[{"author":[{"full_name":"Sanjak, Jaleal S.","last_name":"Sanjak","first_name":"Jaleal S."},{"first_name":"Julia","last_name":"Sidorenko","full_name":"Sidorenko, Julia"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard"},{"full_name":"Thornton, Kevin R.","first_name":"Kevin R.","last_name":"Thornton"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."}],"related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.1806837115","relation":"erratum"}]},"date_created":"2020-04-30T10:45:43Z","date_updated":"2021-01-12T08:15:07Z","oa_version":"None","volume":115,"_id":"7724","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Evidence of directional and stabilizing selection in contemporary humans","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","intvolume":" 115","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."}],"issue":"1","extern":"1","type":"journal_article","doi":"10.1073/pnas.1707227114","date_published":"2018-01-02T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","citation":{"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.","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.","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.","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","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","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."},"article_type":"original","quality_controlled":"1","page":"151-156","day":"02","month":"01","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424","1091-6490"]}},{"article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]},"month":"10","day":"19","date_published":"2018-10-19T00:00:00Z","doi":"10.1038/s41467-018-06851-5","language":[{"iso":"eng"}],"citation":{"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","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.","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.","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."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-018-06851-5"}],"oa":1,"publication":"Nature Communications","article_type":"original","quality_controlled":"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."}],"extern":"1","type":"journal_article","article_number":"4348","author":[{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."},{"full_name":"Ribbeck, Katharina","last_name":"Ribbeck","first_name":"Katharina"}],"oa_version":"Published Version","volume":9,"date_updated":"2021-01-12T08:15:18Z","date_created":"2020-04-30T11:38:01Z","year":"2018","_id":"7754","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","intvolume":" 9","status":"public","title":"Enhanced diffusion by binding to the crosslinks of a polymer gel","publication_status":"published"},{"month":"11","day":"09","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2018-11-09T00:00:00Z","page":"49","publication":"bioRxiv","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."},"main_file_link":[{"url":"https://doi.org/10.1101/466771 ","open_access":"1"}],"oa":1,"extern":"1","abstract":[{"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.","lang":"eng"}],"type":"preprint","date_created":"2020-04-30T13:09:37Z","date_updated":"2021-01-12T08:15:30Z","oa_version":"Preprint","author":[{"full_name":"Bevers, Roel P.J.","last_name":"Bevers","first_name":"Roel P.J."},{"first_name":"Maria","last_name":"Litovchenko","full_name":"Litovchenko, Maria"},{"full_name":"Kapopoulou, Adamandia","first_name":"Adamandia","last_name":"Kapopoulou"},{"full_name":"Braman, Virginie S.","last_name":"Braman","first_name":"Virginie S."},{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Auwerx, Johan","last_name":"Auwerx","first_name":"Johan"},{"full_name":"Hollis, Brian","last_name":"Hollis","first_name":"Brian"},{"last_name":"Deplancke","first_name":"Bart","full_name":"Deplancke, Bart"}],"status":"public","publication_status":"published","title":"Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel","publisher":"Cold Spring Harbor Laboratory","_id":"7783","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":1,"month":"09","day":"01","publication_identifier":{"issn":["2329-4949"]},"publication":"ACM Transactions on Parallel Computing","citation":{"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.","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.","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","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.","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.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018)."},"quality_controlled":"1","doi":"10.1145/3201897","date_published":"2018-09-01T00:00:00Z","language":[{"iso":"eng"}],"article_number":"18","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"4","_id":"6001","year":"2018","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"ThreadScan: Automatic and scalable memory reclamation","status":"public","department":[{"_id":"DaAl"}],"intvolume":" 4","publisher":"Association for Computing Machinery","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"first_name":"William","last_name":"Leiserson","full_name":"Leiserson, William"},{"full_name":"Matveev, Alexander","last_name":"Matveev","first_name":"Alexander"},{"first_name":"Nir","last_name":"Shavit","full_name":"Shavit, Nir"}],"related_material":{"record":[{"id":"779","status":"public","relation":"earlier_version"}]},"date_created":"2019-02-14T13:24:11Z","date_updated":"2023-02-23T13:17:54Z","volume":4,"oa_version":"None"},{"scopus_import":1,"month":"05","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"6th International Conference on Learning Representations","oa":1,"citation":{"short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 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.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","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.","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."},"external_id":{"arxiv":["1802.05668"]},"quality_controlled":"1","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2018-05-03","start_date":"2018-04-30","location":"Vancouver, Canada"},"date_published":"2018-05-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","file_date_updated":"2020-07-14T12:48:03Z","abstract":[{"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.","lang":"eng"}],"_id":"7812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","title":"Model compression via distillation and quantization","status":"public","publication_status":"published","ddc":["000"],"department":[{"_id":"DaAl"}],"author":[{"full_name":"Polino, Antonio","last_name":"Polino","first_name":"Antonio"},{"full_name":"Pascanu, Razvan","last_name":"Pascanu","first_name":"Razvan"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"date_created":"2020-05-10T22:00:51Z","date_updated":"2023-02-23T13:18:41Z","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":308339,"access_level":"open_access","file_name":"2018_ICLR_Polino.pdf","checksum":"a4336c167978e81891970e4e4517a8c3","date_created":"2020-05-26T13:02:00Z","date_updated":"2020-07-14T12:48:03Z","file_id":"7894","relation":"main_file"}]}]