[{"citation":{"mla":"Reber, Stephan A., et al. “Early Life Differences in Behavioral Predispositions in Two Alligatoridae Species.” <i>Animal Cognition</i>, vol. 24, no. 4, Springer Nature, 2021, pp. 753–64, doi:<a href=\"https://doi.org/10.1007/s10071-020-01461-5\">10.1007/s10071-020-01461-5</a>.","short":"S.A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, A. Wilkinson, Animal Cognition 24 (2021) 753–764.","ieee":"S. A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, and A. Wilkinson, “Early life differences in behavioral predispositions in two Alligatoridae species,” <i>Animal Cognition</i>, vol. 24, no. 4. Springer Nature, pp. 753–764, 2021.","ista":"Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. 2021. Early life differences in behavioral predispositions in two Alligatoridae species. Animal Cognition. 24(4), 753–764.","chicago":"Reber, Stephan A., Jinook Oh, Judith Janisch, Colin Stevenson, Shaun Foggett, and Anna Wilkinson. “Early Life Differences in Behavioral Predispositions in Two Alligatoridae Species.” <i>Animal Cognition</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s10071-020-01461-5\">https://doi.org/10.1007/s10071-020-01461-5</a>.","ama":"Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. Early life differences in behavioral predispositions in two Alligatoridae species. <i>Animal Cognition</i>. 2021;24(4):753-764. doi:<a href=\"https://doi.org/10.1007/s10071-020-01461-5\">10.1007/s10071-020-01461-5</a>","apa":"Reber, S. A., Oh, J., Janisch, J., Stevenson, C., Foggett, S., &#38; Wilkinson, A. (2021). Early life differences in behavioral predispositions in two Alligatoridae species. <i>Animal Cognition</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10071-020-01461-5\">https://doi.org/10.1007/s10071-020-01461-5</a>"},"quality_controlled":"1","ddc":["590"],"publisher":"Springer Nature","scopus_import":"1","article_type":"original","department":[{"_id":"SyCr"}],"intvolume":"        24","day":"01","article_processing_charge":"No","oa_version":"Published Version","_id":"9101","title":"Early life differences in behavioral predispositions in two Alligatoridae species","author":[{"full_name":"Reber, Stephan A.","last_name":"Reber","first_name":"Stephan A."},{"id":"403169A4-080F-11EA-9993-BF3F3DDC885E","full_name":"Oh, Jinook","last_name":"Oh","first_name":"Jinook","orcid":"0000-0001-7425-2372"},{"full_name":"Janisch, Judith","first_name":"Judith","last_name":"Janisch"},{"full_name":"Stevenson, Colin","last_name":"Stevenson","first_name":"Colin"},{"last_name":"Foggett","first_name":"Shaun","full_name":"Foggett, Shaun"},{"first_name":"Anna","last_name":"Wilkinson","full_name":"Wilkinson, Anna"}],"date_created":"2021-02-07T23:01:13Z","external_id":{"pmid":["33454828"],"isi":["000608382100001"]},"date_updated":"2025-06-12T06:34:03Z","abstract":[{"text":"Behavioral predispositions are innate tendencies of animals to behave in a given way without the input of learning. They increase survival chances and, due to environmental and ecological challenges, may vary substantially even between closely related taxa. These differences are likely to be especially pronounced in long-lived species like crocodilians. This order is particularly relevant for comparative cognition due to its phylogenetic proximity to birds. Here we compared early life behavioral predispositions in two Alligatoridae species. We exposed American alligator and spectacled caiman hatchlings to three different novel situations: a novel object, a novel environment that was open and a novel environment with a shelter. This was then repeated a week later. During exposure to the novel environments, alligators moved around more and explored a larger range of the arena than the caimans. When exposed to the novel object, the alligators reduced the mean distance to the novel object in the second phase, while the caimans further increased it, indicating diametrically opposite ontogenetic development in behavioral predispositions. Although all crocodilian hatchlings face comparable challenges, e.g., high predation pressure, the effectiveness of parental protection might explain the observed pattern. American alligators are apex predators capable of protecting their offspring against most dangers, whereas adult spectacled caimans are frequently predated themselves. Their distancing behavior might be related to increased predator avoidance and also explain the success of invasive spectacled caimans in the natural habitats of other crocodilians.","lang":"eng"}],"publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-02-09T07:40:14Z","publication":"Animal Cognition","date_published":"2021-07-01T00:00:00Z","volume":24,"publication_identifier":{"issn":["1435-9448"],"eissn":["1435-9456"]},"status":"public","acknowledgement":"We thank Jamie Gilks and Terry Miles for their support at Crocodiles of the World. We are grateful to the Department of Cognitive Biology, University of Vienna for provision of working space and hardware. Finally, we would like to thank Cliodhna Quigley, Rachael Harrison and Urs A. Reber for discussion. Open Access funding provided by Lund University. This project was funded by the Marietta Blau grant (BMFWF) to S. A. R.","type":"journal_article","month":"07","isi":1,"oa":1,"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","creator":"dernst","success":1,"file_id":"9107","date_updated":"2021-02-09T07:40:14Z","file_name":"2021_AnimalCognition_Reber.pdf","checksum":"d9dfa0d1de6d684692b041d936dd858e","content_type":"application/pdf","file_size":1117991,"date_created":"2021-02-09T07:40:14Z","relation":"main_file"}],"has_accepted_license":"1","page":"753-764","doi":"10.1007/s10071-020-01461-5","issue":"4"},{"day":"01","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","_id":"9111","article_type":"original","scopus_import":"1","department":[{"_id":"HeEd"}],"intvolume":"         5","publisher":"Springer Nature","citation":{"apa":"Brown, A., Bobrowski, O., Munch, E., &#38; Wang, B. (2021). Probabilistic convergence and stability of random mapper graphs. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-020-00063-x\">https://doi.org/10.1007/s41468-020-00063-x</a>","ama":"Brown A, Bobrowski O, Munch E, Wang B. Probabilistic convergence and stability of random mapper graphs. <i>Journal of Applied and Computational Topology</i>. 2021;5(1):99-140. doi:<a href=\"https://doi.org/10.1007/s41468-020-00063-x\">10.1007/s41468-020-00063-x</a>","chicago":"Brown, Adam, Omer Bobrowski, Elizabeth Munch, and Bei Wang. “Probabilistic Convergence and Stability of Random Mapper Graphs.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s41468-020-00063-x\">https://doi.org/10.1007/s41468-020-00063-x</a>.","ista":"Brown A, Bobrowski O, Munch E, Wang B. 2021. Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. 5(1), 99–140.","ieee":"A. Brown, O. Bobrowski, E. Munch, and B. Wang, “Probabilistic convergence and stability of random mapper graphs,” <i>Journal of Applied and Computational Topology</i>, vol. 5, no. 1. Springer Nature, pp. 99–140, 2021.","mla":"Brown, Adam, et al. “Probabilistic Convergence and Stability of Random Mapper Graphs.” <i>Journal of Applied and Computational Topology</i>, vol. 5, no. 1, Springer Nature, 2021, pp. 99–140, doi:<a href=\"https://doi.org/10.1007/s41468-020-00063-x\">10.1007/s41468-020-00063-x</a>.","short":"A. Brown, O. Bobrowski, E. Munch, B. Wang, Journal of Applied and Computational Topology 5 (2021) 99–140."},"quality_controlled":"1","ddc":["510"],"date_published":"2021-03-01T00:00:00Z","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Journal of Applied and Computational Topology","file_date_updated":"2021-02-11T14:43:59Z","date_updated":"2025-04-14T07:43:51Z","abstract":[{"text":"We study the probabilistic convergence between the mapper graph and the Reeb graph of a topological space X equipped with a continuous function f:X→R. We first give a categorification of the mapper graph and the Reeb graph by interpreting them in terms of cosheaves and stratified covers of the real line R. We then introduce a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium on point-based graphics, 2007), referred to as the enhanced mapper graph, and demonstrate that such a construction approximates the Reeb graph of (X,f) when it is applied to points randomly sampled from a probability density function concentrated on (X,f). Our techniques are based on the interleaving distance of constructible cosheaves and topological estimation via kernel density estimates. Following Munch and Wang (In: 32nd international symposium on computational geometry, volume 51 of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany, pp 53:1–53:16, 2016), we first show that the mapper graph of (X,f), a constructible R-space (with a fixed open cover), approximates the Reeb graph of the same space. We then construct an isomorphism between the mapper of (X,f) to the mapper of a super-level set of a probability density function concentrated on (X,f). Finally, building on the approach of Bobrowski et al. (Bernoulli 23(1):288–328, 2017b), we show that, with high probability, we can recover the mapper of the super-level set given a sufficiently large sample. Our work is the first to consider the mapper construction using the theory of cosheaves in a probabilistic setting. It is part of an ongoing effort to combine sheaf theory, probability, and statistics, to support topological data analysis with random data.","lang":"eng"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam","last_name":"Brown"},{"full_name":"Bobrowski, Omer","last_name":"Bobrowski","first_name":"Omer"},{"first_name":"Elizabeth","last_name":"Munch","full_name":"Munch, Elizabeth"},{"first_name":"Bei","last_name":"Wang","full_name":"Wang, Bei"}],"title":"Probabilistic convergence and stability of random mapper graphs","date_created":"2021-02-11T14:41:02Z","external_id":{"arxiv":["1909.03488"]},"type":"journal_article","acknowledgement":"AB was supported in part by the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Sklodowska-Curie GrantAgreement No. 754411 and NSF IIS-1513616. OB was supported in part by the Israel Science Foundation, Grant 1965/19. BW was supported in part by NSF IIS-1513616 and DBI-1661375. EM was supported in part by NSF CMMI-1800466, DMS-1800446, and CCF-1907591.We would like to thank the Institute for Mathematics and its Applications for hosting a workshop titled Bridging Statistics and Sheaves in May 2018, where this work was conceived.