[{"quality_controlled":0,"extern":1,"abstract":[{"lang":"eng","text":"Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle."}],"doi":"10.1038/nature11871","date_updated":"2021-01-12T06:54:28Z","date_published":"2013-02-28T00:00:00Z","author":[{"full_name":"Baradaran, Rozbeh ","first_name":"Rozbeh","last_name":"Baradaran"},{"full_name":"Berrisford, John M","first_name":"John","last_name":"Berrisford"},{"full_name":"Minhas, Gurdeep S","last_name":"Minhas","first_name":"Gurdeep"},{"first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Leonid Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5107","date_created":"2018-12-11T11:55:01Z","publisher":"Nature Publishing Group","title":"Crystal structure of the entire respiratory complex i","publication":"Nature","month":"02","citation":{"mla":"Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48, doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>.","short":"R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.","ista":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of the entire respiratory complex i. Nature. 494(7438), 443–448.","ama":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire respiratory complex i. <i>Nature</i>. 2013;494(7438):443-448. doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>","apa":"Baradaran, R., Berrisford, J., Minhas, G., &#38; Sazanov, L. A. (2013). Crystal structure of the entire respiratory complex i. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>","chicago":"Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>.","ieee":"R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure of the entire respiratory complex i,” <i>Nature</i>, vol. 494, no. 7438. Nature Publishing Group, pp. 443–448, 2013."},"day":"28","issue":"7438","status":"public","acknowledgement":"This work was funded by the Medical Research Council.","publication_status":"published","year":"2013","_id":"1978","intvolume":"       494","type":"journal_article","page":"443 - 448","volume":494},{"date_published":"2013-12-01T00:00:00Z","author":[{"last_name":"Bonny","first_name":"Mike","full_name":"Bonny, Mike "},{"first_name":"Elisabeth","last_name":"Fischer Friedrich","full_name":"Fischer-Friedrich, Elisabeth"},{"first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Martin Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Petra","last_name":"Schwille","full_name":"Schwille, Petra "},{"first_name":"Karsten","last_name":"Kruse","full_name":"Kruse, Karsten"}],"date_updated":"2021-01-12T06:54:32Z","doi":"10.1371/journal.pcbi.1003347","abstract":[{"lang":"eng","text":"The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally."}],"extern":1,"quality_controlled":0,"publication":"PLoS Computational Biology","title":"Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation","publisher":"Public Library of Science","date_created":"2018-12-11T11:55:04Z","publist_id":"5095","status":"public","issue":"12","day":"01","citation":{"ama":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>","mla":"Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>, vol. 9, no. 12, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>.","short":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013).","ista":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 9(12).","chicago":"Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille, and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>.","ieee":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation,” <i>PLoS Computational Biology</i>, vol. 9, no. 12. Public Library of Science, 2013.","apa":"Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., &#38; Kruse, K. (2013). Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>"},"month":"12","volume":9,"type":"journal_article","intvolume":"         9","_id":"1988","year":"2013","publication_status":"published"},{"publisher":"Nature Publishing Group","publication":"Nature","title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","publist_id":"5092","date_created":"2018-12-11T11:55:05Z","doi":"10.1038/nature12235","date_updated":"2021-01-12T06:54:33Z","date_published":"2013-07-18T00:00:00Z","author":[{"full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"},{"full_name":"Bachtrog, Doris","first_name":"Doris","last_name":"Bachtrog"}],"extern":1,"quality_controlled":0,"abstract":[{"lang":"eng","text":"Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur."}],"type":"journal_article","volume":499,"page":"332 - 335","year":"2013","publication_status":"published","intvolume":"       499","_id":"1991","issue":"7458","day":"18","status":"public","acknowledgement":"Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B.","month":"07","citation":{"ista":"Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335.","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>, vol. 499, no. 7458, Nature Publishing Group, 2013, pp. 332–35, doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>.","short":"B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.","ama":"Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. 2013;499(7458):332-335. doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>","apa":"Vicoso, B., &#38; Bachtrog, D. (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>.","ieee":"B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome in Drosophila,” <i>Nature</i>, vol. 499, no. 7458. Nature Publishing Group, pp. 332–335, 2013."}},{"day":"01","language":[{"iso":"eng"}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"month":"01","publication_status":"published","intvolume":"      8044","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"alternative_title":["LNCS"],"doi":"10.1007/978-3-642-39799-8_6","date_updated":"2023-09-07T11:40:43Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5399"},{"id":"1400","relation":"dissertation_contains","status":"public"}]},"date_published":"2013-01-01T00:00:00Z","author":[{"full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter","orcid":"0000-0002-0170-7353"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"quality_controlled":"1","scopus_import":1,"conference":{"start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19","name":"CAV: Computer Aided Verification"},"external_id":{"arxiv":["1303.5251"]},"status":"public","oa":1,"citation":{"ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>."