[{"page":"47 - 55","date_updated":"2023-09-19T14:44:14Z","year":"2018","alternative_title":["ICAPS"],"oa":1,"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"AAAI Press","main_file_link":[{"url":"https://arxiv.org/abs/1710.00675","open_access":"1"}],"intvolume":" 2018","date_created":"2018-12-11T11:44:16Z","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","external_id":{"isi":["000492986200006"],"arxiv":["1710.00675"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8021","department":[{"_id":"KrCh"}],"ec_funded":1,"publication_status":"published","status":"public","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies.","lang":"eng"}],"_id":"34","title":"Sensor synthesis for POMDPs with reachability objectives","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Chemlík","full_name":"Chemlík, Martin","first_name":"Martin"},{"last_name":"Topcu","full_name":"Topcu, Ufuk","first_name":"Ufuk"}],"article_processing_charge":"No","volume":2018,"arxiv":1,"oa_version":"Preprint","conference":{"end_date":"2018-06-29","start_date":"2018-06-24","location":"Delft, Netherlands","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"month":"06","citation":{"short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.","ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55.","ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.","apa":"Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.","mla":"Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018."},"day":"01"},{"arxiv":1,"article_processing_charge":"No","month":"06","citation":{"ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. In: 28th International Conference on Automated Planning and Scheduling . AAAI Press; 2018.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional lower bounds for planning problems. 28th International Conference on Automated Planning and Scheduling . ICAPS: International Conference on Automated Planning and Scheduling.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2018). Algorithms and conditional lower bounds for planning problems. In 28th International Conference on Automated Planning and Scheduling . Delft, Netherlands: AAAI Press.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” in 28th International Conference on Automated Planning and Scheduling , Delft, Netherlands, 2018.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In 28th International Conference on Automated Planning and Scheduling . AAAI Press, 2018.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018."},"day":"01","oa_version":"None","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","start_date":"2018-06-24","location":"Delft, Netherlands","end_date":"2018-06-29"},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"publication_status":"published","status":"public","_id":"35","title":"Algorithms and conditional lower bounds for planning problems","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Dvorák","full_name":"Dvorák, Wolfgang","first_name":"Wolfgang"},{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Svozil","full_name":"Svozil, Alexander","first_name":"Alexander"}],"abstract":[{"text":"We consider planning problems for graphs, Markov decision processes (MDPs), and games on graphs. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems where there are k different target sets, and the problems are as follows: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) objective-separation results showing that for MDPs the coverage problem is harder than the sequential target problem.","lang":"eng"}],"publisher":"AAAI Press","main_file_link":[{"url":"https://arxiv.org/abs/1804.07031","open_access":"1"}],"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publist_id":"8020","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:44:17Z","scopus_import":"1","external_id":{"isi":["000492986200007"],"arxiv":["1804.07031"]},"date_published":"2018-06-01T00:00:00Z","date_updated":"2023-09-26T10:41:41Z","publication":"28th International Conference on Automated Planning and Scheduling ","related_material":{"record":[{"status":"public","relation":"later_version","id":"9293"}]},"oa":1,"year":"2018"},{"_id":"36","author":[{"last_name":"Vu","full_name":"Vu, Lam","first_name":"Lam"},{"first_name":"Tingting","last_name":"Zhu","full_name":"Zhu, Tingting"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge","last_name":"Verstraeten"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"last_name":"Gevaert","full_name":"Gevaert, Kris","first_name":"Kris"},{"first_name":"Ive","full_name":"De Smet, Ive","last_name":"De Smet"}],"title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","doi":"10.1093/jxb/ery204","issue":"19","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","publication_status":"published","status":"public","file_date_updated":"2020-07-14T12:46:13Z","ddc":["581"],"month":"08","day":"31","citation":{"mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624."