[{"ec_funded":1,"quality_controlled":"1","citation":{"ista":"Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226.","ieee":"M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis,” <i>PLoS Genetics</i>, vol. 18, no. 7. Public Library of Science, 2022.","mla":"Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>.","apa":"Toups, M. A., Vicoso, B., &#38; Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).","chicago":"Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>.","ama":"Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. 2022;18(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>"},"doi":"10.1371/journal.pgen.1010226","acknowledgement":"JRP was supported by the Swiss National Science Foundation (https://www.snf.ch/en), Sinergia grant 26073998. BV was supported by the European Research Council (https://erc.europa.eu/) under the European Union’s Horizon 2020 research and innovation program, grant number 715257. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nPlants were grown in Lausanne by Aline Revel, and RNA extraction and library preparation were performed by Dessislava Savova Bianchi. All sequencing and the IsoSeq3 analysis were carried out by Center for Integrative Genomics at the University of Lausanne. All other computational analyses were performed on the server at IST Austria.","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7404"]},"year":"2022","intvolume":"        18","pmid":1,"has_accepted_license":"1","external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"isi":1,"file":[{"file_size":1620272,"checksum":"aa4c137f82635e700856c359dccfaa0a","creator":"dernst","date_updated":"2022-08-01T07:49:25Z","file_id":"11708","access_level":"open_access","date_created":"2022-08-01T07:49:25Z","content_type":"application/pdf","success":1,"file_name":"2022_PLoSGenetics_Toups.pdf","relation":"main_file"}],"abstract":[{"lang":"eng","text":"Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism."}],"oa":1,"ddc":["570"],"file_date_updated":"2022-08-01T07:49:25Z","publication":"PLoS Genetics","type":"journal_article","_id":"11703","article_processing_charge":"No","issue":"7","date_created":"2022-07-31T22:01:48Z","oa_version":"Published Version","project":[{"grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"department":[{"_id":"BeVi"}],"author":[{"last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"last_name":"Pannell","first_name":"John R.","full_name":"Pannell, John R."}],"day":"06","status":"public","article_number":"e1010226","volume":18,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","scopus_import":"1","article_type":"original","date_published":"2022-07-06T00:00:00Z","month":"07","date_updated":"2023-08-03T12:17:12Z","publisher":"Public Library of Science","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"isi":1,"external_id":{"isi":["000911392100055"]},"abstract":[{"text":"In Fall 2020, several European countries reported rapid increases in COVID-19 cases along with growing estimates of the effective reproduction rates. Such an acceleration in epidemic spread is usually attributed to time-dependent effects, e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc. In this case however the acceleration occurred when counter measures such as testing and contact tracing exceeded their capacity limit. Considering Austria as an example, here we show that this dynamics can be captured by a time-independent, i.e. autonomous, compartmental model that incorporates these capacity limits. In this model, the epidemic acceleration coincides with the exhaustion of mitigation efforts, resulting in an increasing fraction of undetected cases that drive the effective reproduction rate progressively higher. We demonstrate that standard models which does not include this effect necessarily result in a systematic underestimation of the effective reproduction rate.","lang":"eng"}],"ddc":["510"],"oa":1,"file":[{"checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","file_size":1421256,"creator":"dernst","date_updated":"2022-08-01T08:02:38Z","file_id":"11712","date_created":"2022-08-01T08:02:38Z","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2022_PLoSONE_Budanur.pdf","relation":"main_file"}],"quality_controlled":"1","citation":{"mla":"Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>, vol. 17, no. 7, e0269975, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>.","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975.","ieee":"N. B. Budanur and B. Hof, “An autonomous compartmental model for accelerating epidemics,” <i>PLoS ONE</i>, vol. 17, no. 7. Public Library of Science, 2022.","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022).","chicago":"Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>.","apa":"Budanur, N. B., &#38; Hof, B. (2022). An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>","ama":"Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. 2022;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>"},"doi":"10.1371/journal.pone.0269975","related_material":{"record":[{"relation":"research_data","id":"11711","status":"public"}]},"year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1932-6203"]},"has_accepted_license":"1","intvolume":"        17","scopus_import":"1","article_type":"original","month":"07","date_published":"2022-07-18T00:00:00Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:24:22Z","publisher":"Public Library of Science","oa_version":"Published Version","date_created":"2022-07-31T22:01:48Z","file_date_updated":"2022-08-01T08:02:38Z","publication":"PLoS ONE","article_processing_charge":"No","_id":"11704","type":"journal_article","issue":"7","author":[{"last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"department":[{"_id":"BjHo"}],"day":"18","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"An autonomous compartmental model for accelerating epidemics","volume":17,"status":"public","article_number":"e0269975"},{"month":"08","date_published":"2022-08-26T00:00:00Z","article_type":"original","publisher":"Wiley","date_updated":"2023-08-03T12:23:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","scopus_import":"1","day":"26","article_number":"e202207002","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","volume":61,"_id":"11705","type":"journal_article","article_processing_charge":"Yes (via OA deal)","issue":"35","publication":"Angewandte Chemie - International Edition","file_date_updated":"2023-02-02T08:01:00Z","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","date_created":"2022-07-31T22:01:48Z","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"author":[{"last_name":"Chang","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","last_name":"Liu"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","last_name":"Lee","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598"},{"full_name":"Spadaro, Maria","last_name":"Spadaro","first_name":"Maria"},{"first_name":"Kristopher M.","last_name":"Koskela","full_name":"Koskela, Kristopher M."},{"full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Brutchey, Richard L.","first_name":"Richard L.","last_name":"Brutchey"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"file":[{"file_size":4072650,"checksum":"ad601f2b9e26e46ab4785162be58b5ed","creator":"dernst","date_updated":"2023-02-02T08:01:00Z","file_id":"12476","access_level":"open_access","date_created":"2023-02-02T08:01:00Z","content_type":"application/pdf","success":1,"file_name":"2022_AngewandteChemieInternat_Chang.pdf","relation":"main_file"}],"ddc":["540"],"oa":1,"abstract":[{"text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe.","lang":"eng"}],"external_id":{"isi":["000828274200001"]},"isi":1,"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"language":[{"iso":"eng"}],"year":"2022","intvolume":"        61","has_accepted_license":"1","citation":{"ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. 