[{"ddc":["570"],"title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","status":"public","intvolume":" 224","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6831","oa_version":"Published Version","file":[{"file_size":2314016,"content_type":"application/pdf","creator":"apreinsp","access_level":"open_access","file_name":"2019_NewPhytologist_Puixeu.pdf","checksum":"6370e7567d96b7b562e77d8b89653f80","date_created":"2019-08-27T12:44:54Z","date_updated":"2020-07-14T12:47:42Z","relation":"main_file","file_id":"6833"}],"type":"journal_article","abstract":[{"lang":"eng","text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle."}],"issue":"3","article_type":"original","page":"1108-1120","publication":"New Phytologist","citation":{"short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120."},"date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"year":"2019","date_created":"2019-08-25T22:00:51Z","date_updated":"2023-08-29T07:17:07Z","volume":224,"author":[{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Barrett, Spencer C.H.","first_name":"Spencer C.H.","last_name":"Barrett"}],"related_material":{"record":[{"id":"9803","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000481376500001"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.16050","month":"11","publication_identifier":{"eissn":["1469-8137"]}},{"date_published":"2019-12-01T00:00:00Z","page":"747–760","article_type":"original","citation":{"ista":"Gärtner FR, Massberg S. 2019. Patrolling the vascular borders: Platelets in immunity to infection and cancer. Nature Reviews Immunology. 19(12), 747–760.","apa":"Gärtner, F. R., & Massberg, S. (2019). Patrolling the vascular borders: Platelets in immunity to infection and cancer. Nature Reviews Immunology. Springer Nature. https://doi.org/10.1038/s41577-019-0202-z","ieee":"F. R. Gärtner and S. Massberg, “Patrolling the vascular borders: Platelets in immunity to infection and cancer,” Nature Reviews Immunology, vol. 19, no. 12. Springer Nature, pp. 747–760, 2019.","ama":"Gärtner FR, Massberg S. Patrolling the vascular borders: Platelets in immunity to infection and cancer. Nature Reviews Immunology. 2019;19(12):747–760. doi:10.1038/s41577-019-0202-z","chicago":"Gärtner, Florian R, and Steffen Massberg. “Patrolling the Vascular Borders: Platelets in Immunity to Infection and Cancer.” Nature Reviews Immunology. Springer Nature, 2019. https://doi.org/10.1038/s41577-019-0202-z.","mla":"Gärtner, Florian R., and Steffen Massberg. “Patrolling the Vascular Borders: Platelets in Immunity to Infection and Cancer.” Nature Reviews Immunology, vol. 19, no. 12, Springer Nature, 2019, pp. 747–760, doi:10.1038/s41577-019-0202-z.","short":"F.R. Gärtner, S. Massberg, Nature Reviews Immunology 19 (2019) 747–760."},"publication":"Nature Reviews Immunology","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","intvolume":" 19","title":"Patrolling the vascular borders: Platelets in immunity to infection and cancer","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6824","issue":"12","abstract":[{"text":"Platelets are small anucleate cellular fragments that are released by megakaryocytes and safeguard vascular integrity through a process termed ‘haemostasis’. However, platelets have important roles beyond haemostasis as they contribute to the initiation and coordination of intravascular immune responses. They continuously monitor blood vessel integrity and tightly coordinate vascular trafficking and functions of multiple cell types. In this way platelets act as ‘patrolling officers of the vascular highway’ that help to establish effective immune responses to infections and cancer. Here we discuss the distinct biological features of platelets that allow them to shape immune responses to pathogens and tumour cells, highlighting the parallels between these responses.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41577-019-0202-z","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000499090600011"],"pmid":["31409920"]},"publication_identifier":{"issn":["1474-1733"],"eissn":["1474-1741"]},"month":"12","volume":19,"date_updated":"2023-08-29T07:16:14Z","date_created":"2019-08-20T17:24:32Z","author":[{"full_name":"Gärtner, Florian R","last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"}],"publisher":"Springer Nature","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2019","ec_funded":1},{"month":"08","external_id":{"isi":["000481688700050"],"pmid":["31416964"]},"isi":1,"quality_controlled":"1","doi":"10.1126/science.aau3429","language":[{"iso":"eng"}],"pmid":1,"year":"2019","publisher":"American Association for the Advancement of Science","department":[{"_id":"EdHa"}],"publication_status":"published","author":[{"full_name":"Krndija, Denis","last_name":"Krndija","first_name":"Denis"},{"last_name":"Marjou","first_name":"Fatima El","full_name":"Marjou, Fatima El"},{"first_name":"Boris","last_name":"Guirao","full_name":"Guirao, Boris"},{"first_name":"Sophie","last_name":"Richon","full_name":"Richon, Sophie"},{"full_name":"Leroy, Olivier","last_name":"Leroy","first_name":"Olivier"},{"first_name":"Yohanns","last_name":"Bellaiche","full_name":"Bellaiche, Yohanns"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Vignjevic, Danijela Matic","first_name":"Danijela Matic","last_name":"Vignjevic"}],"volume":365,"date_created":"2019-08-25T22:00:51Z","date_updated":"2023-08-29T07:16:40Z","scopus_import":"1","article_processing_charge":"No","day":"16","citation":{"chicago":"Krndija, Denis, Fatima El Marjou, Boris Guirao, Sophie Richon, Olivier Leroy, Yohanns Bellaiche, Edouard B Hannezo, and Danijela Matic Vignjevic. “Active Cell Migration Is Critical for Steady-State Epithelial Turnover in the Gut.