},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"101 - 106","volume":8044,"year":"2013","_id":"2000","arxiv":1,"series_title":"Lecture Notes in Computer Science","abstract":[{"lang":"eng","text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics."}],"publisher":"Springer","department":[{"_id":"KrCh"}],"title":"TTP: Tool for tumor progression","publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","publist_id":"5077","oa_version":"Preprint","date_created":"2018-12-11T11:55:08Z","ec_funded":1},{"department":[{"_id":"CaUh"}],"title":"Privacy-preserving data sharing for genome-wide association studies","publication":"Journal of Privacy and Confidentiality ","publisher":"Carnegie Mellon University","oa_version":"Published Version","date_created":"2018-12-11T11:55:11Z","publist_id":"5067","author":[{"orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline"},{"full_name":"Slavkovic, Aleksandra","first_name":"Aleksandra","last_name":"Slavkovic"},{"full_name":"Fienberg, Stephen","first_name":"Stephen","last_name":"Fienberg"}],"date_published":"2013-08-01T00:00:00Z","doi":"10.29012/jpc.v5i1.629","date_updated":"2021-01-12T06:54:41Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression."}],"quality_controlled":"1","page":"137 - 166","volume":5,"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://repository.cmu.edu/jpc/vol5/iss1/6","open_access":"1"}],"_id":"2009","intvolume":"         5","publication_status":"published","year":"2013","oa":1,"status":"public","day":"01","issue":"1","citation":{"ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.","chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166."},"language":[{"iso":"eng"}],"month":"08"},{"doi":"10.1214/12-AOS1080","date_updated":"2021-01-12T06:54:42Z","date_published":"2013-04-01T00:00:00Z","author":[{"first_name":"Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Raskutti","first_name":"Garvesh","full_name":"Raskutti, Garvesh"},{"last_name":"Bühlmann","first_name":"Peter","full_name":"Bühlmann, Peter"},{"last_name":"Yu","first_name":"Bin","full_name":"Yu, Bin"}],"quality_controlled":"1","scopus_import":1,"publication_status":"published","intvolume":"        41","main_file_link":[{"open_access":"1","url":"www.doi.org/10.1214/12-AOS1080"}],"day":"01","language":[{"iso":"eng"}],"month":"04","publisher":"Institute of Mathematical Statistics","department":[{"_id":"CaUh"}],"title":"Geometry of the faithfulness assumption in causal inference","publication":"The Annals of Statistics","publist_id":"5066","oa_version":"Published Version","date_created":"2018-12-11T11:55:11Z","arxiv":1,"abstract":[{"text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case.","lang":"eng"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"436 - 463","volume":41,"year":"2013","_id":"2010","external_id":{"arxiv":["1207.0547"]},"issue":"2","status":"public","oa":1,"citation":{"ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013.","chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>.","apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>","mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463."}},{"date_created":"2018-12-11T11:55:33Z","publist_id":"4964","title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution","publication":"PNAS","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. "}],"quality_controlled":0,"extern":1,"date_published":"2013-04-16T00:00:00Z","author":[{"full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"},{"full_name":"Kaiser, Vera B","first_name":"Vera","last_name":"Kaiser"},{"first_name":"Doris","last_name":"Bachtrog","full_name":"Bachtrog, Doris"}],"doi":"10.1073/pnas.1217027110","date_updated":"2021-01-12T06:55:08Z","_id":"2074","intvolume":"       110","publication_status":"published","year":"2013","page":"6453 - 6458","volume":110,"type":"journal_article","citation":{"ama":"Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. 2013;110(16):6453-6458. doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>","short":"B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.","ista":"Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458.","mla":"Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>.","chicago":"Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>.","ieee":"B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” <i>PNAS</i>, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.","apa":"Vicoso, B., Kaiser, V., &#38; Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>"},"month":"04","status":"public","day":"16","issue":"16"},{"date_updated":"2021-01-12T06:55:09Z","doi":"10.1371/journal.pbio.1001643","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Emerson, Jr J.","first_name":"Jr","last_name":"Emerson"},{"full_name":"Zektser, Yulia","first_name":"Yulia","last_name":"Zektser"},{"full_name":"Mahajan, Shivani","first_name":"Shivani","last_name":"Mahajan"},{"first_name":"Doris","last_name":"Bachtrog","full_name":"Bachtrog, Doris"}],"date_published":"2013-08-27T00:00:00Z","extern":1,"quality_controlled":0,"abstract":[{"lang":"eng","text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n"}],"publisher":"Public Library of Science","publication":"PLoS Biology","title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","publist_id":"4962","date_created":"2018-12-11T11:55:34Z","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"},"issue":"8","day":"27","acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB.","status":"public","month":"08","citation":{"chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>.","ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” <i>PLoS Biology</i>, vol. 11, no. 8. Public Library of Science, 2013.","apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., &#38; Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>","ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. 2013;11(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).","short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013).","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>, vol. 11, no. 8, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>."