2022;61(35). doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002.","ieee":"C. Chang <i>et al.</i>, “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35. Wiley, 2022.","mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35, e202207002, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>.","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>","short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>."},"doi":"10.1002/anie.202207002","quality_controlled":"1","ec_funded":1,"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya."},{"citation":{"mla":"Balliu, Alkida, et al. “Local Mending.” <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, vol. 13298, Springer Nature, 2022, pp. 1–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>.","ieee":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela, “Local mending,” in <i>International Colloquium on Structural Information and Communication Complexity</i>, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.","ista":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local mending. International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol. 13298, 1–20.","short":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, J. Suomela, in:, M. Parter (Ed.), International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2022, pp. 1–20.","chicago":"Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki, and Jukka Suomela. “Local Mending.” In <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, 13298:1–20. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>.","apa":"Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., &#38; Suomela, J. (2022). Local mending. In M. Parter (Ed.), <i>International Colloquium on Structural Information and Communication Complexity</i> (Vol. 13298, pp. 1–20). Paderborn, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>","ama":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. Local mending. In: Parter M, ed. <i>International Colloquium on Structural Information and Communication Complexity</i>. Vol 13298. LNCS. Springer Nature; 2022:1-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>"},"doi":"10.1007/978-3-031-09993-9_1","ec_funded":1,"quality_controlled":"1","conference":{"start_date":"2022-06-27","end_date":"2022-06-29","location":"Paderborn, Germany","name":"SIROCCO: Structural Information and Communication Complexity"},"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605. This work was supported in part by the Academy of Finland, Grants 314888 and 333837. The authors would also like to thank David Harris, Neven Villani, and the anonymous reviewers for their very helpful comments and feedback on previous versions of this work.","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031099922"]},"language":[{"iso":"eng"}],"year":"2022","arxiv":1,"intvolume":"     13298","editor":[{"full_name":"Parter, Merav","last_name":"Parter","first_name":"Merav"}],"external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"isi":1,"page":"1-20","oa":1,"abstract":[{"lang":"eng","text":"In this work we introduce the graph-theoretic notion of mendability: for each locally checkable graph problem we can define its mending radius, which captures the idea of how far one needs to modify a partial solution in order to “patch a hole.” We explore how mendability is connected to the existence of efficient algorithms, especially in distributed, parallel, and fault-tolerant settings. It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds in the LOCAL model of distributed computing. One of the surprises is that in paths and cycles, a converse also holds in the following sense: if a problem Π can be solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently solvable but that is also O(1)-mendable. We also explore the structure of the landscape of mendability. For example, we show that in trees, the mending radius of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs the structure is much more diverse."}],"_id":"11707","article_processing_charge":"No","type":"conference","publication":"International Colloquium on Structural Information and Communication Complexity","project":[{"name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"840605"}],"oa_version":"Preprint","date_created":"2022-07-31T22:01:49Z","department":[{"_id":"DaAl"}],"author":[{"full_name":"Balliu, Alkida","first_name":"Alkida","last_name":"Balliu"},{"last_name":"Hirvonen","first_name":"Juho","full_name":"Hirvonen, Juho"},{"full_name":"Melnyk, Darya","first_name":"Darya","last_name":"Melnyk"},{"first_name":"Dennis","last_name":"Olivetti","full_name":"Olivetti, Dennis"},{"orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","last_name":"Rybicki"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"}],"day":"25","status":"public","volume":13298,"title":"Local mending","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08703"}],"scopus_import":"1","series_title":"LNCS","month":"06","date_published":"2022-06-25T00:00:00Z","publisher":"Springer Nature","date_updated":"2023-08-03T12:16:29Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published"},{"department":[{"_id":"BjHo"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11704"}]},"author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"}],"_id":"11711","article_processing_charge":"No","type":"research_data_reference","doi":"10.5281/ZENODO.6802720","citation":{"ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","mla":"Budanur, Nazmi B. <i>Burakbudanur/Autoacc-Public</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>","short":"N.B. Budanur, (2022).","chicago":"Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>.","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>"},"date_created":"2022-08-01T08:06:33Z","oa_version":"Published Version","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"title":"burakbudanur/autoacc-public","has_accepted_license":"1","year":"2022","day":"06","license":"https://creativecommons.org/publicdomain/zero/1.0/","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6802720"}],"publisher":"Zenodo","date_updated":"2023-08-03T12:24:21Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2022-07-06T00:00:00Z","month":"07","ddc":["000"],"oa":1,"abstract":[{"text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\"","lang":"eng"}]},{"external_id":{"pmid":["35562780"]},"oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes."}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"file":[{"checksum":"008156e5340e9789f0f6d82bde4d347a","file_size":1545310,"creator":"dernst","date_updated":"2022-08-01T09:24:42Z","file_id":"11714","access_level":"open_access","date_created":"2022-08-01T09:24:42Z","success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2022_BMCResearchNotes_Nikolic.pdf"}],"doi":"10.1186/s13104-022-06061-9","citation":{"mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","ista":"Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. 15, 173.","ieee":"N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli,” <i>BMC Research Notes</i>, vol. 15. Springer Nature, 2022.","chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","apa":"Nikolic, N., Sauert, M., Albanese, T. G., &#38; Moll, I. (2022). Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>","ama":"Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. 