},"oa_version":"Published Version","file":[{"date_created":"2018-12-18T09:47:51Z","file_id":"5741","date_updated":"2020-07-14T12:46:13Z","content_type":"application/pdf","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":3359316,"file_name":"2018_JournalExperimBotany_Vu.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","volume":69,"has_accepted_license":"1","oa":1,"year":"2018","date_updated":"2023-09-19T10:00:46Z","publication":"Journal of Experimental Botany","page":"4609 - 4624","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8019","department":[{"_id":"JiFr"}],"scopus_import":"1","date_created":"2018-12-11T11:44:17Z","date_published":"2018-08-31T00:00:00Z","external_id":{"isi":["000443568700010"]},"intvolume":" 69","publisher":"Oxford University Press","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1},{"oa":1,"year":"2018","alternative_title":["Methods in Molecular Biology"],"publication":"Morphogen Gradients ","date_updated":"2021-01-12T07:49:03Z","page":"47 - 63","department":[{"_id":"AnKi"}],"publist_id":"8018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-10-16T00:00:00Z","date_created":"2018-12-11T11:44:17Z","scopus_import":"1","series_title":"MIMB","publisher":"Springer Nature","intvolume":" 1863","language":[{"iso":"eng"}],"quality_controlled":"1","type":"book_chapter","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","author":[{"full_name":"Zagórski, Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","orcid":"0000-0001-7896-7762"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998"}],"_id":"37","abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}],"doi":"10.1007/978-1-4939-8772-6_4","publication_identifier":{"isbn":["978-1-4939-8771-9"],"issn":["1064-3745"]},"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"}],"status":"public","publication_status":"published","ec_funded":1,"citation":{"ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4."},"day":"16","month":"10","ddc":["570"],"file_date_updated":"2020-10-13T14:20:37Z","oa_version":"Submitted Version","file":[{"file_id":"8656","date_created":"2020-10-13T14:20:37Z","success":1,"date_updated":"2020-10-13T14:20:37Z","access_level":"open_access","content_type":"application/pdf","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","file_name":"2018_MIMB_Zagorski.pdf","relation":"main_file","file_size":4906815,"creator":"dernst"}],"has_accepted_license":"1","article_processing_charge":"No","volume":1863},{"year":"2018","oa":1,"page":"11006 - 11011","publication":"PNAS","date_updated":"2023-09-18T08:36:49Z","date_published":"2018-10-23T00:00:00Z","external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"date_created":"2018-12-11T11:44:18Z","scopus_import":"1","department":[{"_id":"NiBa"}],"publist_id":"8017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"National Academy of Sciences","intvolume":" 115","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"issue":"43","doi":"10.1073/pnas.1801832115","title":"Selection and gene flow shape genomic islands that control floral guides","author":[{"first_name":"Hugo","full_name":"Tavares, Hugo","last_name":"Tavares"},{"first_name":"Annabel","full_name":"Whitley, Annabel","last_name":"Whitley"},{"orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","full_name":"Field, David"},{"first_name":"Desmond","full_name":"Bradley, Desmond","last_name":"Bradley"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"first_name":"Joane","last_name":"Elleouet","full_name":"Elleouet, Joane"},{"first_name":"Monique","last_name":"Burrus","full_name":"Burrus, Monique"},{"first_name":"Christophe","full_name":"Andalo, Christophe","last_name":"Andalo"},{"last_name":"Li","full_name":"Li, Miaomiao","first_name":"Miaomiao"},{"last_name":"Li","full_name":"Li, Qun","first_name":"Qun"},{"full_name":"Xue, Yongbiao","last_name":"Xue","first_name":"Yongbiao"},{"first_name":"Alexandra B","last_name":"Rebocho","full_name":"Rebocho, Alexandra B"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Enrico","full_name":"Coen, Enrico","last_name":"Coen"}],"_id":"38","acknowledgement":" ERC Grant 201252 (to N.H.B.)","status":"public","publication_status":"published","publication_identifier":{"issn":["00278424"]},"oa_version":"Published Version","citation":{"mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115"},"day":"23","pmid":1,"month":"10","ddc":["570"],"file_date_updated":"2020-07-14T12:46:16Z","has_accepted_license":"1","article_processing_charge":"No","volume":115,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"5683","date_created":"2018-12-17T08:44:03Z","file_name":"11006.full.pdf","relation":"main_file","file_size":1911302,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","date_updated":"2020-07-14T12:46:16Z"}]},{"year":"2018","oa":1,"page":"928 - 938","date_updated":"2023-09-11T13:56:52Z","publication":"Genome Biology and Evolution","scopus_import":"1","date_created":"2018-12-11T11:46:10Z","external_id":{"isi":["000429483700022"]},"date_published":"2018-03-01T00:00:00Z","publist_id":"7445","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"FyKo"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":" 10","publisher":"Oxford University