[{"oa_version":"None","author":[{"first_name":"Ruben","last_name":"van Drongelen","full_name":"van Drongelen, Ruben"},{"full_name":"Pal, Anshuman","last_name":"Pal","first_name":"Anshuman"},{"first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"}],"month":"03","article_number":"032706","citation":{"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","ista":"van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706.","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","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.","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.","short":"R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).","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."},"date_created":"2020-04-30T11:41:38Z","extern":"1","article_type":"original","publication":"Physical Review E","issue":"3","date_published":"2015-03-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","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."}],"_id":"7767","intvolume":" 91","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1103/physreve.91.032706","title":"Collective dynamics of soft active particles","date_updated":"2021-01-12T08:15:24Z","publisher":"American Physical Society","day":"01","publication_status":"published","publication_identifier":{"issn":["1539-3755","1550-2376"]},"year":"2015","article_processing_charge":"No","type":"journal_article","volume":91},{"year":"2015","main_file_link":[{"url":"http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning"}],"conference":{"name":"NIPS: Neural Information Processing Systems"},"article_processing_charge":"No","type":"conference","volume":"2015-January","title":"Streaming min-max hypergraph partitioning","date_updated":"2023-02-23T13:17:09Z","publisher":"Neural Information Processing Systems","day":"01","publication_status":"published","publist_id":"6879","status":"public","date_published":"2015-01-01T00:00:00Z","page":"1900 - 1908","abstract":[{"lang":"eng","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."}],"_id":"777","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Iglesias","first_name":"Jennifer","full_name":"Iglesias, Jennifer"},{"full_name":"Vojnović, Milan","last_name":"Vojnović","first_name":"Milan"}],"oa_version":"None","month":"01","citation":{"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.","ista":"Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 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.","short":"D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, pp. 1900–1908.","mla":"Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08."},"date_created":"2018-12-11T11:48:27Z","extern":"1"},{"_id":"7779","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2015-10-29T00:00:00Z","publication":"arXiv:1510.08820","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"}],"page":"242","date_created":"2020-04-30T12:16:18Z","citation":{"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).","chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","ieee":"C. P. Goodrich, “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, .","apa":"Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820.","ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:151008820. 2015."},"arxiv":1,"extern":"1","month":"10","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"}],"oa_version":"Preprint","article_processing_charge":"No","oa":1,"type":"preprint","main_file_link":[{"url":"https://arxiv.org/abs/1510.08820","open_access":"1"}],"year":"2015","date_updated":"2021-01-12T08:15:28Z","publication_status":"published","day":"29","external_id":{"arxiv":["1510.08820"]},"title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids"},{"author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Kopinsky, Justin","last_name":"Kopinsky","first_name":"Justin"},{"last_name":"Kuznetsov","first_name":"Petr","full_name":"Kuznetsov, Petr"},{"full_name":"Ravi, Srivatsan","first_name":"Srivatsan","last_name":"Ravi"},{"full_name":"Shavit, Nir","first_name":"Nir","last_name":"Shavit"}],"month":"01","citation":{"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.","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.","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.","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","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.","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"},"arxiv":1,"page":"185 - 199","language":[{"iso":"eng"}],"_id":"778","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.","doi":"10.1007/978-3-662-48653-5_13","title":"Inherent limitations of hybrid transactional memory","external_id":{"arxiv":["1405.5689"]},"day":"01","date_updated":"2023-02-23T13:17:35Z","conference":{"name":"DISC: Distributed Computing"},"year":"2015","oa":1,"article_processing_charge":"No","oa_version":"None","extern":"1","alternative_title":["LNCS"],"date_created":"2018-12-11T11:48:27Z","abstract":[{"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.","lang":"eng"}],"publist_id":"6880","status":"public","date_published":"2015-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9363","quality_controlled":"1","publication_status":"published","publisher":"Springer","main_file_link":[{"url":"https://arxiv.org/abs/1405.5689","open_access":"1"}],"type":"conference","volume":9363},{"day":"13","publication_status":"published","date_updated":"2023-02-23T12:35:42Z","publisher":"ACM","doi":"10.1145/2755573.2755600","title":"ThreadScan: Automatic and scalable memory reclamation","type":"conference","volume":"2015-June","article_processing_charge":"No","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"related_material":{"record":[{"id":"6001","relation":"later_version","status":"public"}]},"year":"2015","extern":"1","citation":{"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.","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","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","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.","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.","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."