2022;15. doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>"},"quality_controlled":"1","related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"acknowledgement":"We acknowledge the Max Perutz Labs FACS Facility together with Thomas Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207), to IM. Open access funding provided by the Austrian Science Fund.","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1756-0500"]},"has_accepted_license":"1","pmid":1,"intvolume":"        15","scopus_import":"1","date_published":"2022-05-13T00:00:00Z","month":"05","article_type":"letter_note","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","date_updated":"2022-08-01T09:27:40Z","project":[{"grant_number":"V00738","call_identifier":"FWF","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","_id":"26956E74-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","date_created":"2022-08-01T09:04:27Z","article_processing_charge":"No","_id":"11713","type":"journal_article","publication":"BMC Research Notes","file_date_updated":"2022-08-01T09:24:42Z","author":[{"last_name":"Nikolic","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela"},{"first_name":"Martina","last_name":"Sauert","full_name":"Sauert, Martina"},{"first_name":"Tanino G.","last_name":"Albanese","full_name":"Albanese, Tanino G."},{"last_name":"Moll","first_name":"Isabella","full_name":"Moll, Isabella"}],"department":[{"_id":"CaGu"}],"day":"13","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":15,"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","article_number":"173","status":"public"},{"doi":"10.1016/j.aim.2022.108591","citation":{"ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022.","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","mla":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>.","apa":"Drach, K., &#38; Schleicher, D. (2022). Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).","chicago":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>.","ama":"Drach K, Schleicher D. Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. 2022;408(Part A). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>"},"ec_funded":1,"quality_controlled":"1","acknowledgement":"We are grateful to a number of colleagues for helpful and inspiring discussions during the time when we worked on this project, in particular Dima Dudko, Misha Hlushchanka, John Hubbard, Misha Lyubich, Oleg Kozlovski, and Sebastian van Strien. Finally, we would like to thank our dynamics research group for numerous helpful and enjoyable discussions: Konstantin Bogdanov, Roman Chernov, Russell Lodge, Steffen Maaß, David Pfrang, Bernhard Reinke, Sergey Shemyakov, and Maik Sowinski. We gratefully acknowledge support by the Advanced Grant “HOLOGRAM” (#695 621) of the European Research Council (ERC), as well as hospitality of Cornell University in the spring of 2018 while much of this work was prepared. The first-named author also acknowledges the support of the ERC Advanced Grant “SPERIG” (#885 707).","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0001-8708"]},"has_accepted_license":"1","intvolume":"       408","isi":1,"external_id":{"isi":["000860924200005"]},"oa":1,"ddc":["510"],"abstract":[{"text":"We study rigidity of rational maps that come from Newton's root finding method for polynomials of arbitrary degrees. We establish dynamical rigidity of these maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit can be distinguished in combinatorial terms from all other orbits), or the orbit of this point eventually lands in the filled-in Julia set of a polynomial-like restriction of the original map. As a corollary, we show that the Julia sets of Newton maps in many non-trivial cases are locally connected; in particular, every cubic Newton map without Siegel points has locally connected Julia set.\r\nIn the parameter space of Newton maps of arbitrary degree we obtain the following rigidity result: any two combinatorially equivalent Newton maps are quasiconformally conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable, or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized renormalization concept called “complex box mappings” for which we extend a dynamical rigidity result by Kozlovski and van Strien so as to include irrationally indifferent and renormalizable situations.","lang":"eng"}],"keyword":["General Mathematics"],"file":[{"access_level":"open_access","date_created":"2023-02-02T07:39:09Z","file_id":"12474","relation":"main_file","file_name":"2022_AdvancesMathematics_Drach.pdf","success":1,"content_type":"application/pdf","creator":"dernst","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","file_size":2164036,"date_updated":"2023-02-02T07:39:09Z"}],"project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020","grant_number":"885707"}],"oa_version":"Published Version","date_created":"2022-08-01T17:08:16Z","issue":"Part A","_id":"11717","type":"journal_article","article_processing_charge":"Yes (via OA deal)","publication":"Advances in Mathematics","file_date_updated":"2023-02-02T07:39:09Z","author":[{"id":"fe8209e2-906f-11eb-847d-950f8fc09115","first_name":"Kostiantyn","last_name":"Drach","full_name":"Drach, Kostiantyn","orcid":"0000-0002-9156-8616"},{"full_name":"Schleicher, Dierk","last_name":"Schleicher","first_name":"Dierk"}],"department":[{"_id":"VaKa"}],"day":"29","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Rigidity of Newton dynamics","volume":408,"article_number":"108591","status":"public","scopus_import":"1","month":"10","date_published":"2022-10-29T00:00:00Z","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Elsevier","date_updated":"2023-08-03T12:36:07Z"},{"volume":119,"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","status":"public","article_number":"e2121058119","day":"25","author":[{"last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","last_name":"Chen"},{"full_name":"Alotaibi, Saqer S.","first_name":"Saqer S.","last_name":"Alotaibi"},{"full_name":"Pěnčík, Aleš","last_name":"Pěnčík","first_name":"Aleš"},{"last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"oa_version":"Published Version","date_created":"2022-08-04T20:06:49Z","project":[{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the National Academy of Sciences","file_date_updated":"2022-08-08T07:42:09Z","type":"journal_article","_id":"11723","article_processing_charge":"No","issue":"31","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-10-29T10:12:30Z","publisher":"Proceedings of the National Academy of Sciences","article_type":"original","date_published":"2022-07-25T00:00:00Z","month":"07","scopus_import":"1","has_accepted_license":"1","intvolume":"       119","pmid":1,"year":"2022","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","quality_controlled":"1","citation":{"ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 119(31), e2121058119.","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences 119 (2022).","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>"},"doi":"10.1073/pnas.2121058119","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"keyword":["Multidisciplinary"],"oa":1,"ddc":["580"],"file":[{"date_updated":"2022-08-08T07:42:09Z","creator":"dernst","file_size":2506262,"checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","relation":"main_file","file_name":"2022_PNAS_Li.pdf","content_type":"application/pdf","success":1,"date_created":"2022-08-08T07:42:09Z","access_level":"open_access","file_id":"11747"}],"isi":1,"external_id":{"isi":["000881496900002"],"pmid":["35878023"]}},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"year":"2022","intvolume":"       189","has_accepted_license":"1","citation":{"short":"S.J. Henheik, A.B. Lauritsen, Journal of Statistical Physics 189 (2022).","chicago":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>.","apa":"Henheik, S. J., &#38; Lauritsen, A. B. (2022). The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>","mla":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>, vol. 189, 5, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>.","ista":"Henheik SJ, Lauritsen AB. 2022. The BCS energy gap at high density. Journal of Statistical Physics. 