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aau3429.","mla":"Krndija, Denis, et al. “Active Cell Migration Is Critical for Steady-State Epithelial Turnover in the Gut.” Science, vol. 365, no. 6454, American Association for the Advancement of Science, 2019, pp. 705–10, doi:10.1126/science.aau3429.","short":"D. Krndija, F.E. Marjou, B. Guirao, S. Richon, O. Leroy, Y. Bellaiche, E.B. Hannezo, D.M. Vignjevic, Science 365 (2019) 705–710.","ista":"Krndija D, Marjou FE, Guirao B, Richon S, Leroy O, Bellaiche Y, Hannezo EB, Vignjevic DM. 2019. Active cell migration is critical for steady-state epithelial turnover in the gut. Science. 365(6454), 705–710.","apa":"Krndija, D., Marjou, F. E., Guirao, B., Richon, S., Leroy, O., Bellaiche, Y., … Vignjevic, D. M. (2019). Active cell migration is critical for steady-state epithelial turnover in the gut. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aau3429","ieee":"D. Krndija et al., “Active cell migration is critical for steady-state epithelial turnover in the gut,” Science, vol. 365, no. 6454. American Association for the Advancement of Science, pp. 705–710, 2019.","ama":"Krndija D, Marjou FE, Guirao B, et al. Active cell migration is critical for steady-state epithelial turnover in the gut. Science. 2019;365(6454):705-710. doi:10.1126/science.aau3429"},"publication":"Science","page":"705-710","date_published":"2019-08-16T00:00:00Z","type":"journal_article","issue":"6454","abstract":[{"lang":"eng","text":"Steady-state turnover is a hallmark of epithelial tissues throughout adult life. Intestinal epithelial turnover is marked by continuous cell migration, which is assumed to be driven by mitotic pressure from the crypts. However, the balance of forces in renewal remains ill-defined. Combining biophysical modeling and quantitative three-dimensional tissue imaging with genetic and physical manipulations, we revealed the existence of an actin-related protein 2/3 complex–dependent active migratory force, which explains quantitatively the profiles of cell speed, density, and tissue tension along the villi. Cells migrate collectively with minimal rearrangements while displaying dual—apicobasal and front-back—polarity characterized by actin-rich basal protrusions oriented in the direction of migration. We propose that active migration is a critical component of gut epithelial turnover."}],"_id":"6832","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 365","title":"Active cell migration is critical for steady-state epithelial turnover in the gut","status":"public","oa_version":"None"},{"doi":"10.1016/j.dyepig.2019.107768","language":[{"iso":"eng"}],"external_id":{"isi":["000484870700099"]},"quality_controlled":"1","isi":1,"month":"12","publication_identifier":{"issn":["0143-7208"]},"author":[{"last_name":"Yumusak","first_name":"Cigdem","full_name":"Yumusak, Cigdem"},{"last_name":"Prochazkova","first_name":"Anna Jancik","full_name":"Prochazkova, Anna Jancik"},{"full_name":"Apaydin, Dogukan H","first_name":"Dogukan H","last_name":"Apaydin","id":"2FF891BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1075-8857"},{"last_name":"Seelajaroen","first_name":"Hathaichanok","full_name":"Seelajaroen, Hathaichanok"},{"full_name":"Sariciftci, Niyazi Serdar","first_name":"Niyazi Serdar","last_name":"Sariciftci"},{"full_name":"Weiter, Martin","first_name":"Martin","last_name":"Weiter"},{"full_name":"Krajcovic, Jozef","last_name":"Krajcovic","first_name":"Jozef"},{"full_name":"Qin, Yong","last_name":"Qin","first_name":"Yong"},{"full_name":"Zhang, Wei","first_name":"Wei","last_name":"Zhang"},{"full_name":"Zhan, Jixun","last_name":"Zhan","first_name":"Jixun"},{"full_name":"Kovalenko, Alexander","last_name":"Kovalenko","first_name":"Alexander"}],"date_updated":"2023-08-29T07:11:09Z","date_created":"2019-08-18T22:00:39Z","volume":171,"year":"2019","publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"Elsevier","article_number":"107768","date_published":"2019-12-01T00:00:00Z","publication":"Dyes and Pigments","citation":{"chicago":"Yumusak, Cigdem, Anna Jancik Prochazkova, Dogukan H Apaydin, Hathaichanok Seelajaroen, Niyazi Serdar Sariciftci, Martin Weiter, Jozef Krajcovic, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” Dyes and Pigments. Elsevier, 2019. https://doi.org/10.1016/j.dyepig.2019.107768.","mla":"Yumusak, Cigdem, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” Dyes and Pigments, vol. 171, 107768, Elsevier, 2019, doi:10.1016/j.dyepig.2019.107768.","short":"C. Yumusak, A.J. Prochazkova, D.H. Apaydin, H. Seelajaroen, N.S. Sariciftci, M. Weiter, J. Krajcovic, Y. Qin, W. Zhang, J. Zhan, A. Kovalenko, Dyes and Pigments 171 (2019).","ista":"Yumusak C, Prochazkova AJ, Apaydin DH, Seelajaroen H, Sariciftci NS, Weiter M, Krajcovic J, Qin Y, Zhang W, Zhan J, Kovalenko A. 2019. Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. 171, 107768.","apa":"Yumusak, C., Prochazkova, A. J., Apaydin, D. H., Seelajaroen, H., Sariciftci, N. S., Weiter, M., … Kovalenko, A. (2019). Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. Elsevier. https://doi.org/10.1016/j.dyepig.2019.107768","ieee":"C. Yumusak et al., “Indigoidine - Biosynthesized organic semiconductor,” Dyes and Pigments, vol. 171. Elsevier, 2019.","ama":"Yumusak C, Prochazkova AJ, Apaydin DH, et al. Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. 2019;171. doi:10.1016/j.dyepig.2019.107768"},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6818","title":"Indigoidine - Biosynthesized organic semiconductor","status":"public","intvolume":" 171","abstract":[{"lang":"eng","text":"Indigoidine is a blue natural pigment, which can be efficiently synthetized in E. coli. In addition to its antioxidant and antimicrobial activities indigoidine due to its stability and deep blue color can find an application as an industrial, environmentally friendly dye. Moreover, similarly to its counterpart regular indigo dye, due to its molecular structure, indigoidine is an organic semiconductor. Fully conjugated aromatic moiety and intermolecular hydrogen bonding of indigoidine result in an unusually narrow bandgap for such a small molecule. This, in its turn, result is tight molecular packing in the solid state and opens a path for a wide range of application in organic and bio-electronics, such as electrochemical and field effect transistors, organic solar cells, light and bio-sensors etc."}],"type":"journal_article"},{"date_updated":"2023-08-29T07:11:47Z","date_created":"2019-08-22T07:54:13Z","volume":538,"author":[{"last_name":"Brown","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","full_name":"Brown, Adam"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2019","language":[{"iso":"eng"}],"doi":"10.1016/j.jalgebra.2019.07.027","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.04676"}],"external_id":{"arxiv":["1805.04676"],"isi":["000487176300011"]},"oa":1,"month":"11","publication_identifier":{"issn":["0021-8693"]},"oa_version":"Preprint","status":"public","title":"Arakawa-Suzuki functors for Whittaker modules","intvolume":" 538","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6828","abstract":[{"text":"In this paper we construct a family of exact functors from the category of Whittaker modules of the simple complex Lie algebra of type to the category of finite-dimensional modules of the graded affine Hecke algebra of type . Using results of Backelin [2] and of Arakawa-Suzuki [1], we prove that these functors map standard modules to standard modules (or zero) and simple modules to simple modules (or zero). Moreover, we show that each simple module of the graded affine Hecke algebra appears as the image of a simple Whittaker module. Since the Whittaker category contains the BGG category as a full subcategory, our results generalize results of Arakawa-Suzuki [1], which in turn generalize Schur-Weyl duality between finite-dimensional representations of and representations of the symmetric group .","lang":"eng"}],"type":"journal_article","date_published":"2019-11-15T00:00:00Z","article_type":"original","page":"261-289","publication":"Journal of Algebra","citation":{"ama":"Brown A. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 2019;538:261-289. doi:10.1016/j.jalgebra.2019.07.027","ista":"Brown A. 2019. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 538, 261–289.","apa":"Brown, A. (2019). Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2019.07.027","ieee":"A. Brown, “Arakawa-Suzuki functors for Whittaker modules,” Journal of Algebra, vol. 538. Elsevier, pp. 261–289, 2019.","mla":"Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra, vol. 538, Elsevier, 2019, pp. 261–89, doi:10.1016/j.jalgebra.2019.07.027.","short":"A. Brown, Journal of Algebra 538 (2019) 261–289.","chicago":"Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra. Elsevier, 2019. https://doi.org/10.1016/j.jalgebra.2019.07.027."},"day":"15","article_processing_charge":"No"},{"main_file_link":[{"url":"https://doi.org/10.5061/dryad.n1701c9","open_access":"1"}],"citation":{"chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","mla":"Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019.","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9"},"oa":1,"date_published":"2019-07-22T00:00:00Z","doi":"10.5061/dryad.n1701c9","month":"07","day":"22","article_processing_charge":"No","_id":"9803","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"author":[{"full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma","last_name":"Puixeu Sala"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"full_name":"Field, David","first_name":"David","last_name":"Field"},{"last_name":"Barrett","first_name":"Spencer C.H.","full_name":"Barrett, Spencer C.H."}],"related_material":{"record":[{"id":"14058","status":"public","relation":"used_in_publication"},{"id":"6831","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-06T11:48:42Z","date_updated":"2023-08-29T07:17:07Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle.","lang":"eng"}]},{"abstract":[{"text":"Direct reciprocity is a powerful mechanism for the evolution of cooperation on the basis of repeated interactions1,2,3,4. It requires that interacting individuals are sufficiently equal, such that everyone faces similar consequences when they cooperate or defect. Yet inequality is ubiquitous among humans5,6 and is generally considered to undermine cooperation and welfare7,8,9,10. Most previous models of reciprocity do not include inequality11,12,13,14,15. These models assume that individuals are the same in all