},"date_created":"2018-12-11T11:48:27Z","oa_version":"None","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"full_name":"Leiserson, William","last_name":"Leiserson","first_name":"William"},{"first_name":"Nir","last_name":"Shavit","full_name":"Shavit, Nir"}],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"779","language":[{"iso":"eng"}],"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.","page":"123 - 132","abstract":[{"text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU, are either prohibitively expensive or require significant programming expertise, to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated. 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.","lang":"eng"}],"publist_id":"6876","status":"public","date_published":"2015-06-13T00:00:00Z"},{"date_published":"2015-01-01T00:00:00Z","status":"public","publist_id":"6877","abstract":[{"lang":"eng","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."}],"page":"479 - 491","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.”","language":[{"iso":"eng"}],"_id":"780","intvolume":" 9135","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","oa_version":"Preprint","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"}],"date_created":"2018-12-11T11:48:28Z","arxiv":1,"citation":{"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","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.","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","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.","short":"D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.","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.","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."},"extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1502.05745","open_access":"1"}],"year":"2015","conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming"},"oa":1,"volume":9135,"type":"conference","external_id":{"arxiv":["1502.05745"]},"title":"Polylogarithmic-time leader election in population protocols","doi":"10.1007/978-3-662-47666-6_38","publisher":"Springer","date_updated":"2023-02-23T13:18:11Z","publication_status":"published","day":"01"},{"page":"47 - 56","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"}],"publist_id":"6873","date_published":"2015-07-21T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"781","language":[{"iso":"eng"}],"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"full_name":"Vojnović, Milan","first_name":"Milan","last_name":"Vojnović"}],"oa_version":"None","month":"07","extern":"1","citation":{"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.","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.","short":"D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 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.","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","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","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."},"date_created":"2018-12-11T11:48:28Z","conference":{"name":"PODC: Principles of Distributed Computing"},"year":"2015","type":"conference","volume":"2015-July","article_processing_charge":"No","doi":"10.1145/2767386.2767429","title":"Fast and exact majority in population protocols","day":"21","publication_status":"published","date_updated":"2023-02-23T13:18:35Z","publisher":"ACM"},{"doi":"10.1145/2767386.2767430","title":"Lock-Free algorithms under stochastic schedulers","date_updated":"2023-02-23T13:18:50Z","publisher":"ACM","day":"21","publication_status":"published","year":"2015","conference":{"name":"PODC: Principles of Distributed Computing"},"article_processing_charge":"No","type":"conference","volume":"2015-July","oa_version":"None","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Thomas","last_name":"Sauerwald","full_name":"Sauerwald, Thomas"},{"full_name":"Vojnović, Milan","first_name":"Milan","last_name":"Vojnović"}],"month":"07","date_created":"2018-12-11T11:48:28Z","citation":{"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.","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.","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.","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.","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"},"extern":"1","publist_id":"6874","date_published":"2015-07-21T00:00:00Z","status":"public","page":"251 - 260","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"}],"_id":"782","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"783","language":[{"iso":"eng"}],"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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6875","status":"public","date_published":"2015-07-21T00:00:00Z","page":"365 - 374","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","citation":{"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","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.","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","short":"D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.","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.","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.","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."