[{"citation":{"ama":"Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 2018;208(4):1397-1408. doi:10.1534/genetics.117.300360","ista":"Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. 2018. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 208(4), 1397–1408.","apa":"Lloyd-Jones, L. R., Robinson, M. R., Yang, J., & Visscher, P. M. (2018). Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300360","ieee":"L. R. Lloyd-Jones, M. R. Robinson, J. Yang, and P. M. Visscher, “Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1397–1408, 2018.","mla":"Lloyd-Jones, Luke R., et al. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1397–408, doi:10.1534/genetics.117.300360.","short":"L.R. Lloyd-Jones, M.R. Robinson, J. Yang, P.M. Visscher, Genetics 208 (2018) 1397–1408.","chicago":"Lloyd-Jones, Luke R., Matthew Richard Robinson, Jian Yang, and Peter M. Visscher. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300360."},"publication":"Genetics","page":"1397-1408","article_type":"original","quality_controlled":"1","date_published":"2018-04-01T00:00:00Z","doi":"10.1534/genetics.117.300360","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["0016-6731","1943-2631"]},"month":"04","day":"01","_id":"7723","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Genetics Society of America","intvolume":" 208","title":"Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio","publication_status":"published","status":"public","author":[{"last_name":"Lloyd-Jones","first_name":"Luke R.","full_name":"Lloyd-Jones, Luke R."},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"}],"volume":208,"oa_version":"None","date_created":"2020-04-30T10:45:19Z","date_updated":"2021-01-12T08:15:06Z","type":"journal_article","issue":"4","abstract":[{"text":"Genome-wide association studies (GWAS) have identified thousands of loci that are robustly associated with complex diseases. The use of linear mixed model (LMM) methodology for GWAS is becoming more prevalent due to its ability to control for population structure and cryptic relatedness and to increase power. The odds ratio (OR) is a common measure of the association of a disease with an exposure (e.g., a genetic variant) and is readably available from logistic regression. However, when the LMM is applied to all-or-none traits it provides estimates of genetic effects on the observed 0–1 scale, a different scale to that in logistic regression. This limits the comparability of results across studies, for example in a meta-analysis, and makes the interpretation of the magnitude of an effect from an LMM GWAS difficult. In this study, we derived transformations from the genetic effects estimated under the LMM to the OR that only rely on summary statistics. To test the proposed transformations, we used real genotypes from two large, publicly available data sets to simulate all-or-none phenotypes for a set of scenarios that differ in underlying model, disease prevalence, and heritability. Furthermore, we applied these transformations to GWAS summary statistics for type 2 diabetes generated from 108,042 individuals in the UK Biobank. In both simulation and real-data application, we observed very high concordance between the transformed OR from the LMM and either the simulated truth or estimates from logistic regression. The transformations derived and validated in this study improve the comparability of results from prospective and already performed LMM GWAS on complex diseases by providing a reliable transformation to a common comparative scale for the genetic effects.","lang":"eng"}],"extern":"1"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41588-018-0101-4","date_published":"2018-04-16T00:00:00Z","article_type":"original","quality_controlled":"1","page":"746-753","publication":"Nature Genetics","citation":{"chicago":"Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics. Springer Nature, 2018. https://doi.org/10.1038/s41588-018-0101-4.","short":"J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo, C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu, T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018) 746–753.","mla":"Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics, vol. 50, no. 5, Springer Nature, 2018, pp. 746–53, doi:10.1038/s41588-018-0101-4.","ieee":"J. Zeng et al., “Signatures of negative selection in the genetic architecture of human complex traits,” Nature Genetics, vol. 50, no. 5. Springer Nature, pp. 746–753, 2018.","apa":"Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-018-0101-4","ista":"Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753.","ama":"Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 2018;50(5):746-753. doi:10.1038/s41588-018-0101-4"},"month":"04","day":"16","article_processing_charge":"No","publication_identifier":{"issn":["1061-4036","1546-1718"]},"date_updated":"2021-01-12T08:15:06Z","date_created":"2020-04-30T10:44:57Z","oa_version":"None","volume":50,"author":[{"first_name":"Jian","last_name":"Zeng","full_name":"Zeng, Jian"},{"first_name":"Ronald","last_name":"de Vlaming","full_name":"de Vlaming, Ronald"},{"full_name":"Wu, Yang","first_name":"Yang","last_name":"Wu"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Lloyd-Jones, Luke R.","last_name":"Lloyd-Jones","first_name":"Luke R."},{"full_name":"Yengo, Loic","first_name":"Loic","last_name":"Yengo"},{"full_name":"Yap, Chloe X.","first_name":"Chloe X.","last_name":"Yap"},{"full_name":"Xue, Angli","first_name":"Angli","last_name":"Xue"},{"first_name":"Julia","last_name":"Sidorenko","full_name":"Sidorenko, Julia"},{"last_name":"McRae","first_name":"Allan F.","full_name":"McRae, Allan F."