PhysRevX.7.011012 apa: Fink, J. M., Dombi, A., Vukics, A., Wallraff, A., & Domokos, P. (2017). Observation of the photon blockade breakdown phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.7.011012 chicago: Fink, Johannes M, András Dombi, András Vukics, Andreas Wallraff, and Peter Domokos. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X. American Physical Society, 2017. https://doi.org/10.1103/PhysRevX.7.011012. ieee: J. M. Fink, A. Dombi, A. Vukics, A. Wallraff, and P. Domokos, “Observation of the photon blockade breakdown phase transition,” Physical Review X, vol. 7, no. 1. American Physical Society, 2017. ista: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. 2017. Observation of the photon blockade breakdown phase transition. Physical Review X. 7(1), 011012. mla: Fink, Johannes M., et al. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X, vol. 7, no. 1, 011012, American Physical Society, 2017, doi:10.1103/PhysRevX.7.011012. short: J.M. Fink, A. Dombi, A. Vukics, A. Wallraff, P. Domokos, Physical Review X 7 (2017). date_created: 2018-12-11T11:50:13Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:33:07Z day: '31' ddc: - '539' department: - _id: JoFi doi: 10.1103/PhysRevX.7.011012 external_id: isi: - '000397450500001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:12:52Z date_updated: 2018-12-12T10:12:52Z file_id: '4972' file_name: IST-2017-753-v1+1_PhysRevX.7.011012.pdf file_size: 1172926 relation: main_file file_date_updated: 2018-12-12T10:12:52Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Physical Review X publication_identifier: issn: - '21603308' publication_status: published publisher: American Physical Society publist_id: '6252' pubrep_id: '753' quality_controlled: '1' scopus_import: '1' status: public title: Observation of the photon blockade breakdown phase transition tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1111' abstract: - lang: eng text: Adaptation depends critically on the effects of new mutations and their dependency on the genetic background in which they occur. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape. We analyze populations in the weak-mutation regime and characterize the conditions that enable them to quickly reach the fitness peak as a function of the number of sites under selection. We show that for additive landscapes there is a critical selection strength enabling populations to reach high-fitness genotypes, regardless of the distribution of effects. This threshold scales with the number of sites under selection, effectively setting a limit to adaptation, and results from the inevitable increase in deleterious mutational pressure as the population adapts in a space of discrete genotypes. Furthermore, we show that for the class of all unimodal landscapes this condition is sufficient but not necessary for rapid adaptation, as in some highly epistatic landscapes the critical strength does not depend on the number of sites under selection; effectively removing this barrier to adaptation. article_processing_charge: No article_type: original author: - first_name: Jorge full_name: Heredia, Jorge last_name: Heredia - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340 apa: Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.189340 chicago: Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.189340. ieee: J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017. ista: Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825. mla: Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340. short: J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825. date_created: 2018-12-11T11:50:12Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:35:03Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.116.189340 ec_funded: 1 external_id: isi: - '000394144900025' pmid: - '27881471' intvolume: ' 205' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1534/genetics.116.189340 month: '02' oa: 1 oa_version: Published Version page: 803 - 825 pmid: 1 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Genetics publication_identifier: issn: - '00166731' publication_status: published publisher: Genetics Society of America publist_id: '6256' quality_controlled: '1' scopus_import: '1' status: public title: Selection limits to adaptive walks on correlated landscapes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 205 year: '2017' ... --- _id: '1109' abstract: - lang: eng text: 'Rotation of molecules embedded in He nanodroplets is explored by a combination of fs laser-induced alignment experiments and angulon quasiparticle theory. We demonstrate that at low fluence of the fs alignment pulse, the molecule and its solvation shell can be set into coherent collective rotation lasting long enough to form revivals. With increasing fluence, however, the revivals disappear -- instead, rotational dynamics as rapid as for an isolated molecule is observed during the first few picoseconds. Classical calculations trace this phenomenon to transient decoupling of the molecule from its He shell. Our results open novel opportunities for studying non-equilibrium solute-solvent dynamics and quantum thermalization. ' article_number: '203203' article_processing_charge: No author: - first_name: Benjamin full_name: Shepperson, Benjamin last_name: Shepperson - first_name: Anders full_name: Søndergaard, Anders last_name: Søndergaard - first_name: Lars full_name: Christiansen, Lars last_name: Christiansen - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Robert full_name: Zillich, Robert last_name: Zillich - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Henrik full_name: Stapelfeldt, Henrik last_name: Stapelfeldt citation: ama: 'Shepperson B, Søndergaard A, Christiansen L, et al. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 2017;118(20). doi:10.1103/PhysRevLett.118.203203' apa: 'Shepperson, B., Søndergaard, A., Christiansen, L., Kaczmarczyk, J., Zillich, R., Lemeshko, M., & Stapelfeldt, H. (2017). Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.203203' chicago: 'Shepperson, Benjamin, Anders Søndergaard, Lars Christiansen, Jan Kaczmarczyk, Robert Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.203203.' ieee: 'B. Shepperson et al., “Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free,” Physical Review Letters, vol. 118, no. 20. American Physical Society, 2017.' ista: 'Shepperson B, Søndergaard A, Christiansen L, Kaczmarczyk J, Zillich R, Lemeshko M, Stapelfeldt H. 2017. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 118(20), 203203.' mla: 'Shepperson, Benjamin, et al. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters, vol. 118, no. 20, 203203, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.203203.' short: B. Shepperson, A. Søndergaard, L. Christiansen, J. Kaczmarczyk, R. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:50:12Z date_published: 2017-05-19T00:00:00Z date_updated: 2023-09-20T11:36:17Z day: '19' department: - _id: MiLe doi: 10.1103/PhysRevLett.118.203203 external_id: isi: - '000401664000005' intvolume: ' 118' isi: 1 issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.01977 month: '05' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6260' quality_controlled: '1' scopus_import: '1' status: public title: 'Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1087' abstract: - lang: eng text: Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to. acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Dwight full_name: Barkley, Dwight last_name: Barkley - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14 apa: Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.14 chicago: Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.14. ieee: B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University Press, pp. 1045–1059, 2017. ista: Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059. mla: Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:10.1017/jfm.2017.14. short: B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059. date_created: 2018-12-11T11:50:04Z date_published: 2017-02-25T00:00:00Z date_updated: 2023-09-20T11:47:22Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.14 ec_funded: 1 external_id: isi: - '000394376400044' intvolume: ' 813' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1603.04077 month: '02' oa: 1 oa_version: Submitted Version page: 1045 - 1059 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_identifier: issn: - '00221120' publication_status: published publisher: Cambridge University Press publist_id: '6290' quality_controlled: '1' scopus_import: '1' status: public title: Speed and structure of turbulent fronts in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 813 year: '2017' ... --- _id: '1089' abstract: - lang: eng text: We discuss properties of distributions that are multivariate totally positive of order two (MTP2) related to conditional independence. In particular, we show that any independence model generated by an MTP2 distribution is a compositional semigraphoid which is upward-stable and singleton-transitive. In addition, we prove that any MTP2 distribution satisfying an appropriate support condition is faithful to its concentration graph. Finally, we analyze factorization properties of MTP2 distributions and discuss ways of constructing MTP2 distributions; in particular we give conditions on the log-linear parameters of a discrete distribution which ensure MTP2 and characterize conditional Gaussian distributions which satisfy MTP2. article_processing_charge: No author: - first_name: Shaun full_name: Fallat, Shaun last_name: Fallat - first_name: Steffen full_name: Lauritzen, Steffen last_name: Lauritzen - first_name: Kayvan full_name: Sadeghi, Kayvan last_name: Sadeghi - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Nanny full_name: Wermuth, Nanny last_name: Wermuth - first_name: Piotr full_name: Zwiernik, Piotr last_name: Zwiernik citation: ama: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity in Markov structures. Annals of Statistics. 2017;45(3):1152-1184. doi:10.1214/16-AOS1478 apa: Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., & Zwiernik, P. (2017). Total positivity in Markov structures. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AOS1478 chicago: Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” Annals of Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AOS1478. ieee: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik, “Total positivity in Markov structures,” Annals of Statistics, vol. 45, no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017. ista: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184. mla: Fallat, Shaun, et al. “Total Positivity in Markov Structures.” Annals of Statistics, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp. 1152–84, doi:10.1214/16-AOS1478. short: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals of Statistics 45 (2017) 1152–1184. date_created: 2018-12-11T11:50:05Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:46:53Z day: '01' department: - _id: CaUh doi: 10.1214/16-AOS1478 external_id: isi: - '000404395900008' intvolume: ' 45' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.01290 month: '06' oa: 1 oa_version: Submitted Version page: 1152 - 1184 project: - _id: 2530CA10-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 903-N35 name: 'Gaussian Graphical Models: Theory and Applications' publication: Annals of Statistics publication_identifier: issn: - '00905364' publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6288' quality_controlled: '1' scopus_import: '1' status: public title: Total positivity in Markov structures type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 45 year: '2017' ... --- _id: '1080' abstract: - lang: eng text: Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods. article_number: '14114' article_processing_charge: No author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Alvin full_name: Makohon Moore, Alvin last_name: Makohon Moore - first_name: Jeffrey full_name: Gerold, Jeffrey last_name: Gerold - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christine full_name: Iacobuzio Donahue, Christine last_name: Iacobuzio Donahue - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114 apa: Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114 chicago: Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14114. ieee: J. Reiter et al., “Reconstructing metastatic seeding patterns of human cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114. mla: Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group, 2017, doi:10.1038/ncomms14114. short: J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:02Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:55:31Z day: '31' ddc: - '004' - '006' department: - _id: KrCh doi: 10.1038/ncomms14114 ec_funded: 1 external_id: isi: - '000393096600001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:15:15Z date_updated: 2018-12-12T10:15:15Z file_id: '5133' file_name: IST-2017-786-v1+1_ncomms14114.pdf file_size: 897050 relation: main_file file_date_updated: 2018-12-12T10:15:15Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6301' pubrep_id: '786' quality_controlled: '1' scopus_import: '1' status: public title: Reconstructing metastatic seeding patterns of human cancers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '1085' abstract: - lang: eng text: Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution. article_number: '14251' article_processing_charge: No author: - first_name: Alison full_name: Wright, Alison last_name: Wright - first_name: Iulia full_name: Darolti, Iulia last_name: Darolti - first_name: Natasha full_name: Bloch, Natasha last_name: Bloch - first_name: Vicencio full_name: Oostra, Vicencio last_name: Oostra - first_name: Benjamin full_name: Sandkam, Benjamin last_name: Sandkam - first_name: Séverine full_name: Buechel, Séverine last_name: Buechel - first_name: Niclas full_name: Kolm, Niclas last_name: Kolm - first_name: Felix full_name: Breden, Felix last_name: Breden - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Judith full_name: Mank, Judith last_name: Mank citation: ama: Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 2017;8. doi:10.1038/ncomms14251 apa: Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14251 chicago: Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14251. ieee: A. Wright et al., “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251. mla: Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications, vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251. short: A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:04Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:48:16Z day: '31' ddc: - '570' - '576' department: - _id: BeVi doi: 10.1038/ncomms14251 external_id: isi: - '000392953700001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:15:22Z date_updated: 2018-12-12T10:15:22Z file_id: '5141' file_name: IST-2017-791-v1+1_ncomms14251.pdf file_size: 955256 relation: main_file file_date_updated: 2018-12-12T10:15:22Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6292' pubrep_id: '791' quality_controlled: '1' scopus_import: '1' status: public title: Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '1086' abstract: - lang: eng text: 'Characterisation of G protein-coupled receptors (GPCR) relies on the availability of a toolbox of ligands that selectively modulate different functional states of the receptors. To uncover such molecules, we explored a unique strategy for ligand discovery that takes advantage of the evolutionary conservation of the 600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger), identified and cloned its cognate receptor and determined its pharmacological properties on the insect and human oxytocin/vasopressin receptors. Subsequently, we identified a functional dichotomy: inotocin activated the insect inotocin and the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist ([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor interaction, which led to the identification of key residues of the receptors that are important for ligand functionality and selectivity. These observations could play an important role for development of oxytocin/vasopressin receptor modulators that would enable clear distinction of the physiological and pathological responses of the individual receptor subtypes.' article_processing_charge: No author: - first_name: Maria full_name: Di Giglio, Maria last_name: Di Giglio - first_name: Markus full_name: Muttenthaler, Markus last_name: Muttenthaler - first_name: Kasper full_name: Harpsøe, Kasper last_name: Harpsøe - first_name: Zita full_name: Liutkeviciute, Zita last_name: Liutkeviciute - first_name: Peter full_name: Keov, Peter last_name: Keov - first_name: Thomas full_name: Eder, Thomas last_name: Eder - first_name: Thomas full_name: Rattei, Thomas last_name: Rattei - first_name: Sarah full_name: Arrowsmith, Sarah last_name: Arrowsmith - first_name: Susan full_name: Wray, Susan last_name: Wray - first_name: Ales full_name: Marek, Ales last_name: Marek - first_name: Tomas full_name: Elbert, Tomas last_name: Elbert - first_name: Paul full_name: Alewood, Paul last_name: Alewood - first_name: David full_name: Gloriam, David last_name: Gloriam - first_name: Christian full_name: Gruber, Christian last_name: Gruber citation: ama: Di Giglio M, Muttenthaler M, Harpsøe K, et al. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. 2017;7:41002. doi:10.1038/srep41002 apa: Di Giglio, M., Muttenthaler, M., Harpsøe, K., Liutkeviciute, Z., Keov, P., Eder, T., … Gruber, C. (2017). Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41002 chicago: Di Giglio, Maria, Markus Muttenthaler, Kasper Harpsøe, Zita Liutkeviciute, Peter Keov, Thomas Eder, Thomas Rattei, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41002. ieee: M. Di Giglio et al., “Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide,” Scientific Reports, vol. 7. Nature Publishing Group, p. 41002, 2017. ista: Di Giglio M, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood P, Gloriam D, Gruber C. 2017. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. 7, 41002. mla: Di Giglio, Maria, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports, vol. 7, Nature Publishing Group, 2017, p. 41002, doi:10.1038/srep41002. short: M. Di Giglio, M. Muttenthaler, K. Harpsøe, Z. Liutkeviciute, P. Keov, T. Eder, T. Rattei, S. Arrowsmith, S. Wray, A. Marek, T. Elbert, P. Alewood, D. Gloriam, C. Gruber, Scientific Reports 7 (2017) 41002. date_created: 2018-12-11T11:50:04Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:47:47Z day: '01' ddc: - '570' - '590' doi: 10.1038/srep41002 external_id: isi: - '000393163800001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:14:59Z date_updated: 2018-12-12T10:14:59Z file_id: '5115' file_name: IST-2017-790-v1+1_srep41002_1_.pdf file_size: 1994139 relation: main_file file_date_updated: 2018-12-12T10:14:59Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '41002' publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '6291' pubrep_id: '790' quality_controlled: '1' scopus_import: '1' status: public title: Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1084' abstract: - lang: eng text: 'BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.' article_processing_charge: No author: - first_name: Chong full_name: Fang, Chong last_name: Fang - first_name: Anna A full_name: Nagy-Staron, Anna A id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87 last_name: Nagy-Staron orcid: 0000-0002-1391-8377 - first_name: Martin full_name: Grafe, Martin last_name: Grafe - first_name: Ralf full_name: Heermann, Ralf last_name: Heermann - first_name: Kirsten full_name: Jung, Kirsten last_name: Jung - first_name: Susanne full_name: Gebhard, Susanne last_name: Gebhard - first_name: Thorsten full_name: Mascher, Thorsten last_name: Mascher citation: ama: Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597 apa: Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., & Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.13597 chicago: Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597. ieee: C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017. ista: Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31. mla: Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597. short: C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31. date_created: 2018-12-11T11:50:03Z date_published: 2017-04-01T00:00:00Z date_updated: 2023-09-20T11:48:43Z day: '01' department: - _id: CaGu doi: 10.1111/mmi.13597 external_id: isi: - '000398059200002' intvolume: ' 104' isi: 1 issue: '1' language: - iso: eng month: '04' oa_version: None page: 16 - 31 publication: Molecular Microbiology publication_identifier: issn: - ' 0950382X' publication_status: published publisher: Wiley-Blackwell publist_id: '6294' quality_controlled: '1' scopus_import: '1' status: public title: Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 104 year: '2017' ... --- _id: '1079' abstract: - lang: eng text: We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers. article_number: '6' article_processing_charge: No author: - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Hanne full_name: Van Den Bosch, Hanne last_name: Van Den Bosch citation: ama: Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 2017;20(2). doi:10.1007/s11040-017-9238-0 apa: Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0 chicago: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0. ieee: P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2. Springer, 2017. ista: Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6. mla: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0. short: P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017). date_created: 2018-12-11T11:50:02Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:53:35Z day: '01' department: - _id: RoSe doi: 10.1007/s11040-017-9238-0 external_id: isi: - '000401270000004' intvolume: ' 20' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1603.07368 month: '06' oa: 1 oa_version: Submitted Version project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Mathematical Physics, Analysis and Geometry publication_identifier: issn: - '13850172' publication_status: published publisher: Springer publist_id: '6300' quality_controlled: '1' scopus_import: '1' status: public title: Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 20 year: '2017' ... --- _id: '1077' abstract: - lang: eng text: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima. article_number: '20160139' article_processing_charge: Yes (in subscription journal) author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Harold full_name: Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 - first_name: Tomasz full_name: Włodarski, Tomasz last_name: Włodarski - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139 apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139 chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139. ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017. ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139. mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139. short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017). date_created: 2018-12-11T11:50:01Z date_published: 2017-01-04T00:00:00Z date_updated: 2023-09-20T11:56:34Z day: '04' ddc: - '570' department: - _id: NiBa - _id: JoBo doi: 10.1098/rsif.2016.0139 ec_funded: 1 external_id: isi: - '000393380400001' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-01-18T09:14:02Z date_updated: 2019-01-18T09:14:02Z file_id: '5843' file_name: 2017_JRSI_Redondo.pdf file_size: 1092015 relation: main_file success: 1 file_date_updated: 2019-01-18T09:14:02Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '126' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: Journal of the Royal Society Interface publication_identifier: issn: - '17425689' publication_status: published publisher: Royal Society of London publist_id: '6303' quality_controlled: '1' related_material: record: - id: '9864' relation: research_data status: public scopus_import: '1' status: public title: Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2017' ... --- _id: '1067' abstract: - lang: eng text: Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction. acknowledged_ssus: - _id: PreCl article_processing_charge: No author: - first_name: Hitoshi full_name: Morita, Hitoshi id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87 last_name: Morita - first_name: Silvia full_name: Grigolon, Silvia last_name: Grigolon - first_name: Martin full_name: Bock, Martin last_name: Bock - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Guillaume full_name: Salbreux, Guillaume last_name: Salbreux - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010 apa: Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010 chicago: Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.01.010. ieee: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017. ista: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366. mla: Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010. short: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366. date_created: 2018-12-11T11:49:58Z date_published: 2017-02-27T00:00:00Z date_updated: 2023-09-20T12:06:27Z day: '27' ddc: - '572' - '597' department: - _id: CaHe doi: 10.1016/j.devcel.2017.01.010 ec_funded: 1 external_id: isi: - '000395368300007' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:10:57Z date_updated: 2018-12-12T10:10:57Z file_id: '4849' file_name: IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf file_size: 6866187 relation: main_file file_date_updated: 2018-12-12T10:10:57Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 354 - 366 project: - _id: 2524F500-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '201439' name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish publication: Developmental Cell publication_identifier: issn: - '15345807' publication_status: published publisher: Cell Press publist_id: '6320' pubrep_id: '869' quality_controlled: '1' scopus_import: '1' status: public title: The physical basis of coordinated tissue spreading in zebrafish gastrulation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2017' ... --- _id: '1074' abstract: - lang: eng text: Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance. article_processing_charge: No author: - first_name: Harald full_name: Ringbauer, Harald id: 417FCFF4-F248-11E8-B48F-1D18A9856A87 last_name: Ringbauer orcid: 0000-0002-4884-9682 - first_name: Graham full_name: Coop, Graham last_name: Coop - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220 apa: Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220 chicago: Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220. ieee: H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017. ista: Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351. mla: Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220. short: H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351. date_created: 2018-12-11T11:50:00Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-20T12:00:56Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.116.196220 ec_funded: 1 external_id: isi: - '000395807200023' intvolume: ' 205' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.biorxiv.org/content/early/2016/09/23/076810 month: '03' oa: 1 oa_version: Preprint page: 1335 - 1351 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_identifier: issn: - '00166731' publication_status: published publisher: Genetics Society of America publist_id: '6307' quality_controlled: '1' related_material: record: - id: '200' relation: dissertation_contains status: public scopus_import: '1' status: public title: Inferring recent demography from isolation by distance of long shared sequence blocks type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 205 year: '2017' ... --- _id: '1076' abstract: - lang: eng text: Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed. article_number: '023403' article_processing_charge: No author: - first_name: Michael full_name: Klaiber, Michael last_name: Klaiber - first_name: Jiří full_name: Daněk, Jiří last_name: Daněk - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Karen full_name: Hatsagortsyan, Karen last_name: Hatsagortsyan - first_name: Christoph full_name: Keitel, Christoph last_name: Keitel citation: ama: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403 apa: Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403 chicago: Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403. ieee: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2. American Physical Society, 2017. ista: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403. mla: Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403. short: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017). date_created: 2018-12-11T11:50:01Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:57:23Z day: '01' department: - _id: MiLe doi: 10.1103/PhysRevA.95.023403 ec_funded: 1 external_id: isi: - '000400571700011' intvolume: ' 95' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.07018 month: '02' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Physical Review A - Atomic, Molecular, and Optical Physics' publication_identifier: issn: - '24699926' publication_status: published publisher: American Physical Society publist_id: '6305' quality_controlled: '1' scopus_import: '1' status: public title: Strong-field ionization via a high-order Coulomb-corrected strong-field approximation type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 95 year: '2017' ... --- _id: '1072' abstract: - lang: eng text: Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field. acknowledgement: This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”. article_processing_charge: No article_type: original author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991 apa: Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6991 chicago: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991. ieee: U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” Transactions of the American Mathematical Society, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017. ista: Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762. mla: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991. short: U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762. date_created: 2018-12-11T11:49:59Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-09-20T12:05:56Z day: '01' department: - _id: HeEd doi: 10.1090/tran/6991 ec_funded: 1 external_id: arxiv: - '1312.1231' isi: - '000398030400024' intvolume: ' 369' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1312.1231 month: '05' oa: 1 oa_version: Preprint page: 3741 - 3762 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Transactions of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '6311' quality_controlled: '1' scopus_import: '1' status: public title: The Morse theory of Čech and delaunay complexes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 369 year: '2017' ... --- _id: '1073' abstract: - lang: eng text: Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation. article_processing_charge: No author: - first_name: Martin full_name: Čadek, Martin last_name: Čadek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Lukáš full_name: Vokřínek, Lukáš last_name: Vokřínek citation: ama: Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6 apa: Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9855-6 chicago: Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6. ieee: M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” Discrete & Computational Geometry, vol. 54, no. 4. Springer, pp. 915–965, 2017. ista: Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 54(4), 915–965. mla: Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:10.1007/s00454-016-9855-6. short: M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54 (2017) 915–965. date_created: 2018-12-11T11:50:00Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T12:01:28Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-016-9855-6 external_id: isi: - '000400072700008' intvolume: ' 54' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1307.6444 month: '06' oa: 1 oa_version: Submitted Version page: 915 - 965 publication: Discrete & Computational Geometry publication_identifier: issn: - '01795376' publication_status: published publisher: Springer publist_id: '6309' quality_controlled: '1' scopus_import: '1' status: public title: Algorithmic solvability of the lifting extension problem type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 54 year: '2017' ... --- _id: '1065' abstract: - lang: eng text: 'We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs.' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 citation: ama: Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003 apa: Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003 chicago: Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003. ieee: K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017. ista: Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29. mla: Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp. 25–29, doi:10.1016/j.ipl.2017.02.003. short: K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29. date_created: 2018-12-11T11:49:57Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T12:08:18Z day: '01' ddc: - '000' department: - _id: KrCh - _id: HeEd doi: 10.1016/j.ipl.2017.02.003 ec_funded: 1 external_id: isi: - '000399506600005' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:13:17Z date_updated: 2019-10-15T07:44:51Z file_id: '4998' file_name: IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf file_size: 247657 relation: main_file file_date_updated: 2019-10-15T07:44:51Z has_accepted_license: '1' intvolume: ' 122' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 25 - 29 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Information Processing Letters publication_identifier: issn: - '00200190' publication_status: published publisher: Elsevier publist_id: '6323' pubrep_id: '991' quality_controlled: '1' scopus_import: '1' status: public title: Pushdown reachability with constant treewidth type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 122 year: '2017' ... --- _id: '1063' abstract: - lang: eng text: Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations. article_processing_charge: No author: - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 citation: ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191 apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191 chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191. ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017. ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858. mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191. short: H. Uecker, Evolution 71 (2017) 845–858. date_created: 2018-12-11T11:49:57Z date_published: 2017-04-01T00:00:00Z date_updated: 2023-09-20T12:10:32Z day: '01' department: - _id: NiBa doi: 10.1111/evo.13191 ec_funded: 1 external_id: isi: - '000398545200003' intvolume: ' 71' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://biorxiv.org/content/early/2016/10/14/081042 month: '04' oa: 1 oa_version: Submitted Version page: 845 - 858 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Evolution publication_identifier: issn: - '00143820' publication_status: published publisher: Wiley-Blackwell publist_id: '6327' quality_controlled: '1' scopus_import: '1' status: public title: Evolutionary rescue in randomly mating, selfing, and clonal populations type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 71 year: '2017' ... --- _id: '1066' abstract: - lang: eng text: "Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms." article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006 apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.006. ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” Information and Computation, vol. 254, no. 2. Elsevier, pp. 143–166, 2017. ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166. mla: Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006. short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166. date_created: 2018-12-11T11:49:58Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T12:07:48Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.ic.2016.10.006 ec_funded: 1 external_id: isi: - '000402025600002' intvolume: ' 254' isi: 1 issue: '2' language: - iso: eng month: '06' oa_version: None page: 143 - 166 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '6322' quality_controlled: '1' related_material: record: - id: '5428' relation: earlier_version status: public scopus_import: '1' status: public title: Quantitative fair simulation games type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 254 year: '2017' ... --- _id: '1023' abstract: - lang: eng text: We consider products of independent square non-Hermitian random matrices. More precisely, let X1,…, Xn be independent N × N random matrices with independent entries (real or complex with independent real and imaginary parts) with zero mean and variance 1/N. Soshnikov-O’Rourke [19] and Götze-Tikhomirov [15] showed that the empirical spectral distribution of the product of n random matrices with iid entries converges to (equation found). We prove that if the entries of the matrices X1,…, Xn are independent (but not necessarily identically distributed) and satisfy uniform subexponential decay condition, then in the bulk the convergence of the ESD of X1,…, Xn to (0.1) holds up to the scale N–1/2+ε. article_number: '22' article_processing_charge: No author: - first_name: Yuriy full_name: Nemish, Yuriy id: 4D902E6A-F248-11E8-B48F-1D18A9856A87 last_name: Nemish orcid: 0000-0002-7327-856X citation: ama: Nemish Y. Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP38 apa: Nemish, Y. (2017). Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-EJP38 chicago: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random Matrices with Independent Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP38. ieee: Y. Nemish, “Local law for the product of independent non-Hermitian random matrices with independent entries,” Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics, 2017. ista: Nemish Y. 2017. Local law for the product of independent non-Hermitian random matrices with independent entries. Electronic Journal of Probability. 22, 22. mla: Nemish, Yuriy. “Local Law for the Product of Independent Non-Hermitian Random Matrices with Independent Entries.” Electronic Journal of Probability, vol. 22, 22, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP38. short: Y. Nemish, Electronic Journal of Probability 22 (2017). date_created: 2018-12-11T11:49:44Z date_published: 2017-02-06T00:00:00Z date_updated: 2023-09-22T09:27:51Z day: '06' ddc: - '510' department: - _id: LaEr doi: 10.1214/17-EJP38 external_id: isi: - '000396611900022' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:15:29Z date_updated: 2018-12-12T10:15:29Z file_id: '5149' file_name: IST-2017-802-v1+1_euclid.ejp.1487991681.pdf file_size: 742275 relation: main_file file_date_updated: 2018-12-12T10:15:29Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Electronic Journal of Probability publication_identifier: issn: - '10836489' publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6370' pubrep_id: '802' quality_controlled: '1' scopus_import: '1' status: public title: Local law for the product of independent non-Hermitian random matrices with independent entries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 22 year: '2017' ... --- _id: '1022' abstract: - lang: eng text: We introduce a multiscale topological description of the Megaparsec web-like cosmic matter distribution. Betti numbers and topological persistence offer a powerful means of describing the rich connectivity structure of the cosmic web and of its multiscale arrangement of matter and galaxies. Emanating from algebraic topology and Morse theory, Betti numbers and persistence diagrams represent an extension and deepening of the cosmologically familiar topological genus measure and the related geometric Minkowski functionals. In addition to a description of the mathematical background, this study presents the computational procedure for computing Betti numbers and persistence diagrams for density field filtrations. The field may be computed starting from a discrete spatial distribution of galaxies or simulation particles. The main emphasis of this study concerns an extensive and systematic exploration of the imprint of different web-like morphologies and different levels of multiscale clustering in the corresponding computed Betti numbers and persistence diagrams. To this end, we use Voronoi clustering models as templates for a rich variety of web-like configurations and the fractal-like Soneira-Peebles models exemplify a range of multiscale configurations. We have identified the clear imprint of cluster nodes, filaments, walls, and voids in persistence diagrams, along with that of the nested hierarchy of structures in multiscale point distributions. We conclude by outlining the potential of persistent topology for understanding the connectivity structure of the cosmic web, in large simulations of cosmic structure formation and in the challenging context of the observed galaxy distribution in large galaxy surveys. acknowledgement: Part of this work has been supported by the 7th Framework Programme for Research of the European Commission, under FETOpen grant number 255827 (CGL Computational Geometry Learning) and ERC advanced grant, URSAT (Understanding Random Systems via Algebraic Topology) number 320422. article_processing_charge: No author: - first_name: Pratyush full_name: Pranav, Pratyush last_name: Pranav - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Rien full_name: Van De Weygaert, Rien last_name: Van De Weygaert - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Michael full_name: Kerber, Michael last_name: Kerber - first_name: Bernard full_name: Jones, Bernard last_name: Jones - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Pranav P, Edelsbrunner H, Van De Weygaert R, et al. The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. 2017;465(4):4281-4310. doi:10.1093/mnras/stw2862 apa: Pranav, P., Edelsbrunner, H., Van De Weygaert, R., Vegter, G., Kerber, M., Jones, B., & Wintraecken, M. (2017). The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2862 chicago: Pranav, Pratyush, Herbert Edelsbrunner, Rien Van De Weygaert, Gert Vegter, Michael Kerber, Bernard Jones, and Mathijs Wintraecken. “The Topology of the Cosmic Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2862. ieee: P. Pranav et al., “The topology of the cosmic web in terms of persistent Betti numbers,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 4. Oxford University Press, pp. 4281–4310, 2017. ista: Pranav P, Edelsbrunner H, Van De Weygaert R, Vegter G, Kerber M, Jones B, Wintraecken M. 2017. The topology of the cosmic web in terms of persistent Betti numbers. Monthly Notices of the Royal Astronomical Society. 465(4), 4281–4310. mla: Pranav, Pratyush, et al. “The Topology of the Cosmic Web in Terms of Persistent Betti Numbers.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 4, Oxford University Press, 2017, pp. 4281–310, doi:10.1093/mnras/stw2862. short: P. Pranav, H. Edelsbrunner, R. Van De Weygaert, G. Vegter, M. Kerber, B. Jones, M. Wintraecken, Monthly Notices of the Royal Astronomical Society 465 (2017) 4281–4310. date_created: 2018-12-11T11:49:44Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-22T09:40:55Z day: '01' department: - _id: HeEd doi: 10.1093/mnras/stw2862 external_id: isi: - '000395170200039' intvolume: ' 465' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.04519 month: '01' oa: 1 oa_version: Submitted Version page: 4281 - 4310 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - '00358711' publication_status: published publisher: Oxford University Press publist_id: '6373' quality_controlled: '1' scopus_import: '1' status: public title: The topology of the cosmic web in terms of persistent Betti numbers type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 465 year: '2017' ... --- _id: '1026' abstract: - lang: eng text: The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function. acknowledgement: This work was supported by grants of the European Union Seventh Framework Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the Austrian Science Fund FWF (W1232 MolecularDrugTargets). article_processing_charge: No article_type: original author: - first_name: Viviana full_name: Agus, Viviana last_name: Agus - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: 'Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006' apa: 'Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.006' chicago: 'Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.006.' ieee: 'V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier, pp. 8–14, 2017.' ista: 'Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 48, 8–14.' mla: 'Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology, vol. 48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.' short: V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14. date_created: 2018-12-11T11:49:45Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-22T09:26:06Z day: '01' department: - _id: HaJa doi: 10.1016/j.copbio.2017.02.006 ec_funded: 1 external_id: isi: - '000418313200003' intvolume: ' 48' isi: 1 language: - iso: eng month: '12' oa_version: None page: 8 - 14 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology - _id: 255A6082-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Current Opinion in Biotechnology publication_identifier: issn: - '09581669' publication_status: published publisher: Elsevier publist_id: '6365' quality_controlled: '1' scopus_import: '1' status: public title: 'Optogenetic methods in drug screening: Technologies and applications' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 48 year: '2017' ... --- _id: '1020' abstract: - lang: eng text: Cellulose is the most abundant biopolymer on Earth. Cellulose fibers, such as the one extracted form cotton or woodpulp, have been used by humankind for hundreds of years to make textiles and paper. Here we show how, by engineering light-matter interaction, we can optimize light scattering using exclusively cellulose nanocrystals. The produced material is sustainable, biocompatible, and when compared to ordinary microfiber-based paper, it shows enhanced scattering strength (×4), yielding a transport mean free path as low as 3.5 μm in the visible light range. The experimental results are in a good agreement with the theoretical predictions obtained with a diffusive model for light propagation. acknowledgement: This research was funded by the EPSRC (EP/M027961/1), the Leverhulme Trust (RPG-2014-238), Royal Society (RG140457), the BBSRC David Phillips fellowship (BB/K014617/1), and the European Research Council (ERC-2014-STG H2020 639088). All data created during this research are provided in full in the results section and Supporting Information. They are openly available from figshare and can be accessed at ref 30. article_processing_charge: No author: - first_name: Soraya full_name: Caixeiro, Soraya last_name: Caixeiro - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Olimpia full_name: Onelli, Olimpia last_name: Onelli - first_name: Silvia full_name: Vignolini, Silvia last_name: Vignolini - first_name: Riccardo full_name: Sapienza, Riccardo last_name: Sapienza citation: ama: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 2017;9(9):7885-7890. doi:10.1021/acsami.6b15986 apa: Caixeiro, S., Peruzzo, M., Onelli, O., Vignolini, S., & Sapienza, R. (2017). Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.6b15986 chicago: Caixeiro, Soraya, Matilda Peruzzo, Olimpia Onelli, Silvia Vignolini, and Riccardo Sapienza. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces. American Chemical Society, 2017. https://doi.org/10.1021/acsami.6b15986. ieee: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, and R. Sapienza, “Disordered cellulose based nanostructures for enhanced light scattering,” ACS Applied Materials and Interfaces, vol. 9, no. 9. American Chemical Society, pp. 7885–7890, 2017. ista: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. 2017. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 9(9), 7885–7890. mla: Caixeiro, Soraya, et al. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces, vol. 9, no. 9, American Chemical Society, 2017, pp. 7885–90, doi:10.1021/acsami.6b15986. short: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied Materials and Interfaces 9 (2017) 7885–7890. date_created: 2018-12-11T11:49:44Z date_published: 2017-03-08T00:00:00Z date_updated: 2023-09-22T09:40:14Z day: '08' department: - _id: JoFi doi: 10.1021/acsami.6b15986 external_id: isi: - '000396186000002' intvolume: ' 9' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.01415 month: '03' oa: 1 oa_version: Submitted Version page: 7885 - 7890 publication: ACS Applied Materials and Interfaces publication_identifier: issn: - '19448244' publication_status: published publisher: American Chemical Society publist_id: '6372' quality_controlled: '1' scopus_import: '1' status: public title: Disordered cellulose based nanostructures for enhanced light scattering type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2017' ... --- _id: '1021' abstract: - lang: eng text: Most flows in nature and engineering are turbulent because of their large velocities and spatial scales. Laboratory experiments on rotating quasi-Keplerian flows, for which the angular velocity decreases radially but the angular momentum increases, are however laminar at Reynolds numbers exceeding one million. This is in apparent contradiction to direct numerical simulations showing that in these experiments turbulence transition is triggered by the axial boundaries. We here show numerically that as the Reynolds number increases, turbulence becomes progressively confined to the boundary layers and the flow in the bulk fully relaminarizes. Our findings support that turbulence is unlikely to occur in isothermal constant-density quasi-Keplerian flows. article_processing_charge: No author: - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Lopez Alonso JM, Avila M. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 2017;817:21-34. doi:10.1017/jfm.2017.109 apa: Lopez Alonso, J. M., & Avila, M. (2017). Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.109 chicago: Lopez Alonso, Jose M, and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.109. ieee: J. M. Lopez Alonso and M. Avila, “Boundary layer turbulence in experiments on quasi Keplerian flows,” Journal of Fluid Mechanics, vol. 817. Cambridge University Press, pp. 21–34, 2017. ista: Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34. mla: Lopez Alonso, Jose M., and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics, vol. 817, Cambridge University Press, 2017, pp. 21–34, doi:10.1017/jfm.2017.109. short: J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34. date_created: 2018-12-11T11:49:44Z date_published: 2017-04-25T00:00:00Z date_updated: 2023-09-22T09:39:46Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.109 external_id: isi: - '000398179100006' intvolume: ' 817' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.05527 month: '04' oa: 1 oa_version: Submitted Version page: 21 - 34 project: - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: Journal of Fluid Mechanics publication_identifier: issn: - '00221120' publication_status: published publisher: Cambridge University Press publist_id: '6371' quality_controlled: '1' scopus_import: '1' status: public title: Boundary layer turbulence in experiments on quasi Keplerian flows type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 817 year: '2017' ... --- _id: '1025' abstract: - lang: eng text: Many organ surfaces are covered by a protective epithelial-cell layer. It emerges that such layers are maintained by cell stretching that triggers cell division mediated by the force-sensitive ion-channel protein Piezo1. See Letter p.118 article_processing_charge: No author: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44. doi:10.1038/nature21502' apa: 'Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21502' chicago: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.' ieee: 'C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature, vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.' ista: 'Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643), 43–44.' mla: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature, vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.' short: C.-P.J. Heisenberg, Nature 543 (2017) 43–44. date_created: 2018-12-11T11:49:45Z date_published: 2017-03-02T00:00:00Z date_updated: 2023-09-22T09:26:59Z day: '02' department: - _id: CaHe doi: 10.1038/nature21502 external_id: isi: - '000395671500025' intvolume: ' 543' isi: 1 issue: '7643' language: - iso: eng month: '03' oa_version: None page: 43 - 44 publication: Nature publication_identifier: issn: - '00280836' publication_status: published publisher: Nature Publishing Group publist_id: '6367' quality_controlled: '1' scopus_import: '1' status: public title: 'Cell biology: Stretched divisions' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 543 year: '2017' ... --- _id: '1017' abstract: - lang: eng text: The development of the vertebrate central nervous system is reliant on a complex cascade of biological processes that include mitotic division, relocation of migrating neurons, and the extension of dendritic and axonal processes. Each of these cellular events requires the diverse functional repertoire of the microtubule cytoskeleton for the generation of forces, assembly of macromolecular complexes and transport of molecules and organelles. The tubulins are a multi-gene family that encode for the constituents of microtubules, and have been implicated in a spectrum of neurological disorders. Evidence is building that different tubulins tune the functional properties of the microtubule cytoskeleton dependent on the cell type, developmental profile and subcellular localisation. Here we review of the origins of the functional specification of the tubulin gene family in the developing brain at a transcriptional, translational, and post-transcriptional level. We remind the reader that tubulins are not just loading controls for your average Western blot. article_processing_charge: No author: - first_name: Martin full_name: Breuss, Martin last_name: Breuss - first_name: Ines full_name: Leca, Ines last_name: Leca - first_name: Thomas full_name: Gstrein, Thomas last_name: Gstrein - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: David full_name: Keays, David last_name: Keays citation: ama: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 2017;84:58-67. doi:10.1016/j.mcn.2017.03.002' apa: 'Breuss, M., Leca, I., Gstrein, T., Hansen, A. H., & Keays, D. (2017). Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. Academic Press. https://doi.org/10.1016/j.mcn.2017.03.002' chicago: 'Breuss, Martin, Ines Leca, Thomas Gstrein, Andi H Hansen, and David Keays. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience. Academic Press, 2017. https://doi.org/10.1016/j.mcn.2017.03.002.' ieee: 'M. Breuss, I. Leca, T. Gstrein, A. H. Hansen, and D. Keays, “Tubulins and brain development: The origins of functional specification,” Molecular and Cellular Neuroscience, vol. 84. Academic Press, pp. 58–67, 2017.' ista: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. 2017. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 84, 58–67.' mla: 'Breuss, Martin, et al. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience, vol. 84, Academic Press, 2017, pp. 58–67, doi:10.1016/j.mcn.2017.03.002.' short: M. Breuss, I. Leca, T. Gstrein, A.H. Hansen, D. Keays, Molecular and Cellular Neuroscience 84 (2017) 58–67. date_created: 2018-12-11T11:49:42Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-22T09:42:15Z day: '01' ddc: - '571' department: - _id: SiHi doi: 10.1016/j.mcn.2017.03.002 external_id: isi: - '000415140700007' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:09:19Z date_updated: 2018-12-12T10:09:19Z file_id: '4742' file_name: IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf file_size: 1436377 relation: main_file file_date_updated: 2018-12-12T10:09:19Z has_accepted_license: '1' intvolume: ' 84' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 58 - 67 publication: Molecular and Cellular Neuroscience publication_identifier: issn: - '10447431' publication_status: published publisher: Academic Press publist_id: '6377' pubrep_id: '806' quality_controlled: '1' scopus_import: '1' status: public title: 'Tubulins and brain development: The origins of functional specification' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 84 year: '2017' ... --- _id: '1015' abstract: - lang: eng text: 'Vortices are commonly observed in the context of classical hydrodynamics: from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon such as a tornado, all classical vortices are characterized by an arbitrary circulation value of the local velocity field. On the other hand the appearance of vortices with quantized circulation represents one of the fundamental signatures of macroscopic quantum phenomena. In two-dimensional superfluids quantized vortices play a key role in determining finite-temperature properties, as the superfluid phase and the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless transition. Very recent experiments with two-dimensional superfluid fermions motivate the present work: we present theoretical results based on the renormalization group showing that the universal jump of the superfluid density and the critical temperature crucially depend on the interaction strength, providing a strong benchmark for forthcoming investigations.' article_number: '45702' article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Luca full_name: Salasnich, Luca last_name: Salasnich citation: ama: Bighin G, Salasnich L. Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. 2017;7. doi:10.1038/srep45702 apa: Bighin, G., & Salasnich, L. (2017). Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep45702 chicago: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep45702. ieee: G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional ultracold Fermi gases,” Scientific Reports, vol. 7. Nature Publishing Group, 2017. ista: Bighin G, Salasnich L. 2017. Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. 