},"extern":"1","oa_version":"None","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Vladu, Adrian","first_name":"Adrian","last_name":"Vladu"}],"month":"07","article_processing_charge":"No","oa":1,"type":"conference","volume":"2015-July","year":"2015","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.1001"}],"conference":{"name":"PODC: Principles of Distributed Computing"},"date_updated":"2023-02-23T13:18:55Z","publisher":"ACM","day":"21","publication_status":"published","doi":"10.1145/2767386.2767420","title":"How to elect a leader faster than a tournament"},{"type":"conference","year":"2015","conference":{"end_date":"2015-08-21","start_date":"2015-08-17","name":"SIGCOMM: Special Interest Group on Data Communication","location":"London, United Kindgdom"},"publisher":"ACM","date_updated":"2023-02-23T13:18:57Z","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-3542-3"]},"day":"01","quality_controlled":"1","title":"A high-radix, low-latency optical switch for data centers","doi":"10.1145/2785956.2790035","_id":"784","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-01-01T00:00:00Z","status":"public","publist_id":"6872","abstract":[{"lang":"eng","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."}],"page":"367 - 368","date_created":"2018-12-11T11:48:29Z","citation":{"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","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.","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","short":"D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts, B. Thomsen, in:, ACM, 2015, pp. 367–368.","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.","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.","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."},"extern":"1","month":"01","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Ballani","first_name":"Hitesh","full_name":"Ballani, Hitesh"},{"full_name":"Costa, Paolo","last_name":"Costa","first_name":"Paolo"},{"full_name":"Funnell, Adam","last_name":"Funnell","first_name":"Adam"},{"full_name":"Benjamin, Joshua","first_name":"Joshua","last_name":"Benjamin"},{"first_name":"Philip","last_name":"Watts","full_name":"Watts, Philip"},{"full_name":"Thomsen, Benn","last_name":"Thomsen","first_name":"Benn"}],"oa_version":"None"},{"doi":"10.1093/glycob/cwv059","department":[{"_id":"CaHe"}],"title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","external_id":{"pmid":["26306635"]},"quality_controlled":"1","pmid":1,"day":"01","publication_status":"published","date_updated":"2021-01-12T08:16:33Z","publisher":"Oxford University Press","year":"2015","type":"journal_article","volume":25,"author":[{"last_name":"Engel","first_name":"Jakob","full_name":"Engel, Jakob"},{"orcid":"0000-0002-5795-0133","full_name":"Schmalhorst, Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","first_name":"Philipp S"},{"last_name":"Kruger","first_name":"Anke","full_name":"Kruger, Anke"},{"full_name":"Muller, Christina","last_name":"Muller","first_name":"Christina"},{"last_name":"Buettner","first_name":"Falk","full_name":"Buettner, Falk"},{"last_name":"Routier","first_name":"Françoise","full_name":"Routier, Françoise"}],"oa_version":"None","month":"12","scopus_import":1,"date_created":"2018-12-11T11:48:35Z","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.","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","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","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.","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.","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."},"page":"1423 - 1430","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"}],"publist_id":"6851","issue":"12","publication":"Glycobiology","date_published":"2015-12-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"802","intvolume":" 25","language":[{"iso":"eng"}]},{"doi":"10.1038/nature13838","title":"Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution","quality_controlled":0,"day":"22","publication_status":"published","date_updated":"2021-01-12T08:17:08Z","publisher":"Nature Publishing Group","year":"2015","type":"journal_article","volume":517,"author":[{"first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Florian Schur","orcid":"0000-0003-4790-8078"},{"first_name":"Wim","last_name":"Hagen","full_name":"Hagen, Wim J"},{"first_name":"Michaela","last_name":"Rumlová","full_name":"Rumlová, Michaela"},{"full_name":"Ruml, Tomáš","last_name":"Ruml","first_name":"Tomáš"},{"first_name":"B","last_name":"Müller","full_name":"Müller B"},{"first_name":"Hans","last_name":"Kraüsslich","full_name":"Kraüsslich, Hans Georg"},{"full_name":"Briggs, John A","last_name":"Briggs","first_name":"John"}],"month":"01","extern":1,"citation":{"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.","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.","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.","short":"F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508.","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","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.","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"},"date_created":"2018-12-11T11:48:39Z","page":"505 - 508","abstract":[{"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.","lang":"eng"}],"publication":"Nature","publist_id":"6836","issue":"7535","date_published":"2015-01-22T00:00:00Z","status":"public","_id":"814","intvolume":" 517","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."