[{"has_accepted_license":"1","scopus_import":"1","publication_status":"published","isi":1,"date_published":"2018-03-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"G3: Genes, Genomes, Genetics","date_created":"2018-12-11T11:47:05Z","doi":"10.1534/g3.117.300452","page":"845 - 857","pubrep_id":"990","title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","file_date_updated":"2020-07-14T12:46:56Z","publisher":"Genetics Society of America","license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"7271","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         8","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"system","date_updated":"2020-07-14T12:46:56Z","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","file_size":2251222,"relation":"main_file","file_id":"4905","access_level":"open_access","checksum":"7d9d28b915159078a4ca7add568010e8","date_created":"2018-12-12T10:11:48Z","content_type":"application/pdf"}],"abstract":[{"text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.","lang":"eng"}],"ddc":["570"],"author":[{"first_name":"Attila","orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek"},{"full_name":"Ratheesh, Aparna","first_name":"Aparna","orcid":"0000-0001-7190-0776","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","last_name":"Ratheesh"},{"first_name":"Katarina","full_name":"Valosková, Katarina","last_name":"Valosková","id":"46F146FC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vera","full_name":"Belyaeva, Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wachner, Stephanie","first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner"},{"last_name":"Matsubayashi","first_name":"Yutaka","full_name":"Matsubayashi, Yutaka"},{"last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz","first_name":"Besaiz"},{"last_name":"Stramer","first_name":"Brian","full_name":"Stramer, Brian"},{"last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","full_name":"Siekhaus, Daria E"}],"acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","issue":"3","oa":1,"month":"03","oa_version":"Published Version","related_material":{"record":[{"id":"6530","relation":"research_paper"},{"id":"6543","relation":"research_paper"},{"status":"public","id":"11193","relation":"dissertation_contains"},{"id":"6546","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"DaSi"}],"external_id":{"isi":["000426693300011"]},"date_updated":"2024-03-25T23:30:15Z","status":"public","type":"journal_article","_id":"544","year":"2018","citation":{"short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>.","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>","ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. 2018;8(3):845-857. doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>","ieee":"A. György <i>et al.</i>, “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.","mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>."},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"LifeSc"}],"ec_funded":1,"day":"01","project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"},{"name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","_id":"2637E9C0-B435-11E9-9278-68D0E5697425","grant_number":"LSC16-021 "},{"call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"volume":8},{"date_published":"2018-11-11T00:00:00Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"month":"11","date_created":"2018-12-12T11:39:26Z","author":[{"full_name":"Anonymous, 1","first_name":"1","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"first_name":"4","full_name":"Anonymous, 4","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"5","full_name":"Anonymous, 5"},{"full_name":"Anonymous, 6","first_name":"6","last_name":"Anonymous"}],"has_accepted_license":"1","ddc":["000"],"publication_status":"published","scopus_import":1,"status":"public","publisher":"IST Austria","date_updated":"2025-06-02T08:53:45Z","type":"technical_report","pubrep_id":"1066","page":"27","related_material":{"record":[{"status":"public","id":"6175","relation":"later_version"}]},"file_date_updated":"2020-07-14T12:47:00Z","title":"Cost analysis of nondeterministic probabilistic programs","publication_identifier":{"issn":["2664-1690"]},"citation":{"short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous, Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria, 2018.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, &#38; Anonymous, 6. (2018). <i>Cost analysis of nondeterministic probabilistic programs</i>. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria; 2018.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous, <i>Cost analysis of nondeterministic probabilistic programs</i>. IST Austria, 2018.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria, 27p.","mla":"Anonymous, 1, et al. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","_id":"5457","alternative_title":["IST Austria Technical Report"],"day":"11","abstract":[{"lang":"eng","text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds."}],"file":[{"date_created":"2018-12-12T11:53:32Z","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:47:00Z","relation":"main_file","file_id":"5493","file_size":4202966,"file_name":"IST-2018-1066-v1+1_techreport.pdf","checksum":"ba3adafd36fe200385ccda583063b9eb","access_level":"open_access"},{"date_created":"2019-05-10T13:22:12Z","content_type":"text/plain","creator":"dernst","date_updated":"2020-07-14T12:47:00Z","file_id":"6402","relation":"main_file","file_size":322,"file_name":"authors-names.txt","checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","access_level":"closed"}]},{"date_updated":"2023-09-15T12:06:46Z","status":"public","type":"journal_article","department":[{"_id":"SyCr"}],"external_id":{"isi":["000446693400008"]},"oa":1,"month":"10","oa_version":"Published Version","author":[{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","full_name":"Pull, Christopher","first_name":"Christopher","orcid":"0000-0003-1122-3982"},{"id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","first_name":"Sina"},{"first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"issue":"19","volume":28,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2018.08.063"}],"day":"08","citation":{"ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>.","apa":"Pull, C., Metzler, S., Naderlinger, E., &#38; Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” <i>Current Biology</i>, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. 