189, 5.","ieee":"S. J. Henheik and A. B. Lauritsen, “The BCS energy gap at high density,” <i>Journal of Statistical Physics</i>, vol. 189. Springer Nature, 2022.","ama":"Henheik SJ, Lauritsen AB. The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. 2022;189. doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>"},"doi":"10.1007/s10955-022-02965-9","ec_funded":1,"quality_controlled":"1","acknowledgement":"We are grateful to Robert Seiringer for helpful discussions and many valuable comments\r\non an earlier version of the manuscript. J.H. acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond’ No. 101020331. Open access funding provided by Institute of Science and Technology (IST Austria)","file":[{"content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2022_JourStatisticalPhysics_Henheik.pdf","file_id":"11746","access_level":"open_access","date_created":"2022-08-08T07:36:34Z","date_updated":"2022-08-08T07:36:34Z","checksum":"b398c4dbf65f71d417981d6e366427e9","file_size":419563,"creator":"dernst"}],"oa":1,"ddc":["530"],"abstract":[{"lang":"eng","text":"We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic formula, which strongly depends on the strength of the interaction potential V on the Fermi surface. In combination with the recent result by one of us (Math. Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities, we prove the universality of the ratio of the energy gap and the critical temperature."}],"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"external_id":{"isi":["000833007200002"]},"isi":1,"day":"29","article_number":"5","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":189,"title":"The BCS energy gap at high density","type":"journal_article","_id":"11732","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2022-08-08T07:36:34Z","publication":"Journal of Statistical Physics","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020"}],"oa_version":"Published Version","date_created":"2022-08-05T11:36:56Z","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"author":[{"last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X"},{"orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen"}],"date_published":"2022-07-29T00:00:00Z","month":"07","article_type":"original","publisher":"Springer Nature","date_updated":"2023-09-05T14:57:49Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","scopus_import":"1"},{"has_accepted_license":"1","intvolume":"       119","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"]},"related_material":{"record":[{"relation":"research_data","id":"13064","status":"public"}]},"acknowledgement":"This project was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science and Technology Austria. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant PRG687. Estonian Biobank computations were performed in the High-Performance Computing Centre, University of Tartu.","quality_controlled":"1","citation":{"ama":"Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>","chicago":"Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>.","short":"E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher, M.R. Robinson, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher, P. M., &#38; Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>","mla":"Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121279119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>.","ista":"Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank data. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121279119.","ieee":"E. J. Orliac <i>et al.</i>, “Improving GWAS discovery and genomic prediction accuracy in biobank data,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022."},"doi":"10.1073/pnas.2121279119","abstract":[{"text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies.","lang":"eng"}],"oa":1,"ddc":["570"],"file":[{"checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","file_size":1001164,"creator":"dernst","date_updated":"2022-08-08T07:31:19Z","file_id":"11745","date_created":"2022-08-08T07:31:19Z","access_level":"open_access","content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2022_PNAS_Orliac.pdf"}],"isi":1,"external_id":{"isi":["000881496900003"]},"volume":119,"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","status":"public","article_number":"e2121279119","day":"29","author":[{"full_name":"Orliac, Etienne J.","last_name":"Orliac","first_name":"Etienne J."},{"first_name":"Daniel","last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel"},{"last_name":"Ojavee","first_name":"Sven E.","full_name":"Ojavee, Sven E."},{"first_name":"Kristi","last_name":"Läll","full_name":"Läll, Kristi"},{"first_name":"Reedik","last_name":"Mägi","full_name":"Mägi, Reedik"},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson"}],"department":[{"_id":"MaRo"}],"date_created":"2022-08-07T22:01:56Z","oa_version":"Published Version","file_date_updated":"2022-08-08T07:31:19Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","type":"journal_article","_id":"11733","article_processing_charge":"No","issue":"31","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:40:38Z","publisher":"Proceedings of the National Academy of Sciences","article_type":"original","date_published":"2022-07-29T00:00:00Z","month":"07","scopus_import":"1"},{"scopus_import":"1","date_published":"2022-07-25T00:00:00Z","month":"07","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2023-08-03T12:39:29Z","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","grant_number":"I 1774-B16"}],"oa_version":"Published Version","date_created":"2022-08-07T22:01:57Z","issue":"31","_id":"11734","type":"journal_article","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2022-08-08T07:09:58Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Bouguyon, Eleonore","last_name":"Bouguyon","first_name":"Eleonore"},{"id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","first_name":"Kevin","last_name":"Domanegg","orcid":"0000-0002-1215-4264","full_name":"Domanegg, Kevin"},{"full_name":"Krapp, Anne","last_name":"Krapp","first_name":"Anne"},{"first_name":"Philip","last_name":"Nacry","full_name":"Nacry, Philip"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"last_name":"Lacombe","first_name":"Benoit","full_name":"Lacombe, Benoit"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"}],"department":[{"_id":"EvBe"}],"day":"25","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","volume":119,"article_number":"e2122460119","status":"public","isi":1,"external_id":{"pmid":["35878040"],"isi":["000881496900007"]},"oa":1,"ddc":["570"],"abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"file":[{"checksum":"6e97dedc281247fc3fe238a209f14af0","file_size":3092330,"creator":"dernst","date_updated":"2022-08-08T07:09:58Z","file_id":"11744","access_level":"open_access","date_created":"2022-08-08T07:09:58Z","success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2022_PNAS_Abualia.pdf"}],"doi":"10.1073/pnas.2122460119","citation":{"ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>","apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>.","short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>."