},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"815","intvolume":" 89","abstract":[{"lang":"eng","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"}],"page":"10294 - 10302","status":"public","date_published":"2015-09-22T00:00:00Z","publist_id":"6837","publication":"Journal of Virology","issue":"20","extern":"1","date_created":"2018-12-11T11:48:39Z","citation":{"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","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","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.","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.","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.","short":"F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89 (2015) 10294–10302.","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."},"month":"09","oa_version":"None","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian"},{"last_name":"Dick","first_name":"Robert","full_name":"Dick, Robert"},{"full_name":"Hagen, Wim","last_name":"Hagen","first_name":"Wim"},{"full_name":"Vogt, Volker","first_name":"Volker","last_name":"Vogt"},{"full_name":"Briggs, John","first_name":"John","last_name":"Briggs"}],"volume":89,"type":"journal_article","year":"2015","publication_status":"published","day":"22","publisher":"ASM","date_updated":"2021-01-12T08:17:09Z","title":"The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly","doi":"10.1128/JVI.01502-15","pmid":1,"external_id":{"pmid":["26223638"]},"quality_controlled":"1"},{"related_material":{"record":[{"status":"public","relation":"later_version","id":"9308"},{"relation":"later_version","id":"10220","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8156"}]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"year":"2015","type":"preprint","article_processing_charge":"No","oa":1,"department":[{"_id":"UlWa"}],"title":"Eliminating higher-multiplicity intersections, III. Codimension 2","external_id":{"arxiv":["1511.03501"]},"publication_status":"submitted","day":"15","date_updated":"2023-09-07T13:12:17Z","abstract":[{"lang":"eng","text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample."}],"date_published":"2015-11-15T00:00:00Z","status":"public","publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","_id":"8183","language":[{"iso":"eng"}],"article_number":"1511.03501","month":"11","oa_version":"Preprint","author":[{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard"},{"first_name":"A.","last_name":"Skopenkov","full_name":"Skopenkov, A."},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"arxiv":1,"citation":{"short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, 1511.03501.","chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” arXiv. .","ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv.","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv."},"date_created":"2020-07-30T10:45:19Z"},{"title":"Automatic generation of alternative starting positions for simple traditional board games","date_updated":"2023-02-23T12:25:07Z","day":"01","ec_funded":1,"year":"2015","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5410"}]},"conference":{"end_date":"2015-01-30","start_date":"2015-01-25","name":"AAAI: Conference on Artificial Intelligence","location":"Austin, TX, USA"},"oa":1,"article_processing_charge":"No","month":"01","author":[{"first_name":"Umair","last_name":"Ahmed","full_name":"Ahmed, Umair"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Sumit","last_name":"Gulwani","full_name":"Gulwani, Sumit"}],"citation":{"short":"U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752.","mla":"Ahmed, Umair, et al. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, vol. 2, AAAI Press, 2015, pp. 745–52.","chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2:745–52. AAAI Press, 2015.","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, “Automatic generation of alternative starting positions for simple traditional board games,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, Austin, TX, USA, 2015, vol. 2, pp. 745–752.","ista":"Ahmed U, Chatterjee K, Gulwani S. 2015. Automatic generation of alternative starting positions for simple traditional board games. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2, 745–752.","apa":"Ahmed, U., Chatterjee, K., & Gulwani, S. (2015). Automatic generation of alternative starting positions for simple traditional board games. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 2, pp. 745–752). Austin, TX, USA: AAAI Press.","ama":"Ahmed U, Chatterjee K, Gulwani S. Automatic generation of alternative starting positions for simple traditional board games. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. Vol 2. AAAI Press; 2015:745-752."