},"type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/","volume":11,"year":"2013","publication_status":"published","intvolume":"        11","_id":"2076"},{"year":"2013","publication_status":"published","_id":"2107","intvolume":"        32","type":"journal_article","volume":32,"month":"07","citation":{"ama":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>","short":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","ista":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. 2013. Computational design of actuated deformable characters. ACM Transactions on Graphics. 32(4).","mla":"Skouras, Mélina, et al. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>.","ieee":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, and M. Groß, “Computational design of actuated deformable characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, and Markus Groß. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>.","apa":"Skouras, M., Thomaszewski, B., Coros, S., Bickel, B., &#38; Groß, M. (2013). Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>"},"issue":"4","day":"01","status":"public","acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF","publist_id":"4926","date_created":"2018-12-11T11:55:45Z","publisher":"ACM","publication":"ACM Transactions on Graphics","title":"Computational design of actuated deformable characters","extern":1,"quality_controlled":0,"abstract":[{"lang":"eng","text":"We present a method for fabrication-oriented design of actuated deformable characters that allows a user to automatically create physical replicas of digitally designed characters using rapid manufacturing technologies. Given a deformable character and a set of target poses as input, our method computes a small set of actuators along with their locations on the surface and optimizes the internal material distribution such that the resulting character exhibits the desired deformation behavior. We approach this problem with a dedicated algorithm that combines finite-element analysis, sparse regularization, and constrained optimization. We validate our pipeline on a set of two- and three-dimensional example characters and present results in simulation and physically-fabricated prototypes."}],"date_updated":"2021-01-12T06:55:21Z","doi":"10.1145/2461912.2461979","date_published":"2013-07-01T00:00:00Z","author":[{"full_name":"Skouras, Mélina","last_name":"Skouras","first_name":"Mélina"},{"last_name":"Thomaszewski","first_name":"Bernhard","full_name":"Thomaszewski, Bernhard"},{"last_name":"Coros","first_name":"Stelian","full_name":"Coros, Stelian"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"last_name":"Groß","first_name":"Markus","full_name":"Groß, Markus S"}]},{"publist_id":"4927","date_created":"2018-12-11T11:55:46Z","publisher":"ACM","title":"Computational design of mechanical characters","publication":"ACM Transactions on Graphics","quality_controlled":0,"extern":1,"abstract":[{"lang":"eng","text":"We present an interactive design system that allows non-expert users to create animated mechanical characters. Given an articulated character as input, the user iteratively creates an animation by sketching motion curves indicating how different parts of the character should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices. We demonstrate the versatility of our approach by designing a wide range of mechanical characters, several of which we manufactured using 3D printing. While our pipeline is designed for characters driven by planar mechanisms, significant parts of it extend directly to non-planar mechanisms, allowing us to create characters with compelling 3D motions. "}],"doi":"10.1145/2461912.2461953","date_updated":"2021-01-12T06:55:21Z","date_published":"2013-07-01T00:00:00Z","author":[{"full_name":"Coros, Stelian","last_name":"Coros","first_name":"Stelian"},{"full_name":"Thomaszewski, Bernhard","first_name":"Bernhard","last_name":"Thomaszewski"},{"full_name":"Noris, Gioacchino","first_name":"Gioacchino","last_name":"Noris"},{"full_name":"Sueda, Shinjiro","first_name":"Shinjiro","last_name":"Sueda"},{"full_name":"Forberg, Moira","first_name":"Moira","last_name":"Forberg"},{"full_name":"Sumner, Robert W","last_name":"Sumner","first_name":"Robert"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"}],"publication_status":"published","year":"2013","intvolume":"        32","_id":"2108","type":"journal_article","volume":32,"month":"07","citation":{"ama":"Coros S, Thomaszewski B, Noris G, et al. Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>","short":"S. Coros, B. Thomaszewski, G. Noris, S. Sueda, M. Forberg, R. Sumner, W. Matusik, B. Bickel, ACM Transactions on Graphics 32 (2013).","mla":"Coros, Stelian, et al. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>.","ista":"Coros S, Thomaszewski B, Noris G, Sueda S, Forberg M, Sumner R, Matusik W, Bickel B. 2013. Computational design of mechanical characters. ACM Transactions on Graphics. 32(4).","ieee":"S. Coros <i>et al.</i>, “Computational design of mechanical characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","chicago":"Coros, Stelian, Bernhard Thomaszewski, Gioacchino Noris, Shinjiro Sueda, Moira Forberg, Robert Sumner, Wojciech Matusik, and Bernd Bickel. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>.","apa":"Coros, S., Thomaszewski, B., Noris, G., Sueda, S., Forberg, M., Sumner, R., … Bickel, B. (2013). Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>"},"day":"01","issue":"4","status":"public"},{"status":"public","issue":"6","day":"01","citation":{"ieee":"K. Hildebrand, B. Bickel, and M. Alexa, “Orthogonal slicing for additive manufacturing,” <i>Computers and Graphics (Pergamon)</i>, vol. 37, no. 6. Elsevier, pp. 669–675, 2013.","chicago":"Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Orthogonal Slicing for Additive Manufacturing.” <i>Computers and Graphics (Pergamon)</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">https://doi.org/10.1016/j.cag.2013.05.011</a>.","apa":"Hildebrand, K., Bickel, B., &#38; Alexa, M. (2013). Orthogonal slicing for additive manufacturing. <i>Computers and Graphics (Pergamon)</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">https://doi.org/10.1016/j.cag.2013.05.011</a>","ama":"Hildebrand K, Bickel B, Alexa M. Orthogonal slicing for additive manufacturing. <i>Computers and Graphics (Pergamon)</i>. 