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria).","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"ec_funded":1,"status":"public","volume":5,"page":"99-140","has_accepted_license":"1","issue":"1","doi":"10.1007/s41468-020-00063-x","oa":1,"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"9112","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_created":"2021-02-11T14:43:59Z","file_name":"2020_JourApplCompTopology_Brown.pdf","date_updated":"2021-02-11T14:43:59Z","content_type":"application/pdf","checksum":"3f02e9d47c428484733da0f588a3c069","file_size":2090265}],"language":[{"iso":"eng"}],"arxiv":1,"month":"03"},{"publication_identifier":{"eissn":["2168-0485"]},"status":"public","volume":9,"type":"journal_article","acknowledgement":"M.O.T. acknowledges DST/TMD/HFC/2 K18/58, DST-SERB, MHRD fast track, and DST Nanomission forfinancialassistance. Z.M.B. acknowledges CSIR-SRF fellowship fromMHRD, India. S.A.F. acknowledges support from IST Austria.","isi":1,"month":"02","page":"3104-3111","issue":"8","doi":"10.1021/acssuschemeng.0c07547","year":"2021","language":[{"iso":"eng"}],"publisher":"American Chemical Society","quality_controlled":"1","citation":{"ista":"Manzoor Bhat ZM, Thimmappa R, Dargily NC, Raafik A, Kottaichamy AR, Devendrachari MC, Itagi M,  Makri Nimbegondi Kotresh H, Freunberger SA, Ottakam Thotiyl M. 2021. Ambient condition alcohol reforming to hydrogen with electricity output. ACS Sustainable Chemistry and Engineering. 9(8), 3104–3111.","ieee":"Z. M. Manzoor Bhat <i>et al.</i>, “Ambient condition alcohol reforming to hydrogen with electricity output,” <i>ACS Sustainable Chemistry and Engineering</i>, vol. 9, no. 8. American Chemical Society, pp. 3104–3111, 2021.","mla":"Manzoor Bhat, Zahid Manzoor, et al. “Ambient Condition Alcohol Reforming to Hydrogen with Electricity Output.” <i>ACS Sustainable Chemistry and Engineering</i>, vol. 9, no. 8, American Chemical Society, 2021, pp. 3104–11, doi:<a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">10.1021/acssuschemeng.0c07547</a>.","short":"Z.M. Manzoor Bhat, R. Thimmappa, N.C. Dargily, A. Raafik, A.R. Kottaichamy, M.C. Devendrachari, M. Itagi, H.  Makri Nimbegondi Kotresh, S.A. Freunberger, M. Ottakam Thotiyl, ACS Sustainable Chemistry and Engineering 9 (2021) 3104–3111.","ama":"Manzoor Bhat ZM, Thimmappa R, Dargily NC, et al. Ambient condition alcohol reforming to hydrogen with electricity output. <i>ACS Sustainable Chemistry and Engineering</i>. 2021;9(8):3104-3111. doi:<a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">10.1021/acssuschemeng.0c07547</a>","apa":"Manzoor Bhat, Z. M., Thimmappa, R., Dargily, N. C., Raafik, A., Kottaichamy, A. R., Devendrachari, M. C., … Ottakam Thotiyl, M. (2021). Ambient condition alcohol reforming to hydrogen with electricity output. <i>ACS Sustainable Chemistry and Engineering</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">https://doi.org/10.1021/acssuschemeng.0c07547</a>","chicago":"Manzoor Bhat, Zahid Manzoor, Ravikumar Thimmappa, Neethu Christudas  Dargily, Abdul  Raafik, Alagar Raja  Kottaichamy, Mruthyunjayachari Chattanahalli  Devendrachari, Mahesh Itagi, Harish  Makri Nimbegondi Kotresh, Stefan Alexander Freunberger, and Musthafa  Ottakam Thotiyl. “Ambient Condition Alcohol Reforming to Hydrogen with Electricity Output.” <i>ACS Sustainable Chemistry and Engineering</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">https://doi.org/10.1021/acssuschemeng.0c07547</a>."},"day":"11","oa_version":"None","article_processing_charge":"No","_id":"9113","article_type":"original","scopus_import":"1","department":[{"_id":"StFr"}],"intvolume":"         9","date_updated":"2024-10-09T21:00:24Z","abstract":[{"text":"“Hydrogen economy” could enable a carbon-neutral sustainable energy chain. However, issues with safety, storage, and transport of molecular hydrogen impede its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art reforming is difficult, requiring high temperatures >200 °C and pressures >25 bar, and the resulting H2 is carbonized beyond tolerance levels for direct use in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization energy between the alkaline anode and the acidic cathode drives the process, particularly the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature coefficient of the resulting electromotive force allows us to harvest a large fraction of the output energy from the surrounding, achieving a thermodynamic efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming even under open-air conditions, a challenge that state-of-the-art alcohol reforming failed to overcome. We further show reforming of a wide range of alcohols. The ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously captured and pure H2 produced at mild conditions.","lang":"eng"}],"author":[{"first_name":"Zahid Manzoor","last_name":"Manzoor Bhat","full_name":"Manzoor Bhat, Zahid Manzoor"},{"full_name":"Thimmappa, Ravikumar","first_name":"Ravikumar","last_name":"Thimmappa"},{"full_name":"Dargily, Neethu Christudas ","last_name":"Dargily","first_name":"Neethu Christudas "},{"first_name":"Abdul ","last_name":"Raafik","full_name":"Raafik, Abdul "},{"first_name":"Alagar Raja ","last_name":"Kottaichamy","full_name":"Kottaichamy, Alagar Raja "},{"full_name":"Devendrachari, Mruthyunjayachari Chattanahalli ","last_name":"Devendrachari","first_name":"Mruthyunjayachari Chattanahalli "},{"last_name":"Itagi","first_name":"Mahesh","full_name":"Itagi, Mahesh"},{"full_name":" Makri Nimbegondi Kotresh, Harish","first_name":"Harish","last_name":" Makri Nimbegondi Kotresh"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander"},{"last_name":"Ottakam Thotiyl","first_name":"Musthafa ","full_name":"Ottakam Thotiyl, Musthafa "}],"title":"Ambient condition alcohol reforming to hydrogen with electricity output","date_created":"2021-02-12T09:20:18Z","external_id":{"isi":["000625460400010"]},"date_published":"2021-02-11T00:00:00Z","corr_author":"1","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"ACS Sustainable Chemistry and Engineering"},{"language":[{"iso":"eng"}],"year":"2021","oa":1,"doi":"10.1111/1755-0998.13323","page":"2629-2644","month":"01","isi":1,"type":"journal_article","volume":21,"status":"public","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"publication":"Molecular Ecology Resources","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","pmid":1,"corr_author":"1","date_published":"2021-01-15T00:00:00Z","date_created":"2021-02-14T23:01:14Z","external_id":{"pmid":["33448666"],"isi":["000614183100001"]},"title":"DILS: Demographic inferences with linked selection by using ABC","author":[{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Popovic, Iva","first_name":"Iva","last_name":"Popovic"},{"full_name":"Mazoyer, Clément","first_name":"Clément","last_name":"Mazoyer"},{"full_name":"Spataro, Bruno","last_name":"Spataro","first_name":"Bruno"},{"first_name":"Stéphane","last_name":"Delmotte","full_name":"Delmotte, Stéphane"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"last_name":"Loire","first_name":"Étienne","full_name":"Loire, Étienne"},{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"first_name":"Laurent","last_name":"Duret","full_name":"Duret, Laurent"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"},{"full_name":"Vekemans, Xavier","first_name":"Xavier","last_name":"Vekemans"},{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"}],"abstract":[{"lang":"eng","text":"We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species."}],"date_updated":"2025-06-12T06:34:23Z","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2","open_access":"1"}],"intvolume":"        21","department":[{"_id":"NiBa"}],"scopus_import":"1","article_type":"original","_id":"9119","article_processing_charge":"No","oa_version":"Preprint","day":"15","quality_controlled":"1","citation":{"chicago":"Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>.","ama":"Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. 