},"page":"745 - 752","acknowledgement":"A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n","_id":"1481","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","department":[{"_id":"KrCh"}],"publisher":"AAAI Press","publication_status":"published","main_file_link":[{"url":"https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300","open_access":"1"}],"volume":2,"type":"conference","oa_version":"None","date_created":"2018-12-11T11:52:16Z","scopus_import":1,"status":"public","date_published":"2015-01-01T00:00:00Z","publist_id":"5713","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence","abstract":[{"lang":"eng","text":"Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in the development of mathematical and logical skills, but also in the emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. We present an approach that generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. The presence of such states for standard game variants like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played as the default start state is heavily biased. "}],"intvolume":" 2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes."}],"page":"4741 - 4748","status":"public","date_published":"2015-10-14T00:00:00Z","publist_id":"5709","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1483","language":[{"iso":"eng"}],"month":"10","author":[{"first_name":"Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814"},{"full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kwitt, Roland","first_name":"Roland","last_name":"Kwitt"}],"oa_version":"Preprint","scopus_import":1,"date_created":"2018-12-11T11:52:17Z","citation":{"ama":"Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106","apa":"Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106","ista":"Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748.","ieee":"J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.","chicago":"Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.","mla":"Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.","short":"J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748."},"conference":{"end_date":"2015-06-12","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition","location":"Boston, MA, USA"},"year":"2015","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1412.6821"}],"type":"conference","oa":1,"title":"A stable multi-scale kernel for topological machine learning","department":[{"_id":"HeEd"}],"doi":"10.1109/CVPR.2015.7299106","publication_identifier":{"eisbn":["978-1-4673-6964-0 "]},"publication_status":"published","day":"14","publisher":"IEEE","date_updated":"2021-01-12T06:51:03Z"},{"language":[{"iso":"eng"}],"_id":"1495","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 27th Canadian Conference on Computational Geometry","publist_id":"5684","date_published":"2015-08-01T00:00:00Z","status":"public","page":"128-135","abstract":[{"text":"Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. ","lang":"eng"}],"date_created":"2018-12-11T11:52:21Z","citation":{"apa":"Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk packing. In Proceedings of the 27th Canadian Conference on Computational Geometry (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.","ista":"Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.","ama":"Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings of the 27th Canadian Conference on Computational Geometry. Vol 2015-August. Queen’s University; 2015:128-135.","mla":"Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the 27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s University, 2015, pp. 128–35.","short":"H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.","ieee":"H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in Proceedings of the 27th Canadian Conference on Computational Geometry, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.","chicago":"Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational Geometry, 2015–August:128–35. Queen’s University, 2015."},"scopus_import":1,"oa_version":"Submitted Version","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham"},{"first_name":"Vitaliy","last_name":"Kurlin","full_name":"Kurlin, Vitaliy"}],"month":"08","oa":1,"type":"conference","volume":"2015-August","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.03402"}],"year":"2015","conference":{"start_date":"2015-08-10","end_date":"2015-08-12","location":"Ontario, Canada","name":"CCCG: Canadian Conference on Computational Geometry"},"date_updated":"2021-01-12T06:51:09Z","publisher":"Queen's University","day":"01","publication_status":"published","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"title":"Relaxed disk packing","department":[{"_id":"HeEd"}]},{"oa_version":"Published Version","scopus_import":1,"date_created":"2018-12-11T11:52:22Z","abstract":[{"text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.","lang":"eng"}],"date_published":"2015-07-21T00:00:00Z","status":"public","publication":"Nucleic Acids Research","publist_id":"5682","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 43","department":[{"_id":"GaNo"}],"quality_controlled":"1","publication_status":"published","publisher":"Oxford University