2013;37(6):669-675. doi:<a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">10.1016/j.cag.2013.05.011</a>","mla":"Hildebrand, Kristian, et al. “Orthogonal Slicing for Additive Manufacturing.” <i>Computers and Graphics (Pergamon)</i>, vol. 37, no. 6, Elsevier, 2013, pp. 669–75, doi:<a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">10.1016/j.cag.2013.05.011</a>.","ista":"Hildebrand K, Bickel B, Alexa M. 2013. Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). 37(6), 669–675.","short":"K. Hildebrand, B. Bickel, M. Alexa, Computers and Graphics (Pergamon) 37 (2013) 669–675."},"month":"10","volume":37,"page":"669 - 675","type":"journal_article","_id":"2109","intvolume":"        37","year":"2013","publication_status":"published","author":[{"full_name":"Hildebrand, Kristian","last_name":"Hildebrand","first_name":"Kristian"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Alexa, Marc","first_name":"Marc","last_name":"Alexa"}],"date_published":"2013-10-01T00:00:00Z","doi":"10.1016/j.cag.2013.05.011","date_updated":"2021-01-12T06:55:22Z","abstract":[{"text":"Most additive manufacturing technologies work by layering, i.e. slicing the shape and then generating each slice independently. This introduces an anisotropy into the process, often as different accuracies in the tangential and normal directions, but also in terms of other parameters such as build speed or tensile strength and strain. We model this as an anisotropic cubic element. Our approach then finds a compromise between modeling each part of the shape individually in the best possible direction and using one direction for the whole shape part. In particular, we compute an orthogonal basis and consider only the three basis vectors as slice normals (i.e. fabrication directions). Then we optimize a decomposition of the shape along this basis so that each part can be consistently sliced along one of the basis vectors. In simulation, we show that this approach is superior to slicing the whole shape in one direction, only. It also has clear benefits if the shape is larger than the build volume of the available equipment.","lang":"eng"}],"quality_controlled":0,"extern":1,"publication":"Computers and Graphics (Pergamon)","title":"Orthogonal slicing for additive manufacturing","publisher":"Elsevier","date_created":"2018-12-11T11:55:46Z","publist_id":"4924"},{"quality_controlled":0,"extern":1,"abstract":[{"text":"We present a method for practical physical reproduction and design of homogeneous materials with desired subsurface scattering. Our process uses a collection of different pigments that can be suspended in a clear base material. Our goal is to determine pigment concentrations that best reproduce the appearance and subsurface scattering of a given target material. In order to achieve this task we first fabricate a collection of material samples composed of known mixtures of the available pigments with the base material. We then acquire their reflectance profiles using a custom-built measurement device. We use the same device to measure the reflectance profile of a target material. Based on the database of mappings from pigment concentrations to reflectance profiles, we use an optimization process to compute the concentration of pigments to best replicate the target material appearance. We demonstrate the practicality of our method by reproducing a variety of different translucent materials. We also present a tool that allows the user to explore the range of achievable appearances for a given set of pigments. ","lang":"eng"}],"doi":"10.1145/2461912.2461974","date_updated":"2021-01-12T06:55:22Z","date_published":"2013-07-01T00:00:00Z","author":[{"full_name":"Papas, Marios","first_name":"Marios","last_name":"Papas"},{"full_name":"Regg, Christian","last_name":"Regg","first_name":"Christian"},{"last_name":"Jarosz","first_name":"Wojciech","full_name":"Jarosz, Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"full_name":"Jackson, Philip V","first_name":"Philip","last_name":"Jackson"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"full_name":"Marschner, Steve","last_name":"Marschner","first_name":"Steve"},{"full_name":"Groß, Markus S","first_name":"Markus","last_name":"Groß"}],"publist_id":"4925","date_created":"2018-12-11T11:55:46Z","publisher":"ACM","publication":"ACM Transactions on Graphics","title":"Fabricating translucent materials using continuous pigment mixtures","month":"07","citation":{"ama":"Papas M, Regg C, Jarosz W, et al. Fabricating translucent materials using continuous pigment mixtures. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461974\">10.1145/2461912.2461974</a>","mla":"Papas, Marios, et al. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461974\">10.1145/2461912.2461974</a>.","short":"M. Papas, C. Regg, W. Jarosz, B. Bickel, P. Jackson, W. Matusik, S. Marschner, M. Groß, ACM Transactions on Graphics 32 (2013).","ista":"Papas M, Regg C, Jarosz W, Bickel B, Jackson P, Matusik W, Marschner S, Groß M. 2013. Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. 32(4).","chicago":"Papas, Marios, Christian Regg, Wojciech Jarosz, Bernd Bickel, Philip Jackson, Wojciech Matusik, Steve Marschner, and Markus Groß. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461974\">https://doi.org/10.1145/2461912.2461974</a>.","ieee":"M. Papas <i>et al.</i>, “Fabricating translucent materials using continuous pigment mixtures,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","apa":"Papas, M., Regg, C., Jarosz, W., Bickel, B., Jackson, P., Matusik, W., … Groß, M. (2013). Fabricating translucent materials using continuous pigment mixtures. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461974\">https://doi.org/10.1145/2461912.2461974</a>"},"issue":"4","day":"01","status":"public","year":"2013","publication_status":"published","_id":"2110","intvolume":"        32","type":"journal_article","volume":32},{"intvolume":"        32","_id":"2111","publication_status":"published","year":"2013","volume":32,"type":"journal_article","citation":{"apa":"Bermano, A., Bruschweiler, P., Grundhöfer, A., Iwai, D., Bickel, B., &#38; Groß, M. (2013). Augmenting physical avatars using projector-based illumination. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2508363.2508416\">https://doi.org/10.1145/2508363.2508416</a>","ieee":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, and M. Groß, “Augmenting physical avatars using projector-based illumination,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6. ACM, 2013.","chicago":"Bermano, Amit, Philipp Bruschweiler, Anselm Grundhöfer, Daisuke Iwai, Bernd Bickel, and Markus Groß. “Augmenting Physical Avatars Using Projector-Based Illumination.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2508363.2508416\">https://doi.org/10.1145/2508363.2508416</a>.","ista":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. 2013. Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. 32(6).","short":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","mla":"Bermano, Amit, et al. “Augmenting Physical Avatars Using Projector-Based Illumination.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2508363.2508416\">10.1145/2508363.2508416</a>.","ama":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. Augmenting physical avatars using projector-based illumination. <i>ACM Transactions on Graphics</i>. 2013;32(6). doi:<a href=\"https://doi.org/10.1145/2508363.2508416\">10.1145/2508363.2508416</a>"},"month":"11","status":"public","day":"01","issue":"6","date_created":"2018-12-11T11:55:47Z","publist_id":"4922","title":"Augmenting physical avatars using projector-based illumination","publication":"ACM Transactions on Graphics","publisher":"ACM","abstract":[{"lang":"eng","text":"Animated animatronic figures are a unique way to give physical presence to a character. However, their movement and expressions are often limited due to mechanical constraints. In this paper, we propose a complete process for augmenting physical avatars using projector-based illumination, significantly increasing their expressiveness. Given an input animation, the system decomposes the motion into low-frequency motion that can be physically reproduced by the animatronic head and high-frequency details that are added using projected shading. At the core is a spatio-temporal optimization process that compresses the motion in gradient space, ensuring faithful motion replay while respecting the physical limitations of the system. We also propose a complete multi-camera and projection system, including a novel defocused projection and subsurface scattering compensation scheme. The result of our system is a highly expressive physical avatar that features facial details and motion otherwise unattainable due to physical constraints."}],"extern":1,"quality_controlled":0,"date_published":"2013-11-01T00:00:00Z","author":[{"first_name":"Amit","last_name":"Bermano","full_name":"Bermano, Amit H"},{"last_name":"Bruschweiler","first_name":"Philipp","full_name":"Bruschweiler, Philipp"},{"full_name":"Grundhöfer, Anselm","first_name":"Anselm","last_name":"Grundhöfer"},{"last_name":"Iwai","first_name":"Daisuke","full_name":"Iwai, Daisuke"},{"full_name":"Bernd Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"full_name":"Groß, Markus S","first_name":"Markus","last_name":"Groß"}],"date_updated":"2021-01-12T06:55:23Z","doi":"10.1145/2508363.2508416"},{"publist_id":"4923","date_created":"2018-12-11T11:55:47Z","publisher":"ACM","title":"Modeling and estimation of internal friction in cloth","publication":"ACM Transactions on Graphics","extern":1,"quality_controlled":0,"abstract":[{"lang":"eng","text":"Force-deformation measurements of cloth exhibit significant hysteresis, and many researchers have identified internal friction as the source of this effect. However, it has not been incorporated into computer animation models of cloth. In this paper, we propose a model of internal friction based on an augmented reparameterization of Dahl's model, and we show that this model provides a good match to several important features of cloth hysteresis even with a minimal set of parameters. We also propose novel parameter estimation procedures that are based on simple and inexpensive setups and need only sparse data, as opposed to the complex hardware and dense data acquisition of previous methods. Finally, we provide an algorithm for the efficient simulation of internal friction, and we demonstrate it on simulation examples that show disparate behavior with and without internal friction."}],"date_updated":"2021-01-12T06:55:23Z","doi":"10.1145/2508363.2508389 ","date_published":"2013-11-01T00:00:00Z","author":[{"full_name":"Miguel, Eder","last_name":"Miguel","first_name":"Eder"},{"last_name":"Tamstorf","first_name":"Rasmus","full_name":"Tamstorf, Rasmus"},{"last_name":"Bradley","first_name":"Derek","full_name":"Bradley, Derek J"},{"full_name":"Schvartzman, Sara C","first_name":"Sara","last_name":"Schvartzman"},{"full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski","first_name":"Bernhard"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"},{"full_name":"Marschner, Steve","last_name":"Marschner","first_name":"Steve"},{"first_name":"Miguel","last_name":"Otaduy","full_name":"Otaduy, Miguel A"}],"publication_status":"published","year":"2013","_id":"2112","intvolume":"        32","type":"journal_article","volume":32,"month":"11","citation":{"chicago":"Miguel, Eder, Rasmus Tamstorf, Derek Bradley, Sara Schvartzman, Bernhard Thomaszewski, Bernd Bickel, Wojciech Matusik, Steve Marschner, and Miguel Otaduy. “Modeling and Estimation of Internal Friction in Cloth.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2508363.2508389 \">https://doi.org/10.1145/2508363.2508389 </a>.","ieee":"E. Miguel <i>et al.</i>, “Modeling and estimation of internal friction in cloth,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6. ACM, 2013.","apa":"Miguel, E., Tamstorf, R., Bradley, D., Schvartzman, S., Thomaszewski, B., Bickel, B., … Otaduy, M. (2013). Modeling and estimation of internal friction in cloth. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2508363.2508389 \">https://doi.org/10.1145/2508363.2508389 </a>","ama":"Miguel E, Tamstorf R, Bradley D, et al. Modeling and estimation of internal friction in cloth. <i>ACM Transactions on Graphics</i>. 