[{"_id":"7741","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2021-01-12T08:15:12Z","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population."}],"month":"07","intvolume":" 282","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rspb.2015.0689"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8452","1471-2954"]},"publication_status":"published","issue":"1810","volume":282,"article_number":"20150689","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:10.1098/rspb.2015.0689.","apa":"Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689","ama":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810). doi:10.1098/rspb.2015.0689","short":"M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015).","ieee":"M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird,” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810. The Royal Society, 2015.","chicago":"Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.","ista":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810), 20150689."},"title":"Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird","author":[{"first_name":"Mark James","full_name":"Adams, Mark James","last_name":"Adams"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson"},{"first_name":"Maria-Elena","last_name":"Mannarelli","full_name":"Mannarelli, Maria-Elena"},{"first_name":"Ben J.","full_name":"Hatchwell, Ben J.","last_name":"Hatchwell"}],"external_id":{"pmid":["26063846"]},"article_processing_charge":"No","publisher":"The Royal Society","quality_controlled":"1","oa":1,"day":"07","publication":"Proceedings of the Royal Society B: Biological Sciences","year":"2015","date_published":"2015-07-07T00:00:00Z","doi":"10.1098/rspb.2015.0689","date_created":"2020-04-30T10:58:07Z"},{"article_type":"original","type":"journal_article","status":"public","_id":"7739","article_processing_charge":"No","author":[{"full_name":"Santure, Anna W.","last_name":"Santure","first_name":"Anna W."},{"first_name":"Jocelyn","last_name":"Poissant","full_name":"Poissant, Jocelyn"},{"first_name":"Isabelle","last_name":"De Cauwer","full_name":"De Cauwer, Isabelle"},{"last_name":"van Oers","full_name":"van Oers, Kees","first_name":"Kees"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson"},{"full_name":"Quinn, John L.","last_name":"Quinn","first_name":"John L."},{"first_name":"Martien A. M.","last_name":"Groenen","full_name":"Groenen, Martien A. M."},{"first_name":"Marcel E.","last_name":"Visser","full_name":"Visser, Marcel E."},{"first_name":"Ben C.","full_name":"Sheldon, Ben C.","last_name":"Sheldon"},{"first_name":"Jon","last_name":"Slate","full_name":"Slate, Jon"}],"title":"Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations","date_updated":"2021-01-12T08:15:12Z","citation":{"ista":"Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 24, 6148–6162.","chicago":"Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers, Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology. Wiley, 2015. https://doi.org/10.1111/mec.13452.","ieee":"A. W. Santure et al., “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” Molecular Ecology, vol. 24. Wiley, pp. 6148–6162, 2015.","short":"A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L. Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology 24 (2015) 6148–6162.","apa":"Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R., Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.13452","ama":"Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452","mla":"Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology, vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","main_file_link":[{"url":"https://doi.org/10.1111/mec.13452","open_access":"1"}],"oa":1,"publisher":"Wiley","quality_controlled":"1","intvolume":" 24","month":"12","abstract":[{"lang":"eng","text":"Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations."}],"oa_version":"Published Version","page":"6148-6162","date_created":"2020-04-30T10:51:01Z","doi":"10.1111/mec.13452","date_published":"2015-12-10T00:00:00Z","volume":24,"publication_status":"published","year":"2015","publication_identifier":{"issn":["0962-1083"]},"language":[{"iso":"eng"}],"publication":"Molecular Ecology","day":"10"},{"type":"conference","conference":{"name":"PPoPP: Principles and Practice of Parallel Pogramming"},"status":"public","_id":"776","publist_id":"6878","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Justin","last_name":"Kopinsky","full_name":"Kopinsky, Justin"},{"last_name":"Li","full_name":"Li, Jerry","first_name":"Jerry"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"article_processing_charge":"No","title":"The SprayList: A scalable relaxed priority queue","date_updated":"2023-02-23T13:16:43Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.","short":"D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20.","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel Pogramming, 2015, vol. 2015–January, pp. 11–20.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList: A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523","ama":"Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015. https://doi.org/10.1145/2688500.2688523.","ista":"Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming vol. 2015–January, 11–20."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","month":"01","abstract":[{"lang":"eng","text":"High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by "spraying" themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(plog3p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log3p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. Furthermore, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution."}],"oa_version":"None","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle\r\nand Intel corporations.","page":"11 - 20","volume":"2015-January","date_published":"2015-01-24T00:00:00Z","doi":"10.1145/2688500.2688523","date_created":"2018-12-11T11:48:26Z","publication_status":"published","year":"2015","day":"24","language":[{"iso":"eng"}]},{"intvolume":" 114","month":"06","publisher":"American Physical Society","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior."}],"date_created":"2020-04-30T11:41:08Z","date_published":"2015-06-04T00:00:00Z","doi":"10.1103/physrevlett.114.225501","volume":114,"issue":"22","publication":"Physical Review Letters","language":[{"iso":"eng"}],"day":"04","year":"2015","publication_status":"published","publication_identifier":{"issn":["0031-9007","1079-7114"]},"status":"public","type":"journal_article","article_type":"original","article_number":"225501","_id":"7765","title":"The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior","article_processing_charge":"No","author":[{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:15:23Z","citation":{"chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/physrevlett.114.225501.","ista":"Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 114(22), 225501.","mla":"Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.","apa":"Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501","ama":"Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior,” Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015)."}},{"article_number":"032706","_id":"7767","status":"public","article_type":"original","type":"journal_article","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.” Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015, doi:10.1103/physreve.91.032706.","short":"R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).","ieee":"R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics of soft active particles,” Physical Review E, vol. 91, no. 3. American Physical Society, 2015.","apa":"van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective dynamics of soft active particles. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.91.032706","ama":"van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706","chicago":"Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema. “Collective Dynamics of Soft Active Particles.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.","ista":"van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706."},"date_updated":"2021-01-12T08:15:24Z","title":"Collective dynamics of soft active particles","author":[{"last_name":"van Drongelen","full_name":"van Drongelen, Ruben","first_name":"Ruben"},{"first_name":"Anshuman","last_name":"Pal","full_name":"Pal, Anshuman"},{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"},{"last_name":"Idema","full_name":"Idema, Timon","first_name":"Timon"}],"article_processing_charge":"No","oa_version":"None","abstract":[{"text":"We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength of these interactions leads to migrating swarms, rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble motion, alternating between migration and either rotating or jammed states. Interestingly, although a migrating swarm moves slower than an individual particle, the diffusion constant can be up to three orders of magnitude larger, suggesting that collective motion can be highly advantageous, for example, when searching for food.","lang":"eng"}],"month":"03","intvolume":" 91","quality_controlled":"1","publisher":"American Physical Society","day":"01","language":[{"iso":"eng"}],"publication":"Physical Review E","publication_identifier":{"issn":["1539-3755","1550-2376"]},"publication_status":"published","year":"2015","doi":"10.1103/physreve.91.032706","volume":91,"date_published":"2015-03-01T00:00:00Z","issue":"3","date_created":"2020-04-30T11:41:38Z"},{"type":"journal_article","article_type":"original","status":"public","_id":"7766","article_processing_charge":"No","author":[{"first_name":"Daniel M.","last_name":"Sussman","full_name":"Sussman, Daniel M."},{"first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"title":"Disordered surface vibrations in jammed sphere packings","date_updated":"2021-01-12T08:15:23Z","citation":{"mla":"Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:10.1039/c4sm02905d.","ieee":"D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751.","apa":"Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c4sm02905d","ama":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d","chicago":"Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","quality_controlled":"1","publisher":"Royal Society of Chemistry","intvolume":" 11","month":"02","abstract":[{"lang":"eng","text":"We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached."}],"oa_version":"None","page":"2745-2751","date_created":"2020-04-30T11:41:23Z","date_published":"2015-02-15T00:00:00Z","volume":11,"issue":"14","doi":"10.1039/c4sm02905d","year":"2015","publication_status":"published","publication_identifier":{"issn":["1744-683X","1744-6848"]},"publication":"Soft Matter","language":[{"iso":"eng"}],"day":"15"},{"month":"01","main_file_link":[{"url":"http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning"}],"publisher":"Neural Information Processing Systems","oa_version":"None","abstract":[{"text":"In many applications, the data is of rich structure that can be represented by a hypergraph, where the data items are represented by vertices and the associations among items are represented by hyperedges. Equivalently, we are given an input bipartite graph with two types of vertices: items, and associations (which we refer to as topics). We consider the problem of partitioning the set of items into a given number of components such that the maximum number of topics covered by a component is minimized. This is a clustering problem with various applications, e.g. partitioning of a set of information objects such as documents, images, and videos, and load balancing in the context of modern computation platforms.Inthis paper, we focus on the streaming computation model for this problem, in which items arrive online one at a time and each item must be assigned irrevocably to a component at its arrival time. Motivated by scalability requirements, we focus on the class of streaming computation algorithms with memory limited to be at most linear in the number of components. We show that a greedy assignment strategy is able to recover a hidden co-clustering of items under a natural set of recovery conditions. We also report results of an extensive empirical evaluation, which demonstrate that this greedy strategy yields superior performance when compared with alternative approaches.","lang":"eng"}],"date_created":"2018-12-11T11:48:27Z","date_published":"2015-01-01T00:00:00Z","volume":"2015-January","page":"1900 - 1908","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","status":"public","conference":{"name":"NIPS: Neural Information Processing Systems"},"type":"conference","_id":"777","title":"Streaming min-max hypergraph partitioning","article_processing_charge":"No","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Iglesias","full_name":"Iglesias, Jennifer","first_name":"Jennifer"},{"first_name":"Milan","last_name":"Vojnović","full_name":"Vojnović, Milan"}],"publist_id":"6879","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-02-23T13:17:09Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.","ama":"Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning. In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.","apa":"Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.","short":"D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, pp. 1900–1908.","ieee":"D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015, vol. 2015–January, pp. 1900–1908.","chicago":"Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing Systems, 2015.","ista":"Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908."}},{"publist_id":"6880","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Kopinsky","full_name":"Kopinsky, Justin","first_name":"Justin"},{"first_name":"Petr","full_name":"Kuznetsov, Petr","last_name":"Kuznetsov"},{"last_name":"Ravi","full_name":"Ravi, Srivatsan","first_name":"Srivatsan"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"external_id":{"arxiv":["1405.5689"]},"article_processing_charge":"No","title":"Inherent limitations of hybrid transactional memory","citation":{"short":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, pp. 185–199.","ieee":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent limitations of hybrid transactional memory,” presented at the DISC: Distributed Computing, 2015, vol. 9363, pp. 185–199.","apa":"Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015). Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13","ama":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13","mla":"Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.","ista":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363, 185–199.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi, and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99. Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"185 - 199","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-662-48653-5_13","date_created":"2018-12-11T11:48:27Z","year":"2015","day":"01","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"P. Kuznetsov-The author is supported by the Agence Nationale de la Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.","date_updated":"2023-02-23T13:17:35Z","extern":"1","type":"conference","conference":{"name":"DISC: Distributed Computing"},"status":"public","_id":"778","volume":9363,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.5689"}],"month":"01","intvolume":" 9363","abstract":[{"lang":"eng","text":"Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead."}],"oa_version":"None"},{"_id":"7779","status":"public","type":"preprint","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","ista":"Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820, .","mla":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","short":"C.P. Goodrich, ArXiv:1510.08820 (2015).","ieee":"C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of disordered solids,” arXiv:1510.08820. 2015.","ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:151008820. 2015.","apa":"Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820."},"date_updated":"2021-01-12T08:15:28Z","title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids","author":[{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"}],"external_id":{"arxiv":["1510.08820"]},"article_processing_charge":"No","oa_version":"Preprint","abstract":[{"text":"The fact that a disordered material is not constrained in its properties in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential for novel material design. However, unlike their crystalline\r\ncounterparts, disordered solids are not well understood. One of the primary\r\nobstacles is the lack of a theoretical framework for thinking about disorder\r\nand its relation to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition with diverging length scales and clean power-law\r\nsignatures. This critical point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the potential to provide the essential theoretical\r\nfoundation necessary for a unified understanding of the mechanics of disordered\r\nsolids. We begin by showing that jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact nonlinearities.\" We then investigate\r\nthe critical nature of the transition, focusing on diverging length scales and\r\nfinite-size effects. Next, we argue that jamming plays the same role for\r\ndisordered solids as the perfect crystal plays for crystalline solids. Not only\r\ncan it be considered an idealized starting point for understanding disordered\r\nmaterials, but it can even influence systems that have a relatively high amount\r\nof crystalline order. The behavior of solids can thus be thought of as existing\r\non a spectrum, with the perfect crystal and the jamming transition at opposing\r\nends. Finally, we introduce a new principle wherein the contribution of an\r\nindividual bond to one global property is independent of its contribution to\r\nanother. This principle allows the different global responses of a disordered\r\nsystem to be manipulated independently and provides a great deal of flexibility\r\nin designing materials with unique, textured and tunable properties.","lang":"eng"}],"month":"10","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1510.08820","open_access":"1"}],"day":"29","publication":"arXiv:1510.08820","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","date_published":"2015-10-29T00:00:00Z","date_created":"2020-04-30T12:16:18Z","page":"242"},{"acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle corporation. In particular, we would like to thank Dave Dice, Alex Kogan, and Mark Moir from the Oracle Scalable Synchronization Research Group for very useful feedback on earlier drafts of this paper.","oa_version":"None","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. In this paper, 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. Initial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free."}],"month":"06","publisher":"ACM","language":[{"iso":"eng"}],"day":"13","publication_status":"published","year":"2015","date_created":"2018-12-11T11:48:27Z","doi":"10.1145/2755573.2755600","date_published":"2015-06-13T00:00:00Z","volume":"2015-June","related_material":{"record":[{"id":"6001","status":"public","relation":"later_version"}]},"page":"123 - 132","_id":"779","status":"public","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-02-23T12:35:42Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. ThreadScan: Automatic and Scalable Memory Reclamation. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:10.1145/2755573.2755600.","ama":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. ThreadScan: Automatic and scalable memory reclamation. In: Vol 2015-June. ACM; 2015:123-132. doi:10.1145/2755573.2755600","apa":"Alistarh, D.-A., Matveev, A., Leiserson, W., & Shavit, N. (2015). ThreadScan: Automatic and scalable memory reclamation (Vol. 2015–June, pp. 123–132). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2755573.2755600","ieee":"D.-A. Alistarh, A. Matveev, W. Leiserson, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2015, vol. 2015–June, pp. 123–132.","short":"D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp. 123–132.","chicago":"Alistarh, Dan-Adrian, Alexander Matveev, William Leiserson, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation,” 2015–June:123–32. ACM, 2015. https://doi.org/10.1145/2755573.2755600.","ista":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. 2015. ThreadScan: Automatic and scalable memory reclamation. SPAA: Symposium on Parallelism in Algorithms and Architectures vol. 2015–June, 123–132."