2021;21:2629-2644. doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>","apa":"Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>","short":"C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644.","mla":"Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>, vol. 21, Wiley, 2021, pp. 2629–44, doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>.","ieee":"C. Fraisse <i>et al.</i>, “DILS: Demographic inferences with linked selection by using ABC,” <i>Molecular Ecology Resources</i>, vol. 21. Wiley, pp. 2629–2644, 2021.","ista":"Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644."},"publisher":"Wiley"},{"file_date_updated":"2021-02-15T09:31:07Z","publication":"Letters in Mathematical Physics","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"20","date_published":"2021-02-12T00:00:00Z","title":"The BCS energy gap at low density","author":[{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard"}],"date_created":"2021-02-15T09:27:14Z","external_id":{"isi":["000617531900001"]},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"lang":"eng","text":"We show that the energy gap for the BCS gap equation is\r\nΞ=μ(8e−2+o(1))exp(π2μ−−√a)\r\nin the low density limit μ→0. Together with the similar result for the critical temperature by Hainzl and Seiringer (Lett Math Phys 84: 99–107, 2008), this shows that, in the low density limit, the ratio of the energy gap and critical temperature is a universal constant independent of the interaction potential V. The results hold for a class of potentials with negative scattering length a and no bound states."}],"date_updated":"2025-04-15T06:53:09Z","department":[{"_id":"GradSch"}],"intvolume":"       111","scopus_import":"1","article_type":"original","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","_id":"9121","day":"12","ddc":["510"],"citation":{"short":"A.B. Lauritsen, Letters in Mathematical Physics 111 (2021).","mla":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” <i>Letters in Mathematical Physics</i>, vol. 111, 20, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01358-5\">10.1007/s11005-021-01358-5</a>.","ieee":"A. B. Lauritsen, “The BCS energy gap at low density,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","ista":"Lauritsen AB. 2021. The BCS energy gap at low density. Letters in Mathematical Physics. 111, 20.","chicago":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01358-5\">https://doi.org/10.1007/s11005-021-01358-5</a>.","ama":"Lauritsen AB. The BCS energy gap at low density. <i>Letters in Mathematical Physics</i>. 2021;111. doi:<a href=\"https://doi.org/10.1007/s11005-021-01358-5\">10.1007/s11005-021-01358-5</a>","apa":"Lauritsen, A. B. (2021). The BCS energy gap at low density. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01358-5\">https://doi.org/10.1007/s11005-021-01358-5</a>"},"quality_controlled":"1","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"9122","access_level":"open_access","success":1,"creator":"dernst","date_created":"2021-02-15T09:31:07Z","relation":"main_file","content_type":"application/pdf","checksum":"eaf1b3ff5026f120f0929a5c417dc842","file_size":329332,"date_updated":"2021-02-15T09:31:07Z","file_name":"2021_LettersMathPhysics_Lauritsen.pdf"}],"language":[{"iso":"eng"}],"oa":1,"year":"2021","has_accepted_license":"1","doi":"10.1007/s11005-021-01358-5","month":"02","isi":1,"acknowledgement":"Most of this work was done as part of the author’s master’s thesis. The author would like to thank Jan Philip Solovej for his supervision of this process.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria)","type":"journal_article","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"volume":111,"status":"public","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]}},{"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_created":"2021-02-17T17:48:46Z","external_id":{"isi":["000605080300001"]},"author":[{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","full_name":"De Nicola, Stefano","last_name":"De Nicola","first_name":"Stefano","orcid":"0000-0002-4842-6671"}],"title":"Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation","date_updated":"2025-04-14T07:43:51Z","abstract":[{"lang":"eng","text":"While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publication":"Journal of Statistical Mechanics: Theory and Experiment","file_date_updated":"2021-02-19T14:04:40Z","date_published":"2021-01-05T00:00:00Z","article_number":"013101","quality_controlled":"1","citation":{"chicago":"De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States: Field Theory and Stochastic Simulation.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">https://doi.org/10.1088/1742-5468/abc7c7</a>.","ama":"De Nicola S. Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2021;2021(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">10.1088/1742-5468/abc7c7</a>","apa":"De Nicola, S. (2021). Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">https://doi.org/10.1088/1742-5468/abc7c7</a>","mla":"De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States: Field Theory and Stochastic Simulation.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2021, no. 1, 013101, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">10.1088/1742-5468/abc7c7</a>.","short":"S. De Nicola, Journal of Statistical Mechanics: Theory and Experiment 2021 (2021).","ieee":"S. De Nicola, “Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2021, no. 1. IOP Publishing, 2021.","ista":"De Nicola S. 2021. Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory and Experiment. 2021(1), 013101."},"ddc":["530"],"publisher":"IOP Publishing","scopus_import":"1","article_type":"original","intvolume":"      2021","department":[{"_id":"MaSe"}],"day":"05","_id":"9158","article_processing_charge":"No","oa_version":"Published Version","month":"01","isi":1,"year":"2021","oa":1,"file":[{"access_level":"open_access","success":1,"creator":"dernst","file_id":"9172","file_size":1693609,"content_type":"application/pdf","checksum":"64e2aae4837790db26e1dd1986c69c07","date_updated":"2021-02-19T14:04:40Z","file_name":"2021_JourStatMech_deNicola.pdf","date_created":"2021-02-19T14:04:40Z","relation":"main_file"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"1","doi":"10.1088/1742-5468/abc7c7","has_accepted_license":"1","volume":2021,"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability","Statistical and Nonlinear Physics"],"publication_identifier":{"issn":["1742-5468"]},"status":"public","ec_funded":1,"acknowledgement":"S D N would like to thank M J Bhaseen, J Chalker, B Doyon, V Gritsev, A Lamacraft,\r\nA Michailidis and M Serbyn for helpful feedback and stimulating conversations. S D N\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and\r\nfrom the European Union’s Horizon 2020 research and innovation program under the\r\nMarie Sk\blodowska-Curie Grant Agreement No. 754411. S D N also acknowledges funding\r\nfrom the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to Non-\r\nEquilibrium Systems (CANES) under Grant EP/L015854/1. S D N is grateful to IST\r\nAustria for providing open access funding.","type":"journal_article"},{"day":"01","_id":"9168","article_processing_charge":"No","oa_version":"Published Version","article_type":"original","scopus_import":"1","intvolume":"       217","department":[{"_id":"NiBa"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Genetics Society of America","quality_controlled":"1","citation":{"chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>. Genetics Society of America, 2021. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. 2021;217(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>","apa":"Fraisse, C., &#38; Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” <i>Genetics</i>, vol. 217, no. 2. Genetics Society of America, 2021.","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>.","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025."},"date_published":"2021-02-01T00:00:00Z","article_number":"iyaa025","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","publication":"Genetics","date_updated":"2025-06-12T06:34:41Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"abstract":[{"text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.","lang":"eng"}],"project":[{"call_identifier":"FWF","grant_number":"M02463","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-02-18T14:41:30Z","external_id":{"isi":["000637218100005"],"pmid":["33724409"]},"author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}],"title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","type":"journal_article","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","publication_identifier":{"issn":["1943-2631"]},"status":"public","volume":217,"issue":"2","doi":"10.1093/genetics/iyaa025","year":"2021","oa":1,"language":[{"iso":"eng"}],"isi":1,"month":"02"},{"acknowledgement":"I would like to thank M. Zdanwociz for various mathematical discussions which lead to this article, Tamas Hausel for hosting me in his research group at IST Austria and the anonymous referee for their helpful suggestions and comments. This research has received funding from the European Union's Horizon 2020 Marie Sklodowska-Curie Actions Grant No. 754411 and Institue of Science and Technology Austria IST-PLUS Grant No. 754411.","type":"journal_article","volume":167,"publication_identifier":{"issn":["0007-4497"]},"ec_funded":1,"status":"public","oa":1,"year":"2021","language":[{"iso":"eng"}],"doi":"10.1016/j.bulsci.2021.102957","issue":"03","month":"03","arxiv":1,"isi":1,"article_type":"original","scopus_import":"1","department":[{"_id":"TaHa"}],"intvolume":"       167","day":"01","article_processing_charge":"No","oa_version":"Preprint","_id":"9173","quality_controlled":"1","citation":{"chicago":"Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular Enriques Surface.” <i>Bulletin Des Sciences Mathematiques</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">https://doi.org/10.1016/j.bulsci.2021.102957</a>.","apa":"Srivastava, T. K. (2021). Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. <i>Bulletin Des Sciences Mathematiques</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">https://doi.org/10.1016/j.bulsci.2021.102957</a>","ama":"Srivastava TK. Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. <i>Bulletin des Sciences Mathematiques</i>. 2021;167(03). doi:<a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">10.1016/j.bulsci.2021.102957</a>","mla":"Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular Enriques Surface.” <i>Bulletin Des Sciences Mathematiques</i>, vol. 167, no. 03, 102957, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">10.1016/j.bulsci.2021.102957</a>.","short":"T.K. Srivastava, Bulletin Des Sciences Mathematiques 167 (2021).","ieee":"T. K. Srivastava, “Pathologies of the Hilbert scheme of points of a supersingular Enriques surface,” <i>Bulletin des Sciences Mathematiques</i>, vol. 167, no. 03. Elsevier, 2021.","ista":"Srivastava TK. 2021. Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. Bulletin des Sciences Mathematiques. 167(03), 102957."},"publisher":"Elsevier","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Bulletin des Sciences Mathematiques","date_published":"2021-03-01T00:00:00Z","article_number":"102957","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"4D046628-F248-11E8-B48F-1D18A9856A87","full_name":"Srivastava, Tanya K","first_name":"Tanya K","last_name":"Srivastava"}],"title":"Pathologies of the Hilbert scheme of points of a supersingular Enriques surface","date_created":"2021-02-21T23:01:20Z","external_id":{"isi":["000623881600009"],"arxiv":["2010.08976"]},"main_file_link":[{"url":"https://arxiv.org/abs/2010.08976","open_access":"1"}],"date_updated":"2025-04-14T07:43:51Z","abstract":[{"lang":"eng","text":"We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem."}]},{"keyword":["Cell Biology","Cellular and Molecular Neuroscience"],"volume":145,"ec_funded":1,"status":"public","publication_identifier":{"issn":["0197-0186"]},"acknowledgement":"We thank Melissa Stouffer for critically reading the manuscript. This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung n[f + b] life science call grant (C13-002) to S.H. and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","type":"journal_article","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"05","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-08-11T12:30:38Z","relation":"main_file","file_size":7083499,"checksum":"c6d7a40089cd29e289f9b22e75768304","content_type":"application/pdf","date_updated":"2021-08-11T12:30:38Z","file_name":"2021_NCI_Pauler.pdf","file_id":"9883","access_level":"open_access","success":1,"creator":"kschuh"}],"oa":1,"year":"2021","has_accepted_license":"1","doi":"10.1016/j.neuint.2021.104986","issue":"5","ddc":["570"],"citation":{"ista":"Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. 2021. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry International. 145(5), 104986.","ieee":"F. Pauler, Q. Hudson, S. Laukoter, and S. Hippenmeyer, “Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond,” <i>Neurochemistry International</i>, vol. 145, no. 5. Elsevier, 2021.","short":"F. Pauler, Q. Hudson, S. Laukoter, S. Hippenmeyer, Neurochemistry International 145 (2021).","mla":"Pauler, Florian, et al. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” <i>Neurochemistry International</i>, vol. 145, no. 5, 104986, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">10.1016/j.neuint.2021.104986</a>.","apa":"Pauler, F., Hudson, Q., Laukoter, S., &#38; Hippenmeyer, S. (2021). Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. <i>Neurochemistry International</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">https://doi.org/10.1016/j.neuint.2021.104986</a>","ama":"Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. <i>Neurochemistry International</i>. 2021;145(5). doi:<a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">10.1016/j.neuint.2021.104986</a>","chicago":"Pauler, Florian, Quanah Hudson, Susanne Laukoter, and Simon Hippenmeyer. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” <i>Neurochemistry International</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">https://doi.org/10.1016/j.neuint.2021.104986</a>."},"quality_controlled":"1","publisher":"Elsevier","department":[{"_id":"SiHi"}],"intvolume":"       145","scopus_import":"1","article_type":"original","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","_id":"9188","day":"01","title":"Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond","author":[{"last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Quanah","last_name":"Hudson","full_name":"Hudson, Quanah"},{"full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","last_name":"Laukoter","first_name":"Susanne"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"date_created":"2021-02-23T12:31:43Z","external_id":{"pmid":["33600873"],"isi":["000635575000005"]},"project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"}],"abstract":[{"text":"Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues.","lang":"eng"}],"date_updated":"2025-04-14T07:43:04Z","file_date_updated":"2021-08-11T12:30:38Z","publication":"Neurochemistry International","pmid":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"104986","date_published":"2021-05-01T00:00:00Z"},{"author":[{"full_name":"Zhao, Y","last_name":"Zhao","first_name":"Y"},{"last_name":"Wu","first_name":"L","full_name":"Wu, L"},{"last_name":"Fu","first_name":"Q","full_name":"Fu, Q"},{"first_name":"D","last_name":"Wang","full_name":"Wang, D"},{"full_name":"Li, J","last_name":"Li","first_name":"J"},{"full_name":"Yao, B","last_name":"Yao","first_name":"B"},{"last_name":"Yu","first_name":"S","full_name":"Yu, S"},{"full_name":"Jiang, L","last_name":"Jiang","first_name":"L"},{"full_name":"Qian, J","first_name":"J","last_name":"Qian"},{"last_name":"Zhou","first_name":"X","full_name":"Zhou, X"},{"first_name":"L","last_name":"Han","full_name":"Han, L"},{"last_name":"Zhao","first_name":"S","full_name":"Zhao, S"},{"full_name":"Ma, C","last_name":"Ma","first_name":"C"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"full_name":"Luo, C","first_name":"C","last_name":"Luo"},{"last_name":"Dong","first_name":"Q","full_name":"Dong, Q"},{"full_name":"Li, S","first_name":"S","last_name":"Li"},{"full_name":"Zhang, L","last_name":"Zhang","first_name":"L"},{"first_name":"X","last_name":"Jiang","full_name":"Jiang, X"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"first_name":"H","last_name":"Luo","full_name":"Luo, H"},{"last_name":"Li","first_name":"K","full_name":"Li, K"},{"last_name":"Yang","first_name":"J","full_name":"Yang, J"},{"full_name":"Luo, Q","first_name":"Q","last_name":"Luo"},{"last_name":"Li","first_name":"L","full_name":"Li, L"},{"full_name":"Peng, S","first_name":"S","last_name":"Peng"},{"last_name":"Huang","first_name":"H","full_name":"Huang, H"},{"last_name":"Zuo","first_name":"Z","full_name":"Zuo, Z"},{"full_name":"Liu, C","last_name":"Liu","first_name":"C"},{"first_name":"L","last_name":"Wang","full_name":"Wang, L"},{"last_name":"Li","first_name":"C","full_name":"Li, C"},{"first_name":"X","last_name":"He","full_name":"He, X"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Y","last_name":"Du","full_name":"Du, Y"}],"title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","date_created":"2021-02-24T10:07:21Z","external_id":{"pmid":["33576018"],"isi":["000625398600001"]},"abstract":[{"text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.","lang":"eng"}],"date_updated":"2023-11-07T08:18:36Z","file_date_updated":"2023-11-02T17:02:11Z","publication":"Plant, Cell & Environment","publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-01T00:00:00Z","ddc":["580"],"citation":{"chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” <i>Plant, Cell &#38; Environment</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/pce.14029\">https://doi.org/10.1111/pce.14029</a>.","ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. <i>Plant, Cell &#38; Environment</i>. 