7, 45702. mla: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” Scientific Reports, vol. 7, 45702, Nature Publishing Group, 2017, doi:10.1038/srep45702. short: G. Bighin, L. Salasnich, Scientific Reports 7 (2017). date_created: 2018-12-11T11:49:42Z date_published: 2017-04-04T00:00:00Z date_updated: 2023-09-22T09:43:10Z day: '04' ddc: - '539' department: - _id: MiLe doi: 10.1038/srep45702 external_id: isi: - '000398148100001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:12:32Z date_updated: 2018-12-12T10:12:32Z file_id: '4950' file_name: IST-2017-809-v1+1_srep45702.pdf file_size: 478289 relation: main_file file_date_updated: 2018-12-12T10:12:32Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: issn: - '20452322' publication_status: published publisher: Nature Publishing Group publist_id: '6380' pubrep_id: '809' quality_controlled: '1' scopus_import: '1' status: public title: Vortices and antivortices in two-dimensional ultracold Fermi gases tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1016' abstract: - lang: eng text: The integrity and dynamic properties of the microtubule cytoskeleton are indispensable for the development of the mammalian brain. Consequently, mutations in the genes that encode the structural component (the α/β-tubulin heterodimer) can give rise to severe, sporadic neurodevelopmental disorders. These are commonly referred to as the tubulinopathies. Here we report the addition of recessive quadrupedalism, also known as Uner Tan syndrome (UTS), to the growing list of diseases caused by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to the identifying quadrupedal locomotion, all three patients showed severe cerebellar hypoplasia. None, however, displayed the basal ganglia malformations typically associated with TUBB2B mutations. Functional analysis of the R390Q substitution revealed that it did not affect the ability of β-tubulin to fold or become assembled into the α/β-heterodimer, nor did it influence the incorporation of mutant-containing heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2 did not affect growth under basal conditions, but did result in increased sensitivity to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation on microtubule function. The TUBB2B mutation described here represents an unusual recessive mode of inheritance for missense-mediated tubulinopathies and reinforces the sensitivity of the developing cerebellum to microtubule defects. article_processing_charge: No author: - first_name: Martin full_name: Breuss, Martin last_name: Breuss - first_name: Thai full_name: Nguyen, Thai last_name: Nguyen - first_name: Anjana full_name: Srivatsan, Anjana last_name: Srivatsan - first_name: Ines full_name: Leca, Ines last_name: Leca - first_name: Guoling full_name: Tian, Guoling last_name: Tian - first_name: Tanja full_name: Fritz, Tanja last_name: Fritz - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Damir full_name: Musaev, Damir last_name: Musaev - first_name: Jennifer full_name: Mcevoy Venneri, Jennifer last_name: Mcevoy Venneri - first_name: James full_name: Kiely, James last_name: Kiely - first_name: Rasim full_name: Rosti, Rasim last_name: Rosti - first_name: Eric full_name: Scott, Eric last_name: Scott - first_name: Uner full_name: Tan, Uner last_name: Tan - first_name: Richard full_name: Kolodner, Richard last_name: Kolodner - first_name: Nicholas full_name: Cowan, Nicholas last_name: Cowan - first_name: David full_name: Keays, David last_name: Keays - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson citation: ama: Breuss M, Nguyen T, Srivatsan A, et al. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. 2017;26(2):258-269. doi:10.1093/hmg/ddw383 apa: Breuss, M., Nguyen, T., Srivatsan, A., Leca, I., Tian, G., Fritz, T., … Gleeson, J. (2017). Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddw383 chicago: Breuss, Martin, Thai Nguyen, Anjana Srivatsan, Ines Leca, Guoling Tian, Tanja Fritz, Andi H Hansen, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” Human Molecular Genetics. Oxford University Press, 2017. https://doi.org/10.1093/hmg/ddw383. ieee: M. Breuss et al., “Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability,” Human Molecular Genetics, vol. 26, no. 2. Oxford University Press, pp. 258–269, 2017. ista: Breuss M, Nguyen T, Srivatsan A, Leca I, Tian G, Fritz T, Hansen AH, Musaev D, Mcevoy Venneri J, Kiely J, Rosti R, Scott E, Tan U, Kolodner R, Cowan N, Keays D, Gleeson J. 2017. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. 26(2), 258–269. mla: Breuss, Martin, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” Human Molecular Genetics, vol. 26, no. 2, Oxford University Press, 2017, pp. 258–69, doi:10.1093/hmg/ddw383. short: M. Breuss, T. Nguyen, A. Srivatsan, I. Leca, G. Tian, T. Fritz, A.H. Hansen, D. Musaev, J. Mcevoy Venneri, J. Kiely, R. Rosti, E. Scott, U. Tan, R. Kolodner, N. Cowan, D. Keays, J. Gleeson, Human Molecular Genetics 26 (2017) 258–269. date_created: 2018-12-11T11:49:42Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-22T09:42:42Z day: '01' department: - _id: SiHi doi: 10.1093/hmg/ddw383 external_id: isi: - '000397066400002' intvolume: ' 26' isi: 1 issue: '2' language: - iso: eng month: '01' oa_version: None page: 258 - 269 publication: Human Molecular Genetics publication_identifier: issn: - '09646906' publication_status: published publisher: Oxford University Press publist_id: '6379' quality_controlled: '1' scopus_import: '1' status: public title: Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 26 year: '2017' ... --- _id: '1018' abstract: - lang: eng text: In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The crosstalk between cytokinin response and light is known for a long time. However, the molecular mechanism underlying the interactionbetween light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT-1 (CKI1), encoding the constitutively active sensor histidine kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE 1 (HY1) which encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertiblephytochromes. Our analysis confirmed the light-dependent regulation oftheCKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors PHYTOCHROME INTERACTING FACTOR 3 (PIF3) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlatewithmisregulation of MSP signaling, changedcytokinin sensitivity and developmental aberrations,previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light- and cytokinin-controlled plant development. article_processing_charge: No author: - first_name: Tereza full_name: Dobisova, Tereza last_name: Dobisova - first_name: Vendula full_name: Hrdinova, Vendula last_name: Hrdinova - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Sarka full_name: Michlickova, Sarka last_name: Michlickova - first_name: Ivana full_name: Urbankova, Ivana last_name: Urbankova - first_name: Romana full_name: Hejatkova, Romana last_name: Hejatkova - first_name: Petra full_name: Zadnikova, Petra last_name: Zadnikova - first_name: Markéta full_name: Pernisová, Markéta last_name: Pernisová - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko citation: ama: Dobisova T, Hrdinova V, Cuesta C, et al. Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. 2017;174(1):387-404. doi:10.1104/pp.16.01964 apa: Dobisova, T., Hrdinova, V., Cuesta, C., Michlickova, S., Urbankova, I., Hejatkova, R., … Hejátko, J. (2017). Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01964 chicago: Dobisova, Tereza, Vendula Hrdinova, Candela Cuesta, Sarka Michlickova, Ivana Urbankova, Romana Hejatkova, Petra Zadnikova, Markéta Pernisová, Eva Benková, and Jan Hejátko. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls Cytokinin Related Development.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01964. ieee: T. Dobisova et al., “Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 387–404, 2017. ista: Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R, Zadnikova P, Pernisová M, Benková E, Hejátko J. 2017. Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development. Plant Physiology. 174(1), 387–404. mla: Dobisova, Tereza, et al. “Light Regulated Expression of Sensor Histidine Kinase CKI1 Controls Cytokinin Related Development.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 387–404, doi:10.1104/pp.16.01964. short: T. Dobisova, V. Hrdinova, C. Cuesta, S. Michlickova, I. Urbankova, R. Hejatkova, P. Zadnikova, M. Pernisová, E. Benková, J. Hejátko, Plant Physiology 174 (2017) 387–404. date_created: 2018-12-11T11:49:43Z date_published: 2017-05-17T00:00:00Z date_updated: 2023-09-22T09:41:48Z day: '17' department: - _id: EvBe doi: 10.1104/pp.16.01964 external_id: isi: - '000402057200028' intvolume: ' 174' isi: 1 issue: '1' language: - iso: eng month: '05' oa_version: None page: 387 - 404 publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '6375' quality_controlled: '1' scopus_import: '1' status: public title: Light regulated expression of sensor histidine kinase CKI1 controls cytokinin related development type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 174 year: '2017' ... --- _id: '1019' abstract: - lang: eng text: As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline. article_processing_charge: No author: - first_name: Eliza full_name: Argyridou, Eliza last_name: Argyridou - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Annabella full_name: Königer, Annabella last_name: Königer - first_name: John full_name: Parsch, John last_name: Parsch citation: ama: Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 2017;119(1):27-34. doi:10.1038/hdy.2017.12 apa: Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12 chicago: Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12. ieee: E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,” Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017. ista: Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 119(1), 27–34. mla: Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1, Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12. short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34. date_created: 2018-12-11T11:49:43Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-09-22T09:41:21Z day: '01' department: - _id: BeVi doi: 10.1038/hdy.2017.12 external_id: isi: - '000405397800004' intvolume: ' 119' isi: 1 issue: '1' language: - iso: eng month: '07' oa_version: None page: 27 - 34 publication: Heredity publication_identifier: issn: - 0018067X publication_status: published publisher: Nature Publishing Group publist_id: '6374' quality_controlled: '1' related_material: record: - id: '9861' relation: research_data status: public scopus_import: '1' status: public title: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 119 year: '2017' ... --- _id: '9861' abstract: - lang: eng text: As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline. article_processing_charge: No author: - first_name: Eliza full_name: Argyridou, Eliza last_name: Argyridou - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Annabella full_name: Königer, Annabella last_name: Königer - first_name: John full_name: Parsch, John last_name: Parsch citation: ama: 'Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. 2017. doi:10.5061/dryad.02f6r' apa: 'Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Dryad. https://doi.org/10.5061/dryad.02f6r' chicago: 'Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Dryad, 2017. https://doi.org/10.5061/dryad.02f6r.' ieee: 'E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.” Dryad, 2017.' ista: 'Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster, Dryad, 10.5061/dryad.02f6r.' mla: 'Argyridou, Eliza, et al. Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster. Dryad, 2017, doi:10.5061/dryad.02f6r.' short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017). date_created: 2021-08-10T08:12:52Z date_published: 2017-02-14T00:00:00Z date_updated: 2023-09-22T09:41:20Z day: '14' department: - _id: BeVi doi: 10.5061/dryad.02f6r main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.02f6r month: '02' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1019' relation: used_in_publication status: public status: public title: 'Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '1006' abstract: - lang: eng text: 'Background: The phenomenon of immune priming, i.e. enhanced protection following a secondary exposure to a pathogen, has now been demonstrated in a wide range of invertebrate species. Despite accumulating phenotypic evidence, knowledge of its mechanistic underpinnings is currently very limited. Here we used the system of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus thuringiensis (Bt) to further our molecular understanding of the oral immune priming phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants) of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon later challenge exposure, using a whole-transcriptome sequencing approach. Results: Whereas gene expression of individuals primed with the orally non-pathogenic strain showed minor changes to controls, we found that priming with the pathogenic strain induced regulation of a large set of distinct genes, many of which are known immune candidates. Intriguingly, the immune repertoire activated upon priming and subsequent challenge qualitatively differed from the one mounted upon infection with Bt without previous priming. Moreover, a large subset of priming-specific genes showed an inverse regulation compared to their regulation upon challenge only. Conclusions: Our data demonstrate that gene expression upon infection is strongly affected by previous immune priming. We hypothesise that this shift in gene expression indicates activation of a more targeted and efficient response towards a previously encountered pathogen, in anticipation of potential secondary encounter.' article_processing_charge: No author: - first_name: Jenny full_name: Greenwood, Jenny last_name: Greenwood - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Sarah full_name: Behrens, Sarah last_name: Behrens - first_name: Daniela full_name: Essar, Daniela last_name: Essar - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: Greenwood J, Milutinovic B, Peuß R, et al. Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. 2017;18(1):329. doi:10.1186/s12864-017-3705-7 apa: Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-017-3705-7 chicago: Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics. BioMed Central, 2017. https://doi.org/10.1186/s12864-017-3705-7. ieee: J. Greenwood et al., “Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,” BMC Genomics, vol. 18, no. 1. BioMed Central, p. 329, 2017. ista: Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. 18(1), 329. mla: Greenwood, Jenny, et al. “Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics, vol. 18, no. 1, BioMed Central, 2017, p. 329, doi:10.1186/s12864-017-3705-7. short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, BMC Genomics 18 (2017) 329. date_created: 2018-12-11T11:49:39Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-22T09:47:44Z day: '26' ddc: - '570' department: - _id: SyCr doi: 10.1186/s12864-017-3705-7 external_id: isi: - '000400625200004' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:46Z date_updated: 2018-12-12T10:16:46Z file_id: '5236' file_name: IST-2017-814-v1+1_s12864-017-3705-7.pdf file_size: 2379672 relation: main_file file_date_updated: 2018-12-12T10:16:46Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '329' publication: BMC Genomics publication_identifier: issn: - '14712164' publication_status: published publisher: BioMed Central publist_id: '6392' pubrep_id: '814' quality_controlled: '1' related_material: record: - id: '9859' relation: research_data status: public - id: '9860' relation: research_data status: public scopus_import: '1' status: public title: Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 18 year: '2017' ... --- _id: '1011' abstract: - lang: eng text: Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly equivalent, are standard models for interprocedural analysis. Yet RSMs are more convenient as they (a) explicitly model function calls and returns, and (b) specify many natural parameters for algorithmic analysis, e.g., the number of entries and exits. We consider a general framework where RSM transitions are labeled from a semiring and path properties are algebraic with semiring operations, which can model, e.g., interprocedural reachability and dataflow analysis problems. Our main contributions are new algorithms for several fundamental problems. As compared to a direct translation of RSMs to PDSs and the best-known existing bounds of PDSs, our analysis algorithm improves the complexity for finite-height semirings (that subsumes reachability and standard dataflow properties). We further consider the problem of extracting distance values from the representation structures computed by our algorithm, and give efficient algorithms that distinguish the complexity of a one-time preprocessing from the complexity of each individual query. Another advantage of our algorithm is that our improvements carry over to the concurrent setting, where we improve the bestknown complexity for the context-bounded analysis of concurrent RSMs. Finally, we provide a prototype implementation that gives a significant speed-up on several benchmarks from the SLAM/SDV project. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Samarth full_name: Mishra, Samarth last_name: Mishra - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. Faster algorithms for weighted recursive state machines. In: Yang H, ed. Vol 10201. Springer; 2017:287-313. doi:10.1007/978-3-662-54434-1_11' apa: 'Chatterjee, K., Kragl, B., Mishra, S., & Pavlogiannis, A. (2017). Faster algorithms for weighted recursive state machines. In H. Yang (Ed.) (Vol. 10201, pp. 287–313). Presented at the ESOP: European Symposium on Programming, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54434-1_11' chicago: Chatterjee, Krishnendu, Bernhard Kragl, Samarth Mishra, and Andreas Pavlogiannis. “Faster Algorithms for Weighted Recursive State Machines.” edited by Hongseok Yang, 10201:287–313. Springer, 2017. https://doi.org/10.1007/978-3-662-54434-1_11. ieee: 'K. Chatterjee, B. Kragl, S. Mishra, and A. Pavlogiannis, “Faster algorithms for weighted recursive state machines,” presented at the ESOP: European Symposium on Programming, Uppsala, Sweden, 2017, vol. 10201, pp. 287–313.' ista: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. 2017. Faster algorithms for weighted recursive state machines. ESOP: European Symposium on Programming, LNCS, vol. 10201, 287–313.' mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Weighted Recursive State Machines. Edited by Hongseok Yang, vol. 10201, Springer, 2017, pp. 287–313, doi:10.1007/978-3-662-54434-1_11. short: K. Chatterjee, B. Kragl, S. Mishra, A. Pavlogiannis, in:, H. Yang (Ed.), Springer, 2017, pp. 287–313. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'ESOP: European Symposium on Programming' start_date: 2017-04-22 date_created: 2018-12-11T11:49:41Z date_published: 2017-03-19T00:00:00Z date_updated: 2023-09-22T09:44:50Z day: '19' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-662-54434-1_11 ec_funded: 1 editor: - first_name: Hongseok full_name: Yang, Hongseok last_name: Yang external_id: isi: - '000681702400011' intvolume: ' 10201' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1701.04914 month: '03' oa: 1 oa_version: Submitted Version page: 287 - 313 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6384' quality_controlled: '1' scopus_import: '1' status: public title: Faster algorithms for weighted recursive state machines type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10201 year: '2017' ... --- _id: '1004' abstract: - lang: eng text: The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment. article_processing_charge: No author: - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 2017;45:82-89. doi:10.1016/j.gde.2017.03.010 apa: Ötvös, K., & Benková, E. (2017). Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2017.03.010 chicago: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development. Elsevier, 2017. https://doi.org/10.1016/j.gde.2017.03.010. ieee: K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” Current Opinion in Genetics & Development, vol. 45. Elsevier, pp. 82–89, 2017. ista: Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 45, 82–89. mla: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development, vol. 45, Elsevier, 2017, pp. 82–89, doi:10.1016/j.gde.2017.03.010. short: K. Ötvös, E. Benková, Current Opinion in Genetics & Development 45 (2017) 82–89. date_created: 2018-12-11T11:49:38Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-09-22T09:48:15Z day: '01' ddc: - '575' department: - _id: EvBe doi: 10.1016/j.gde.2017.03.010 external_id: isi: - '000404880400013' pmid: - '28391060' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-04-17T08:00:36Z date_updated: 2019-04-17T08:00:36Z file_id: '6336' file_name: Otvos_Benkova_CurOpDevBiol_2017.pdf file_size: 364133 relation: main_file success: 1 file_date_updated: 2019-04-17T08:00:36Z has_accepted_license: '1' intvolume: ' 45' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 82 - 89 pmid: 1 project: - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development publication: Current Opinion in Genetics & Development publication_identifier: issn: - 0959437X publication_status: published publisher: Elsevier publist_id: '6394' pubrep_id: '1017' quality_controlled: '1' scopus_import: '1' status: public title: Spatiotemporal mechanisms of root branching tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 45 year: '2017' ... --- _id: '1010' abstract: - lang: eng text: 'We prove a local law in the bulk of the spectrum for random Gram matrices XX∗, a generalization of sample covariance matrices, where X is a large matrix with independent, centered entries with arbitrary variances. The limiting eigenvalue density that generalizes the Marchenko-Pastur law is determined by solving a system of nonlinear equations. Our entrywise and averaged local laws are on the optimal scale with the optimal error bounds. They hold both in the square case (hard edge) and in the properly rectangular case (soft edge). In the latter case we also establish a macroscopic gap away from zero in the spectrum of XX∗. ' article_number: '25' article_processing_charge: No author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Alt J, Erdös L, Krüger TH. Local law for random Gram matrices. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP42 apa: Alt, J., Erdös, L., & Krüger, T. H. (2017). Local law for random Gram matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-EJP42 chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Law for Random Gram Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP42. ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local law for random Gram matrices,” Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics, 2017. ista: Alt J, Erdös L, Krüger TH. 2017. Local law for random Gram matrices. Electronic Journal of Probability. 