},{"full_name":"Powell, Joseph E.","last_name":"Powell","first_name":"Joseph E."},{"last_name":"Montgomery","first_name":"Grant W.","full_name":"Montgomery, Grant W."},{"first_name":"Andres","last_name":"Metspalu","full_name":"Metspalu, Andres"},{"last_name":"Esko","first_name":"Tonu","full_name":"Esko, Tonu"},{"first_name":"Greg","last_name":"Gibson","full_name":"Gibson, Greg"},{"full_name":"Wray, Naomi R.","first_name":"Naomi R.","last_name":"Wray"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."},{"first_name":"Jian","last_name":"Yang","full_name":"Yang, Jian"}],"publication_status":"published","status":"public","title":"Signatures of negative selection in the genetic architecture of human complex traits","publisher":"Springer Nature","intvolume":" 50","year":"2018","_id":"7722","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits."}],"issue":"5","type":"journal_article"},{"_id":"7724","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"Proceedings of the National Academy of Sciences","intvolume":" 115","publication_status":"published","title":"Evidence of directional and stabilizing selection in contemporary humans","status":"public","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.1806837115"}]},"author":[{"first_name":"Jaleal S.","last_name":"Sanjak","full_name":"Sanjak, Jaleal S."},{"full_name":"Sidorenko, Julia","last_name":"Sidorenko","first_name":"Julia"},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Thornton, Kevin R.","first_name":"Kevin R.","last_name":"Thornton"},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."}],"volume":115,"oa_version":"None","date_updated":"2021-01-12T08:15:07Z","date_created":"2020-04-30T10:45:43Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species."}],"extern":"1","citation":{"ista":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 115(1), 151–156.","ieee":"J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher, “Evidence of directional and stabilizing selection in contemporary humans,” Proceedings of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National Academy of Sciences, pp. 151–156, 2018.","apa":"Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher, P. M. (2018). Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114","ama":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114","chicago":"Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R. Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114.","mla":"Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences, vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56, doi:10.1073/pnas.1707227114.","short":"J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings of the National Academy of Sciences 115 (2018) 151–156."},"publication":"Proceedings of the National Academy of Sciences","page":"151-156","article_type":"original","quality_controlled":"1","date_published":"2018-01-02T00:00:00Z","doi":"10.1073/pnas.1707227114","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"article_processing_charge":"No","month":"01","day":"02"},{"status":"public","title":"Enhanced diffusion by binding to the crosslinks of a polymer gel","publication_status":"published","publisher":"Springer Nature","intvolume":" 9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7754","year":"2018","date_created":"2020-04-30T11:38:01Z","date_updated":"2021-01-12T08:15:18Z","volume":9,"oa_version":"Published Version","author":[{"first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."},{"full_name":"Ribbeck, Katharina","last_name":"Ribbeck","first_name":"Katharina"}],"article_number":"4348","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex."}],"quality_controlled":"1","article_type":"original","publication":"Nature Communications","citation":{"ieee":"C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer Nature, 2018.","apa":"Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06851-5","ista":"Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348.","ama":"Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5","chicago":"Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5.","short":"C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018).","mla":"Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature, 2018, doi:10.1038/s41467-018-06851-5."},"main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-06851-5","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2018-10-19T00:00:00Z","doi":"10.1038/s41467-018-06851-5","day":"19","month":"10","article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]}},{"date_published":"2018-11-09T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. 2018.","ieee":"R. P. J. Bevers et al., “Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018.","apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. Cold Spring Harbor Laboratory.","ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv, .","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018).","mla":"Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv, Cold Spring Harbor Laboratory, 2018.","chicago":"Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring Harbor Laboratory, 2018."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/466771 "}],"publication":"bioRxiv","page":"49","article_processing_charge":"No","month":"11","day":"09","author":[{"full_name":"Bevers, Roel P.J.","last_name":"Bevers","first_name":"Roel P.J."