},"quality_controlled":"1","acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"]},"has_accepted_license":"1","pmid":1,"intvolume":"       119"},{"external_id":{"isi":["000830989200018"]},"isi":1,"file":[{"content_type":"application/pdf","success":1,"file_name":"Chen-2022-High-LevelPuzzle_authorVersion.pdf","relation":"main_file","file_id":"11992","access_level":"open_access","date_created":"2022-08-28T07:56:19Z","date_updated":"2022-08-28T07:56:19Z","file_size":16896871,"checksum":"0b51651be45b1b33f2072bd5d2686c69","creator":"bbickel"}],"ddc":["000"],"oa":1,"abstract":[{"text":"Interlocking puzzles are intriguing geometric games where the puzzle pieces are held together based on their geometric arrangement, preventing the puzzle from falling apart. High-level-of-difficulty, or simply high-level, interlocking puzzles are a subclass of interlocking puzzles that require multiple moves to take out the first subassembly from the puzzle. Solving a high-level interlocking puzzle is a challenging task since one has to explore many different configurations of the puzzle pieces until reaching a configuration where the first subassembly can be taken out. Designing a high-level interlocking puzzle with a user-specified level of difficulty is even harder since the puzzle pieces have to be interlocking in all the configurations before the first subassembly is taken out.\r\n\r\nIn this paper, we present a computational approach to design high-level interlocking puzzles. The core idea is to represent all possible configurations of an interlocking puzzle as well as transitions among these configurations using a rooted, undirected graph called a disassembly graph and leverage this graph to find a disassembly plan that requires a minimal number of moves to take out the first subassembly from the puzzle. At the design stage, our algorithm iteratively constructs the geometry of each puzzle piece to expand the disassembly graph incrementally, aiming to achieve a user-specified level of difficulty. We show that our approach allows efficient generation of high-level interlocking puzzles of various shape complexities, including new solutions not attainable by state-of-the-art approaches.","lang":"eng"}],"acknowledgement":"We thank the reviewers for the valuable comments, David Gontier for sharing the source code of the baseline design approach, Christian Hafner for proofreading the paper, Keenan Crane for the 3D model of Cow, and Thingiverse for the 3D models of Moai and Owl. This work was supported by the SUTD Start-up Research Grant (Number: SRG ISTD 2019 148), the Swiss National Science Foundation (NCCR Digital Fabrication Agreement #51NF40-141853), and\r\nthe European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 715767 – MATERIALIZABLE).","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/unlocking-interlocking-riddles/","description":"News on ISTA website"}]},"doi":"10.1145/3528223.3530071","citation":{"mla":"Chen, Rulin, et al. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 150, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>.","ieee":"R. Chen, Z. Wang, P. Song, and B. Bickel, “Computational design of high-level interlocking puzzles,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ista":"Chen R, Wang Z, Song P, Bickel B. 2022. Computational design of high-level interlocking puzzles. ACM Transactions on Graphics. 41(4), 150.","chicago":"Chen, Rulin, Ziqi Wang, Peng Song, and Bernd Bickel. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>.","short":"R. Chen, Z. Wang, P. Song, B. Bickel, ACM Transactions on Graphics 41 (2022).","apa":"Chen, R., Wang, Z., Song, P., &#38; Bickel, B. (2022). Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>","ama":"Chen R, Wang Z, Song P, Bickel B. Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>"},"quality_controlled":"1","ec_funded":1,"intvolume":"        41","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"year":"2022","scopus_import":"1","publisher":"Association for Computing Machinery","date_updated":"2023-08-03T13:21:22Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","month":"07","date_published":"2022-07-22T00:00:00Z","article_type":"original","department":[{"_id":"BeBi"}],"author":[{"full_name":"Chen, Rulin","last_name":"Chen","first_name":"Rulin"},{"full_name":"Wang, Ziqi","last_name":"Wang","first_name":"Ziqi"},{"first_name":"Peng","last_name":"Song","full_name":"Song, Peng"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel"}],"issue":"4","_id":"11735","article_processing_charge":"No","type":"journal_article","publication":"ACM Transactions on Graphics","file_date_updated":"2022-08-28T07:56:19Z","project":[{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"date_created":"2022-08-07T22:01:57Z","oa_version":"Submitted Version","article_number":"150","status":"public","title":"Computational design of high-level interlocking puzzles","volume":41,"day":"22"},{"status":"public","article_number":"65","volume":41,"title":"Estimation of yarn-level simulation models for production fabrics","day":"22","department":[{"_id":"ChWo"}],"author":[{"full_name":"Sperl, Georg","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl"},{"first_name":"Rosa M.","last_name":"Sánchez-Banderas","full_name":"Sánchez-Banderas, Rosa M."},{"full_name":"Li, Manwen","last_name":"Li","first_name":"Manwen"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Otaduy","first_name":"Miguel A.","full_name":"Otaduy, Miguel A."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"ACM Transactions on Graphics","article_processing_charge":"No","_id":"11736","issue":"4","type":"journal_article","date_created":"2022-08-07T22:01:58Z","oa_version":"Published Version","date_updated":"2023-08-03T12:38:30Z","publisher":"Association for Computing Machinery","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","date_published":"2022-07-22T00:00:00Z","month":"07","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3528223.3530167","open_access":"1"}],"intvolume":"        41","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"language":[{"iso":"eng"}],"year":"2022","acknowledgement":"We wish to thank the anonymous reviewers for their helpful comments. To develop this project, we were helped by many people both at Under Armour (Clay Dean, Randall Harward, Kyle Blakely, Craig Simile, Michael Seiz, Brooke Malone, Brittainy McFarland, Emilie Phan, Lindsey Kern, Courtney Oswald, Haley Barkley, Bob Chin, Adam Bayer, Connie Kwok, Marielle Newman, Nick Pence, Allison Hicks, Allison White, Candace Rubenstein, Jeremy Stangland, Fred Fagergren, Michael Mazzoleni, Nathaniel Berry, Manuel Frank) and SEDDI (Gabriel Cirio, Alejandro Rodríguez, Sofía Dominguez, Alicia Nicas, Elena Garcés, Daniel Rodríguez, David Pascual, Manuel Godoy, Sergio Suja, Sergio Ruiz, Roberto Condori, Alberto Martín, Graham Sullivan). We also thank the members of the Visual Computing Group at IST Austria and the Multimodal Simulation Lab at URJC for their feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing, and it was funded in part by the European Research Council (ERC Consolidator Grant 772738 TouchDesign).","related_material":{"link":[{"description":"News on the ISTA website","url":"https://ista.ac.at/en/news/digital-yarn-real-socks/","relation":"press_release"}],"record":[{"status":"public","id":"12358","relation":"dissertation_contains"}]},"quality_controlled":"1","citation":{"apa":"Sperl, G., Sánchez-Banderas, R. M., Li, M., Wojtan, C., &#38; Otaduy, M. A. (2022). Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>","chicago":"Sperl, Georg, Rosa M. Sánchez-Banderas, Manwen Li, Chris Wojtan, and Miguel A. Otaduy. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>.","short":"G. Sperl, R.M. Sánchez-Banderas, M. Li, C. Wojtan, M.A. Otaduy, ACM Transactions on Graphics 41 (2022).","ista":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. 2022. Estimation of yarn-level simulation models for production fabrics. ACM Transactions on Graphics. 41(4), 65.","ieee":"G. Sperl, R. M. Sánchez-Banderas, M. Li, C. Wojtan, and M. A. Otaduy, “Estimation of yarn-level simulation models for production fabrics,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","mla":"Sperl, Georg, et al. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 65, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>.","ama":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>"},"doi":"10.1145/3528223.3530167","abstract":[{"text":"This paper introduces a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compiled a database from physical tests of several different knitted fabrics used in the textile industry. These data span different types of complex knit patterns, yarn compositions, and fabric finishes, and the results demonstrate diverse physical properties like stiffness, nonlinearity, and anisotropy.\r\n\r\nWe then develop a system for approximating these mechanical responses with yarn-level cloth simulation. To do so, we introduce an efficient pipeline for converting between fabric-level data and yarn-level simulation, including a novel swatch-level approximation for speeding up computation, and some small-but-necessary extensions to yarn-level models used in computer graphics. The dataset used for this paper can be found at http://mslab.es/projects/YarnLevelFabrics.","lang":"eng"}],"oa":1,"external_id":{"isi":["000830989200114"]},"isi":1},{"arxiv":1,"intvolume":"        54","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"year":"2022","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme grant 716117 and by the AustrianScience Fund (FWF) through grants F65 and W1245.","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10022"}]},"citation":{"ama":"Forkert DL, Maas J, Portinale L. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(4):4297-4333. doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>","mla":"Forkert, Dominik L., et al. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4, Society for Industrial and Applied Mathematics, 2022, pp. 4297–333, doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>.","ista":"Forkert DL, Maas J, Portinale L. 2022. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. SIAM Journal on Mathematical Analysis. 54(4), 4297–4333.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4. Society for Industrial and Applied Mathematics, pp. 4297–4333, 2022.","short":"D.L. Forkert, J. Maas, L. Portinale, SIAM Journal on Mathematical Analysis 54 (2022) 4297–4333.","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>.","apa":"Forkert, D. L., Maas, J., &#38; Portinale, L. (2022). Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>"},"doi":"10.1137/21M1410968","quality_controlled":"1","ec_funded":1,"oa":1,"keyword":["Fokker--Planck equation","gradient flow","evolutionary $\\Gamma$-convergence"],"abstract":[{"lang":"eng","text":"We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality."}],"external_id":{"arxiv":["2008.10962"],"isi":["000889274600001"]},"isi":1,"page":"4297-4333","status":"public","title":"Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","volume":54,"day":"18","department":[{"_id":"JaMa"}],"author":[{"last_name":"Forkert","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","full_name":"Forkert, Dominik L"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas"},{"last_name":"Portinale","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"}],"issue":"4","_id":"11739","article_processing_charge":"No","type":"journal_article","publication":"SIAM Journal on Mathematical Analysis","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2022-08-07T22:01:59Z","oa_version":"Preprint","publisher":"Society for Industrial and Applied Mathematics","date_updated":"2023-08-03T12:37:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_published":"2022-07-18T00:00:00Z","month":"07","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2008.10962"}]},{"external_id":{"arxiv":["2005.07103"],"isi":["000836200300001"]},"isi":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","file":[{"content_type":"application/pdf","success":1,"file_name":"2022_ElecJournCombinatorics_Cooley.pdf","relation":"main_file","file_id":"11742","date_created":"2022-08-08T06:28:52Z","access_level":"open_access","date_updated":"2022-08-08T06:28:52Z","file_size":1768663,"checksum":"057c676dcee70236aa234d4ce6138c69","creator":"dernst"}],"ddc":["510"],"oa":1,"abstract":[{"lang":"eng","text":"We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].\r\nWe consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition."}],"acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","doi":"10.37236/10607","citation":{"ama":"Cooley O, Del Giudice N, Kang M, Sprüssel P. Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. 2022;29(3). doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>","ieee":"O. Cooley, N. Del Giudice, M. Kang, and P. Sprüssel, “Phase transition in cohomology groups of non-uniform random simplicial complexes,” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3. Electronic Journal of Combinatorics, 2022.","ista":"Cooley O, Del Giudice N, Kang M, Sprüssel P. 2022. Phase transition in cohomology groups of non-uniform random simplicial complexes. Electronic Journal of Combinatorics. 29(3), P3.27.","mla":"Cooley, Oliver, et al. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3, P3.27, Electronic Journal of Combinatorics, 2022, doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>.","apa":"Cooley, O., Del Giudice, N., Kang, M., &#38; Sprüssel, P. (2022). Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>","chicago":"Cooley, Oliver, Nicola Del Giudice, Mihyun Kang, and Philipp Sprüssel. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2022. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>.","short":"O. Cooley, N. Del Giudice, M. Kang, P. Sprüssel, Electronic Journal of Combinatorics 29 (2022)."},"quality_controlled":"1","intvolume":"        29","arxiv":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1077-8926"]},"year":"2022","scopus_import":"1","publisher":"Electronic Journal of Combinatorics","date_updated":"2023-08-03T12:37:54Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_published":"2022-07-29T00:00:00Z","month":"07","article_type":"original","department":[{"_id":"MaKw"}],"author":[{"full_name":"Cooley, Oliver","last_name":"Cooley","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","first_name":"Oliver"},{"full_name":"Del Giudice, Nicola","first_name":"Nicola","last_name":"Del Giudice"},{"full_name":"Kang, Mihyun","first_name":"Mihyun","last_name":"Kang"},{"full_name":"Sprüssel, Philipp","last_name":"Sprüssel","first_name":"Philipp"}],"_id":"11740","issue":"3","type":"journal_article","article_processing_charge":"No","publication":"Electronic Journal of Combinatorics","file_date_updated":"2022-08-08T06:28:52Z","oa_version":"Published Version","date_created":"2022-08-07T22:01:59Z","article_number":"P3.27","status":"public","volume":29,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png"},"title":"Phase transition in cohomology groups of non-uniform random simplicial complexes","day":"29"},{"month":"09","date_published":"2022-09-23T00:00:00Z","date_updated":"2023-08-03T13:38:46Z","publisher":"Springer