Press","doi":"10.1093/gbe/evy049","issue":"3","abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"_id":"384","author":[{"first_name":"Peter","full_name":"Hönigschmid, Peter","last_name":"Hönigschmid"},{"full_name":"Bykova, Nadya","last_name":"Bykova","first_name":"Nadya"},{"last_name":"Schneider","full_name":"Schneider, René","first_name":"René"},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Frishman","full_name":"Frishman, Dmitrij","first_name":"Dmitrij"}],"title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","status":"public","publication_status":"published","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","oa_version":"Published Version","month":"03","ddc":["576"],"file_date_updated":"2020-07-14T12:46:16Z","day":"01","citation":{"chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938."},"pubrep_id":"999","volume":10,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"458a7c2c2e79528567edfeb0f326cbe0","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:16Z","file_size":691602,"relation":"main_file","creator":"system","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","date_created":"2018-12-12T10:08:07Z","file_id":"4667"}]},{"volume":210,"article_processing_charge":"No","month":"12","day":"04","citation":{"ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429."},"oa_version":"Preprint","publication_identifier":{"issn":["00166731"]},"publication_status":"published","status":"public","_id":"39","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"Replicability of introgression under linked, polygenic selection","doi":"10.1534/genetics.118.301429","issue":"4","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"intvolume":" 210","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"publisher":"Genetics Society of America","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"scopus_import":"1","date_created":"2018-12-11T11:44:18Z","date_published":"2018-12-04T00:00:00Z","external_id":{"isi":["000452315900021"]},"date_updated":"2023-09-18T08:10:29Z","publication":"Genetics","article_type":"original","page":"1411-1427","oa":1,"year":"2018"},{"publist_id":"7435","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1712.07925"]},"extern":"1","date_published":"2018-01-10T00:00:00Z","date_created":"2018-12-11T11:46:13Z","main_file_link":[{"url":"https://arxiv.org/abs/1712.07925","open_access":"1"}],"intvolume":" 18","publisher":"American Chemical Society","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","oa":1,"year":"2018","publication":"Nano Letters","date_updated":"2021-01-12T07:53:20Z","page":"223 - 228","day":"10","citation":{"chicago":"Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.7b03953.","mla":"Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters, vol. 18, no. 1, American Chemical Society, 2018, pp. 223–28, doi:10.1021/acs.nanolett.7b03953.","ieee":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,” Nano Letters, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018.","apa":"Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., & Gedik, N. (2018). Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b03953","short":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018) 223–228.","ama":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 2018;18(1):223-228. doi:10.1021/acs.nanolett.7b03953","ista":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1), 223–228."},"month":"01","oa_version":"Submitted Version","arxiv":1,"volume":18,"author":[{"last_name":"Mahmood","full_name":"Mahmood, Fahad","first_name":"Fahad"},{"orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek"},{"first_name":"Yi","full_name":"Lee, Yi","last_name":"Lee"},{"first_name":"Jing","last_name":"Kong","full_name":"Kong, Jing"},{"full_name":"Gedik, Nuh","last_name":"Gedik","first_name":"Nuh"}],"title":"Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2","_id":"394","issue":"1","abstract":[{"lang":"eng","text":"The valley pseudospin in monolayer transition metal dichalcogenides (TMDs) has been proposed as a new way to manipulate information in various optoelectronic devices. This relies on a large valley polarization that remains stable over long time scales (hundreds of nanoseconds). However, time-resolved measurements report valley lifetimes of only a few picoseconds. This has been attributed to mechanisms such as phonon-mediated intervalley scattering and a precession of the valley pseudospin through electron-hole exchange. Here we use transient spin grating to directly measure the valley depolarization lifetime in monolayer MoSe2. We find a fast valley decay rate that scales linearly with the excitation density at different temperatures. This establishes the presence of strong exciton-exciton Coulomb exchange interactions enhancing the valley depolarization. Our work highlights the microscopic processes inhibiting the efficient use of the exciton valley pseudospin in monolayer TMDs. "}],"doi":"10.1021/acs.nanolett.7b03953","publication_status":"published","status":"public"},{"project":[{"name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published","_id":"395","supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"}],"title":"The