[{"day":"01","publication":"Communications on Pure and Applied Mathematics","isi":1,"year":"2018","date_published":"2018-03-01T00:00:00Z","doi":"10.1002/cpa.21717","date_created":"2018-12-11T11:46:31Z","page":"577 - 614","acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614."},"title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","author":[{"last_name":"Frank","full_name":"Frank, Rupert","first_name":"Rupert"},{"last_name":"Phan Thanh","full_name":"Phan Thanh, Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Nam"},{"full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch","first_name":"Hanne"}],"publist_id":"7377","external_id":{"isi":["000422675800004"],"arxiv":["1606.07355"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":71,"oa_version":"Preprint","abstract":[{"text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential.","lang":"eng"}],"month":"03","intvolume":" 71","main_file_link":[{"url":"https://arxiv.org/abs/1606.07355","open_access":"1"}],"date_updated":"2023-09-19T10:09:40Z","department":[{"_id":"RoSe"}],"_id":"446","status":"public","type":"journal_article","article_type":"original"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786"},"title":"Tread lightly interpreting polygenic tests of selection","external_id":{"isi":["000429094400005"]},"article_processing_charge":"No","author":[{"last_name":"Novembre","full_name":"Novembre, John","first_name":"John"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publist_id":"7393","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","publication":"Genetics","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:46:26Z","date_published":"2018-04-01T00:00:00Z","doi":"10.1534/genetics.118.300786","page":"1351 - 1355","_id":"430","pubrep_id":"1012","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["576"],"date_updated":"2023-09-19T10:17:30Z","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","abstract":[{"text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly.","lang":"eng"}],"intvolume":" 208","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":500129,"date_updated":"2020-07-14T12:46:26Z","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","date_created":"2018-12-12T10:12:40Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"3d838dc285df394376555b794b6a5ad1","file_id":"4958"}],"publication_status":"published","issue":"4","volume":208},{"author":[{"first_name":"Wen","full_name":"Ma, Wen","last_name":"Ma"},{"first_name":"Paris","last_name":"Veltsos","full_name":"Veltsos, Paris"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"full_name":"Rodrigues, Nicolas","last_name":"Rodrigues","first_name":"Nicolas"},{"full_name":"Sermier, Roberto","last_name":"Sermier","first_name":"Roberto"},{"first_name":"Daniel","last_name":"Jeffries","full_name":"Jeffries, Daniel"},{"first_name":"Nicolas","last_name":"Perrin","full_name":"Perrin, Nicolas"}],"publist_id":"7714","article_processing_charge":"No","external_id":{"isi":["000436494200026"]},"title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","citation":{"short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"294","date_published":"2018-06-12T00:00:00Z","doi":"10.3390/genes9060294","date_created":"2018-12-11T11:45:09Z","isi":1,"has_accepted_license":"1","year":"2018","day":"12","publication":"Genes","publisher":"MDPI AG","quality_controlled":"1","oa":1,"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:45:22Z","date_updated":"2023-09-19T10:15:31Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"199","volume":9,"issue":"6","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5905","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","creator":"dernst","file_size":3985796,"date_updated":"2020-07-14T12:45:22Z","file_name":"2018_Genes_Ma.pdf","date_created":"2019-02-01T07:52:28Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 9","abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"oa_version":"Published Version"},{"status":"public","type":"journal_article","_id":"543","department":[{"_id":"GaTk"}],"date_updated":"2023-09-19T10:16:35Z","intvolume":" 115","month":"01","main_file_link":[{"url":"https://doi.org/10.1101/152660 ","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits.","lang":"eng"}],"volume":115,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26"}],"title":"Toward a unified theory of efficient, predictive, and sparse coding","external_id":{"isi":["000419128700049"]},"article_processing_charge":"No","author":[{"first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","last_name":"Chalk"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7273","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115.","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115."},"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","date_created":"2018-12-11T11:47:04Z","doi":"10.1073/pnas.1711114115","date_published":"2018-01-02T00:00:00Z","page":"186 - 191","publication":"PNAS","day":"02","year":"2018","isi":1},{"title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","publist_id":"7403","author":[{"last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal","first_name":"Kinjal"},{"first_name":"Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Claude-Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022."},"quality_controlled":"1","publisher":"Biophysical Society","oa":1,"doi":"10.1016/j.bpj.2017.12.022","date_published":"2018-02-27T00:00:00Z","date_created":"2018-12-11T11:46:23Z","page":"968 - 977","day":"27","publication":"Biophysical Journal","isi":1,"year":"2018","status":"public","type":"journal_article","_id":"421","department":[{"_id":"EdHa"}],"date_updated":"2023-09-19T10:13:55Z","month":"02","intvolume":" 114","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.01486"}],"oa_version":"Submitted Version","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"volume":114,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published"}]