2013;32(6). doi:<a href=\"https://doi.org/10.1145/2508363.2508389 \">10.1145/2508363.2508389 </a>","ista":"Miguel E, Tamstorf R, Bradley D, Schvartzman S, Thomaszewski B, Bickel B, Matusik W, Marschner S, Otaduy M. 2013. Modeling and estimation of internal friction in cloth. ACM Transactions on Graphics. 32(6).","short":"E. Miguel, R. Tamstorf, D. Bradley, S. Schvartzman, B. Thomaszewski, B. Bickel, W. Matusik, S. Marschner, M. Otaduy, ACM Transactions on Graphics 32 (2013).","mla":"Miguel, Eder, et al. “Modeling and Estimation of Internal Friction in Cloth.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2508363.2508389 \">10.1145/2508363.2508389 </a>."},"day":"01","issue":"6","acknowledgement":"This work was supported in part by the European Research Council (ERC-2011-StG-280135 Animetrics) and the Spanish Ministry of Economy (TIN2012-35840).","status":"public"},{"date_published":"2013-09-23T00:00:00Z","author":[{"first_name":"Olivier","last_name":"Rouiller","full_name":"Rouiller, Olivier"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"full_name":"Kautz, Jan","first_name":"Jan","last_name":"Kautz"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"full_name":"Alexa, Marc","first_name":"Marc","last_name":"Alexa"}],"doi":"10.1109/MCG.2013.82 ","date_updated":"2021-01-12T06:55:23Z","abstract":[{"text":"A new method fabricates custom surface reflectance and spatially varying bidirectional reflectance distribution functions (svBRDFs). Researchers optimize a microgeometry for a range of normal distribution functions and simulate the resulting surface's effective reflectance. Using the simulation's results, they reproduce an input svBRDF's appearance by distributing the microgeometry on the printed material's surface. This method lets people print svBRDFs on planar samples with current 3D printing technology, even with a limited set of printing materials. It extends naturally to printing svBRDFs on arbitrary shapes.","lang":"eng"}],"quality_controlled":0,"extern":1,"title":"3D printing spatially varying BRDFs","publication":"IEEE Computer Graphics and Applications","publisher":"IEEE","date_created":"2018-12-11T11:55:47Z","publist_id":"4920","status":"public","day":"23","issue":"6","citation":{"ama":"Rouiller O, Bickel B, Kautz J, Matusik W, Alexa M. 3D printing spatially varying BRDFs. <i>IEEE Computer Graphics and Applications</i>. 2013;33(6):48-57. doi:<a href=\"https://doi.org/10.1109/MCG.2013.82 \">10.1109/MCG.2013.82 </a>","short":"O. Rouiller, B. Bickel, J. Kautz, W. Matusik, M. Alexa, IEEE Computer Graphics and Applications 33 (2013) 48–57.","ista":"Rouiller O, Bickel B, Kautz J, Matusik W, Alexa M. 2013. 3D printing spatially varying BRDFs. IEEE Computer Graphics and Applications. 33(6), 48–57.","mla":"Rouiller, Olivier, et al. “3D Printing Spatially Varying BRDFs.” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6, IEEE, 2013, pp. 48–57, doi:<a href=\"https://doi.org/10.1109/MCG.2013.82 \">10.1109/MCG.2013.82 </a>.","chicago":"Rouiller, Olivier, Bernd Bickel, Jan Kautz, Wojciech Matusik, and Marc Alexa. “3D Printing Spatially Varying BRDFs.” <i>IEEE Computer Graphics and Applications</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/MCG.2013.82 \">https://doi.org/10.1109/MCG.2013.82 </a>.","ieee":"O. Rouiller, B. Bickel, J. Kautz, W. Matusik, and M. Alexa, “3D printing spatially varying BRDFs,” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6. IEEE, pp. 48–57, 2013.","apa":"Rouiller, O., Bickel, B., Kautz, J., Matusik, W., &#38; Alexa, M. (2013). 3D printing spatially varying BRDFs. <i>IEEE Computer Graphics and Applications</i>. IEEE. <a href=\"https://doi.org/10.1109/MCG.2013.82 \">https://doi.org/10.1109/MCG.2013.82 </a>"},"month":"09","page":"48 - 57","volume":33,"type":"journal_article","_id":"2113","intvolume":"        33","publication_status":"published","year":"2013"},{"status":"public","issue":"6","day":"01","citation":{"mla":"Bickel, Bernd, and Marc Alexa. “Computational Aspects of Fabrication: Modeling, Design and 3d Printing.” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6, IEEE, 2013, pp. 24–25, doi:<a href=\"https://doi.org/10.1109/MCG.2013.89\">10.1109/MCG.2013.89</a>.","short":"B. Bickel, M. Alexa, IEEE Computer Graphics and Applications 33 (2013) 24–25.","ista":"Bickel B, Alexa M. 2013. Computational aspects of fabrication: Modeling, design and 3d printing. IEEE Computer Graphics and Applications. 33(6), 24–25.","ama":"Bickel B, Alexa M. Computational aspects of fabrication: Modeling, design and 3d printing. <i>IEEE Computer Graphics and Applications</i>. 2013;33(6):24-25. doi:<a href=\"https://doi.org/10.1109/MCG.2013.89\">10.1109/MCG.2013.89</a>","apa":"Bickel, B., &#38; Alexa, M. (2013). Computational aspects of fabrication: Modeling, design and 3d printing. <i>IEEE Computer Graphics and Applications</i>. IEEE. <a href=\"https://doi.org/10.1109/MCG.2013.89\">https://doi.org/10.1109/MCG.2013.89</a>","ieee":"B. Bickel and M. Alexa, “Computational aspects of fabrication: Modeling, design and 3d printing,” <i>IEEE Computer Graphics and Applications</i>, vol. 33, no. 6. IEEE, pp. 24–25, 2013.","chicago":"Bickel, Bernd, and Marc Alexa. “Computational Aspects of Fabrication: Modeling, Design and 3d Printing.” <i>IEEE Computer Graphics and Applications</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/MCG.2013.89\">https://doi.org/10.1109/MCG.2013.89</a>."