2021;44(6):1846-1857. doi:<a href=\"https://doi.org/10.1111/pce.14029\">10.1111/pce.14029</a>","apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. <i>Plant, Cell &#38; Environment</i>. Wiley. <a href=\"https://doi.org/10.1111/pce.14029\">https://doi.org/10.1111/pce.14029</a>","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell &#38; Environment 44 (2021) 1846–1857.","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” <i>Plant, Cell &#38; Environment</i>, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:<a href=\"https://doi.org/10.1111/pce.14029\">10.1111/pce.14029</a>.","ieee":"Y. Zhao <i>et al.</i>, “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” <i>Plant, Cell &#38; Environment</i>, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell &#38; Environment. 44(6), 1846–1857."},"quality_controlled":"1","publisher":"Wiley","department":[{"_id":"JiFr"}],"intvolume":"        44","article_type":"original","scopus_import":"1","article_processing_charge":"No","oa_version":"Submitted Version","_id":"9189","day":"01","month":"06","isi":1,"language":[{"iso":"eng"}],"file":[{"file_id":"14481","access_level":"open_access","creator":"amally","success":1,"date_created":"2023-11-02T17:02:11Z","relation":"main_file","file_name":"Zhao PlantCellEnv 2021_accepted.pdf","date_updated":"2023-11-02T17:02:11Z","content_type":"application/pdf","file_size":8437528,"checksum":"a812418fede076741c9c4dc07f317068"}],"oa":1,"year":"2021","has_accepted_license":"1","page":"1846-1857","doi":"10.1111/pce.14029","issue":"6","volume":44,"status":"public","publication_identifier":{"eissn":["1365-3040"],"issn":["0140-7791"]},"type":"journal_article"},{"abstract":[{"text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"contributor":[{"contributor_type":"project_member","first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carina","last_name":"Baskett","contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David"},{"last_name":"Pickup","first_name":"Melinda","contributor_type":"project_member","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"date_updated":"2025-04-15T08:20:40Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","author":[{"first_name":"Parvathy","last_name":"Surendranadh","orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","first_name":"Louise S"},{"full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","last_name":"Baskett","first_name":"Carina"},{"orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2021-02-24T17:49:21Z","month":"02","has_accepted_license":"1","related_material":{"record":[{"relation":"earlier_version","id":"8254","status":"public"},{"id":"11321","status":"public","relation":"later_version"},{"id":"11411","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:9192","date_published":"2021-02-26T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/x-zip-compressed","checksum":"f85537815809a8a4b7da9d01163f88c0","file_size":5934452,"file_name":"Data_Code.zip","date_updated":"2021-02-24T17:45:13Z","relation":"main_file","date_created":"2021-02-24T17:45:13Z","success":1,"creator":"larathoo","access_level":"open_access","file_id":"9193"}],"file_date_updated":"2021-02-24T17:45:13Z","oa":1,"year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","status":"public","ddc":["576"],"citation":{"ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021).","mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>.","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","oa_version":"Published Version","type":"research_data","_id":"9192","day":"26","department":[{"_id":"GradSch"},{"_id":"NiBa"}]},{"publication_identifier":{"isbn":["9781450383394"]},"ec_funded":1,"status":"public","keyword":["hybrid automaton","membership","system identification"],"type":"conference","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","arxiv":1,"isi":1,"month":"05","has_accepted_license":"1","conference":{"start_date":"2021-05-19","end_date":"2021-05-21","location":"Nashville, TN, United States","name":"HSCC: Hybrid Systems - Computation and Control"},"page":"2102.12734","doi":"10.1145/3447928.3456704","oa":1,"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","success":1,"creator":"kschuh","file_id":"9424","checksum":"4c1202c1abf71384c3ee6fea88c2f80e","file_size":1474786,"content_type":"application/pdf","date_updated":"2021-05-25T13:53:22Z","file_name":"2021_HSCC_Soto.pdf","date_created":"2021-05-25T13:53:22Z","relation":"main_file"}],"language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","citation":{"apa":"Garcia Soto, M., Henzinger, T. A., &#38; Schilling, C. (2021). Synthesis of hybrid automata with affine dynamics from time-series data. In <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i> (p. 2102.12734). Nashville, TN, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3447928.3456704\">https://doi.org/10.1145/3447928.3456704</a>","ama":"Garcia Soto M, Henzinger TA, Schilling C. Synthesis of hybrid automata with affine dynamics from time-series data. In: <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>. Association for Computing Machinery; 2021:2102.12734. doi:<a href=\"https://doi.org/10.1145/3447928.3456704\">10.1145/3447928.3456704</a>","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” In <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, 2102.12734. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3447928.3456704\">https://doi.org/10.1145/3447928.3456704</a>.","ista":"Garcia Soto M, Henzinger TA, Schilling C. 2021. Synthesis of hybrid automata with affine dynamics from time-series data. HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 2102.12734.","mla":"Garcia Soto, Miriam, et al. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, Association for Computing Machinery, 2021, p. 2102.12734, doi:<a href=\"https://doi.org/10.1145/3447928.3456704\">10.1145/3447928.3456704</a>.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Association for Computing Machinery, 2021, p. 2102.12734.","ieee":"M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of hybrid automata with affine dynamics from time-series data,” in <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, Nashville, TN, United States, 2021, p. 2102.12734."},"ddc":["000"],"day":"01","oa_version":"Published Version","article_processing_charge":"No","_id":"9200","scopus_import":"1","department":[{"_id":"ToHe"}],"date_updated":"2025-07-10T12:01:40Z","abstract":[{"lang":"eng","text":"Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach."}],"project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"title":"Synthesis of hybrid automata with affine dynamics from time-series data","author":[{"orcid":"0000-0003-2936-5719","first_name":"Miriam","last_name":"Garcia Soto","full_name":"Garcia Soto, Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065"}],"external_id":{"isi":["000932821700028"],"arxiv":["2102.12734"]},"date_created":"2021-02-26T16:30:39Z","date_published":"2021-05-01T00:00:00Z","corr_author":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control","file_date_updated":"2021-05-25T13:53:22Z"},{"volume":14,"status":"public","publication_identifier":{"eissn":["1996-1944"]},"acknowledgement":"This work was supported by European Regional Development Funds and the Framework 7\r\nprogram under project UNION (FP7-NMP 310250). GSN acknowledges support from the US National Science Foundation under grant No. DMR-1748188. DC acknowledges support from COLCIENCIAS under project 120480863414. ","type":"journal_article","month":"02","isi":1,"file":[{"file_id":"9218","access_level":"open_access","success":1,"creator":"dernst","date_created":"2021-03-03T07:32:01Z","relation":"main_file","checksum":"76d6c7f97b810ce504ab151c9bf3524e","content_type":"application/pdf","file_size":2722517,"date_updated":"2021-03-03T07:32:01Z","file_name":"2021_Materials_Cadavid.pdf"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","oa":1,"doi":"10.3390/ma14040853","issue":"4","has_accepted_license":"1","ddc":["540"],"quality_controlled":"1","citation":{"short":"D. Cadavid, K. Wei, Y. Liu, Y. Zhang, M. Li, A. Genç, T. Berestok, M. Ibáñez, A. Shavel, G.S. Nolas, A. Cabot, Materials 14 (2021).","mla":"Cadavid, Doris, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” <i>Materials</i>, vol. 14, no. 4, 853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ma14040853\">10.3390/ma14040853</a>.","ieee":"D. Cadavid <i>et al.</i>, “Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks,” <i>Materials</i>, vol. 14, no. 4. MDPI, 2021.","ista":"Cadavid D, Wei K, Liu Y, Zhang Y, Li M, Genç A, Berestok T, Ibáñez M, Shavel A, Nolas GS, Cabot A. 2021. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. Materials. 14(4), 853.","chicago":"Cadavid, Doris, Kaya Wei, Yu Liu, Yu Zhang, Mengyao Li, Aziz Genç, Taisiia Berestok, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” <i>Materials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ma14040853\">https://doi.org/10.3390/ma14040853</a>.","apa":"Cadavid, D., Wei, K., Liu, Y., Zhang, Y., Li, M., Genç, A., … Cabot, A. (2021). Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. <i>Materials</i>. MDPI. <a href=\"https://doi.org/10.3390/ma14040853\">https://doi.org/10.3390/ma14040853</a>","ama":"Cadavid D, Wei K, Liu Y, et al. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. <i>Materials</i>. 