relevant aspects. Here we introduce a general framework to study direct reciprocity among unequal individuals. Our model allows for multiple sources of inequality. Subjects can differ in their endowments, their productivities and in how much they benefit from public goods. We find that extreme inequality prevents cooperation. But if subjects differ in productivity, some endowment inequality can be necessary for cooperation to prevail. Our mathematical predictions are supported by a behavioural experiment in which we vary the endowments and productivities of the subjects. We observe that overall welfare is maximized when the two sources of heterogeneity are aligned, such that more productive individuals receive higher endowments. By contrast, when endowments and productivities are misaligned, cooperation quickly breaks down. Our findings have implications for policy-makers concerned with equity, efficiency and the provisioning of public goods.","lang":"eng"}],"issue":"7770","type":"journal_article","oa_version":"Submitted Version","file":[{"checksum":"a6e0e3168bf62de624e7772cdfaeb26f","date_updated":"2020-07-14T12:47:42Z","date_created":"2020-05-14T10:00:32Z","file_id":"7828","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":18577756,"access_level":"open_access","file_name":"2019_Nature_Hauser.pdf"}],"_id":"6836","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["000"],"title":"Social dilemmas among unequals","intvolume":" 572","day":"22","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-08-22T00:00:00Z","publication":"Nature","citation":{"chicago":"Hauser, Oliver P., Christian Hilbe, Krishnendu Chatterjee, and Martin A. Nowak. “Social Dilemmas among Unequals.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1488-5.","mla":"Hauser, Oliver P., et al. “Social Dilemmas among Unequals.” Nature, vol. 572, no. 7770, Springer Nature, 2019, pp. 524–27, doi:10.1038/s41586-019-1488-5.","short":"O.P. Hauser, C. Hilbe, K. Chatterjee, M.A. Nowak, Nature 572 (2019) 524–527.","ista":"Hauser OP, Hilbe C, Chatterjee K, Nowak MA. 2019. Social dilemmas among unequals. Nature. 572(7770), 524–527.","apa":"Hauser, O. P., Hilbe, C., Chatterjee, K., & Nowak, M. A. (2019). Social dilemmas among unequals. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1488-5","ieee":"O. P. Hauser, C. Hilbe, K. Chatterjee, and M. A. Nowak, “Social dilemmas among unequals,” Nature, vol. 572, no. 7770. Springer Nature, pp. 524–527, 2019.","ama":"Hauser OP, Hilbe C, Chatterjee K, Nowak MA. Social dilemmas among unequals. Nature. 2019;572(7770):524-527. doi:10.1038/s41586-019-1488-5"},"article_type":"letter_note","page":"524-527","file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"author":[{"full_name":"Hauser, Oliver P.","last_name":"Hauser","first_name":"Oliver P."},{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/too-much-inequality-impedes-support-for-public-goods-according-to-research-published-in-nature/","description":"News on IST Homepage","relation":"press_release"}]},"date_updated":"2023-08-29T07:42:54Z","date_created":"2019-09-01T22:00:56Z","volume":572,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"month":"08","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"doi":"10.1038/s41586-019-1488-5","language":[{"iso":"eng"}],"external_id":{"isi":["000482219600045"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"686-696","publication":"Journal of Anatomy","citation":{"short":"N. Picco, S. Hippenmeyer, J. Rodarte, C. Streicher, Z. Molnár, P.K. Maini, T.E. Woolley, Journal of Anatomy 235 (2019) 686–696.","mla":"Picco, Noemi, et al. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” Journal of Anatomy, vol. 235, no. 3, Wiley, 2019, pp. 686–96, doi:10.1111/joa.13001.","chicago":"Picco, Noemi, Simon Hippenmeyer, Julio Rodarte, Carmen Streicher, Zoltán Molnár, Philip K. Maini, and Thomas E. Woolley. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” Journal of Anatomy. Wiley, 2019. https://doi.org/10.1111/joa.13001.","ama":"Picco N, Hippenmeyer S, Rodarte J, et al. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 2019;235(3):686-696. doi:10.1111/joa.13001","ieee":"N. Picco et al., “A mathematical insight into cell labelling experiments for clonal analysis,” Journal of Anatomy, vol. 235, no. 3. Wiley, pp. 686–696, 2019.","apa":"Picco, N., Hippenmeyer, S., Rodarte, J., Streicher, C., Molnár, Z., Maini, P. K., & Woolley, T. E. (2019). A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. Wiley. https://doi.org/10.1111/joa.13001","ista":"Picco N, Hippenmeyer S, Rodarte J, Streicher C, Molnár Z, Maini PK, Woolley TE. 2019. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 235(3), 686–696."