},"title":"ThreadScan: Automatic and scalable memory reclamation","article_processing_charge":"No","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Matveev","full_name":"Matveev, Alexander","first_name":"Alexander"},{"last_name":"Leiserson","full_name":"Leiserson, William","first_name":"William"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"publist_id":"6876"},{"date_updated":"2023-02-23T13:18:11Z","citation":{"ista":"Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in population protocols. ICALP: International Colloquium on Automota, Languages and Programming vol. 9135, 479–491.","chicago":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.","ieee":"D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in population protocols,” presented at the ICALP: International Colloquium on Automota, Languages and Programming, 2015, vol. 9135, pp. 479–491.","short":"D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.","ama":"Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population protocols. In: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38","apa":"Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP: International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38","mla":"Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Rati","full_name":"Gelashvili, Rati","last_name":"Gelashvili"}],"publist_id":"6877","external_id":{"arxiv":["1502.05745"]},"title":"Polylogarithmic-time leader election in population protocols","_id":"780","type":"conference","conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming"},"status":"public","publication_status":"published","year":"2015","day":"01","language":[{"iso":"eng"}],"page":"479 - 491","doi":"10.1007/978-3-662-47666-6_38","volume":9135,"date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:48:28Z","abstract":[{"text":"Population protocols are networks of finite-state agents, interacting randomly, and updating their states using simple rules. Despite their extreme simplicity, these systems have been shown to cooperatively perform complex computational tasks, such as simulating register machines to compute standard arithmetic functions. The election of a unique leader agent is a key requirement in such computational constructions. Yet, the fastest currently known population protocol for electing a leader only has linear convergence time, and it has recently been shown that no population protocol using a constant number of states per node may overcome this linear bound. In this paper, we give the first population protocol for leader election with polylogarithmic convergence time, using polylogarithmic memory states per node. The protocol structure is quite simple: each node has an associated value, and is either a leader (still in contention) or a minion (following some leader). A leader keeps incrementing its value and “defeats” other leaders in one-to-one interactions, and will drop from contention and become a minion if it meets a leader with higher value. Importantly, a leader also drops out if it meets a minion with higher absolute value. While these rules are quite simple, the proof that this algorithm achieves polylogarithmic convergence time is non-trivial. In particular, the argument combines careful use of concentration inequalities with anti-concentration bounds, showing that the leaders’ values become spread apart as the execution progresses, which in turn implies that straggling leaders get quickly eliminated. We complement our analysis with empirical results, showing that our protocol converges extremely fast, even for large network sizes.","lang":"eng"}],"oa_version":"Preprint","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.05745"}],"oa":1,"month":"01","intvolume":" 9135"},{"oa_version":"None","abstract":[{"text":"Population protocols, roughly defined as systems consisting of large numbers of simple identical agents, interacting at random and updating their state following simple rules, are an important research topic at the intersection of distributed computing and biology. One of the fundamental tasks that a population protocol may solve is majority: each node starts in one of two states; the goal is for all nodes to reach a correct consensus on which of the two states was initially the majority. Despite considerable research effort, known protocols for this problem are either exact but slow (taking linear parallel time to converge), or fast but approximate (with non-zero probability of error). In this paper, we show that this trade-off between preciasion and speed is not inherent. We present a new protocol called Average and Conquer (AVC) that solves majority ex-actly in expected parallel convergence time O(log n/(sε) + log n log s), where n is the number of nodes, εn is the initial node advantage of the majority state, and s = Ω(log n log log n) is the number of states the protocol employs. This shows that the majority problem can be solved exactly in time poly-logarithmic in n, provided that the memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case of four memory states per node, and a lower bound of Ω(logn) parallel time for protocols using any number of memory states per node.per node, and a lower bound of (log n) parallel time for protocols using any number of memory states per node.","lang":"eng"}],"month":"07","publisher":"ACM","day":"21","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","date_published":"2015-07-21T00:00:00Z","doi":"10.1145/2767386.2767429","volume":"2015-July","date_created":"2018-12-11T11:48:28Z","page":"47 - 56","_id":"781","status":"public","type":"conference","conference":{"name":"PODC: Principles of Distributed Computing"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429.","ista":"Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in population protocols. PODC: Principles of Distributed Computing vol. 2015–July, 47–56.","mla":"Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols. Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429.","short":"D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.","ieee":"D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority in population protocols,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 47–56.","apa":"Alistarh, D.-A., Gelashvili, R., & Vojnović, M. (2015). Fast and exact majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767429","ama":"Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429"},"date_updated":"2023-02-23T13:18:35Z","title":"Fast and exact majority in population protocols","publist_id":"6873","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"last_name":"Vojnović","full_name":"Vojnović, Milan","first_name":"Milan"}],"article_processing_charge":"No"},{"article_processing_charge":"No","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"first_name":"Thomas","last_name":"Sauerwald","full_name":"Sauerwald, Thomas"},{"first_name":"Milan","last_name":"Vojnović","full_name":"Vojnović, Milan"}],"publist_id":"6874","title":"Lock-Free algorithms under stochastic schedulers","citation":{"apa":"Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms under stochastic schedulers (Vol. 2015–July, pp. 251–260). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767430","ama":"Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic schedulers. In: Vol 2015-July. ACM; 2015:251-260. doi:10.1145/2767386.2767430","ieee":"D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under stochastic schedulers,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 251–260.","short":"D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260.","mla":"Alistarh, Dan-Adrian, et al. Lock-Free Algorithms under Stochastic Schedulers. Vol. 2015–July, ACM, 2015, pp. 251–60, doi:10.1145/2767386.2767430.","ista":"Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic schedulers. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.","chicago":"Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free Algorithms under Stochastic Schedulers,” 2015–July:251–60. ACM, 2015. https://doi.org/10.1145/2767386.2767430."},"date_updated":"2023-02-23T13:18:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","conference":{"name":"PODC: Principles of Distributed Computing"},"type":"conference","status":"public","_id":"782","page":"251 - 260","date_created":"2018-12-11T11:48:28Z","date_published":"2015-07-21T00:00:00Z","doi":"10.1145/2767386.2767430","volume":"2015-July","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"day":"21","publisher":"ACM","month":"07","abstract":[{"text":"In this work, we consider the following random process, mo- Tivated by the analysis of lock-free concurrent algorithms under high memory contention. In each round, a new scheduling step is allocated to one of n threads, according to a distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability pi. When some thread first reaches a set threshold of executed steps, it registers a win, completing its current operation, and resets its step count to 1. At the same time, threads whose step count was close to the threshold also get reset because of the win, but to 0 steps, being penalized for almost winning. We are interested in two questions: how often does some thread complete an operation (system latency), and how often does a specific thread complete an operation (individual latency)? We provide asymptotically tight bounds for the system and individual latency of this general concurrency pattern, for arbitrary scheduling distributions p. Surprisingly, a sim- ple characterization exists: in expectation, the system will complete a new operation every Θ(1/p 2) steps, while thread i will complete a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right, as it requires a careful analysis of how the higher norms of the vector p inuence the thread step counts and latencies in this random process. Our result offers a simple connection between the scheduling distribution and the average performance of concurrent algorithms, which has several applications.","lang":"eng"}],"oa_version":"None"},{"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.1001"}],"publisher":"ACM","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement during this work, and the anonymous reviewers for their very useful suggestions.","oa_version":"None","abstract":[{"text":"The problem of electing a leader from among n contenders is one of the fundamental questions in distributed computing. In its simplest formulation, the task is as follows: given n processors, all participants must eventually return a win or lose indication, such that a single contender may win. Despite a considerable amount of work on leader election, the following question is still open: can we elect a leader in an asynchronous fault-prone system faster than just running a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper, we answer this question in the affirmative, improving on a decades-old upper bound. We introduce two new algorithmic ideas to reduce the time complexity of electing a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application of our algorithm is a new upper bound for the tight renaming problem, assigning n items to the n participants in expected O(log2 n) time and O(n2) messages. We complement our results with lower bound of Ω(n2) messages for solving these two problems, closing the question of their message complexity.","lang":"eng"}],"date_created":"2018-12-11T11:48:28Z","doi":"10.1145/2767386.2767420","volume":"2015-July","date_published":"2015-07-21T00:00:00Z","page":"365 - 374","language":[{"iso":"eng"}],"day":"21","publication_status":"published","year":"2015","status":"public","conference":{"name":"PODC: Principles of Distributed Computing"},"type":"conference","_id":"783","title":"How to elect a leader faster than a tournament","article_processing_charge":"No","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"first_name":"Adrian","last_name":"Vladu","full_name":"Vladu, Adrian"}],"publist_id":"6875","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-02-23T13:18:55Z","citation":{"ista":"Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420.","short":"D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.","ieee":"D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster than a tournament,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 365–374.","ama":"Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament. In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420","apa":"Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420","mla":"Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament. Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420."}},{"publist_id":"6872","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Ballani, Hitesh","last_name":"Ballani","first_name":"Hitesh"},{"first_name":"Paolo","full_name":"Costa, Paolo","last_name":"Costa"},{"first_name":"Adam","full_name":"Funnell, Adam","last_name":"Funnell"},{"first_name":"Joshua","full_name":"Benjamin, Joshua","last_name":"Benjamin"},{"first_name":"Philip","full_name":"Watts, Philip","last_name":"Watts"},{"first_name":"Benn","full_name":"Thomsen, Benn","last_name":"Thomsen"}],"title":"A high-radix, low-latency optical switch for data centers","date_updated":"2023-02-23T13:18:57Z","citation":{"ista":"Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special Interest Group on Data Communication, 367–368.","chicago":"Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.","ieee":"D.-A. Alistarh et al., “A high-radix, low-latency optical switch for data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom, 2015, pp. 367–368.","short":"D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts, B. Thomsen, in:, ACM, 2015, pp. 367–368.","apa":"Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts, P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035","ama":"Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035","mla":"Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","conference":{"start_date":"2015-08-17","end_date":"2015-08-21","location":"London, United Kindgdom","name":"SIGCOMM: Special Interest Group on Data Communication"},"status":"public","_id":"784","page":"367 - 368","date_published":"2015-01-01T00:00:00Z","doi":"10.1145/2785956.2790035","date_created":"2018-12-11T11:48:29Z","publication_identifier":{"isbn":["978-1-4503-3542-3"]},"year":"2015","publication_status":"published","day":"01","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"ACM","month":"01","abstract":[{"text":"We demonstrate an optical switch design that can scale up to a thousand ports with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our design uses a broadcast and select architecture, based on a passive star coupler and fast tunable transceivers. In addition we employ time division multiplexing to achieve very low switching latency. Our demo shows the feasibility of the switch data plane using a small testbed, comprising two transmitters and a receiver, connected through a star coupler.","lang":"eng"}],"oa_version":"None"},{"year":"2015","publication_status":"published","day":"01","publication":"Glycobiology","language":[{"iso":"eng"}],"page":"1423 - 1430","date_published":"2015-12-01T00:00:00Z","doi":"10.1093/glycob/cwv059","volume":25,"issue":"12","date_created":"2018-12-11T11:48:35Z","abstract":[{"text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.","lang":"eng"}],"oa_version":"None","pmid":1,"publisher":"Oxford University Press","quality_controlled":"1","scopus_import":1,"month":"12","intvolume":" 25","citation":{"ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430.","chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.","ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430. doi:10.1093/glycob/cwv059","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., & Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059","ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:10.1093/glycob/cwv059."},"date_updated":"2021-01-12T08:16:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jakob","full_name":"Engel, Jakob","last_name":"Engel"},{"first_name":"Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","orcid":"0000-0002-5795-0133","full_name":"Schmalhorst, Philipp S"},{"first_name":"Anke","last_name":"Kruger","full_name":"Kruger, Anke"},{"full_name":"Muller, Christina","last_name":"Muller","first_name":"Christina"},{"first_name":"Falk","full_name":"Buettner, Falk","last_name":"Buettner"},{"full_name":"Routier, Françoise","last_name":"Routier","first_name":"Françoise"}],"publist_id":"6851","external_id":{"pmid":["26306635"]},"title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","department":[{"_id":"CaHe"}],"_id":"802","type":"journal_article","status":"public"},{"citation":{"ieee":"F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20. ASM, pp. 10294–10302, 2015.","short":"F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89 (2015) 10294–10302.","apa":"Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15","ama":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15","mla":"Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15.","ista":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.","chicago":"Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology. ASM, 2015. https://doi.org/10.1128/JVI.01502-15."},"date_updated":"2021-01-12T08:17:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","external_id":{"pmid":["26223638"]},"publist_id":"6837","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","last_name":"Schur"},{"last_name":"Dick","full_name":"Dick, Robert","first_name":"Robert"},{"full_name":"Hagen, Wim","last_name":"Hagen","first_name":"Wim"},{"last_name":"Vogt","full_name":"Vogt, Volker","first_name":"Volker"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John"}],"title":"The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly","_id":"815","type":"journal_article","status":"public","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"Journal of Virology","day":"22","page":"10294 - 10302","date_created":"2018-12-11T11:48:39Z","doi":"10.1128/JVI.01502-15","date_published":"2015-09-22T00:00:00Z","issue":"20","volume":89,"abstract":[{"text":"The polyprotein Gag is the primary structural component of retroviruses. Gag consists of independently folded domains connected by flexible linkers. Interactions between the conserved capsid (CA) domains of Gag mediate formation of hexameric protein lattices that drive assembly of immature virus particles. Proteolytic cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses from an immature form into an infectious form. Within the assembled Gag lattices of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts similar quaternary arrangements, while the N-terminal domain of CA is packed in very different manners. Here, we have used cryo-electron tomography and subtomogram averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus (RSV) Gag particles and have determined the structure of CA and the surrounding regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA adopts a novel arrangement in which the upstream p10 domain folds back into the CA lattice. In this position the cleavage site between CA and p10 appears to be inaccessible to PR. Below CA, an extended density is consistent with the presence of a six-helix bundle formed by the spacer-peptide region. We have also assessed the affect of lattice assembly on proteolytic processing by exogenous PR. The cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding consistent with structural regulation of proteolytic maturation.\r\n","lang":"eng"}],"oa_version":"None","pmid":1,"quality_controlled":"1","publisher":"ASM","intvolume":" 89","month":"09"},{"publication":"Nature","day":"22","year":"2015","publication_status":"published","date_created":"2018-12-11T11:48:39Z","volume":517,"date_published":"2015-01-22T00:00:00Z","doi":"10.1038/nature13838","issue":"7535","page":"505 - 508","acknowledgement":"This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples, and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich and T. Bharat for technical support and/or discussion. This study was technically supported by the European Molecular Biology Laboratory IT services unit.","abstract":[{"lang":"eng","text":"Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments."}],"intvolume":" 517","month":"01","quality_controlled":0,"publisher":"Nature Publishing Group","extern":1,"date_updated":"2021-01-12T08:17:08Z","citation":{"mla":"Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838.","apa":"Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H., & Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838","ama":"Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508. doi:10.1038/nature13838","short":"F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508.","ieee":"F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature Publishing Group, pp. 505–508, 2015.","chicago":"Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature13838.","ista":"Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 517(7535), 505–508."},"title":"Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution","publist_id":"6836","author":[{"first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Florian Schur","last_name":"Schur"},{"first_name":"Wim","full_name":"Hagen, Wim J","last_name":"Hagen"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"first_name":"Tomáš","last_name":"Ruml","full_name":"Ruml, Tomáš"},{"first_name":"B","last_name":"Müller","full_name":"Müller B"},{"last_name":"Kraüsslich","full_name":"Kraüsslich, Hans Georg","first_name":"Hans"},{"last_name":"Briggs","full_name":"Briggs, John A","first_name":"John"}],"_id":"814","status":"public","type":"journal_article"},{"article_number":"AB101","_id":"8242","status":"public","type":"journal_article","article_type":"original","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology, vol. 135, no. 2, AB101, Elsevier, 2015, doi:10.1016/j.jaci.2014.12.1263.","apa":"Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim, E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2014.12.1263","ama":"Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 2015;135(2). doi:10.1016/j.jaci.2014.12.1263","short":"L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova, K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 135 (2015).","ieee":"L. Einhorn et al., “Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients,” Journal of Allergy and Clinical Immunology, vol. 135, no. 2. Elsevier, 2015.","chicago":"Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida, Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology. Elsevier, 2015. https://doi.org/10.1016/j.jaci.2014.12.1263.","ista":"Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 135(2), AB101."