2021;14(4). doi:<a href=\"https://doi.org/10.3390/ma14040853\">10.3390/ma14040853</a>"},"publisher":"MDPI","intvolume":"        14","department":[{"_id":"MaIb"}],"scopus_import":"1","article_type":"original","_id":"9206","article_processing_charge":"No","oa_version":"Published Version","day":"10","external_id":{"isi":["000624094100001"],"pmid":["33578981"]},"date_created":"2021-02-28T23:01:24Z","author":[{"first_name":"Doris","last_name":"Cadavid","full_name":"Cadavid, Doris"},{"first_name":"Kaya","last_name":"Wei","full_name":"Wei, Kaya"},{"first_name":"Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"first_name":"Taisiia","last_name":"Berestok","full_name":"Berestok, Taisiia"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"full_name":"Nolas, George S.","first_name":"George S.","last_name":"Nolas"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"title":"Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks","abstract":[{"text":"The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS. ","lang":"eng"}],"date_updated":"2025-06-12T06:35:03Z","file_date_updated":"2021-03-03T07:32:01Z","publication":"Materials","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","pmid":1,"article_number":"853","date_published":"2021-02-10T00:00:00Z"},{"volume":912,"publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"status":"public","ec_funded":1,"acknowledgement":"We thank Y. Duguet, S. Gomé, G. Lemoult, T. Liu, B. Semin and L.S. Tuckerman for\r\nfruitful discussions. \r\nThis work was supported by a grant, TRANSFLOW, provided by the Agence Nationale de\r\nla Recherche (ANR). A.M.P. was partially supported by the French Embassy in Russia (I.I. Mechnikov scholarship) and by the Russian Science Foundation (project no. 18-79-00189). L.K. was partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","type":"journal_article","month":"02","isi":1,"year":"2021","oa":1,"file":[{"access_level":"open_access","creator":"dernst","success":1,"file_id":"9220","file_name":"2021_JourFluidMechanics_Klotz.pdf","date_updated":"2021-03-03T09:49:34Z","content_type":"application/pdf","file_size":4124471,"checksum":"b8020d6338667673e34fde0608913dd2","date_created":"2021-03-03T09:49:34Z","relation":"main_file"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1017/jfm.2020.1089","has_accepted_license":"1","quality_controlled":"1","citation":{"chicago":"Klotz, Lukasz, A. M. Pavlenko, and J. E. Wesfreid. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/jfm.2020.1089\">https://doi.org/10.1017/jfm.2020.1089</a>.","apa":"Klotz, L., Pavlenko, A. M., &#38; Wesfreid, J. E. (2021). Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2020.1089\">https://doi.org/10.1017/jfm.2020.1089</a>","ama":"Klotz L, Pavlenko AM, Wesfreid JE. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. <i>Journal of Fluid Mechanics</i>. 2021;912. doi:<a href=\"https://doi.org/10.1017/jfm.2020.1089\">10.1017/jfm.2020.1089</a>","short":"L. Klotz, A.M. Pavlenko, J.E. Wesfreid, Journal of Fluid Mechanics 912 (2021).","mla":"Klotz, Lukasz, et al. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” <i>Journal of Fluid Mechanics</i>, vol. 912, A24, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/jfm.2020.1089\">10.1017/jfm.2020.1089</a>.","ieee":"L. Klotz, A. M. Pavlenko, and J. E. Wesfreid, “Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow,” <i>Journal of Fluid Mechanics</i>, vol. 912. Cambridge University Press, 2021.","ista":"Klotz L, Pavlenko AM, Wesfreid JE. 2021. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. Journal of Fluid Mechanics. 912, A24."},"ddc":["530"],"publisher":"Cambridge University Press","scopus_import":"1","article_type":"original","intvolume":"       912","department":[{"_id":"BjHo"}],"day":"15","_id":"9207","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"date_created":"2021-02-28T23:01:25Z","external_id":{"isi":["000618034400001"]},"author":[{"orcid":"0000-0003-1740-7635","first_name":"Lukasz","last_name":"Klotz","full_name":"Klotz, Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlenko, A. M.","last_name":"Pavlenko","first_name":"A. M."},{"last_name":"Wesfreid","first_name":"J. E.","full_name":"Wesfreid, J. E."}],"title":"Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow","date_updated":"2025-04-14T07:43:51Z","abstract":[{"text":"In this paper we experimentally study the transitional range of Reynolds numbers in\r\nplane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures\r\ntriggered by a strong impulsive jet and the large-scale flow generated around these\r\nstructures. We present a detailed investigation of the large-scale flow and show how\r\nits amplitude depends on Reynolds number and amplitude perturbation. In addition,\r\nwe characterize the initial dynamics of the localized turbulent spot, which includes the\r\ncoupling between the small and large scales, as well as the dependence of the advection\r\nspeed on the large-scale flow generated around the spot. Finally, we provide the first\r\nexperimental measurements of the large-scale flow around an oblique turbulent band.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publication":"Journal of Fluid Mechanics","file_date_updated":"2021-03-03T09:49:34Z","date_published":"2021-02-15T00:00:00Z","article_number":"A24"},{"ddc":["510"],"citation":{"chicago":"Volhejn, Vaclav, and Christoph Lampert. “Does SGD Implicitly Optimize for Smoothness?” In <i>42nd German Conference on Pattern Recognition</i>, 12544:246–59. LNCS. Springer, 2021. <a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">https://doi.org/10.1007/978-3-030-71278-5_18</a>.","ama":"Volhejn V, Lampert C. Does SGD implicitly optimize for smoothness? In: <i>42nd German Conference on Pattern Recognition</i>. Vol 12544. LNCS. Springer; 2021:246-259. doi:<a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">10.1007/978-3-030-71278-5_18</a>","apa":"Volhejn, V., &#38; Lampert, C. (2021). Does SGD implicitly optimize for smoothness? In <i>42nd German Conference on Pattern Recognition</i> (Vol. 12544, pp. 246–259). Tübingen, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">https://doi.org/10.1007/978-3-030-71278-5_18</a>","ieee":"V. Volhejn and C. Lampert, “Does SGD implicitly optimize for smoothness?,” in <i>42nd German Conference on Pattern Recognition</i>, Tübingen, Germany, 2021, vol. 12544, pp. 246–259.","mla":"Volhejn, Vaclav, and Christoph Lampert. “Does SGD Implicitly Optimize for Smoothness?” <i>42nd German Conference on Pattern Recognition</i>, vol. 12544, Springer, 2021, pp. 246–59, doi:<a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">10.1007/978-3-030-71278-5_18</a>.","short":"V. Volhejn, C. Lampert, in:, 42nd German Conference on Pattern Recognition, Springer, 2021, pp. 246–259.","ista":"Volhejn V, Lampert C. 2021. Does SGD implicitly optimize for smoothness? 42nd German Conference on Pattern Recognition. DAGM GCPR: German Conference on Pattern Recognition LNCS vol. 12544, 246–259."},"quality_controlled":"1","publisher":"Springer","intvolume":"     12544","department":[{"_id":"ChLa"}],"scopus_import":"1","_id":"9210","article_processing_charge":"No","oa_version":"Submitted Version","day":"17","date_created":"2021-03-01T09:01:16Z","external_id":{"isi":["001500603200018"]},"author":[{"id":"d5235fb4-7a6d-11eb-b254-f25d12d631a8","full_name":"Volhejn, Vaclav","first_name":"Vaclav","last_name":"Volhejn"},{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"title":"Does SGD implicitly optimize for smoothness?","abstract":[{"lang":"eng","text":"Modern neural networks can easily fit their training set perfectly. Surprisingly, despite being “overfit” in this way, they tend to generalize well to future data, thereby defying the classic bias–variance trade-off of machine learning theory. Of the many possible explanations, a prevalent one is that training by stochastic gradient descent (SGD) imposes an implicit bias that leads it to learn simple functions, and these simple functions generalize well. However, the specifics of this implicit bias are not well understood.\r\nIn this work, we explore the smoothness conjecture which states that SGD is implicitly biased towards learning functions that are smooth. We propose several measures to formalize the intuitive notion of smoothness, and we conduct experiments to determine whether SGD indeed implicitly optimizes for these measures. Our findings rule out the possibility that smoothness measures based on first-order derivatives are being implicitly enforced. They are supportive, though, of the smoothness conjecture for measures based on second-order derivatives."