},"date_published":"2019-09-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Studying the progression of the proliferative and differentiative patterns of neural stem cells at the individual cell level is crucial to the understanding of cortex development and how the disruption of such patterns can lead to malformations and neurodevelopmental diseases. However, our understanding of the precise lineage progression programme at single-cell resolution is still incomplete due to the technical variations in lineage- tracing approaches. One of the key challenges involves developing a robust theoretical framework in which we can integrate experimental observations and introduce correction factors to obtain a reliable and representative description of the temporal modulation of proliferation and differentiation. In order to obtain more conclusive insights, we carry out virtual clonal analysis using mathematical modelling and compare our results against experimental data. Using a dataset obtained with Mosaic Analysis with Double Markers, we illustrate how the theoretical description can be exploited to interpret and reconcile the disparity between virtual and experimental results.","lang":"eng"}],"issue":"3","status":"public","ddc":["570"],"title":"A mathematical insight into cell labelling experiments for clonal analysis","intvolume":" 235","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6844","file":[{"creator":"dernst","file_size":1192994,"content_type":"application/pdf","file_name":"2019_JournalAnatomy_Picco.pdf","access_level":"open_access","date_created":"2019-09-02T12:05:18Z","date_updated":"2020-07-14T12:47:42Z","checksum":"160f960844b204057f20896e0e1f8ee7","file_id":"6845","relation":"main_file"}],"oa_version":"Published Version","month":"09","publication_identifier":{"eissn":["1469-7580"],"issn":["0021-8782"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000482426800017"]},"language":[{"iso":"eng"}],"doi":"10.1111/joa.13001","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"SiHi"}],"year":"2019","date_updated":"2023-08-29T07:19:39Z","date_created":"2019-09-02T11:57:28Z","volume":235,"author":[{"last_name":"Picco","first_name":"Noemi","full_name":"Picco, Noemi"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"id":"3C70A038-F248-11E8-B48F-1D18A9856A87","last_name":"Rodarte","first_name":"Julio","full_name":"Rodarte, Julio"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Molnár, Zoltán","last_name":"Molnár","first_name":"Zoltán"},{"last_name":"Maini","first_name":"Philip K.","full_name":"Maini, Philip K."},{"last_name":"Woolley","first_name":"Thomas E.","full_name":"Woolley, Thomas E."}]},{"abstract":[{"text":"Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance.","lang":"eng"}],"type":"journal_article","file":[{"date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-09T07:22:12Z","checksum":"23d3978cf4739a89ce2c3e779f9305ca","relation":"main_file","file_id":"6862","content_type":"application/pdf","file_size":411491,"creator":"dernst","file_name":"2019_AnnualReview_Sella.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"6855","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","title":"Thinking about the evolution of complex traits in the era of genome-wide association studies","ddc":["576"],"status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"05","scopus_import":"1","date_published":"2019-07-05T00:00:00Z","citation":{"ista":"Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493.","apa":"Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316","ieee":"G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” Annual Review of Genomics and Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019.","ama":"Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 2019;20:461-493. doi:10.1146/annurev-genom-083115-022316","chicago":"Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316.","mla":"Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316.","short":"G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493."},"publication":"Annual Review of Genomics and Human Genetics","page":"461-493","file_date_updated":"2020-07-14T12:47:42Z","author":[{"last_name":"Sella","first_name":"Guy","full_name":"Sella, Guy"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"volume":20,"date_updated":"2023-08-29T07:49:38Z","date_created":"2019-09-07T14:28:29Z","pmid":1,"year":"2019","publisher":"Annual Reviews","department":[{"_id":"NiBa"}],"publication_status":"published","publication_identifier":{"eissn":["1545-293X"],"issn":["1527-8204"]},"month":"07","doi":"10.1146/annurev-genom-083115-022316","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000485148400020"],"pmid":["31283361"]},"oa":1,"isi":1,"quality_controlled":"1"},{"scopus_import":"1","day":"13","article_processing_charge":"No","publication":"Journal of Statistical Mechanics: Theory and Experiment","citation":{"chicago":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab190d.","short":"K. Mysliwy, M. Napiórkowski, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","mla":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6, 063101, IOP Publishing, 2019, doi:10.1088/1742-5468/ab190d.","apa":"Mysliwy, K., & Napiórkowski, M. (2019). Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab190d","ieee":"K. Mysliwy and M. Napiórkowski, “Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019.","ista":"Mysliwy K, Napiórkowski M. 2019. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063101.","ama":"Mysliwy K, Napiórkowski M. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab190d"},"date_published":"2019-06-13T00:00:00Z","type":"journal_article","abstract":[{"text":"We discuss thermodynamic properties of harmonically trapped\r\nimperfect quantum gases. The spatial inhomogeneity of these systems imposes\r\na redefinition of the mean-field interparticle potential energy as compared\r\nto the homogeneous case. In our approach, it takes the form a\r\n2N2 ωd, where\r\nN is the number of particles, ω—the harmonic trap frequency, d—system’s\r\ndimensionality, and a is a parameter characterizing the interparticle interaction.