2018;28(19):R1139-R1140. doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>"},"article_type":"original","year":"2018","_id":"55","publist_id":"7999","publisher":"Cell Press","doi":"10.1016/j.cub.2018.08.063","page":"R1139 - R1140","title":"Protection against the lethal side effects of social immunity in ants","date_published":"2018-10-08T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:23Z","publication":"Current Biology","publication_status":"published","scopus_import":"1","isi":1,"abstract":[{"lang":"eng","text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation."}],"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        28"},{"intvolume":"       360","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","abstract":[{"text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).","lang":"eng"}],"scopus_import":1,"publication_status":"published","publication":"Communications in Mathematical Physics","date_created":"2018-12-11T11:47:09Z","language":[{"iso":"eng"}],"date_published":"2018-05-01T00:00:00Z","title":"The Bogoliubov free energy functional II: The dilute Limit","page":"347-403","doi":"10.1007/s00220-017-3064-x","arxiv":1,"publisher":"Springer","publist_id":"7260","_id":"554","year":"2018","citation":{"ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. 2018;360(1):347-403. doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1. Springer, pp. 347–403, 2018.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>.","apa":"Napiórkowski, M. M., Reuvers, R., &#38; Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403."},"publication_identifier":{"issn":["00103616"]},"day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05953"}],"volume":360,"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"issue":"1","author":[{"full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski"},{"last_name":"Reuvers","first_name":"Robin","full_name":"Reuvers, Robin"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"month":"05","oa":1,"oa_version":"Submitted Version","external_id":{"arxiv":["1511.05953"]},"department":[{"_id":"RoSe"}],"type":"journal_article","date_updated":"2021-01-12T08:02:35Z","status":"public"},{"volume":50,"day":"01","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/125524/"}],"citation":{"mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>, vol. 50, Elsevier, 2018, pp. 65–74, doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>.","ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. 2018;50:65-74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” <i>Current Opinion in Structural Biology</i>, vol. 50. Elsevier, pp. 65–74, 2018.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>.","apa":"Richter, R., Baranova, N. S., Day, A., &#38; Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>"},"year":"2018","_id":"555","article_type":"original","type":"journal_article","date_updated":"2023-09-11T14:07:03Z","status":"public","external_id":{"isi":["000443661300011"]},"department":[{"_id":"MaLo"}],"oa":1,"month":"06","oa_version":"Submitted Version","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","author":[{"last_name":"Richter","first_name":"Ralf","full_name":"Richter, Ralf"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","full_name":"Baranova, Natalia","first_name":"Natalia","orcid":"0000-0002-3086-9124"},{"last_name":"Day","first_name":"Anthony","full_name":"Day, Anthony"},{"full_name":"Kwok, Jessica","first_name":"Jessica","last_name":"Kwok"}],"abstract":[{"lang":"eng","text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions."}],"quality_controlled":"1","intvolume":"        50","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","publist_id":"7259","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","page":"65 - 74","doi":"10.1016/j.sbi.2017.12.002","date_created":"2018-12-11T11:47:09Z","publication":"Current Opinion in Structural Biology","language":[{"iso":"eng"}],"date_published":"2018-06-01T00:00:00Z","scopus_import":"1","publication_status":"published","isi":1},{"ec_funded":1,"day":"13","article_processing_charge":"Yes (via OA deal)","volume":19,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"year":"2018","_id":"556","article_type":"original","publication_identifier":{"issn":["1424-0637"]},"citation":{"apa":"Betea, D., Bouttier, J., Nejjar, P., &#38; Vuletic, M. 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The free boundary Schur process and applications I. <i>Annales Henri Poincare</i>. 2018;19(12):3663-3742. doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>","ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>."},"external_id":{"arxiv":["1704.05809"]},"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"type":"journal_article","status":"public","date_updated":"2024-02-20T10:48:17Z","issue":"12","author":[{"first_name":"Dan","full_name":"Betea, Dan","last_name":"Betea"},{"full_name":"Bouttier, Jeremie","first_name":"Jeremie","last_name":"Bouttier"},{"first_name":"Peter","full_name":"Nejjar, Peter","last_name":"Nejjar","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vuletic","full_name":"Vuletic, Mirjana","first_name":"Mirjana"}],"ddc":["500"],"oa_version":"Published Version","month":"11","oa":1,"abstract":[{"lang":"eng","text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions."}],"file":[{"access_level":"open_access","checksum":"0c38abe73569b7166b7487ad5d23cc68","file_size":3084674,"relation":"main_file","file_id":"5866","file_name":"2018_Annales_Betea.pdf","date_updated":"2020-07-14T12:47:03Z","creator":"dernst","date_created":"2019-01-21T15:18:55Z","content_type":"application/pdf"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:03Z","title":"The free boundary Schur process and applications I","doi":"10.1007/s00023-018-0723-1","page":"3663-3742","arxiv":1,"publisher":"Springer Nature","publist_id":"7258","scopus_import":"1","publication_status":"published","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Annales Henri Poincare","date_created":"2018-12-11T11:47:09Z","date_published":"2018-11-13T00:00:00Z"},{"citation":{"mla":"Bergmiller, Tobias, and Nela Nikolic. <i>Time-Lapse Microscopy Data</i>. 