}],"date_updated":"2025-09-10T10:00:33Z","publication":"42nd German Conference on Pattern Recognition","file_date_updated":"2022-08-12T07:27:58Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","date_published":"2021-03-17T00:00:00Z","volume":12544,"status":"public","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030712778"],"issn":["0302-9743"]},"series_title":"LNCS","type":"conference","month":"03","isi":1,"file":[{"date_created":"2022-08-12T07:27:58Z","relation":"main_file","content_type":"application/pdf","checksum":"3e3628ab1cf658d82524963f808004ea","file_size":420234,"date_updated":"2022-08-12T07:27:58Z","file_name":"2020_GCPR_submitted_Volhejn.pdf","file_id":"11820","access_level":"open_access","success":1,"creator":"dernst"}],"language":[{"iso":"eng"}],"year":"2021","oa":1,"doi":"10.1007/978-3-030-71278-5_18","page":"246-259","conference":{"start_date":"2020-09-28","location":"Tübingen, Germany","end_date":"2020-10-01","name":"DAGM GCPR: German Conference on Pattern Recognition "},"has_accepted_license":"1"},{"month":"07","isi":1,"year":"2021","oa":1,"language":[{"iso":"eng"}],"issue":"7","doi":"10.1101/cshperspect.a039941","volume":13,"publication_identifier":{"issn":["1943-0264"]},"status":"public","acknowledgement":"We apologize to all the authors whose scientific work could not be cited and discussed because of space restrictions. We thank Dr. Inge Verstraeten (ISTAustria) and Dr. Juan Carlos Montesinos-Lopez (ETH Zürich) for helpful suggestions. This work was supported by the DOC Fellowship Programme of the Austrian Academy of Sciences (25008) to C.A.","type":"journal_article","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"external_id":{"isi":["000692069100001"],"pmid":["33558367"]},"date_created":"2021-03-01T10:08:32Z","author":[{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","first_name":"Nicola"},{"last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Auxin-regulated lateral root organogenesis","date_updated":"2025-04-15T06:37:14Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039941"}],"abstract":[{"lang":"eng","text":"Plant fitness is largely dependent on the root, the underground organ, which, besides its anchoring function, supplies the plant body with water and all nutrients necessary for growth and development. To exploit the soil effectively, roots must constantly integrate environmental signals and react through adjustment of growth and development. Important components of the root management strategy involve a rapid modulation of the root growth kinetics and growth direction, as well as an increase of the root system radius through formation of lateral roots (LRs). At the molecular level, such a fascinating growth and developmental flexibility of root organ requires regulatory networks that guarantee stability of the developmental program but also allows integration of various environmental inputs. The plant hormone auxin is one of the principal endogenous regulators of root system architecture by controlling primary root growth and formation of LR. In this review, we discuss recent progress in understanding molecular networks where auxin is one of the main players shaping the root system and acting as mediator between endogenous cues and environmental factors."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","publication":"Cold Spring Harbor Perspectives in Biology","date_published":"2021-07-01T00:00:00Z","article_number":"a039941","corr_author":"1","quality_controlled":"1","citation":{"ama":"Cavallari N, Artner C, Benková E. Auxin-regulated lateral root organogenesis. <i>Cold Spring Harbor Perspectives in Biology</i>. 2021;13(7). doi:<a href=\"https://doi.org/10.1101/cshperspect.a039941\">10.1101/cshperspect.a039941</a>","apa":"Cavallari, N., Artner, C., &#38; Benková, E. (2021). Auxin-regulated lateral root organogenesis. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a039941\">https://doi.org/10.1101/cshperspect.a039941</a>","chicago":"Cavallari, Nicola, Christina Artner, and Eva Benková. “Auxin-Regulated Lateral Root Organogenesis.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2021. <a href=\"https://doi.org/10.1101/cshperspect.a039941\">https://doi.org/10.1101/cshperspect.a039941</a>.","ista":"Cavallari N, Artner C, Benková E. 2021. Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. 13(7), a039941.","ieee":"N. Cavallari, C. Artner, and E. Benková, “Auxin-regulated lateral root organogenesis,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 13, no. 7. Cold Spring Harbor Laboratory Press, 2021.","mla":"Cavallari, Nicola, et al. “Auxin-Regulated Lateral Root Organogenesis.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 13, no. 7, a039941, Cold Spring Harbor Laboratory Press, 2021, doi:<a href=\"https://doi.org/10.1101/cshperspect.a039941\">10.1101/cshperspect.a039941</a>.","short":"N. Cavallari, C. Artner, E. Benková, Cold Spring Harbor Perspectives in Biology 13 (2021)."},"publisher":"Cold Spring Harbor Laboratory Press","scopus_import":"1","article_type":"original","intvolume":"        13","department":[{"_id":"EvBe"}],"day":"01","_id":"9212","article_processing_charge":"No","oa_version":"Published Version"},{"issue":"4","doi":"10.1016/j.aop.2021.168415","language":[{"iso":"eng"}],"oa":1,"year":"2021","arxiv":1,"isi":1,"month":"04","type":"journal_article","status":"public","publication_identifier":{"issn":["0003-4916"],"eissn":["1096-035X"]},"volume":427,"article_number":"168415","date_published":"2021-04-01T00:00:00Z","publication":"Annals of Physics","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.04501"}],"date_updated":"2025-07-10T12:01:41Z","author":[{"full_name":"Abanin, D. A.","first_name":"D. A.","last_name":"Abanin"},{"first_name":"J. H.","last_name":"Bardarson","full_name":"Bardarson, J. H."},{"first_name":"G.","last_name":"De Tomasi","full_name":"De Tomasi, G."},{"full_name":"Gopalakrishnan, S.","first_name":"S.","last_name":"Gopalakrishnan"},{"full_name":"Khemani, V.","last_name":"Khemani","first_name":"V."},{"full_name":"Parameswaran, S. A.","first_name":"S. A.","last_name":"Parameswaran"},{"first_name":"F.","last_name":"Pollmann","full_name":"Pollmann, F."},{"first_name":"A. C.","last_name":"Potter","full_name":"Potter, A. C."},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"first_name":"R.","last_name":"Vasseur","full_name":"Vasseur, R."}],"title":"Distinguishing localization from chaos: Challenges in finite-size systems","external_id":{"arxiv":["1911.04501"],"isi":["000634879800007"]},"date_created":"2021-03-07T23:01:25Z","article_processing_charge":"No","oa_version":"Preprint","_id":"9224","day":"01","department":[{"_id":"MaSe"}],"intvolume":"       427","scopus_import":"1","article_type":"original","publisher":"Elsevier","quality_controlled":"1","citation":{"short":"D.A. Abanin, J.H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S.A. Parameswaran, F. Pollmann, A.C. Potter, M. Serbyn, R. Vasseur, Annals of Physics 427 (2021).","mla":"Abanin, D. A., et al. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” <i>Annals of Physics</i>, vol. 427, no. 4, 168415, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aop.2021.168415\">10.1016/j.aop.2021.168415</a>.","ieee":"D. A. Abanin <i>et al.</i>, “Distinguishing localization from chaos: Challenges in finite-size systems,” <i>Annals of Physics</i>, vol. 427, no. 4. Elsevier, 2021.","ista":"Abanin DA, Bardarson JH, De Tomasi G, Gopalakrishnan S, Khemani V, Parameswaran SA, Pollmann F, Potter AC, Serbyn M, Vasseur R. 2021. Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. 427(4), 168415.","chicago":"Abanin, D. A., J. H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S. A. Parameswaran, F. Pollmann, A. C. Potter, Maksym Serbyn, and R. Vasseur. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” <i>Annals of Physics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aop.2021.168415\">https://doi.org/10.1016/j.aop.2021.168415</a>.","ama":"Abanin DA, Bardarson JH, De Tomasi G, et al. Distinguishing localization from chaos: Challenges in finite-size systems. <i>Annals of Physics</i>. 2021;427(4). doi:<a href=\"https://doi.org/10.1016/j.aop.2021.168415\">10.1016/j.aop.2021.168415</a>","apa":"Abanin, D. A., Bardarson, J. H., De Tomasi, G., Gopalakrishnan, S., Khemani, V., Parameswaran, S. A., … Vasseur, R. (2021). Distinguishing localization from chaos: Challenges in finite-size systems. <i>Annals of Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aop.2021.168415\">https://doi.org/10.1016/j.aop.2021.168415</a>"}},{"volume":148,"publication_identifier":{"eissn":["1477-9129"]},"status":"public","acknowledgement":"This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844). Deposited in PMC for release after 12 months.","type":"journal_article","month":"02","isi":1,"year":"2021","oa":1,"language":[{"iso":"eng"}],"doi":"10.1242/dev.176065","issue":"2","quality_controlled":"1","citation":{"chicago":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” <i>Development</i>. The Company of Biologists, 2021. <a href=\"https://doi.org/10.1242/dev.176065\">https://doi.org/10.1242/dev.176065</a>.","ama":"Tkačik G, Gregor T. The many bits of positional information. <i>Development</i>. 2021;148(2). doi:<a href=\"https://doi.org/10.1242/dev.176065\">10.1242/dev.176065</a>","apa":"Tkačik, G., &#38; Gregor, T. (2021). The many bits of positional information. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.176065\">https://doi.org/10.1242/dev.176065</a>","ieee":"G. Tkačik and T. Gregor, “The many bits of positional information,” <i>Development</i>, vol. 148, no. 2. The Company of Biologists, 2021.","short":"G. Tkačik, T. Gregor, Development 148 (2021).","mla":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” <i>Development</i>, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:<a href=\"https://doi.org/10.1242/dev.176065\">10.1242/dev.176065</a>.","ista":"Tkačik G, Gregor T. 2021. The many bits of positional information. Development. 