\r\nWe provide arguments that this model corresponds to the limiting case of\r\na long-ranged interparticle potential of vanishingly small amplitude. This\r\nconclusion is drawn from a computation similar to the well-known Kac scaling\r\nprocedure, which is presented here in a form adapted to the case of an isotropic\r\nharmonic trap. We show that within the model, the imperfect gas of trapped\r\nrepulsive bosons undergoes the Bose–Einstein condensation provided d > 1.\r\nThe main result of our analysis is that in d = 1 the gas of attractive imperfect\r\nfermions with a = −aF < 0 is thermodynamically equivalent to the gas of\r\nrepulsive bosons with a = aB > 0 provided the parameters aF and aB fulfill\r\nthe relation aB + aF = \u001f. This result supplements similar recent conclusion\r\nabout thermodynamic equivalence of two-dimensional (2D) uniform imperfect\r\nrepulsive Bose and attractive Fermi gases.","lang":"eng"}],"issue":"6","status":"public","title":"Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps","intvolume":" 2019","_id":"6840","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"06","publication_identifier":{"eissn":["1742-5468"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa":1,"external_id":{"arxiv":["1810.02209"],"isi":["000471650100001"]},"main_file_link":[{"url":"https://arxiv.org/abs/1810.02209","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1088/1742-5468/ab190d","article_number":"063101","ec_funded":1,"publication_status":"published","publisher":"IOP Publishing","department":[{"_id":"RoSe"}],"year":"2019","date_updated":"2023-08-29T07:19:13Z","date_created":"2019-09-01T22:00:59Z","volume":2019,"author":[{"first_name":"Krzysztof","last_name":"Mysliwy","id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof"},{"last_name":"Napiórkowski","first_name":"Marek","full_name":"Napiórkowski, Marek"}]},{"status":"public","title":"On isometric embeddings of Wasserstein spaces – the discrete case","intvolume":" 480","_id":"6843","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The aim of this short paper is to offer a complete characterization of all (not necessarily surjective) isometric embeddings of the Wasserstein space Wp(X), where S is a countable discrete metric space and 0
Journal of Mathematical Analysis and Applications, vol. 480, no. 2, 123435, Elsevier, 2019, doi:10.1016/j.jmaa.2019.123435.","chicago":"Gehér, György Pál, Tamás Titkos, and Daniel Virosztek. “On Isometric Embeddings of Wasserstein Spaces – the Discrete Case.” Journal of Mathematical Analysis and Applications. Elsevier, 2019. https://doi.org/10.1016/j.jmaa.2019.123435.","ama":"Gehér GP, Titkos T, Virosztek D. On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. 2019;480(2). doi:10.1016/j.jmaa.2019.123435","ieee":"G. P. Gehér, T. Titkos, and D. Virosztek, “On isometric embeddings of Wasserstein spaces – the discrete case,” Journal of Mathematical Analysis and Applications, vol. 480, no. 2. Elsevier, 2019.","apa":"Gehér, G. P., Titkos, T., & Virosztek, D. (2019). On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. Elsevier. https://doi.org/10.1016/j.jmaa.2019.123435","ista":"Gehér GP, Titkos T, Virosztek D. 2019. On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. 480(2), 123435."},"date_published":"2019-12-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","publication_status":"published","publisher":"Elsevier","department":[{"_id":"LaEr"}],"year":"2019","date_created":"2019-09-01T22:01:01Z","date_updated":"2023-08-29T07:18:50Z","volume":480,"author":[{"last_name":"Gehér","first_name":"György Pál","full_name":"Gehér, György Pál"},{"full_name":"Titkos, Tamás","last_name":"Titkos","first_name":"Tamás"},{"first_name":"Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel"}],"article_number":"123435","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.01101"}],"oa":1,"external_id":{"arxiv":["1809.01101"],"isi":["000486563900031"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.jmaa.2019.123435","month":"12","publication_identifier":{"issn":["0022247X"],"eissn":["10960813"]}},{"date_published":"2019-11-01T00:00:00Z","article_type":"original","citation":{"ista":"Destagnol KN, Sofos E. 2019. Rational points and prime values of polynomials in moderately many variables. Bulletin des Sciences Mathematiques. 156(11), 102794.","apa":"Destagnol, K. N., & Sofos, E. (2019). Rational points and prime values of polynomials in moderately many variables. Bulletin Des Sciences Mathematiques. Elsevier. https://doi.org/10.1016/j.bulsci.2019.102794","ieee":"K. N. Destagnol and E. Sofos, “Rational points and prime values of polynomials in moderately many variables,” Bulletin des Sciences Mathematiques, vol. 156, no. 11. Elsevier, 2019.","ama":"Destagnol KN, Sofos E. Rational points and prime values of polynomials in moderately many variables. Bulletin des Sciences Mathematiques. 2019;156(11). doi:10.1016/j.bulsci.2019.102794","chicago":"Destagnol, Kevin N, and Efthymios Sofos. “Rational Points and Prime Values of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques. Elsevier, 2019. https://doi.org/10.1016/j.bulsci.2019.102794.","mla":"Destagnol, Kevin N., and Efthymios Sofos. “Rational Points and Prime Values of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques, vol. 156, no. 11, 102794, Elsevier, 2019, doi:10.1016/j.bulsci.2019.102794.","short":"K.N. Destagnol, E. Sofos, Bulletin Des Sciences Mathematiques 156 (2019)."