},"date_updated":"2021-01-12T08:17:42Z","title":"Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients","author":[{"first_name":"Lukas","full_name":"Einhorn, Lukas","last_name":"Einhorn"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas","full_name":"Fazekas, Judit","orcid":"0000-0002-8777-3502"},{"full_name":"Muhr, Martina","last_name":"Muhr","first_name":"Martina"},{"full_name":"Schoos, Alexandra","last_name":"Schoos","first_name":"Alexandra"},{"full_name":"Oida, Kumiko","last_name":"Oida","first_name":"Kumiko"},{"first_name":"Josef","full_name":"Singer, Josef","last_name":"Singer"},{"first_name":"Lucia","last_name":"Panakova","full_name":"Panakova, Lucia"},{"first_name":"Krisztina","full_name":"Manzano-Szalai, Krisztina","last_name":"Manzano-Szalai"},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"}],"article_processing_charge":"No","oa_version":"None","month":"02","intvolume":" 135","quality_controlled":"1","publisher":"Elsevier","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Allergy and Clinical Immunology","publication_identifier":{"issn":["0091-6749"]},"publication_status":"published","year":"2015","issue":"2","doi":"10.1016/j.jaci.2014.12.1263","date_published":"2015-02-01T00:00:00Z","volume":135,"date_created":"2020-08-10T11:54:09Z"},{"year":"2015","publication_status":"published","day":"20","publication":"Bio-protocol","date_published":"2015-04-20T00:00:00Z","doi":"10.21769/BioProtoc.1446","issue":"8","volume":5,"date_created":"2018-12-11T11:48:44Z","abstract":[{"lang":"eng","text":"Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis."}],"acknowledgement":"European Research Council with a Starting Independent Research grant: ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas Fendrych for critical reading and comments. The protocol was developed based on previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). ","quality_controlled":0,"publisher":"Bio-protocol LLC","month":"04","intvolume":" 5","date_updated":"2021-01-12T08:18:07Z","citation":{"chicago":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol. Bio-protocol LLC, 2015. https://doi.org/10.21769/BioProtoc.1446.","ista":"Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 5(8).","mla":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:10.21769/BioProtoc.1446.","short":"P. Marhavý, E. Benková, Bio-Protocol 5 (2015).","ieee":"P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis in arabidopsis,” Bio-protocol, vol. 5, no. 8. Bio-protocol LLC, 2015.","ama":"Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 2015;5(8). doi:10.21769/BioProtoc.1446","apa":"Marhavý, P., & Benková, E. (2015). Real time analysis of lateral root organogenesis in arabidopsis. Bio-Protocol. Bio-protocol LLC. https://doi.org/10.21769/BioProtoc.1446"},"extern":1,"author":[{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Peter Marhavy","last_name":"Marhavy"},{"full_name":"Eva Benková","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"publist_id":"6816","title":"Real time analysis of lateral root organogenesis in arabidopsis","_id":"832","type":"journal_article","status":"public"},{"abstract":[{"text":"The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.","lang":"eng"}],"oa_version":"Published Version","publisher":"Springer Nature","quality_controlled":"1","intvolume":" 6","month":"10","year":"2015","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"publication":"Nature Communications","day":"05","date_created":"2020-09-18T10:07:36Z","doi":"10.1038/ncomms9361","volume":6,"date_published":"2015-10-05T00:00:00Z","_id":"8456","article_number":"8361","type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","date_updated":"2021-01-12T08:19:24Z","citation":{"ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361","apa":"Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms9361","ieee":"P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.","short":"P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015).","mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015, doi:10.1038/ncomms9361.","ista":"Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361.","chicago":"Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"full_name":"Ma, Peixiang","last_name":"Ma","first_name":"Peixiang"},{"first_name":"Yi","last_name":"Xue","full_name":"Xue, Yi"},{"first_name":"Nicolas","full_name":"Coquelle, Nicolas","last_name":"Coquelle"},{"last_name":"Haller","full_name":"Haller, Jens D.","first_name":"Jens D."},{"first_name":"Tairan","last_name":"Yuwen","full_name":"Yuwen, Tairan"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"last_name":"Mikhailovskii","full_name":"Mikhailovskii, Oleg","first_name":"Oleg"},{"first_name":"Dieter","full_name":"Willbold, Dieter","last_name":"Willbold"},{"first_name":"Jacques-Philippe","full_name":"Colletier, Jacques-Philippe","last_name":"Colletier"},{"full_name":"Skrynnikov, Nikolai R.","last_name":"Skrynnikov","first_name":"Nikolai R."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"title":"Observing the overall rocking motion of a protein in a crystal"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ieee":"P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708, 2015.","short":"P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.","apa":"Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418","ama":"Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418","mla":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.","ista":"Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708.","chicago":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015. https://doi.org/10.1002/9780470034590.emrstm1418."},"date_updated":"2021-01-12T08:19:24Z","title":"Conformational exchange processes in biological systems: Detection by solid-state NMR","article_processing_charge":"No","author":[{"last_name":"Ma","full_name":"Ma, Peixiang","first_name":"Peixiang"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"}],"_id":"8457","status":"public","article_type":"original","type":"journal_article","publication":"eMagRes","language":[{"iso":"eng"}],"day":"10","year":"2015","publication_status":"published","publication_identifier":{"isbn":["9780470034590","9780470058213"]},"date_created":"2020-09-18T10:07:45Z","date_published":"2015-09-10T00:00:00Z","doi":"10.1002/9780470034590.emrstm1418","issue":"3","volume":4,"page":"699-708","oa_version":"None","abstract":[{"text":"We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed.","lang":"eng"}],"intvolume":" 4","month":"09","quality_controlled":"1","publisher":"Wiley"},{"quality_controlled":"1","publisher":"Oxford University Press","intvolume":" 32","month":"02","abstract":[{"text":"The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.","lang":"eng"}],"oa_version":"None","page":"542 - 554","date_created":"2018-12-11T11:48:49Z","date_published":"2015-02-01T00:00:00Z","doi":"10.1093/molbev/msu318","volume":32,"issue":"2","publication_status":"published","year":"2015","publication":"Molecular Biology and Evolution","language":[{"iso":"eng"}],"day":"01","type":"journal_article","status":"public","_id":"848","author":[{"full_name":"Usmanova, Dinara","last_name":"Usmanova","first_name":"Dinara"},{"full_name":"Ferretti, Luca","last_name":"Ferretti","first_name":"Luca"},{"full_name":"Povolotskaya, Inna","last_name":"Povolotskaya","first_name":"Inna"},{"first_name":"Peter","full_name":"Vlasov, Peter","last_name":"Vlasov"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"publist_id":"6804","title":"A model of substitution trajectories in sequence space and long-term protein evolution","date_updated":"2021-01-12T08:19:33Z","citation":{"chicago":"Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/molbev/msu318.","ista":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.","short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.","ieee":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu318","ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"month":"06","intvolume":" 28","publisher":"IOP Publishing","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7]."}],"doi":"10.1088/0951-7715/28/8/2699","issue":"8","volume":28,"date_published":"2015-06-30T00:00:00Z","date_created":"2020-09-18T10:46:43Z","page":"2699-2720","day":"30","language":[{"iso":"eng"}],"publication":"Nonlinearity","publication_identifier":{"issn":["0951-7715","1361-6544"]},"year":"2015","publication_status":"published","status":"public","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"type":"journal_article","article_type":"original","_id":"8498","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","author":[{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"},{"first_name":"K","last_name":"Zhang","full_name":"Zhang, K"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:41Z","citation":{"mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.","apa":"Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699","ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015.","chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015. https://doi.org/10.1088/0951-7715/28/8/2699.","ista":"Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720."}},{"page":"71-149","date_created":"2020-09-18T10:46:50Z","issue":"1","date_published":"2015-02-05T00:00:00Z","doi":"10.4171/jems/499","volume":17,"publication_status":"published","year":"2015","publication_identifier":{"issn":["1435-9855"]},"publication":"Journal of the European Mathematical Society","language":[{"iso":"eng"}],"day":"05","publisher":"European Mathematical Society Publishing House","quality_controlled":"1","intvolume":" 17","month":"02","abstract":[{"text":"We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Journal of the European Mathematical Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:10.4171/jems/499.","ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 2015;17(1):71-149. doi:10.4171/jems/499","apa":"Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149.","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” Journal of the European Mathematical Society, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.","chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.","ista":"Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"8499"},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"9057","file_date_updated":"2021-02-02T13:22:19Z","date_updated":"2023-02-23T13:47:52Z","extern":"1","ddc":["530"],"scopus_import":"1","month":"05","intvolume":" 1","abstract":[{"text":"Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":1,"issue":"4","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","file":[{"file_name":"2015_ScienceAdvances_Palacci.pdf","date_created":"2021-02-02T13:22:19Z","file_size":2416780,"date_updated":"2021-02-02T13:22:19Z","creator":"cziletti","success":1,"file_id":"9058","checksum":"b97d62433581875c1b85210c5f6ae370","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"article_number":"e1400214","author":[{"last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"},{"first_name":"Stefano","last_name":"Sacanna","full_name":"Sacanna, Stefano"},{"first_name":"Anaïs","full_name":"Abramian, Anaïs","last_name":"Abramian"},{"first_name":"Jérémie","full_name":"Barral, Jérémie","last_name":"Barral"},{"first_name":"Kasey","last_name":"Hanson","full_name":"Hanson, Kasey"},{"first_name":"Alexander Y.","last_name":"Grosberg","full_name":"Grosberg, Alexander Y."