148(2), dev176065."},"publisher":"The Company of Biologists","article_type":"original","scopus_import":"1","intvolume":"       148","department":[{"_id":"GaTk"}],"day":"01","_id":"9226","article_processing_charge":"No","oa_version":"Published Version","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"date_created":"2021-03-07T23:01:25Z","external_id":{"pmid":["33526425"],"isi":["000613906000007"]},"title":"The many bits of positional information","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"date_updated":"2025-04-14T09:28:43Z","main_file_link":[{"url":"https://doi.org/10.1242/dev.176065","open_access":"1"}],"abstract":[{"text":"Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","pmid":1,"publication":"Development","date_published":"2021-02-01T00:00:00Z","article_number":"dev176065"},{"month":"01","isi":1,"year":"2021","language":[{"iso":"eng"}],"conference":{"name":"CALDAM: Conference on Algorithms and Discrete Applied Mathematics","location":"Rupnagar, India","end_date":"2021-02-13","start_date":"2021-02-11"},"page":"346-358","doi":"10.1007/978-3-030-67899-9_28","volume":12601,"publication_identifier":{"isbn":["9783030678982"],"issn":["0302-9743"],"eissn":["1611-3349"]},"status":"public","type":"conference","title":"Experimental evaluation of a local search approximation algorithm for the multiway cut problem","author":[{"full_name":"Bloch-Hansen, Andrew","last_name":"Bloch-Hansen","first_name":"Andrew"},{"first_name":"Nasim","last_name":"Samei","id":"C1531CAE-36E9-11EA-845F-33AA3DDC885E","full_name":"Samei, Nasim"},{"full_name":"Solis-Oba, Roberto","first_name":"Roberto","last_name":"Solis-Oba"}],"date_created":"2021-03-07T23:01:25Z","external_id":{"isi":["001433483100028"]},"date_updated":"2025-09-10T10:01:54Z","abstract":[{"text":"In the multiway cut problem we are given a weighted undirected graph   G=(V,E)  and a set   T⊆V  of k terminals. The goal is to find a minimum weight set of edges   E′⊆E  with the property that by removing   E′  from G all the terminals become disconnected. In this paper we present a simple local search approximation algorithm for the multiway cut problem with approximation ratio   2−2k . We present an experimental evaluation of the performance of our local search algorithm and show that it greatly outperforms the isolation heuristic of Dalhaus et al. and it has similar performance as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and Buchbinder et al. which have the currently best known approximation ratios for this problem.","lang":"eng"}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Conference on Algorithms and Discrete Applied Mathematics","date_published":"2021-01-28T00:00:00Z","citation":{"apa":"Bloch-Hansen, A., Samei, N., &#38; Solis-Oba, R. (2021). Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In <i>Conference on Algorithms and Discrete Applied Mathematics</i> (Vol. 12601, pp. 346–358). Rupnagar, India: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">https://doi.org/10.1007/978-3-030-67899-9_28</a>","ama":"Bloch-Hansen A, Samei N, Solis-Oba R. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In: <i>Conference on Algorithms and Discrete Applied Mathematics</i>. Vol 12601. Springer Nature; 2021:346-358. doi:<a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">10.1007/978-3-030-67899-9_28</a>","chicago":"Bloch-Hansen, Andrew, Nasim Samei, and Roberto Solis-Oba. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” In <i>Conference on Algorithms and Discrete Applied Mathematics</i>, 12601:346–58. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">https://doi.org/10.1007/978-3-030-67899-9_28</a>.","ista":"Bloch-Hansen A, Samei N, Solis-Oba R. 2021. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. Conference on Algorithms and Discrete Applied Mathematics. CALDAM: Conference on Algorithms and Discrete Applied Mathematics, LNCS, vol. 12601, 346–358.","ieee":"A. Bloch-Hansen, N. Samei, and R. Solis-Oba, “Experimental evaluation of a local search approximation algorithm for the multiway cut problem,” in <i>Conference on Algorithms and Discrete Applied Mathematics</i>, Rupnagar, India, 2021, vol. 12601, pp. 346–358.","mla":"Bloch-Hansen, Andrew, et al. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” <i>Conference on Algorithms and Discrete Applied Mathematics</i>, vol. 12601, Springer Nature, 2021, pp. 346–58, doi:<a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">10.1007/978-3-030-67899-9_28</a>.","short":"A. Bloch-Hansen, N. Samei, R. Solis-Oba, in:, Conference on Algorithms and Discrete Applied Mathematics, Springer Nature, 2021, pp. 346–358."},"quality_controlled":"1","publisher":"Springer Nature","scopus_import":"1","alternative_title":["LNCS"],"department":[{"_id":"VlKo"}],"intvolume":"     12601","day":"28","article_processing_charge":"No","oa_version":"None","_id":"9227"},{"doi":"10.1016/j.tics.2021.01.007","issue":"4","page":"265-268","has_accepted_license":"1","file":[{"date_created":"2022-05-27T07:31:24Z","relation":"main_file","date_updated":"2022-05-27T07:31:24Z","file_name":"2021_TrendsCognitiveSciences_Achakulvisut.pdf","content_type":"application/pdf","file_size":380720,"checksum":"87e39ea7bd266b976e8631b66979214d","file_id":"11415","access_level":"open_access","creator":"dernst","success":1}],"language":[{"iso":"eng"}],"year":"2021","oa":1,"isi":1,"month":"04","type":"journal_article","acknowledgement":"We thank all of our volunteers from the NMC conferences (list of names in the appendix). We also thank the NSF for support from 1734220 to B.W., and DARPA for support to T.A.","status":"public","publication_identifier":{"issn":["1364-6613"],"eissn":["1879-307X"]},"volume":25,"date_published":"2021-04-01T00:00:00Z","file_date_updated":"2022-05-27T07:31:24Z","publication":"Trends in Cognitive Sciences","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"publication_status":"published","abstract":[{"text":"Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned.","lang":"eng"}],"date_updated":"2023-08-07T13:59:07Z","external_id":{"pmid":["33608214"],"isi":["000627418000001"]},"date_created":"2021-03-07T23:01:25Z","author":[{"full_name":"Achakulvisut, Titipat","last_name":"Achakulvisut","first_name":"Titipat"},{"first_name":"Tulakan","last_name":"Ruangrong","full_name":"Ruangrong, Tulakan"},{"last_name":"Mineault","first_name":"Patrick","full_name":"Mineault, Patrick"},{"full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","last_name":"Vogels","first_name":"Tim P"},{"first_name":"Megan A.K.","last_name":"Peters","full_name":"Peters, Megan A.K."},{"first_name":"Panayiota","last_name":"Poirazi","full_name":"Poirazi, Panayiota"},{"first_name":"Christopher","last_name":"Rozell","full_name":"Rozell, Christopher"},{"last_name":"Wyble","first_name":"Brad","full_name":"Wyble, Brad"},{"full_name":"Goodman, Dan F.M.","last_name":"Goodman","first_name":"Dan F.M."},{"last_name":"Kording","first_name":"Konrad Paul","full_name":"Kording, Konrad Paul"}],"title":"Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences","_id":"9228","oa_version":"Submitted Version","article_processing_charge":"No","day":"01","intvolume":"        25","department":[{"_id":"TiVo"}],"article_type":"original","scopus_import":"1","publisher":"Elsevier","ddc":["570"],"quality_controlled":"1","citation":{"ama":"Achakulvisut T, Ruangrong T, Mineault P, et al. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. <i>Trends in Cognitive Sciences</i>. 2021;25(4):265-268. doi:<a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">10.1016/j.tics.2021.01.007</a>","apa":"Achakulvisut, T., Ruangrong, T., Mineault, P., Vogels, T. P., Peters, M. A. K., Poirazi, P., … Kording, K. P. (2021). Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. <i>Trends in Cognitive Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">https://doi.org/10.1016/j.tics.2021.01.007</a>","chicago":"Achakulvisut, Titipat, Tulakan Ruangrong, Patrick Mineault, Tim P Vogels, Megan A.K. Peters, Panayiota Poirazi, Christopher Rozell, Brad Wyble, Dan F.M. Goodman, and Konrad Paul Kording. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” <i>Trends in Cognitive Sciences</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">https://doi.org/10.1016/j.tics.2021.01.007</a>.","ista":"Achakulvisut T, Ruangrong T, Mineault P, Vogels TP, Peters MAK, Poirazi P, Rozell C, Wyble B, Goodman DFM, Kording KP. 2021. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 25(4), 265–268.","short":"T. Achakulvisut, T. Ruangrong, P. Mineault, T.P. Vogels, M.A.K. Peters, P. Poirazi, C. Rozell, B. Wyble, D.F.M. Goodman, K.P. Kording, Trends in Cognitive Sciences 25 (2021) 265–268.","mla":"Achakulvisut, Titipat, et al. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” <i>Trends in Cognitive Sciences</i>, vol. 25, no. 4, Elsevier, 2021, pp. 265–68, doi:<a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">10.1016/j.tics.2021.01.007</a>.","ieee":"T. Achakulvisut <i>et al.</i>, “Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences,” <i>Trends in Cognitive Sciences</i>, vol. 25, no. 4. Elsevier, pp. 265–268, 2021."}}]