branched chain amino acids in autism spectrum disorders ","author":[{"id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara","full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu"}],"doi":"10.15479/AT:ISTA:th_992","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. "}],"file":[{"embargo_to":"open_access","file_id":"6217","date_created":"2019-04-05T09:19:17Z","file_name":"2018_Thesis_Tarlungeanu_source.docx","file_size":43684035,"creator":"dernst","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"9f5231c96e0ad945040841a8630232da","date_updated":"2021-02-11T23:30:15Z"},{"embargo":"2018-03-15","file_size":30511532,"relation":"main_file","creator":"dernst","file_name":"2018_Thesis_Tarlungeanu.pdf","date_updated":"2021-02-11T11:17:16Z","content_type":"application/pdf","checksum":"0c33c370aa2010df5c552db57a6d01e9","access_level":"open_access","date_created":"2019-04-05T09:19:17Z","file_id":"6218"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-02-11T23:30:15Z","month":"03","ddc":["570","616"],"citation":{"apa":"Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.","mla":"Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992."},"pubrep_id":"992","day":"01","oa_version":"Published Version","date_updated":"2023-09-07T12:38:59Z","page":"88","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1183"}]},"oa":1,"alternative_title":["ISTA Thesis"],"year":"2018","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7434","department":[{"_id":"GaNo"}],"date_created":"2018-12-11T11:46:14Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"date_published":"2018-03-01T00:00:00Z"},{"status":"public","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"doi":"10.1145/3178487.3178489","abstract":[{"lang":"eng","text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. "}],"issue":"1","_id":"397","title":"Harnessing epoch-based reclamation for efficient range queries","author":[{"last_name":"Arbel Raviv","full_name":"Arbel Raviv, Maya","first_name":"Maya"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"}],"volume":53,"article_processing_charge":"No","oa_version":"None","conference":{"location":"Vienna, Austria","start_date":"2018-02-24","end_date":"2018-02-28","name":"PPoPP: Principles and Practice of Parallel Programming"},"month":"02","citation":{"mla":"Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489.","chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.","ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","apa":"Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489","ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27."},"day":"10","page":"14 - 27","date_updated":"2023-09-11T14:10:25Z","alternative_title":["PPoPP"],"year":"2018","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","isi":1,"publisher":"ACM","intvolume":" 53","date_created":"2018-12-11T11:46:14Z","scopus_import":"1","external_id":{"isi":["000446161100002"]},"date_published":"2018-02-10T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7430","department":[{"_id":"DaAl"}]},{"external_id":{"isi":["000432942700070"]},"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","oa_version":"None","date_created":"2018-12-11T11:46:15Z","day":"01","department":[{"_id":"BeBi"}],"citation":{"mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.","chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096","short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.","ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578.","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096","ieee":"P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018."},"month":"05","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7431","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","volume":13,"article_processing_charge":"No","intvolume":" 13","publisher":"Elsevier","year":"2018","abstract":[{"lang":"eng","text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices."}],"doi":"10.1016/j.wneu.2018.02.096","author":[{"first_name":"Philippe","last_name":"Dodier","full_name":"Dodier, Philippe"},{"full_name":"Frischer, Josa","last_name":"Frischer","first_name":"Josa"},{"full_name":"Wang, Wei","last_name":"Wang","first_name":"Wei"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Mallouhi, Ammar","last_name":"Mallouhi","first_name":"Ammar"},{"full_name":"Serles, Wolfgang","last_name":"Serles","first_name":"Wolfgang"},{"full_name":"Gruber, Andreas","last_name":"Gruber","first_name":"Andreas"},{"first_name":"Engelbert","last_name":"Knosp","full_name":"Knosp, Engelbert"},{"first_name":"Gerhard","full_name":"Bavinzski, Gerhard","last_name":"Bavinzski"}],"title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","_id":"398","status":"public","publication_status":"published","page":"e568-e578","publication":"World Neurosurgery","date_updated":"2023-09-11T14:12:33Z"},{"publist_id":"7432","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"RoSe"}],"scopus_import":"1","date_created":"2018-12-11T11:46:15Z","external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"date_published":"2018-01-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.01822"}],"intvolume":" 