},"publication":"Bulletin des Sciences Mathematiques","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 156","status":"public","title":"Rational points and prime values of polynomials in moderately many variables","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6835","issue":"11","abstract":[{"lang":"eng","text":"We derive the Hasse principle and weak approximation for fibrations of certain varieties in the spirit of work by Colliot-Thélène–Sansuc and Harpaz–Skorobogatov–Wittenberg. Our varieties are defined through polynomials in many variables and part of our work is devoted to establishing Schinzel's hypothesis for polynomials of this kind. This last part is achieved by using arguments behind Birch's well-known result regarding the Hasse principle for complete intersections with the notable difference that we prove our result in 50% fewer variables than in the classical Birch setting. We also study the problem of square-free values of an integer polynomial with 66.6% fewer variables than in the Birch setting."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.bulsci.2019.102794","isi":1,"quality_controlled":"1","external_id":{"isi":["000496342100002"],"arxiv":["1801.03082"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1801.03082","open_access":"1"}],"publication_identifier":{"issn":["0007-4497"]},"month":"11","volume":156,"date_updated":"2023-08-29T07:18:02Z","date_created":"2019-09-01T22:00:55Z","author":[{"full_name":"Destagnol, Kevin N","last_name":"Destagnol","first_name":"Kevin N","id":"44DDECBC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sofos","first_name":"Efthymios","full_name":"Sofos, Efthymios"}],"department":[{"_id":"TiBr"}],"publisher":"Elsevier","publication_status":"published","year":"2019","article_number":"102794"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41556-019-0369-3","isi":1,"quality_controlled":"1","external_id":{"isi":["000478029000003"],"pmid":["31371826"]},"month":"08","publication_identifier":{"eissn":["1476-4679"]},"date_updated":"2023-08-29T07:42:20Z","date_created":"2019-09-01T22:00:57Z","volume":21,"author":[{"orcid":"0000-0001-9970-7804","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","last_name":"Tavano","first_name":"Ste","full_name":"Tavano, Ste"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Springer Nature","year":"2019","pmid":1,"date_published":"2019-08-01T00:00:00Z","page":"918-920","publication":"Nature Cell Biology","citation":{"chicago":"Tavano, Ste, and Carl-Philipp J Heisenberg. “Migrasomes Take Center Stage.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0369-3.","mla":"Tavano, Ste, and Carl-Philipp J. Heisenberg. “Migrasomes Take Center Stage.” Nature Cell Biology, vol. 21, no. 8, Springer Nature, 2019, pp. 918–20, doi:10.1038/s41556-019-0369-3.","short":"S. Tavano, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 918–920.","ista":"Tavano S, Heisenberg C-PJ. 2019. Migrasomes take center stage. Nature Cell Biology. 21(8), 918–920.","apa":"Tavano, S., & Heisenberg, C.-P. J. (2019). Migrasomes take center stage. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0369-3","ieee":"S. Tavano and C.-P. J. Heisenberg, “Migrasomes take center stage,” Nature Cell Biology, vol. 21, no. 8. Springer Nature, pp. 918–920, 2019.","ama":"Tavano S, Heisenberg C-PJ. Migrasomes take center stage. Nature Cell Biology. 2019;21(8):918-920. doi:10.1038/s41556-019-0369-3"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"None","status":"public","title":"Migrasomes take center stage","intvolume":" 21","_id":"6837","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Migrasomes are a recently discovered type of extracellular vesicles that are characteristically generated along retraction fibers in migrating cells. Two studies now show how migrasomes are formed and how they function in the physiologically relevant context of the developing zebrafish embryo.","lang":"eng"}],"issue":"8","type":"journal_article"},{"day":"02","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-09-02T00:00:00Z","publication":"Scientific Reports","citation":{"ieee":"M. Fenu et al., “A novel magnet-based scratch method for standardisation of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019.","apa":"Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7","ista":"Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625.","ama":"Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-48930-7","chicago":"Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7.","short":"M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019).","mla":"Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:10.1038/s41598-019-48930-7."},"abstract":[{"text":"A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-16T12:42:40Z","checksum":"9cfd986d4108e288cc72276ef047ab0c","relation":"main_file","file_id":"6879","file_size":3523795,"content_type":"application/pdf","creator":"dernst","file_name":"2019_ScientificReports_Fenu.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6867","ddc":["570"],"title":"A novel magnet-based scratch method for standardisation of wound-healing assays","status":"public","intvolume":" 9","month":"09","publication_identifier":{"eissn":["20452322"]},"doi":"10.1038/s41598-019-48930-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000483697800007"],"pmid":["31477739"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:42Z","article_number":"12625","author":[{"full_name":"Fenu, M.","last_name":"Fenu","first_name":"M."