22, 25. mla: Alt, Johannes, et al. “Local Law for Random Gram Matrices.” Electronic Journal of Probability, vol. 22, 25, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP42. short: J. Alt, L. Erdös, T.H. Krüger, Electronic Journal of Probability 22 (2017). date_created: 2018-12-11T11:49:40Z date_published: 2017-03-08T00:00:00Z date_updated: 2023-09-22T09:45:23Z day: '08' ddc: - '510' - '539' department: - _id: LaEr doi: 10.1214/17-EJP42 ec_funded: 1 external_id: arxiv: - '1606.07353' isi: - '000396611900025' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:13:39Z date_updated: 2018-12-12T10:13:39Z file_id: '5024' file_name: IST-2017-807-v1+1_euclid.ejp.1488942016.pdf file_size: 639384 relation: main_file file_date_updated: 2018-12-12T10:13:39Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Journal of Probability publication_identifier: issn: - '10836489' publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6386' pubrep_id: '807' quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: '1' status: public title: Local law for random Gram matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 22 year: '2017' ... --- _id: '1009' abstract: - lang: eng text: A standard objective in partially-observable Markov decision processes (POMDPs) is to find a policy that maximizes the expected discounted-sum payoff. However, such policies may still permit unlikely but highly undesirable outcomes, which is problematic especially in safety-critical applications. Recently, there has been a surge of interest in POMDPs where the goal is to maximize the probability to ensure that the payoff is at least a given threshold, but these approaches do not consider any optimization beyond satisfying this threshold constraint. In this work we go beyond both the “expectation” and “threshold” approaches and consider a “guaranteed payoff optimization (GPO)” problem for POMDPs, where we are given a threshold t and the objective is to find a policy σ such that a) each possible outcome of σ yields a discounted-sum payoff of at least t, and b) the expected discounted-sum payoff of σ is optimal (or near-optimal) among all policies satisfying a). We present a practical approach to tackle the GPO problem and evaluate it on standard POMDP benchmarks. acknowledgement: 'he research leading to these results was supported by the Austrian Science Fund (FWF) NFN Grant no. S11407-N23 (RiSE/SHiNE); two ERC Starting grants (279307: Graph Games, 279499: inVEST); the Vienna Science and Tech- nology Fund (WWTF) through project ICT15-003; and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734].' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny - first_name: Guillermo full_name: Pérez, Guillermo last_name: Pérez - first_name: Jean full_name: Raskin, Jean last_name: Raskin - first_name: Djordje full_name: Zikelic, Djordje last_name: Zikelic citation: ama: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. Optimizing expectation with guarantees in POMDPs. In: Proceedings of the 31st AAAI Conference on Artificial Intelligence. Vol 5. AAAI Press; 2017:3725-3732.' apa: 'Chatterjee, K., Novotný, P., Pérez, G., Raskin, J., & Zikelic, D. (2017). Optimizing expectation with guarantees in POMDPs. In Proceedings of the 31st AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3725–3732). San Francisco, CA, United States: AAAI Press.' chicago: Chatterjee, Krishnendu, Petr Novotný, Guillermo Pérez, Jean Raskin, and Djordje Zikelic. “Optimizing Expectation with Guarantees in POMDPs.” In Proceedings of the 31st AAAI Conference on Artificial Intelligence, 5:3725–32. AAAI Press, 2017. ieee: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, and D. Zikelic, “Optimizing expectation with guarantees in POMDPs,” in Proceedings of the 31st AAAI Conference on Artificial Intelligence, San Francisco, CA, United States, 2017, vol. 5, pp. 3725–3732. ista: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. 2017. Optimizing expectation with guarantees in POMDPs. Proceedings of the 31st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 5, 3725–3732.' mla: Chatterjee, Krishnendu, et al. “Optimizing Expectation with Guarantees in POMDPs.” Proceedings of the 31st AAAI Conference on Artificial Intelligence, vol. 5, AAAI Press, 2017, pp. 3725–32. short: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, D. Zikelic, in:, Proceedings of the 31st AAAI Conference on Artificial Intelligence, AAAI Press, 2017, pp. 3725–3732. conference: end_date: 2017-02-10 location: San Francisco, CA, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2017-02-04 date_created: 2018-12-11T11:49:40Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-22T09:46:41Z day: '01' department: - _id: KrCh ec_funded: 1 external_id: isi: - '000485630703107' intvolume: ' 5' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/download/14354/14092 month: '01' oa: 1 oa_version: Submitted Version page: 3725 - 3732 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Proceedings of the 31st AAAI Conference on Artificial Intelligence publication_status: published publisher: AAAI Press publist_id: '6387' quality_controlled: '1' scopus_import: '1' status: public title: Optimizing expectation with guarantees in POMDPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 5 year: '2017' ... --- _id: '9859' abstract: - lang: eng text: 'Lists of all differentially expressed genes in the different priming-challenge treatments (compared to the fully naïve control; xlsx file). Relevant columns include the following: sample_1 and sample_2 – treatment groups being compared; Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change) – log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated compared with sample 2, positive means sample 2 upregulated compared with sample 1; cuffdiff test_statistic – test statistic of differential expression test; p_value – p-value of differential expression test; q_value (FDR correction) – adjusted P-value of differential expression test. (XLSX 598 kb)' article_processing_charge: No author: - first_name: Jenny full_name: Greenwood, Jenny last_name: Greenwood - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Sarah full_name: Behrens, Sarah last_name: Behrens - first_name: Daniela full_name: Essar, Daniela last_name: Essar - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d1.v1' apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1' chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature, 2017. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1.' ieee: 'J. Greenwood et al., “Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.” Springer Nature, 2017.' ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae, Springer Nature, 10.6084/m9.figshare.c.3756974_d1.v1.' mla: 'Greenwood, Jenny, et al. Additional File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d1.v1.' short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (2017). date_created: 2021-08-10T07:59:02Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-22T09:47:44Z day: '26' department: - _id: SyCr doi: 10.6084/m9.figshare.c.3756974_d1.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1 month: '04' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '1006' relation: used_in_publication status: public status: public title: 'Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9860' article_processing_charge: No author: - first_name: Jenny full_name: Greenwood, Jenny last_name: Greenwood - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Sarah full_name: Behrens, Sarah last_name: Behrens - first_name: Daniela full_name: Essar, Daniela last_name: Essar - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d5.v1' apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1' chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature, 2017. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1.' ieee: 'J. Greenwood et al., “Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.” Springer Nature, 2017.' ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae, Springer Nature, 10.6084/m9.figshare.c.3756974_d5.v1.' mla: 'Greenwood, Jenny, et al. Additional File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d5.v1.' short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (2017). date_created: 2021-08-10T08:07:12Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-22T09:47:44Z day: '26' department: - _id: SyCr doi: 10.6084/m9.figshare.c.3756974_d5.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1 month: '04' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '1006' relation: used_in_publication status: public status: public title: 'Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '1002' abstract: - lang: eng text: " We present an interactive design system to create functional mechanical \ objects. Our computational approach allows novice users to retarget an existing mechanical template to a user-specified input shape. Our proposed representation for a mechanical template encodes a parameterized mechanism, mechanical constraints that ensure a physically valid configuration, spatial relationships of mechanical parts to the user-provided shape, and functional constraints that specify an intended functionality. We provide an intuitive interface and optimization-in-the-loop approach for finding a valid configuration of the mechanism and the shape to ensure that higher-level functional goals are met. Our algorithm interactively optimizes the mechanism while the user manipulates the placement of mechanical components and the shape. Our system allows users to efficiently explore various design choices and to synthesize customized mechanical objects that can be fabricated with rapid prototyping technologies. We demonstrate the efficacy of our approach by retargeting various mechanical templates to different shapes and fabricating the resulting functional mechanical objects.\r\n" alternative_title: - ACM Transactions on Graphics article_number: '81' article_processing_charge: No author: - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Duygu full_name: Ceylan, Duygu last_name: Ceylan - first_name: Wilmot full_name: Li, Wilmot last_name: Li - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. Functionality-aware retargeting of mechanisms to 3D shapes. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073710' apa: 'Zhang, R., Auzinger, T., Ceylan, D., Li, W., & Bickel, B. (2017). Functionality-aware retargeting of mechanisms to 3D shapes (Vol. 36). Presented at the SIGGRAPH: Computer Graphics and Interactive Techniques, Los Angeles, CA, United States : ACM. https://doi.org/10.1145/3072959.3073710' chicago: Zhang, Ran, Thomas Auzinger, Duygu Ceylan, Wilmot Li, and Bernd Bickel. “Functionality-Aware Retargeting of Mechanisms to 3D Shapes,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073710. ieee: 'R. Zhang, T. Auzinger, D. Ceylan, W. Li, and B. Bickel, “Functionality-aware retargeting of mechanisms to 3D shapes,” presented at the SIGGRAPH: Computer Graphics and Interactive Techniques, Los Angeles, CA, United States , 2017, vol. 36, no. 4.' ista: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. 2017. Functionality-aware retargeting of mechanisms to 3D shapes. SIGGRAPH: Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 81.' mla: Zhang, Ran, et al. Functionality-Aware Retargeting of Mechanisms to 3D Shapes. Vol. 36, no. 4, 81, ACM, 2017, doi:10.1145/3072959.3073710. short: R. Zhang, T. Auzinger, D. Ceylan, W. Li, B. Bickel, in:, ACM, 2017. conference: end_date: 2017-08-03 location: 'Los Angeles, CA, United States ' name: 'SIGGRAPH: Computer Graphics and Interactive Techniques' start_date: 2017-07-30 date_created: 2018-12-11T11:49:38Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-22T09:49:31Z day: '01' ddc: - '003' - '004' department: - _id: BeBi doi: 10.1145/3072959.3073710 ec_funded: 1 external_id: isi: - '000406432100049' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:09:05Z date_updated: 2018-12-12T10:09:05Z file_id: '4728' file_name: IST-2018-1050-v1+1_MechRet.pdf file_size: 25463895 relation: main_file file_date_updated: 2018-12-12T10:09:05Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '4' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '6396' pubrep_id: '1050' quality_controlled: '1' related_material: record: - id: '8386' relation: dissertation_contains status: public scopus_import: '1' status: public title: Functionality-aware retargeting of mechanisms to 3D shapes type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 36 year: '2017' ...