},"month":"12","volume":33,"page":"24 - 25","type":"journal_article","intvolume":"        33","_id":"2114","year":"2013","publication_status":"published","author":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Marc","last_name":"Alexa","full_name":"Alexa, Marc"}],"date_published":"2013-12-01T00:00:00Z","date_updated":"2021-01-12T06:55:24Z","doi":"10.1109/MCG.2013.89","abstract":[{"text":"3D printing is considered a disruptive technology with a potentially tremendous socioeconomic impact. The three articles in this special issue illustrate how novel computer graphics approaches are advancing such digital fabrication.","lang":"eng"}],"quality_controlled":0,"extern":1,"publication":"IEEE Computer Graphics and Applications","title":"Computational aspects of fabrication: Modeling, design and 3d printing","publisher":"IEEE","date_created":"2018-12-11T11:55:48Z","publist_id":"4921"},{"publist_id":"4917","date_created":"2018-12-11T11:55:49Z","publisher":"Institute of Mathematical Statistics","publication":"Electronic Journal of Probability","title":"Poisson stochastic integration in Banach spaces","extern":1,"quality_controlled":0,"abstract":[{"text":"We prove new upper and lower bounds for Banach space-valued stochastic integrals with respect to a compensated Poisson random measure. Our estimates apply to Banach spaces with non-trivial martingale (co)type and extend various results in the literature. We also develop a Malliavin framework to interpret Poisson stochastic integrals as vector-valued Skorohod integrals, and prove a Clark-Ocone representation formula.","lang":"eng"}],"doi":"10.1214/EJP.v18-2945 ","date_updated":"2021-01-12T06:55:24Z","date_published":"2013-11-18T00:00:00Z","author":[{"last_name":"Dirksen","first_name":"Sjoerd","full_name":"Dirksen, Sjoerd"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Jan Maas","last_name":"Maas","orcid":"0000-0002-0845-1338","first_name":"Jan"},{"full_name":"van Neerven, Jan M","first_name":"Jan","last_name":"Van Neerven"}],"year":"2013","publication_status":"published","_id":"2117","main_file_link":[{"url":"http://arxiv.org/abs/1307.7901 ","open_access":"1"}],"intvolume":"        18","type":"journal_article","volume":18,"month":"11","citation":{"ista":"Dirksen S, Maas J, Van Neerven J. 2013. Poisson stochastic integration in Banach spaces. Electronic Journal of Probability. 18.","short":"S. Dirksen, J. Maas, J. Van Neerven, Electronic Journal of Probability 18 (2013).","mla":"Dirksen, Sjoerd, et al. “Poisson Stochastic Integration in Banach Spaces.” <i>Electronic Journal of Probability</i>, vol. 18, Institute of Mathematical Statistics, 2013, doi:<a href=\"https://doi.org/10.1214/EJP.v18-2945 \">10.1214/EJP.v18-2945 </a>.","ama":"Dirksen S, Maas J, Van Neerven J. Poisson stochastic integration in Banach spaces. <i>Electronic Journal of Probability</i>. 2013;18. doi:<a href=\"https://doi.org/10.1214/EJP.v18-2945 \">10.1214/EJP.v18-2945 </a>","apa":"Dirksen, S., Maas, J., &#38; Van Neerven, J. (2013). Poisson stochastic integration in Banach spaces. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/EJP.v18-2945 \">https://doi.org/10.1214/EJP.v18-2945 </a>","ieee":"S. Dirksen, J. Maas, and J. Van Neerven, “Poisson stochastic integration in Banach spaces,” <i>Electronic Journal of Probability</i>, vol. 18. Institute of Mathematical Statistics, 2013.","chicago":"Dirksen, Sjoerd, Jan Maas, and Jan Van Neerven. “Poisson Stochastic Integration in Banach Spaces.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/EJP.v18-2945 \">https://doi.org/10.1214/EJP.v18-2945 </a>."},"day":"18","acknowledgement":"The first and third named authors were supported by VICI subsidy 639.033.604 of the Netherlands Organisation for Scientific Research (NWO). The first and second named authors were supported by the German Research Foundation in the Collaborative Research C","oa":1,"status":"public"},{"publisher":"Society for Industrial and Applied Mathematics ","publication":"SIAM Journal on Mathematical Analysis","title":"Gromov-Hausdorff convergence of discrete transportation metrics","publist_id":"4904","date_created":"2018-12-11T11:55:53Z","doi":"10.1137/120886315 ","date_updated":"2021-01-12T06:55:29Z","date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Nicola","last_name":"Gigli","full_name":"Gigli, Nicola"},{"first_name":"Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","full_name":"Jan Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":0,"extern":1,"abstract":[{"text":"This paper continues the investigation of `Wasserstein-like' transportation distances for probability measures on discrete sets. We prove that the discrete transportation metrics on the d-dimensional discrete torus with mesh size 1/N converge, when N→∞, to the standard 2-Wasserstein distance W_2 on the continuous torus in the sense of Gromov-Hausdorff. This is the first convergence result for the recently developed discrete transportation metrics. The result shows the compatibility between these metrics and the well-established 2-Wasserstein metric. \n\n\n","lang":"eng"}],"type":"journal_article","volume":45,"page":"879 - 899","year":"2013","publication_status":"published","_id":"2129","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.6501"}],"intvolume":"        45","issue":"2","day":"01","oa":1,"acknowledgement":"JM acknowledges support by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO).","status":"public","month":"01","citation":{"ieee":"N. Gigli and J. Maas, “Gromov-Hausdorff convergence of discrete transportation metrics,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 45, no. 2. Society for Industrial and Applied Mathematics , pp. 879–899, 2013.","chicago":"Gigli, Nicola, and Jan Maas. “Gromov-Hausdorff Convergence of Discrete Transportation Metrics.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics , 2013. <a href=\"https://doi.org/10.1137/120886315 \">https://doi.org/10.1137/120886315 </a>.","apa":"Gigli, N., &#38; Maas, J. (2013). Gromov-Hausdorff convergence of discrete transportation metrics. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/120886315 \">https://doi.org/10.1137/120886315 </a>","ama":"Gigli N, Maas J. Gromov-Hausdorff convergence of discrete transportation metrics. <i>SIAM Journal on Mathematical Analysis</i>. 2013;45(2):879-899. doi:<a href=\"https://doi.org/10.1137/120886315 \">10.1137/120886315 </a>","mla":"Gigli, Nicola, and Jan Maas. “Gromov-Hausdorff Convergence of Discrete Transportation Metrics.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 45, no. 2, Society for Industrial and Applied Mathematics , 2013, pp. 879–99, doi:<a href=\"https://doi.org/10.1137/120886315 \">10.1137/120886315 </a>.","ista":"Gigli N, Maas J. 2013. Gromov-Hausdorff convergence of discrete transportation metrics. SIAM Journal on Mathematical Analysis. 45(2), 879–899.","short":"N. Gigli, J. Maas, SIAM Journal on Mathematical Analysis 45 (2013) 879–899."}},{"citation":{"ama":"Lemeshko M. Manipulating scattering of ultracold atoms with light-induced dissipation. <i>Frontiers Physics</i>. 