},{"first_name":"David J.","full_name":"Pine, David J.","last_name":"Pine"},{"first_name":"Paul M.","last_name":"Chaikin","full_name":"Chaikin, Paul M."}],"external_id":{"pmid":["26601175"],"arxiv":["1505.05111"]},"article_processing_charge":"No","title":"Artificial rheotaxis","citation":{"ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214.","short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).","ieee":"J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"American Association for the Advancement of Science ","quality_controlled":"1","oa":1,"doi":"10.1126/sciadv.1400214","date_published":"2015-05-01T00:00:00Z","date_created":"2021-02-02T13:15:02Z","has_accepted_license":"1","year":"2015","day":"01","publication":"Science Advances"},{"quality_controlled":0,"publisher":"Public Library of Science","intvolume":" 10","month":"05","abstract":[{"lang":"eng","text":"The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1."}],"acknowledgement":"Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, \"Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)\" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.","date_created":"2018-12-11T11:49:08Z","volume":10,"issue":"5","doi":"10.1371/journal.pone.0125888","date_published":"2015-05-11T00:00:00Z","year":"2015","publication_status":"published","publication":"PLoS One","day":"11","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"906","publist_id":"6742","author":[{"full_name":"Arkhipova, Oksana V","last_name":"Arkhipova","first_name":"Oksana"},{"first_name":"Margarita","full_name":"Meer, Margarita V","last_name":"Meer"},{"last_name":"Mikoulinskaia","full_name":"Mikoulinskaia, Galina V","first_name":"Galina"},{"first_name":"Marina","last_name":"Zakharova","full_name":"Zakharova, Marina V"},{"first_name":"Alexander","full_name":"Galushko, Alexander S","last_name":"Galushko"},{"full_name":"Akimenko, Vasilii K","last_name":"Akimenko","first_name":"Vasilii"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","citation":{"chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.","ista":"Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).","mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.","ieee":"O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","ama":"Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888"},"date_updated":"2021-01-12T08:21:48Z","extern":1},{"type":"journal_article","article_type":"original","status":"public","_id":"9141","date_updated":"2022-01-24T13:45:41Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014JC010598"}],"month":"06","intvolume":" 120","abstract":[{"text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere.","lang":"eng"}],"oa_version":"Published Version","volume":120,"issue":"7","publication_identifier":{"issn":["2169-9275"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Adrien","last_name":"Lefauve","full_name":"Lefauve, Adrien"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller"},{"last_name":"Melet","full_name":"Melet, Angélique","first_name":"Angélique"}],"article_processing_charge":"No","title":"A three-dimensional map of tidal dissipation over abyssal hills","citation":{"chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598","ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","quality_controlled":"1","publisher":"American Geophysical Union","oa":1,"page":"4760-4777","doi":"10.1002/2014jc010598","date_published":"2015-06-08T00:00:00Z","date_created":"2021-02-15T14:21:49Z","year":"2015","day":"08","publication":"Journal of Geophysical Research: Oceans"},{"_id":"928","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2021-01-12T08:21:58Z","extern":"1","ddc":["539","570"],"file_date_updated":"2020-07-14T12:48:15Z","abstract":[{"text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events.","lang":"eng"}],"oa_version":"Published Version","month":"10","intvolume":" 4","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5769","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","file_size":7202224,"date_updated":"2020-07-14T12:48:15Z","creator":"dernst","file_name":"2015_eLife_Sehring.pdf","date_created":"2018-12-20T15:50:56Z"}],"language":[{"iso":"eng"}],"volume":4,"article_number":"e09206","citation":{"ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","ieee":"I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015.","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206.","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6512","author":[{"first_name":"Ivonne","full_name":"Sehring, Ivonne","last_name":"Sehring"},{"first_name":"Pierre","full_name":"Recho, Pierre","last_name":"Recho"},{"first_name":"Elsa","full_name":"Denker, Elsa","last_name":"Denker"},{"last_name":"Kourakis","full_name":"Kourakis, Matthew","first_name":"Matthew"},{"first_name":"Birthe","last_name":"Mathiesen","full_name":"Mathiesen, Birthe"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Dong, Bo","last_name":"Dong","first_name":"Bo"},{"last_name":"Jiang","full_name":"Jiang, Di","first_name":"Di"}],"title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"has_accepted_license":"1","year":"2015","day":"21","publication":"eLife","doi":"10.7554/eLife.09206","date_published":"2015-10-21T00:00:00Z","date_created":"2018-12-11T11:49:15Z"},{"citation":{"chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","external_id":{"arxiv":["1501.04816"]},"article_processing_charge":"No","author":[{"last_name":"Krivelevich","full_name":"Krivelevich, Michael","first_name":"Michael"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan"},{"first_name":"Benny","full_name":"Sudakov, Benny","last_name":"Sudakov"}],"title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2015","publication":"Electronic Notes in Discrete Mathematics","day":"01","page":"181-187","date_created":"2021-06-21T06:40:34Z","doi":"10.1016/j.endm.2015.06.027","date_published":"2015-11-01T00:00:00Z","_id":"9575","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-02-23T14:01:28Z","extern":"1","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1501.04816","open_access":"1"}],"scopus_import":"1","intvolume":" 49","month":"11","publication_status":"published","publication_identifier":{"issn":["1571-0653"]},"language":[{"iso":"eng"}],"volume":49},{"article_processing_charge":"No","author":[{"full_name":"Leung, H.S.","last_name":"Leung","first_name":"H.S."},{"last_name":"Leung","full_name":"Leung, P.S.S.","first_name":"P.S.S."},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"},{"first_name":"A.H.W.","full_name":"Ngan, A.H.W.","last_name":"Ngan"}],"title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","date_updated":"2023-02-23T14:04:28Z","citation":{"ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"9673","page":"1-25","date_created":"2021-07-15T14:09:32Z","doi":"10.1016/j.ijplas.2014.09.009","date_published":"2015-04-01T00:00:00Z","volume":67,"year":"2015","publication_status":"published","publication_identifier":{"issn":["0749-6419"]},"language":[{"iso":"eng"}],"publication":"International Journal of Plasticity","day":"01","publisher":"Elsevier","scopus_import":"1","intvolume":" 67","month":"04","abstract":[{"text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation.","lang":"eng"}],"oa_version":"None"},{"article_processing_charge":"No","external_id":{"arxiv":["1511.08668"]},"author":[{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"},{"first_name":"Gareth A.","last_name":"Tribello","full_name":"Tribello, Gareth A."},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"title":"Solid-liquid interfacial free energy out of equilibrium","citation":{"ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_number":"180102","date_created":"2021-07-19T10:07:22Z","doi":"10.1103/physrevb.92.180102","date_published":"2015-11-01T00:00:00Z","year":"2015","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"01","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2021-08-09T12:38:49Z","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"9688","volume":92,"issue":"18","publication_status":"published","publication_identifier":{"eissn":["1550-235X"],"issn":["1098-0121"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.08668"}],"scopus_import":"1","intvolume":" 92","month":"11","abstract":[{"text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.","lang":"eng"}],"oa_version":"Preprint"},{"_id":"9711","type":"research_data_reference","status":"public","citation":{"chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, 10.1371/journal.pbio.1002299.s001.","mla":"Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001","ieee":"G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015)."},"date_updated":"2023-02-23T10:07:02Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004"},{"first_name":"Tugce","last_name":"Batur","full_name":"Batur, Tugce"},{"last_name":"Guvenek","full_name":"Guvenek, Aysegul","first_name":"Aysegul"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay Hazal","first_name":"Dilay Hazal"},{"first_name":"Erdal","full_name":"Toprak, Erdal","last_name":"Toprak"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"department":[{"_id":"ToBo"}],"title":"Excel file containing the raw data for all figures","oa_version":"Published Version","publisher":"Public Library of Science","month":"11","year":"2015","day":"18","date_created":"2021-07-23T11:53:50Z","doi":"10.1371/journal.pbio.1002299.s001","related_material":{"record":[{"id":"1619","status":"public","relation":"used_in_publication"}]},"date_published":"2015-11-18T00:00:00Z"},{"citation":{"ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology. Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624.","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp. 615–624, 2015.","mla":"Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X"},{"first_name":"Jesicca","full_name":"Caspar, Jesicca","last_name":"Caspar"},{"full_name":"Theodorou, Panagiotis","last_name":"Theodorou","first_name":"Panagiotis"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"last_name":"Paxton","full_name":"Paxton, Robert","first_name":"Robert"}],"publist_id":"5245","external_id":{"pmid":["25646973"]},"article_processing_charge":"No","title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","has_accepted_license":"1","year":"2015","day":"03","publication":"Journal of Animal Ecology","page":"615 - 624","doi":"10.1111/1365-2656.12345","date_published":"2015-03-03T00:00:00Z","date_created":"2018-12-11T11:54:23Z","acknowledgement":"We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, The Scottish Government and The Wellcome Trust, under the Living with Environmental Change Partnership.","publisher":"Wiley","quality_controlled":"1","oa":1,"date_updated":"2023-02-23T14:06:09Z","ddc":["570"],"department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:45:19Z","_id":"1855","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"460","publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":1823045,"date_created":"2018-12-12T10:18:29Z","file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"542a0b9b07e78050a81b35f26f0b82da","file_id":"5350"}],"language":[{"iso":"eng"}],"issue":"3","volume":84,"related_material":{"record":[{"relation":"research_data","id":"9720","status":"public"}]},"abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 84"},{"date_updated":"2023-02-23T14:06:12Z","department":[{"_id":"SyCr"}],"_id":"1830","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":370,"issue":"1669","related_material":{"record":[{"relation":"research_data","status":"public","id":"9721"}]},"ec_funded":1,"abstract":[{"text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/","open_access":"1"}],"month":"05","intvolume":" 370","citation":{"mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015, doi:10.1098/rstb.2014.0108.","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. 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Series B, Biological Sciences 370 (2015).","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. 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Series B, Biological Sciences","doi":"10.1098/rstb.2014.0108","date_published":"2015-05-26T00:00:00Z","date_created":"2018-12-11T11:54:15Z","acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","quality_controlled":"1","publisher":"Royal Society, The","oa":1},{"_id":"9721","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:16:22Z","citation":{"chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. 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In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}],"month":"12","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.dj2bf"}],"day":"29","year":"2015","date_published":"2015-12-29T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1830"}]},"doi":"10.5061/dryad.dj2bf","date_created":"2021-07-26T09:38:36Z"},{"date_updated":"2023-02-23T10:16:13Z","citation":{"ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). 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Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"full_name":"Friedlander, Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"last_name":"Mayo","full_name":"Mayo, Avraham E.","first_name":"Avraham E."},{"first_name":"Tsvi","full_name":"Tlusty, Tsvi","last_name":"Tlusty"},{"full_name":"Alon, Uri","last_name":"Alon","first_name":"Uri"}],"department":[{"_id":"GaTk"}],"title":"Supporting information text","_id":"9718","type":"research_data_reference","status":"public","year":"2015","day":"23","date_created":"2021-07-26T08:35:23Z","date_published":"2015-03-23T00:00:00Z","related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pcbi.1004055.s001","oa_version":"Published Version","publisher":"Public Library of Science","month":"03"},{"article_number":"e0127657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” PLoS One, vol. 10, no. 6. Public Library of Science, 2015.","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6). doi:10.1371/journal.pone.0127657","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657."},"title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","publist_id":"5318","author":[{"full_name":"Symonova, Olga","last_name":"Symonova","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"day":"01","publication":"PLoS One","has_accepted_license":"1","year":"2015","date_published":"2015-06-01T00:00:00Z","doi":"10.1371/journal.pone.0127657","date_created":"2018-12-11T11:54:02Z","_id":"1793","status":"public","pubrep_id":"454","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-02-23T14:06:33Z","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:16Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth."}],"month":"06","intvolume":" 10","scopus_import":1,"file":[{"checksum":"d20f26461ca575276ad3ed9ce4bfc787","file_id":"5150","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","date_created":"2018-12-12T10:15:30Z","file_size":1850825,"date_updated":"2020-07-14T12:45:16Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"9737","status":"public"}]},"issue":"6","volume":10},{"date_published":"2015-06-01T00:00:00Z","doi":"10.1371/journal.pone.0127657.s001","related_material":{"record":[{"status":"public","id":"1793","relation":"used_in_publication"}]},"date_created":"2021-07-28T06:20:13Z","day":"01","year":"2015","month":"06","publisher":"Public Library of Science","oa_version":"Published Version","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"author":[{"last_name":"Symonova","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga"},{"first_name":"Christopher","last_name":"Topp","full_name":"Topp, Christopher"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001","mla":"Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001."},"date_updated":"2023-02-23T10:14:42Z","status":"public","type":"research_data_reference","_id":"9737"},{"date_updated":"2023-02-23T14:07:51Z","ddc":["576"],"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"GaTk"}],"_id":"1827","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"452","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b8aa66f450ff8de393014b87ec7d2efb","file_id":"5161","date_updated":"2020-07-14T12:45:17Z","file_size":1811647,"creator":"system","date_created":"2018-12-12T10:15:39Z","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf"}],"ec_funded":1,"related_material":{"record":[{"id":"9718","status":"public","relation":"research_data"},{"id":"9773","status":"public","relation":"research_data"}]},"issue":"3","volume":11,"abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 11","month":"03","citation":{"ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055","apa":"Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mayo, Avraham","last_name":"Mayo","first_name":"Avraham"},{"first_name":"Tsvi","full_name":"Tlusty, Tsvi","last_name":"Tlusty"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"publist_id":"5278","title":"Evolution of bow-tie architectures in biology","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"year":"2015","has_accepted_license":"1","publication":"PLoS Computational Biology","day":"23","date_created":"2018-12-11T11:54:14Z","date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055","oa":1,"quality_controlled":"1","publisher":"Public Library of Science"},{"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"NiBa"}],"date_updated":"2023-02-23T14:07:48Z","ddc":["570","576"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"453","_id":"1809","volume":10,"issue":"5","related_material":{"record":[{"relation":"research_data","status":"public","id":"9715"},{"status":"public","id":"9772","relation":"research_data"}]},"publication_status":"published","file":[{"file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","date_created":"2018-12-12T10:09:07Z","creator":"system","file_size":2748982,"date_updated":"2020-07-14T12:45:17Z","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_id":"4730","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"05","intvolume":" 10","abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"oa_version":"Published Version","publist_id":"5299","author":[{"last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"title":"Indirect genetic effects and the dynamics of social interactions","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-05-18T00:00:00Z","doi":"10.1371/journal.pone.0126907","date_created":"2018-12-11T11:54:07Z","has_accepted_license":"1","year":"2015","day":"18","publication":"PLoS One","quality_controlled":"1","publisher":"Public Library of Science","oa":1},{"oa_version":"Published Version","month":"05","publisher":"Public Library of Science","day":"18","year":"2015","date_created":"2021-08-05T12:55:20Z","doi":"10.1371/journal.pone.0126907.s003","related_material":{"record":[{"status":"public","id":"1809","relation":"used_in_publication"}]},"date_published":"2015-05-18T00:00:00Z","_id":"9772","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:15:25Z","citation":{"ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003","mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003."},"title":"Description of the agent based simulations","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}]},{"month":"03","publisher":"Public Library of Science","oa_version":"Published Version","date_created":"2021-08-05T12:58:07Z","doi":"10.1371/journal.pcbi.1004055.s002","date_published":"2015-03-23T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"1827","status":"public"}]},"day":"23","year":"2015","status":"public","type":"research_data_reference","_id":"9773","title":"Evolutionary simulation code","department":[{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"last_name":"Mayo","full_name":"Mayo, Avraham E.","first_name":"Avraham E."},{"last_name":"Tlusty","full_name":"Tlusty, Tsvi","first_name":"Tsvi"},{"first_name":"Uri","full_name":"Alon, Uri","last_name":"Alon"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:16:13Z","citation":{"ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002","mla":"Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002."}},{"title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","publist_id":"6419","author":[{"first_name":"Ilija","full_name":"Zeljkovic, Ilija","last_name":"Zeljkovic"},{"first_name":"Yoshinori","last_name":"Okada","full_name":"Okada, Yoshinori"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sankar","full_name":"Sankar, Raman","first_name":"Raman"},{"full_name":"Walkup, Daniel","last_name":"Walkup","first_name":"Daniel"},{"first_name":"Wenwen","full_name":"Zhou, Wenwen","last_name":"Zhou"},{"first_name":"Junwei","full_name":"Liu, Junwei","last_name":"Liu"},{"first_name":"Guoqing","full_name":"Chang, Guoqing","last_name":"Chang"},{"first_name":"Yungjui","full_name":"Wang, Yungjui","last_name":"Wang"},{"first_name":"Md","last_name":"Hasan","full_name":"Hasan, Md Z"},{"first_name":"Fangcheng","last_name":"Chou","full_name":"Chou, Fangcheng"},{"first_name":"Hsin","last_name":"Lin","full_name":"Lin, Hsin"},{"last_name":"Bansil","full_name":"Bansil, Arun","first_name":"Arun"},{"first_name":"Liang","full_name":"Fu, Liang","last_name":"Fu"},{"first_name":"Vidya","full_name":"Madhavan, Vidya","last_name":"Madhavan"}],"extern":1,"citation":{"ista":"Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324.","chicago":"Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials. Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.","short":"I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324.","ieee":"I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” Nature Materials, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 2015;14(3):318-324. doi:10.1038/nmat4215","apa":"Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. Nature Publishing Group. https://doi.org/10.1038/nmat4215","mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215."},"date_updated":"2021-01-12T08:22:24Z","status":"public","type":"journal_article","_id":"981","date_created":"2018-12-11T11:49:31Z","volume":14,"doi":"10.1038/nmat4215","date_published":"2015-03-01T00:00:00Z","issue":"3","page":"318 - 324","publication":"Nature Materials","day":"01","publication_status":"published","year":"2015","intvolume":" 14","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1403.4906","open_access":"1"}],"oa":1,"publisher":"Nature Publishing Group","quality_controlled":0,"acknowledgement":"We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.","abstract":[{"lang":"eng","text":"The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials."}]},{"extern":1,"citation":{"short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015.","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047","mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047.","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4).","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047."},"date_updated":"2021-01-12T08:22:25Z","title":"Criterion for many-body localization-delocalization phase transition","publist_id":"6418","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","last_name":"Serbyn"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"},{"first_name":"Dmitry","full_name":"Abanin, Dmitry A","last_name":"Abanin"}],"_id":"982","status":"public","type":"journal_article","publication":"Physical Review X","day":"01","publication_status":"published","year":"2015","date_created":"2018-12-11T11:49:32Z","volume":5,"date_published":"2015-01-01T00:00:00Z","issue":"4","doi":"10.1103/PhysRevX.5.041047","acknowledgement":"We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","abstract":[{"lang":"eng","text":"We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions."}],"intvolume":" 5","month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.01635"}],"publisher":"American Physical Society","quality_controlled":0},{"main_file_link":[{"url":"https://arxiv.org/abs/1501.05155","open_access":"1"}],"month":"09","intvolume":" 11","abstract":[{"lang":"eng","text":"Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms."}],"oa_version":"Preprint","issue":"12","volume":11,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"99","date_updated":"2021-01-12T08:22:28Z","extern":"1","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"acknowledgement":"Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation.","page":"1017 - 1021","date_published":"2015-09-14T00:00:00Z","doi":"10.1038/nphys3461","date_created":"2018-12-11T11:44:37Z","year":"2015","day":"14","publication":"Nature Physics","author":[{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"},{"full_name":"Albrecht, S M","last_name":"Albrecht","first_name":"S M"},{"full_name":"Kiršanskas, Gediminas","last_name":"Kiršanskas","first_name":"Gediminas"},{"full_name":"Chang, W","last_name":"Chang","first_name":"W"},{"first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth"},{"first_name":"Peter","last_name":"Krogstrup","full_name":"Krogstrup, Peter"},{"full_name":"Jespersen, Thomas","last_name":"Jespersen","first_name":"Thomas"},{"first_name":"Jesper","last_name":"Nygård","full_name":"Nygård, Jesper"},{"last_name":"Flensberg","full_name":"Flensberg, Karsten","first_name":"Karsten"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"}],"publist_id":"7955","external_id":{"arxiv":["1501.05155"]},"title":"Parity lifetime of bound states in a proximitized semiconductor nanowire","citation":{"mla":"Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.","ama":"Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021. doi:10.1038/nphys3461","apa":"Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461","ieee":"A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015.","short":"A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021.","chicago":"Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.","ista":"Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting."}],"oa_version":"None","publisher":"American Mathematical Society","quality_controlled":"1","month":"12","intvolume":" 144","publication_identifier":{"issn":["0002-9939","1088-6826"]},"publication_status":"published","year":"2015","day":"21","publication":"Proceedings of the American Mathematical Society","language":[{"iso":"eng"}],"page":"1553-1560","volume":144,"issue":"4","doi":"10.1090/proc/12796","date_published":"2015-12-21T00:00:00Z","date_created":"2020-09-18T10:46:14Z","_id":"8495","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2021-01-12T08:19:40Z","citation":{"chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.","ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.","ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 2015;144(4):1553-1560. doi:10.1090/proc/12796","apa":"Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12796"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Abed","last_name":"Bounemoura","full_name":"Bounemoura, Abed"},{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"}],"article_processing_charge":"No","title":"A note on micro-instability for Hamiltonian systems close to integrable"},{"publication":"PNAS","day":"28","publication_status":"published","year":"2015","date_created":"2018-12-11T11:48:55Z","issue":"30","volume":112,"doi":"10.1073/pnas.1511328112","date_published":"2015-07-28T00:00:00Z","page":"9328 - 9333","acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\n","abstract":[{"text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF.","lang":"eng"}],"intvolume":" 112","month":"07","quality_controlled":0,"publisher":"National Academy of Sciences","extern":1,"date_updated":"2021-01-12T08:20:26Z","citation":{"ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112.","ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112","ieee":"C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112."},"title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","publist_id":"6783","author":[{"first_name":"Colin","full_name":"Kretz, Colin A","last_name":"Kretz"},{"first_name":"Manhong","last_name":"Dai","full_name":"Dai, Manhong"},{"full_name":"Soylemez, Onuralp","last_name":"Soylemez","first_name":"Onuralp"},{"full_name":"Yee, Andrew","last_name":"Yee","first_name":"Andrew"},{"last_name":"Desch","full_name":"Desch, Karl C","first_name":"Karl"},{"last_name":"Siemieniak","full_name":"Siemieniak, David R","first_name":"David"},{"full_name":"Tomberg, Kärt","last_name":"Tomberg","first_name":"Kärt"},{"last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Meng, Fan","last_name":"Meng","first_name":"Fan"},{"first_name":"David","last_name":"Ginsburg","full_name":"Ginsburg, David B"}],"_id":"866","status":"public","type":"journal_article"},{"title":"Topological features of rugged fitness landscapes in sequence space","publist_id":"6764","author":[{"first_name":"Dmitry","last_name":"Kondrashov","full_name":"Kondrashov, Dmitry A"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"extern":1,"date_updated":"2021-01-12T08:21:16Z","citation":{"ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009.","ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009","apa":"Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009","ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015.","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009."},"status":"public","type":"journal_article","_id":"886","date_created":"2018-12-11T11:49:01Z","doi":"10.1016/j.tig.2014.09.009","volume":31,"date_published":"2015-01-01T00:00:00Z","issue":"1","page":"24 - 33","publication":"Trends in Genetics","day":"01","year":"2015","publication_status":"published","intvolume":" 31","month":"01","publisher":"Elsevier","quality_controlled":0,"acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.","abstract":[{"text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.","lang":"eng"}]},{"quality_controlled":"1","publisher":"Oxford University Press","year":"2015","day":"18","publication":"Nucleic Acids Research","page":"1905-1917","doi":"10.1093/nar/gkv021","date_published":"2015-02-18T00:00:00Z","date_created":"2021-01-19T11:01:01Z","citation":{"ama":"Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021","apa":"Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021","short":"N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.","ieee":"N. Richet et al., “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015.","mla":"Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:10.1093/nar/gkv021.","ista":"Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917.","chicago":"Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nicolas","last_name":"Richet","full_name":"Richet, Nicolas"},{"full_name":"Liu, Danni","last_name":"Liu","first_name":"Danni"},{"full_name":"Legrand, Pierre","last_name":"Legrand","first_name":"Pierre"},{"first_name":"Christophe","full_name":"Velours, Christophe","last_name":"Velours"},{"last_name":"Corpet","full_name":"Corpet, Armelle","first_name":"Armelle"},{"first_name":"Albane","full_name":"Gaubert, Albane","last_name":"Gaubert"},{"last_name":"Bakail","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M"},{"last_name":"Moal-Raisin","full_name":"Moal-Raisin, Gwenaelle","first_name":"Gwenaelle"},{"last_name":"Guerois","full_name":"Guerois, Raphael","first_name":"Raphael"},{"first_name":"Christel","full_name":"Compper, Christel","last_name":"Compper"},{"first_name":"Arthur","last_name":"Besle","full_name":"Besle, Arthur"},{"first_name":"Berengère","full_name":"Guichard, Berengère","last_name":"Guichard"},{"full_name":"Almouzni, Genevieve","last_name":"Almouzni","first_name":"Genevieve"},{"last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise","first_name":"Françoise"}],"external_id":{"pmid":["25618846"]},"article_processing_charge":"No","title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","abstract":[{"text":"MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","month":"02","intvolume":" 43","publication_identifier":{"issn":["1362-4962","0305-1048"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":43,"issue":"3","_id":"9017","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-23T13:46:50Z","extern":"1"}]