Press","volume":43,"type":"journal_article","file_date_updated":"2020-07-14T12:44:58Z","article_number":"e146","month":"07","author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph"},{"full_name":"Kulinski, Tomasz","first_name":"Tomasz","last_name":"Kulinski"},{"full_name":"Guenzl, Philipp","last_name":"Guenzl","first_name":"Philipp"},{"last_name":"Bammer","first_name":"Philipp","full_name":"Bammer, Philipp"},{"full_name":"Barlow, Denise","last_name":"Barlow","first_name":"Denise"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Hudson, Quanah","last_name":"Hudson","first_name":"Quanah"}],"file":[{"content_type":"application/pdf","file_name":"2015_NucleicAcidsRes_Andergassen.pdf","relation":"main_file","checksum":"385b83854fd0eb2e4f386867da2823e2","creator":"dernst","file_size":6863297,"file_id":"5768","access_level":"open_access","date_updated":"2020-07-14T12:44:58Z","date_created":"2018-12-20T14:18:57Z"}],"citation":{"ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 2015;43(21). doi:10.1093/nar/gkv727","ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146.","apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv727","chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.","ieee":"D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” Nucleic Acids Research, vol. 43, no. 21. Oxford University Press, 2015.","short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).","mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727."},"ddc":["570"],"issue":"21","acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna.","_id":"1497","language":[{"iso":"eng"}],"title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","doi":"10.1093/nar/gkv727","day":"21","date_updated":"2021-01-12T06:51:09Z","has_accepted_license":"1","year":"2015","oa":1},{"title":"The need for language support for fault-tolerant distributed systems","doi":"10.4230/LIPIcs.SNAPL.2015.90","publication_identifier":{"isbn":["978-3-939897-80-4 "]},"day":"01","date_updated":"2020-08-11T10:09:14Z","has_accepted_license":"1","series_title":"Leibniz International Proceedings in Informatics","conference":{"end_date":"2015-05-06","start_date":"2015-05-03","name":"SNAPL: Summit oN Advances in Programming Languages","location":"Asilomar, CA, United States"},"year":"2015","ec_funded":1,"oa":1,"month":"01","file_date_updated":"2020-07-14T12:44:58Z","author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_name":"IST-2016-499-v1+1_9.pdf","relation":"main_file","checksum":"cf5e94baa89a2dc4c5de01abc676eda8","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:14:02Z","date_updated":"2020-07-14T12:44:58Z","file_size":489362,"file_id":"5050"}],"citation":{"ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90.","mla":"Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.","ama":"Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90","ista":"Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102."},"ddc":["005"],"page":"90 - 102","pubrep_id":"499","_id":"1498","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"quality_controlled":"1","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","volume":32,"type":"conference","oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"date_created":"2018-12-11T11:52:22Z","abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.","lang":"eng"}],"date_published":"2015-01-01T00:00:00Z","status":"public","publist_id":"5681","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 32"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 42","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-01-01T00:00:00Z","status":"public","publist_id":"5680","abstract":[{"lang":"eng","text":"We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata."}],"date_created":"2018-12-11T11:52:22Z","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","volume":42,"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"quality_controlled":"1","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"acknowledgement":"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734.","_id":"1499","language":[{"iso":"eng"}],"pubrep_id":"498","page":"142 - 154","citation":{"mla":"Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.","short":"J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154.","chicago":"Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142.","ieee":"J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.","ista":"Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.","apa":"Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142","ama":"Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142"},"ddc":["000","003"],"month":"01","file_date_updated":"2020-07-14T12:44:58Z","file":[{"date_updated":"2020-07-14T12:44:58Z","date_created":"2018-12-12T10:08:12Z","access_level":"open_access","file_id":"4672","file_size":623563,"creator":"system","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_name":"IST-2016-498-v1+1_32.pdf","relation":"main_file","content_type":"application/pdf"}],"author":[{"last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"last_name":"Larsen","first_name":"Kim","full_name":"Larsen, Kim"},{"full_name":"Laursen, Simon","first_name":"Simon","last_name":"Laursen"},{"last_name":"Srba","first_name":"Jiří","full_name":"Srba, Jiří"}],"oa":1,"year":"2015","ec_funded":1,"has_accepted_license":"1","conference":{"location":"Madrid, Spain","name":"CONCUR: Concurrency Theory","start_date":"2015-09-01","end_date":"2015-09-04"},"date_updated":"2021-01-12T06:51:10Z","day":"01","title":"Polynomial time decidability of weighted synchronization under partial observability","doi":"10.4230/LIPIcs.CONCUR.2015.142"}]