Nature","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","day":"23","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Abstract monitors for quantitative specifications","volume":13498,"publication":"22nd International Conference on Runtime Verification","file_date_updated":"2023-01-20T07:34:50Z","_id":"11775","type":"conference","article_processing_charge":"Yes","oa_version":"Published Version","date_created":"2022-08-08T17:09:09Z","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac"}],"file":[{"creator":"dernst","file_size":477110,"checksum":"05c7dcfbb9053a98f46441fb2eccb213","date_updated":"2023-01-20T07:34:50Z","access_level":"open_access","date_created":"2023-01-20T07:34:50Z","file_id":"12317","relation":"main_file","file_name":"2022_LNCS_RV_Henzinger.pdf","content_type":"application/pdf","success":1}],"abstract":[{"lang":"eng","text":"Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time. "}],"oa":1,"ddc":["000"],"external_id":{"isi":["000866539700011"]},"isi":1,"page":"200-220","alternative_title":["LNCS"],"publication_identifier":{"issn":["0302-9743"]},"language":[{"iso":"eng"}],"year":"2022","intvolume":"     13498","has_accepted_license":"1","quality_controlled":"1","ec_funded":1,"citation":{"short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference on Runtime Verification, Springer Nature, 2022, pp. 200–220.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract Monitors for Quantitative Specifications.” In <i>22nd International Conference on Runtime Verification</i>, 13498:200–220. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2022). Abstract monitors for quantitative specifications. In <i>22nd International Conference on Runtime Verification</i> (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>","mla":"Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.” <i>22nd International Conference on Runtime Verification</i>, vol. 13498, Springer Nature, 2022, pp. 200–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for quantitative specifications,” in <i>22nd International Conference on Runtime Verification</i>, Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative specifications. 22nd International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 13498, 200–220.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications. In: <i>22nd International Conference on Runtime Verification</i>. Vol 13498. Springer Nature; 2022:200-220. doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>"},"doi":"10.1007/978-3-031-17196-3_11","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","conference":{"location":"Tbilisi, Georgia","end_date":"2022-09-30","start_date":"2022-09-28","name":"RV: Runtime Verification"}},{"publisher":"Institute of Science and Technology","date_updated":"2023-06-22T09:56:36Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","date_published":"2022-08-11T00:00:00Z","month":"08","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"author":[{"full_name":"Wild, Pascal","last_name":"Wild","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","first_name":"Pascal"}],"type":"dissertation","_id":"11777","article_processing_charge":"No","file_date_updated":"2022-08-11T16:09:19Z","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"date_created":"2022-08-10T15:51:19Z","oa_version":"Published Version","status":"public","title":"High-dimensional expansion and crossing numbers of simplicial complexes","day":"11","alternative_title":["ISTA Thesis"],"page":"170","supervisor":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"file":[{"content_type":"text/x-python","relation":"supplementary_material","file_name":"flags.py","file_id":"11780","access_level":"open_access","date_created":"2022-08-10T15:34:04Z","date_updated":"2022-08-10T15:34:04Z","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","file_size":16828,"description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","creator":"pwild"},{"file_id":"11781","access_level":"open_access","date_created":"2022-08-10T15:34:10Z","content_type":"text/x-c++src","file_name":"lowerbound.cpp","relation":"supplementary_material","file_size":12226,"checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","description":"Code for proof of Lemma 8.20 in Thesis","creator":"pwild","date_updated":"2022-08-10T15:34:10Z"},{"date_updated":"2022-08-10T15:34:17Z","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","file_size":3240,"creator":"pwild","description":"Code for proof of Proposition 7.9 in Thesis","content_type":"text/x-python","file_name":"upperbound.py","relation":"supplementary_material","file_id":"11782","date_created":"2022-08-10T15:34:17Z","access_level":"open_access"},{"title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","date_updated":"2022-08-11T16:08:33Z","creator":"pwild","file_size":5086282,"checksum":"4e96575b10cbe4e0d0db2045b2847774","relation":"main_file","file_name":"finalthesisPascalWildPDFA.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2022-08-11T16:08:33Z","file_id":"11809"},{"file_size":18150068,"checksum":"92d94842a1fb6dca5808448137573b2e","creator":"pwild","date_updated":"2022-08-11T16:09:19Z","file_id":"11810","access_level":"closed","date_created":"2022-08-11T16:09:19Z","content_type":"application/zip","relation":"source_file","file_name":"ThesisSubmission.zip"}],"oa":1,"ddc":["500","516","514"],"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise."}],"citation":{"short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>.","apa":"Wild, P. (2022). <i>High-dimensional expansion and crossing numbers of simplicial complexes</i>. Institute of Science and Technology. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>","mla":"Wild, Pascal. <i>High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes</i>. Institute of Science and Technology, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>.","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>"},"doi":"10.15479/at:ista:11777","ec_funded":1,"has_accepted_license":"1","publication_identifier":{"isbn":["978-3-99078-021-3"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"year":"2022"},{"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:46:28Z","publisher":"AIP Publishing","article_type":"original","month":"06","date_published":"2022-06-10T00:00:00Z","scopus_import":"1","title":"Low-energy spectrum and dynamics of the weakly interacting Bose gas","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":63,"status":"public","article_number":"061102","day":"10","author":[{"last_name":"Bossmann","first_name":"Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea"}],"department":[{"_id":"RoSe"}],"oa_version":"Published Version","date_created":"2022-08-11T06:37:52Z","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication":"Journal of Mathematical Physics","file_date_updated":"2022-08-11T07:03:02Z","_id":"11783","article_processing_charge":"Yes (via OA deal)","issue":"6","type":"journal_article","abstract":[{"text":"We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix.","lang":"eng"}],"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"ddc":["530"],"oa":1,"file":[{"date_updated":"2022-08-11T07:03:02Z","creator":"dernst","checksum":"d0d32c338c1896680174be88c70968fa","file_size":5957888,"relation":"main_file","file_name":"2022_JourMathPhysics_Bossmann.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","date_created":"2022-08-11T07:03:02Z","file_id":"11784"}],"isi":1,"external_id":{"isi":["000809648100002"],"arxiv":["2203.00730"]},"has_accepted_license":"1","intvolume":"        63","arxiv":1,"year":"2022","publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"language":[{"iso":"eng"}],"acknowledgement":"The author thanks Nataˇsa Pavlovic, Sören Petrat, Peter Pickl, Robert Seiringer, and Avy Soffer for the collaboration on Refs. 1, 2 and 21. Funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skℓodowska-Curie Grant Agreement\r\nNo. 754411 is gratefully acknowledged.","ec_funded":1,"quality_controlled":"1","doi":"10.1063/5.0089983","citation":{"ama":"Bossmann L. Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. 2022;63(6). doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>","mla":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6, 061102, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>.","ista":"Bossmann L. 2022. Low-energy spectrum and dynamics of the weakly interacting Bose gas. Journal of Mathematical Physics. 63(6), 061102.","ieee":"L. Bossmann, “Low-energy spectrum and dynamics of the weakly interacting Bose gas,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6. AIP Publishing, 2022.","short":"L. Bossmann, Journal of Mathematical Physics 63 (2022).","chicago":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>.","apa":"Bossmann, L. (2022). Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>"}},{"conference":{"location":"Tel Aviv, Israel","start_date":"2022-10-23","end_date":"2022-10-27","name":"ECCV: European Conference on Computer Vision"},"doi":"10.1007/978-3-031-19803-8_21","citation":{"ama":"Prach B, Lampert C. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In: <i>Computer Vision – ECCV 2022</i>. Vol 13681. Springer Nature; 2022:350-365. doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>","apa":"Prach, B., &#38; Lampert, C. (2022). Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In <i>Computer Vision – ECCV 2022</i> (Vol. 13681, pp. 350–365). Tel Aviv, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>","short":"B. Prach, C. Lampert, in:, Computer Vision – ECCV 2022, Springer Nature, 2022, pp. 350–365.","chicago":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” In <i>Computer Vision – ECCV 2022</i>, 13681:350–65. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>.","ieee":"B. Prach and C. Lampert, “Almost-orthogonal layers for efficient general-purpose Lipschitz networks,” in <i>Computer Vision – ECCV 2022</i>, Tel Aviv, Israel, 2022, vol. 13681, pp. 350–365.","ista":"Prach B, Lampert C. 2022. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. Computer Vision – ECCV 2022. ECCV: European Conference on Computer Vision, LNCS, vol. 13681, 350–365.","mla":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” <i>Computer Vision – ECCV 2022</i>, vol. 13681, Springer Nature, 2022, pp. 350–65, doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>."},"quality_controlled":"1","intvolume":"     13681","arxiv":1,"year":"2022","publication_identifier":{"isbn":["9783031198021"],"eisbn":["9783031198038"]},"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"page":"350-365","external_id":{"arxiv":["2208.03160"]},"oa":1,"abstract":[{"lang":"eng","text":"It is a highly desirable property for deep networks to be robust against\r\nsmall input changes. One popular way to achieve this property is by designing\r\nnetworks with a small Lipschitz constant. In this work, we propose a new\r\ntechnique for constructing such Lipschitz networks that has a number of\r\ndesirable properties: it can be applied to any linear network layer\r\n(fully-connected or convolutional), it provides formal guarantees on the\r\nLipschitz constant, it is easy to implement and efficient to run, and it can be\r\ncombined with any training objective and optimization method. In fact, our\r\ntechnique is the first one in the literature that achieves all of these\r\nproperties simultaneously. Our main contribution is a rescaling-based weight\r\nmatrix parametrization that guarantees each network layer to have a Lipschitz\r\nconstant of at most 1 and results in the learned weight matrices to be close to\r\northogonal. Hence we call such layers almost-orthogonal Lipschitz (AOL).\r\nExperiments and ablation studies in the context of image classification with\r\ncertified robust accuracy confirm that AOL layers achieve results that are on\r\npar with most existing methods. Yet, they are simpler to implement and more\r\nbroadly applicable, because they do not require computationally expensive\r\nmatrix orthogonalization or inversion steps as part of the network\r\narchitecture. We provide code at https://github.com/berndprach/AOL."}],"author":[{"full_name":"Prach, Bernd","first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","last_name":"Prach"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"date_created":"2022-08-12T15:09:47Z","oa_version":"Preprint","_id":"11839","type":"conference","article_processing_charge":"No","publication":"Computer Vision – ECCV 2022","title":"Almost-orthogonal layers for efficient general-purpose Lipschitz networks","volume":13681,"status":"public","day":"23","scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2208.03160","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","date_updated":"2023-05-03T08:00:46Z","month":"10","date_published":"2022-10-23T00:00:00Z"},{"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Adsorption free energy predicts amyloid protein nucleation rates","volume":119,"article_number":"e2109718119","status":"public","day":"28","author":[{"last_name":"Toprakcioglu","first_name":"Zenon","full_name":"Toprakcioglu, Zenon"},{"last_name":"Kamada","first_name":"Ayaka","full_name":"Kamada, Ayaka"},{"last_name":"Michaels","first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T."},{"first_name":"Mengqi","last_name":"Xie","full_name":"Xie, Mengqi"},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"first_name":"Jiapeng","last_name":"Wei","full_name":"Wei, Jiapeng"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Vendruscolo, Michele","first_name":"Michele","last_name":"Vendruscolo"},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"department":[{"_id":"AnSa"}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960"}],"oa_version":"Published Version","date_created":"2022-08-14T22:01:45Z","type":"journal_article","_id":"11841","article_processing_charge":"No","issue":"31","publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2023-10-04T09:05:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2023-10-04T09:06:52Z","date_published":"2022-07-28T00:00:00Z","month":"07","article_type":"original","scopus_import":"1","has_accepted_license":"1","intvolume":"       119","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969). We are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.), the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for Misfolding Diseases (CMD).","doi":"10.1073/pnas.2109718119","citation":{"ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2109718119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>.","ista":"Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A, Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2109718119.","ieee":"Z. Toprakcioglu <i>et al.</i>, “Adsorption free energy predicts amyloid protein nucleation rates,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>.","apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>"},"quality_controlled":"1","ec_funded":1,"oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process."}],"file":[{"file_name":"2022_PNAS_Toprakcioglu.pdf","relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2023-10-04T09:05:44Z","access_level":"open_access","file_id":"14386","date_updated":"2023-10-04T09:05:44Z","creator":"dernst","file_size":2476021,"checksum":"0fe3878896cbeb6c44e29222ec2f336a"}],"isi":1,"external_id":{"isi":["000903753500002"]}}]