},{"full_name":"Litovchenko, Maria","first_name":"Maria","last_name":"Litovchenko"},{"last_name":"Kapopoulou","first_name":"Adamandia","full_name":"Kapopoulou, Adamandia"},{"full_name":"Braman, Virginie S.","first_name":"Virginie S.","last_name":"Braman"},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"first_name":"Johan","last_name":"Auwerx","full_name":"Auwerx, Johan"},{"first_name":"Brian","last_name":"Hollis","full_name":"Hollis, Brian"},{"first_name":"Bart","last_name":"Deplancke","full_name":"Deplancke, Bart"}],"oa_version":"Preprint","date_updated":"2021-01-12T08:15:30Z","date_created":"2020-04-30T13:09:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7783","year":"2018","publisher":"Cold Spring Harbor Laboratory","publication_status":"published","status":"public","title":"Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel","abstract":[{"lang":"eng","text":"The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies."}],"extern":"1","type":"preprint"},{"_id":"6001","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2018","title":"ThreadScan: Automatic and scalable memory reclamation","publication_status":"published","status":"public","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"intvolume":" 4","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leiserson, William","last_name":"Leiserson","first_name":"William"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"related_material":{"record":[{"id":"779","status":"public","relation":"earlier_version"}]},"date_updated":"2023-02-23T13:17:54Z","date_created":"2019-02-14T13:24:11Z","oa_version":"None","volume":4,"article_number":"18","type":"journal_article","abstract":[{"text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.","lang":"eng"}],"issue":"4","publication":"ACM Transactions on Parallel Computing","citation":{"ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897","apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.","ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018).","mla":"Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.","chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897."},"quality_controlled":"1","doi":"10.1145/3201897","date_published":"2018-09-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"09","publication_identifier":{"issn":["2329-4949"]}},{"publication":"6th International Conference on Learning Representations","external_id":{"arxiv":["1802.05668"]},"oa":1,"citation":{"ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018."},"quality_controlled":"1","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Vancouver, Canada","start_date":"2018-04-30","end_date":"2018-05-03"},"date_published":"2018-05-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"05","day":"01","article_processing_charge":"No","has_accepted_license":"1","year":"2018","_id":"7812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Model compression via distillation and quantization","publication_status":"published","ddc":["000"],"department":[{"_id":"DaAl"}],"author":[{"full_name":"Polino, Antonio","first_name":"Antonio","last_name":"Polino"},{"first_name":"Razvan","last_name":"Pascanu","full_name":"Pascanu, Razvan"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"date_updated":"2023-02-23T13:18:41Z","date_created":"2020-05-10T22:00:51Z","file":[{"date_created":"2020-05-26T13:02:00Z","date_updated":"2020-07-14T12:48:03Z","checksum":"a4336c167978e81891970e4e4517a8c3","relation":"main_file","file_id":"7894","content_type":"application/pdf","file_size":308339,"creator":"dernst","file_name":"2018_ICLR_Polino.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"conference","file_date_updated":"2020-07-14T12:48:03Z","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}]},{"publication_identifier":{"issn":["0044-8249"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1002/ange.201802277","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"extern":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:48:06Z","volume":130,"date_updated":"2021-01-12T08:16:21Z","date_created":"2020-06-19T08:33:24Z","author":[{"full_name":"Mahne, Nika","last_name":"Mahne","first_name":"Nika"},{"first_name":"Sara E.","last_name":"Renfrew","full_name":"Renfrew, Sara E."},{"last_name":"McCloskey","first_name":"Bryan D.","full_name":"McCloskey, Bryan D."},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"publisher":"Wiley","publication_status":"published","year":"2018","has_accepted_license":"1","article_processing_charge":"No","day":"04","date_published":"2018-05-04T00:00:00Z","page":"5627-5631","article_type":"original","citation":{"chicago":"Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277.","short":"N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie 130 (2018) 5627–5631.","mla":"Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018, pp. 5627–31, doi:10.1002/ange.201802277.","ieee":"N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie, vol. 130, no. 19. Wiley, pp. 5627–5631, 2018.","apa":"Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277","ista":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 130(19), 5627–5631.","ama":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 2018;130(19):5627-5631. doi:10.1002/ange.201802277"},"publication":"Angewandte Chemie","issue":"19","abstract":[{"text":"Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien, und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen >3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2 + O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir, dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird. Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.","lang":"ger"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"7988","date_updated":"2020-07-14T12:48:06Z","date_created":"2020-06-19T11:58:06Z","checksum":"81506e0f7079e1e3591f3cd9f626bf67","file_name":"2018_AngChemieDT_Mahne.pdf","access_level":"open_access","content_type":"application/pdf","file_size":674789,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 130","status":"public","title":"Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff","ddc":["540"],"_id":"7983","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","issue":"1","abstract":[{"text":"The neural code of cortical processing remains uncracked; however, it must necessarily rely on faithful signal propagation between cortical areas. In this issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation balanced by local inhibition can enable reliable signal propagation in data-constrained network models of macaque cortex. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8015","intvolume":" 98","title":"Cortical signal propagation: Balance, amplify, transmit","status":"public","oa_version":"Published Version","article_processing_charge":"No","day":"04","citation":{"chicago":"Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028.","mla":"Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.","short":"J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9.","ista":"Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify, transmit. Neuron. 98(1), 8–9.","apa":"Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance, amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028","ieee":"J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify, transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.","ama":"Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit. Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028"},"publication":"Neuron","page":"8-9","article_type":"original","date_published":"2018-04-04T00:00:00Z","extern":"1","pmid":1,"year":"2018","publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Stroud, Jake P.","first_name":"Jake P.","last_name":"Stroud"},{"last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"}],"volume":98,"date_updated":"2021-01-12T08:16:31Z","date_created":"2020-06-25T12:53:39Z","publication_identifier":{"issn":["0896-6273"]},"month":"04","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2018.03.028","open_access":"1"}],"external_id":{"pmid":["29621492"]},"quality_controlled":"1","doi":"10.1016/j.neuron.2018.03.028","language":[{"iso":"eng"}]},{"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2018","volume":21,"date_created":"2020-06-30T13:18:02Z","date_updated":"2021-01-12T08:16:46Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41593-018-0307-x","relation":"erratum"}]},"author":[{"last_name":"Stroud","first_name":"Jake P.","full_name":"Stroud, Jake P."},{"full_name":"Porter, Mason A.","last_name":"Porter","first_name":"Mason A."},{"full_name":"Hennequin, Guillaume","first_name":"Guillaume","last_name":"Hennequin"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P","full_name":"Vogels, Tim P"}],"extern":"1","quality_controlled":"1","external_id":{"pmid":["30482949"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41593-018-0276-0","publication_identifier":{"issn":["1097-6256","1546-1726"]},"month":"12","intvolume":" 21","title":"Motor primitives in space and time via targeted gain modulation in cortical networks","status":"public","_id":"8073","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"Submitted Version","type":"journal_article","issue":"12","abstract":[{"text":"Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support the generation of complex movements. Although recent neuronal-network models capture many qualitative aspects of M1 dynamics, they can generate only a few distinct movements. Additionally, it is unclear how M1 efficiently controls movements over a wide range of shapes and speeds. We demonstrate that modulation of neuronal input–output gains in recurrent neuronal-network models with a fixed architecture can dramatically reorganize neuronal activity and thus downstream muscle outputs. Consistent with the observation of diffuse neuromodulatory projections to M1, a relatively small number of modulatory control units provide sufficient flexibility to adjust high-dimensional network activity using a simple reward-based learning rule. Furthermore, it is possible to assemble novel movements from previously learned primitives, and one can separately change movement speed while preserving movement shape. Our results provide a new perspective on the role of modulatory systems in controlling recurrent cortical activity.","lang":"eng"}],"page":"1774-1783","article_type":"original","citation":{"apa":"Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0","ieee":"J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives in space and time via targeted gain modulation in cortical networks,” Nature Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018.","ista":"Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 21(12), 1774–1783.","ama":"Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0","chicago":"Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0.","short":"J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience 21 (2018) 1774–1783.","mla":"Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12, Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0."},"publication":"Nature Neuroscience","date_published":"2018-12-01T00:00:00Z","article_processing_charge":"No","day":"01"}]