2013;1(17). doi:<a href=\"https://doi.org/10.3389/fphy.2013.00017\">10.3389/fphy.2013.00017</a>","ista":"Lemeshko M. 2013. Manipulating scattering of ultracold atoms with light-induced dissipation. Frontiers Physics. 1(17).","mla":"Lemeshko, Mikhail. “Manipulating Scattering of Ultracold Atoms with Light-Induced Dissipation.” <i>Frontiers Physics</i>, vol. 1, no. 17, Frontiers Media, 2013, doi:<a href=\"https://doi.org/10.3389/fphy.2013.00017\">10.3389/fphy.2013.00017</a>.","short":"M. Lemeshko, Frontiers Physics 1 (2013).","ieee":"M. Lemeshko, “Manipulating scattering of ultracold atoms with light-induced dissipation,” <i>Frontiers Physics</i>, vol. 1, no. 17. Frontiers Media, 2013.","chicago":"Lemeshko, Mikhail. “Manipulating Scattering of Ultracold Atoms with Light-Induced Dissipation.” <i>Frontiers Physics</i>. Frontiers Media, 2013. <a href=\"https://doi.org/10.3389/fphy.2013.00017\">https://doi.org/10.3389/fphy.2013.00017</a>.","apa":"Lemeshko, M. (2013). Manipulating scattering of ultracold atoms with light-induced dissipation. <i>Frontiers Physics</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fphy.2013.00017\">https://doi.org/10.3389/fphy.2013.00017</a>"},"month":"10","status":"public","acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory","oa":1,"day":"07","issue":"17","_id":"2139","intvolume":"         1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.8129"}],"publication_status":"published","year":"2013","volume":1,"type":"journal_article","abstract":[{"text":"Recently it has been shown that pairs of atoms can form metastable bonds due to non-conservative forces induced by dissipation [Lemeshko&amp;Weimer, Nature Comm. 4, 2230 (2013)]. Here we study the dynamics of interaction-induced coherent population trapping - the process responsible for the formation of dissipatively bound molecules. We derive the effective dissipative potentials induced between ultracold atoms by laser light, and study the time evolution of the scattering states. We demonstrate that binding occurs on short timescales of ~10 microseconds, even if the initial kinetic energy of the atoms significantly exceeds the depth of the dissipative potential. Dissipatively-bound molecules with preordained bond lengths and vibrational wavefunctions can be created and detected in current experiments with ultracold atoms.","lang":"eng"}],"extern":1,"quality_controlled":0,"author":[{"full_name":"Mikhail Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"date_published":"2013-10-07T00:00:00Z","date_updated":"2021-01-12T06:55:32Z","doi":"10.3389/fphy.2013.00017","date_created":"2018-12-11T11:55:56Z","publist_id":"4885","title":"Manipulating scattering of ultracold atoms with light-induced dissipation","publication":"Frontiers Physics","publisher":"Frontiers Media"},{"page":"317 - 328","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"2181","has_accepted_license":"1","year":"2013","acknowledgement":" and an Elise Richter Fellowship (Austrian Science Fund V00125). ","status":"public","oa":1,"citation":{"ama":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. Quantitative relaxation of concurrent data structures. In: <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>. ACM; 2013:317-328. doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>","ista":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. 2013. Quantitative relaxation of concurrent data structures. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 317–328.","mla":"Henzinger, Thomas A., et al. “Quantitative Relaxation of Concurrent Data Structures.” <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, ACM, 2013, pp. 317–28, doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>.","short":"T.A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, A. Sokolova, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 317–328.","chicago":"Henzinger, Thomas A, Christoph Kirsch, Hannes Payer, Ali Sezgin, and Ana Sokolova. “Quantitative Relaxation of Concurrent Data Structures.” In <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, 317–28. ACM, 2013. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>.","ieee":"T. A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, and A. Sokolova, “Quantitative relaxation of concurrent data structures,” in <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i>, Rome, Italy, 2013, pp. 317–328.","apa":"Henzinger, T. A., Kirsch, C., Payer, H., Sezgin, A., &#38; Sokolova, A. (2013). Quantitative relaxation of concurrent data structures. In <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i> (pp. 317–328). Rome, Italy: ACM. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>"},"publication_identifier":{"isbn":["978-1-4503-1832-7"]},"publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","title":"Quantitative relaxation of concurrent data structures","department":[{"_id":"ToHe"}],"publisher":"ACM","ec_funded":1,"date_created":"2018-12-11T11:56:11Z","oa_version":"Submitted Version","publist_id":"4801","abstract":[{"text":"There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all &quot;legal&quot; sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones.","lang":"eng"}],"file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:14:33Z","relation":"main_file","creator":"system","access_level":"open_access","file_size":294689,"checksum":"adf465e70948f4e80e48057524516456","file_name":"IST-2014-198-v1+1_popl128-henzinger-clean.pdf","file_id":"5086","date_updated":"2020-07-14T12:45:31Z"}],"publication_status":"published","ddc":["000","004"],"day":"01","month":"01","language":[{"iso":"eng"}],"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:45:31Z","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2013-01-25","location":"Rome, Italy","start_date":"2013-01-23"},"date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"first_name":"Hannes","last_name":"Payer","full_name":"Payer, Hannes"},{"last_name":"Sezgin","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali"},{"full_name":"Sokolova, Ana","first_name":"Ana","last_name":"Sokolova"}],"pubrep_id":"198","date_updated":"2023-02-21T16:06:49Z","doi":"10.1145/2429069.2429109","related_material":{"record":[{"relation":"later_version","status":"deleted","id":"10901"}]},"scopus_import":1,"quality_controlled":"1"}]