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Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"file":[{"date_created":"2018-12-12T13:04:39Z","content_type":"application/zip","date_updated":"2020-07-14T12:47:04Z","creator":"system","access_level":"open_access","checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637","file_size":3558703796,"relation":"main_file","file_name":"IST-2018-74-v1+2_15-11-05.zip"},{"content_type":"application/zip","date_created":"2018-12-12T13:04:55Z","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","file_id":"5638","file_size":1830422606,"relation":"main_file","checksum":"bf26649af310ef6892d68576515cde6d","access_level":"open_access"},{"date_created":"2018-12-12T13:05:11Z","content_type":"application/zip","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","file_id":"5639","relation":"main_file","file_size":2140849248,"checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","access_level":"open_access"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","oa_version":"Published Version","date_created":"2018-12-12T12:31:35Z","month":"02","oa":1,"date_published":"2018-02-07T00:00:00Z","author":[{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela"}],"has_accepted_license":"1","ddc":["579"],"type":"research_data","status":"public","publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/publicdomain/zero/1.0/","publist_id":"7385","date_updated":"2024-02-21T13:44:45Z","title":"Time-lapse microscopy data","file_date_updated":"2020-07-14T12:47:04Z","keyword":["microscopy","microfluidics"],"datarep_id":"74","department":[{"_id":"CaGu"}],"doi":"10.15479/AT:ISTA:74","related_material":{"record":[{"relation":"research_paper","id":"438","status":"public"}]}},{"file":[{"access_level":"open_access","checksum":"53c17082848e12f3c2e1b4185b578208","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","file_size":1737958,"file_id":"5600","relation":"main_file","date_updated":"2020-07-14T12:47:05Z","creator":"system","content_type":"application/zip","date_created":"2018-12-12T13:02:34Z"}],"abstract":[{"lang":"eng","text":"Graph matching problems for large displacement optical flow of RGB-D images."}],"day":"04","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","contributor":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","contributor_type":"researcher","first_name":"Paul"}],"year":"2018","_id":"5573","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"H. 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Villányi, (2018).","apa":"Villányi, M. (2018). Data Check IOP Scopus vs. Publisher. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:86\">https://doi.org/10.15479/AT:ISTA:86</a>","ama":"Villányi M. Data Check IOP Scopus vs. Publisher. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:86\">10.15479/AT:ISTA:86</a>","ieee":"M. Villányi, “Data Check IOP Scopus vs. Publisher.” Institute of Science and Technology Austria, 2018.","ista":"Villányi M. 2018. Data Check IOP Scopus vs. Publisher, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:86\">10.15479/AT:ISTA:86</a>.","mla":"Villányi, Márton. <i>Data Check IOP Scopus vs. Publisher</i>. 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"}],"citation":{"apa":"Villányi, M. (2018). Data Check RSC Scopus vs. FWF. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:87\">https://doi.org/10.15479/AT:ISTA:87</a>","chicago":"Villányi, Márton. “Data Check RSC Scopus vs. FWF.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:87\">https://doi.org/10.15479/AT:ISTA:87</a>.","short":"M. Villányi, (2018).","ieee":"M. Villányi, “Data Check RSC Scopus vs. FWF.” Institute of Science and Technology Austria, 2018.","ama":"Villányi M. Data Check RSC Scopus vs. FWF. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:87\">10.15479/AT:ISTA:87</a>","ista":"Villányi M. 2018. Data Check RSC Scopus vs. FWF, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:87\">10.15479/AT:ISTA:87</a>.","mla":"Villányi, Márton. <i>Data Check RSC Scopus vs. FWF</i>. 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Tkačik, (2018).","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>.","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 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The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs  were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. "}],"day":"29","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"ddc":["570"],"has_accepted_license":"1","author":[{"last_name":"Deny","full_name":"Deny, Stephane","first_name":"Stephane"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"full_name":"Botella-Soler, Vicente","first_name":"Vicente","last_name":"Botella-Soler"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","full_name":"Martius, Georg S","first_name":"Georg S"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"date_published":"2018-03-29T00:00:00Z","month":"03","date_created":"2018-12-12T12:31:39Z","oa":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"292"}]},"doi":"10.15479/AT:ISTA:98","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"datarep_id":"98","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"file_date_updated":"2020-07-14T12:47:07Z","title":"Nonlinear decoding of a complex movie from the mammalian retina","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:45:26Z","status":"public","type":"research_data"},{"has_accepted_license":"1","author":[{"first_name":"Claudia","full_name":"Igler, Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","full_name":"Lagator, Mato"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C"}],"ddc":["576"],"date_published":"2018-07-20T00:00:00Z","oa_version":"Published Version","oa":1,"date_created":"2018-12-12T12:31:40Z","month":"07","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"doi":"10.15479/AT:ISTA:108","related_material":{"record":[{"id":"67","relation":"research_paper","status":"public"},{"relation":"research_paper","id":"6371","status":"public"}]},"file_date_updated":"2020-07-14T12:47:07Z","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","datarep_id":"108","status":"public","publisher":"Institute of Science and Technology Austria","date_updated":"2024-03-25T23:30:27Z","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","_id":"5585","citation":{"mla":"Igler, Claudia, et al. <i>Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 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