121","publisher":"IOP Publishing Ltd.","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"oa":1,"year":"2018","date_updated":"2023-09-08T13:30:51Z","publication":"EPL","article_type":"original","article_number":"10007","month":"01","day":"01","citation":{"chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007"},"oa_version":"Preprint","arxiv":1,"volume":121,"article_processing_charge":"No","_id":"399","author":[{"first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"first_name":"Robin","full_name":"Reuvers, Robin","last_name":"Reuvers"},{"last_name":"Solovej","full_name":"Solovej, Jan","first_name":"Jan"}],"title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","doi":"10.1209/0295-5075/121/10007","issue":"1","abstract":[{"text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.","lang":"eng"}],"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"}],"acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","publication_status":"published","status":"public"},{"file":[{"date_created":"2018-12-12T10:16:28Z","file_id":"5216","file_size":22803163,"creator":"system","relation":"main_file","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","date_updated":"2020-07-14T12:46:22Z","content_type":"application/pdf","checksum":"7a2243668f215821bc6aecad0320079a","access_level":"open_access"}],"has_accepted_license":"1","article_processing_charge":"No","volume":37,"day":"04","citation":{"apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325."},"pubrep_id":"1049","ddc":["003","004"],"file_date_updated":"2020-07-14T12:46:22Z","month":"08","oa_version":"Submitted Version","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"status":"public","publication_status":"published","ec_funded":1,"author":[{"first_name":"Nobuyuki","full_name":"Umetani, Nobuyuki","last_name":"Umetani"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd"}],"title":"Learning three-dimensional flow for interactive aerodynamic design","_id":"4","issue":"4","abstract":[{"lang":"eng","text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body."}],"doi":"10.1145/3197517.3201325","intvolume":" 37","publisher":"ACM","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"BeBi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8053","date_published":"2018-08-04T00:00:00Z","external_id":{"isi":["000448185000050"]},"scopus_import":"1","date_created":"2018-12-11T11:44:06Z","publication":"ACM Trans. Graph.","date_updated":"2023-09-13T08:46:15Z","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","description":"News on IST Homepage"}]},"article_number":"89","oa":1,"year":"2018"},{"_id":"40","title":"The consequences of an introgression event","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"doi":"10.1111/mec.14950","abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"issue":"24","publication_identifier":{"issn":["1365294X"]},"publication_status":"published","status":"public","ddc":["576"],"month":"12","pmid":1,"file_date_updated":"2020-07-14T12:46:22Z","citation":{"ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950."},"day":"31","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2018_MolecularEcology_BartonNick.pdf","creator":"apreinsp","file_size":295452,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:22Z","file_id":"6652","date_created":"2019-07-19T06:54:46Z"}],"article_processing_charge":"Yes (via OA deal)","volume":27,"has_accepted_license":"1","oa":1,"year":"2018","date_updated":"2023-09-19T10:06:08Z","publication":"Molecular Ecology","page":"4973-4975","article_type":"letter_note","related_material":{"record":[{"relation":"research_data","status":"public","id":"9805"}]},"publist_id":"8014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:44:18Z","scopus_import":"1","date_published":"2018-12-31T00:00:00Z","external_id":{"pmid":["30599087"],"isi":["000454600500001"]},"publisher":"Wiley","intvolume":" 27","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1},{"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","status":"public","ec_funded":1,"author":[{"first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746"},{"first_name":"Alissa","full_name":"Geisinge, Alissa","last_name":"Geisinge"},{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"last_name":"Loss","full_name":"Loss, Michael","first_name":"Michael"}],"title":"Persistence of translational symmetry in the BCS model with radial pair interaction","_id":"400","issue":"5","abstract":[{"text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case.","lang":"eng"}],"doi":"10.1007/s00023-018-0665-7","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"system","file_size":582680,"file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","date_updated":"2020-07-14T12:46:22Z","content_type":"application/pdf","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","access_level":"open_access","date_created":"2018-12-12T10:12:47Z","file_id":"4966"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":19,"day":"01","citation":{"mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.","ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018."},"pubrep_id":"1011","month":"05","file_date_updated":"2020-07-14T12:46:22Z","ddc":["510"],"oa_version":"Published Version","publication":"Annales Henri Poincare","date_updated":"2023-09-15T12:04:15Z","page":"1507 - 1527","oa":1,"year":"2018","intvolume":" 19","publisher":"Springer","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"RoSe"}],"publist_id":"7429","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000429799900008"]},"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:46:15Z"},{"ddc":["539","570"],"file_date_updated":"2020-07-14T12:46:22Z","month":"03","day":"23","citation":{"apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5.","chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5."},"pubrep_id":"996","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"87a427bc2e8724be3dd22a4efdd21a33","date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","file_size":3780491,"relation":"main_file","creator":"system","file_id":"4902","date_created":"2018-12-12T10:11:45Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":9,"article_processing_charge":"No","has_accepted_license":"1","_id":"401","author":[{"last_name":"Qin","full_name":"Qin, Xiang","first_name":"Xiang"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"last_name":"Mangeat","full_name":"Mangeat, Thomas","first_name":"Thomas"},{"first_name":"Chang","last_name":"Liu","full_name":"Liu, Chang"},{"first_name":"Pralay","last_name":"Majumder","full_name":"Majumder, Pralay"},{"last_name":"Liu","full_name":"Liu, Jjiaying","first_name":"Jjiaying"},{"full_name":"Choesmel Cadamuro, Valerie","last_name":"Choesmel Cadamuro","first_name":"Valerie"},{"full_name":"Mcdonald, Jocelyn","last_name":"Mcdonald","first_name":"Jocelyn"},{"last_name":"Liu","full_name":"Liu, Yinyao","first_name":"Yinyao"},{"first_name":"Bin","full_name":"Yi, Bin","last_name":"Yi"},{"first_name":"Xiaobo","last_name":"Wang","full_name":"Wang, Xiaobo"}],"title":"A biochemical network controlling basal myosin oscillation","doi":"10.1038/s41467-018-03574-5","issue":"1","abstract":[{"text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation.","lang":"eng"}],"publication_status":"published","status":"public","publist_id":"7427","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"EdHa"}],"scopus_import":"1","date_created":"2018-12-11T11:46:16Z","date_published":"2018-03-23T00:00:00Z","external_id":{"isi":["000428165400009"]},"intvolume":" 9","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"oa":1,"year":"2018","date_updated":"2023-09-08T11:41:45Z","publication":"Nature Communications","article_number":"1210"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aal3662"}],"intvolume":" 359","publisher":"American Association for the Advancement of Science","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7428","department":[{"_id":"MiSi"}],"scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"}],"date_created":"2018-12-11T11:46:16Z","date_published":"2018-03-23T00:00:00Z","external_id":{"isi":["000428043600047"],"pmid":["29567714"]},"date_updated":"2024-03-25T23:30:05Z","publication":"Science","article_type":"original","page":"1408 - 1411","related_material":{"record":[{"id":"6947","relation":"dissertation_contains","status":"public"}]},"oa":1,"year":"2018","volume":359,"article_processing_charge":"No","month":"03","pmid":1,"day":"23","citation":{"apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662","ieee":"M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018.","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411.","ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662","chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.","mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662."},"oa_version":"Published Version","project":[{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"}],"ec_funded":1,"publication_status":"published","acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","status":"public","_id":"402","author":[{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"orcid":"0000-0003-3470-6119","last_name":"Assen","full_name":"Assen, Frank P","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1073-744X","last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"full_name":"Schachner, Helga","last_name":"Schachner","first_name":"Helga"},{"full_name":"Asfour, Gabriele","last_name":"Asfour","first_name":"Gabriele"},{"full_name":"Bagó Horváth, Zsuzsanna","last_name":"Bagó Horváth","first_name":"Zsuzsanna"},{"first_name":"Jens","full_name":"Stein, Jens","last_name":"Stein"},{"first_name":"Pavel","last_name":"Uhrin","full_name":"Uhrin, Pavel"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"}],"title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","doi":"10.1126/science.aal3662","issue":"6382","abstract":[{"lang":"eng","text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined."}]},{"acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","publication_status":"published","status":"public","author":[{"first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"full_name":"Fuchs, Armin","last_name":"Fuchs","first_name":"Armin"},{"last_name":"Dadarou","full_name":"Dadarou, Despoina","first_name":"Despoina"},{"first_name":"Andrea","full_name":"Barta, Andrea","last_name":"Barta"},{"full_name":"Doonan, John","last_name":"Doonan","first_name":"John"}],"title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","_id":"403","issue":"6","abstract":[{"text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved.","lang":"eng"}],"doi":"10.1111/tpj.13914","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"dernst","file_size":1543354,"file_name":"2018_PlantJourn_Cavallari.pdf","date_updated":"2020-07-14T12:46:22Z","checksum":"d9d3ad3215ac0e581731443fca312266","content_type":"application/pdf","access_level":"open_access","date_created":"2019-02-06T11:40:54Z","file_id":"5934"}],"has_accepted_license":"1","volume":94,"article_processing_charge":"No","day":"01","citation":{"chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018."},"month":"06","file_date_updated":"2020-07-14T12:46:22Z","ddc":["580"],"oa_version":"Published Version","publication":"The Plant Journal","date_updated":"2023-09-19T10:07:08Z","page":"1010 - 1022","oa":1,"year":"2018","intvolume":" 94","publisher":"Wiley","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"EvBe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7426","date_published":"2018-06-01T00:00:00Z","external_id":{"isi":["000434365500008"]},"scopus_import":"1","date_created":"2018-12-11T11:46:17Z"},{"ddc":["510"],"file_date_updated":"2020-07-14T12:46:22Z","month":"01","citation":{"ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.","apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796."},"day":"30","oa_version":"Published Version","file":[{"file_id":"6992","date_created":"2019-11-07T12:20:25Z","file_name":"2018_SIAM_Fischer.pdf","creator":"dernst","relation":"main_file","file_size":557338,"date_updated":"2020-07-14T12:46:22Z","access_level":"open_access","content_type":"application/pdf","checksum":"89a8eae7c52bb356c04f52b44bff4b5a"}],"article_processing_charge":"No","volume":50,"has_accepted_license":"1","_id":"404","title":"Existence of positive solutions to stochastic thin-film equations","author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X"},{"last_name":"Grün","full_name":"Grün, Günther","first_name":"Günther"}],"doi":"10.1137/16M1098796","abstract":[{"lang":"eng","text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n"}],"issue":"1","publication_status":"published","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7425","department":[{"_id":"JuFi"}],"date_created":"2018-12-11T11:46:17Z","scopus_import":"1","external_id":{"isi":["000426630900015"]},"date_published":"2018-01-30T00:00:00Z","publisher":"Society for Industrial and Applied Mathematics ","intvolume":" 50","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"oa":1,"year":"2018","date_updated":"2023-09-11T13:59:22Z","publication":"SIAM Journal on Mathematical Analysis","page":"411 - 455","article_type":"original"},{"doi":"10.1371/journal.pone.0193049","issue":"3","abstract":[{"lang":"eng","text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. "}],"_id":"406","author":[{"first_name":"Katarína","last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína"},{"first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","last_name":"Mitchell","full_name":"Mitchell, Gabriel"},{"last_name":"Harpaz","full_name":"Harpaz, Roy","first_name":"Roy"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Probabilistic models of individual and collective animal behavior","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","status":"public","publication_status":"published","project":[{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"oa_version":"Submitted Version","ddc":["530","571"],"month":"03","file_date_updated":"2020-07-14T12:46:22Z","day":"07","pubrep_id":"995","citation":{"ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049."},"article_processing_charge":"Yes","volume":13,"has_accepted_license":"1","file":[{"file_id":"5165","date_created":"2018-12-12T10:15:43Z","date_updated":"2020-07-14T12:46:22Z","access_level":"open_access","content_type":"application/pdf","checksum":"684229493db75b43e98a46cd922da497","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","relation":"main_file","creator":"system","file_size":6887358}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","oa":1,"related_material":{"record":[{"id":"9831","relation":"research_data","status":"public"}]},"date_updated":"2023-09-15T12:06:19Z","publication":"PLoS One","scopus_import":"1","date_created":"2018-12-11T11:46:18Z","date_published":"2018-03-07T00:00:00Z","external_id":{"isi":["000426896800032"]},"publist_id":"7423","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GaTk"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":" 13","publisher":"Public Library of Science"}]