},{"full_name":"Bettermann, T.","last_name":"Bettermann","first_name":"T."},{"full_name":"Vogl, C.","last_name":"Vogl","first_name":"C."},{"first_name":"Nasser","last_name":"Darwish-Miranda","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser"},{"full_name":"Schramel, J.","last_name":"Schramel","first_name":"J."},{"first_name":"F.","last_name":"Jenner","full_name":"Jenner, F."},{"first_name":"I.","last_name":"Ribitsch","full_name":"Ribitsch, I."}],"date_created":"2019-09-15T22:00:42Z","date_updated":"2023-08-29T07:55:15Z","volume":9,"year":"2019","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"Bio"}]},{"scopus_import":"1","day":"23","article_processing_charge":"No","publication":"Science","citation":{"mla":"Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” Science, vol. 365, no. 6455, eaaw9144, AAAS, 2019, doi:10.1126/science.aaw9144.","short":"L. Zhou, L.A. Sazanov, Science 365 (2019).","chicago":"Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” Science. AAAS, 2019. https://doi.org/10.1126/science.aaw9144.","ama":"Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. 2019;365(6455). doi:10.1126/science.aaw9144","ista":"Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144.","apa":"Zhou, L., & Sazanov, L. A. (2019). Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. AAAS. https://doi.org/10.1126/science.aaw9144","ieee":"L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase,” Science, vol. 365, no. 6455. AAAS, 2019."},"date_published":"2019-08-23T00:00:00Z","type":"journal_article","abstract":[{"text":"V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation across theplasma membrane using the rotary-catalysis mechanism. They belong to the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthasesin overall architecture. We solved cryo–electron microscopy structures of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs, in three rotationalstates and two substates. These structures indicate substantial flexibility betweenV1and Voin a working enzyme, which results from mechanical competition between centralshaft rotation and resistance from the peripheral stalks. We also describedetails of adenosine diphosphate inhibition release, V1-Votorque transmission, andproton translocation, which are relevant for the entire V-type ATPase family.","lang":"eng"}],"issue":"6455","title":"Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase","status":"public","intvolume":" 365","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6859","oa_version":"None","month":"08","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000482464000043"],"pmid":["31439765"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.aaw9144","article_number":"eaaw9144","publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"AAAS","year":"2019","pmid":1,"date_created":"2019-09-07T19:04:45Z","date_updated":"2023-08-29T07:52:02Z","volume":365,"author":[{"full_name":"Zhou, Long","orcid":"0000-0002-1864-8951","id":"3E751364-F248-11E8-B48F-1D18A9856A87","last_name":"Zhou","first_name":"Long"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/","description":"News on IST Website","relation":"press_release"}]}},{"publication":"National Science Review","citation":{"short":"N.H. Barton, National Science Review 6 (2019) 291–292.","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113.","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.","ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292."},"article_type":"review","page":"291-292","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6858","title":"Is speciation driven by cycles of mixing and isolation?","ddc":["570"],"status":"public","intvolume":" 6","oa_version":"Published Version","file":[{"file_name":"2019_NSR_Barton.pdf","access_level":"open_access","creator":"dernst","file_size":106463,"content_type":"application/pdf","file_id":"8595","relation":"main_file","date_created":"2020-10-02T09:16:44Z","date_updated":"2020-10-02T09:16:44Z","success":1,"checksum":"571d60fa21a568607d1fd04e119da88c"}],"type":"journal_article","issue":"2","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000467957400025"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1093/nsr/nwy113","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["2053-714X"],"issn":["2095-5138"]},"year":"2019","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"date_created":"2019-09-07T14:43:02Z","date_updated":"2023-08-29T07:51:09Z","volume":6,"file_date_updated":"2020-10-02T09:16:44Z"},{"year":"2019","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"eLife Sciences Publications","author":[{"full_name":"Byczkowicz, Niklas","last_name":"Byczkowicz","first_name":"Niklas"},{"first_name":"Abdelmoneim","last_name":"Eshra","full_name":"Eshra, Abdelmoneim"},{"last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Trevisiol, Andrea","first_name":"Andrea","last_name":"Trevisiol"},{"full_name":"Hirrlinger, Johannes","last_name":"Hirrlinger","first_name":"Johannes"},{"last_name":"Kole","first_name":"Maarten Hp","full_name":"Kole, Maarten Hp"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"first_name":"Stefan","last_name":"Hallermann","full_name":"Hallermann, Stefan"}],"date_updated":"2023-08-30T06:17:06Z","date_created":"2019-09-15T22:00:43Z","volume":8,"article_number":"e42766","file_date_updated":"2020-07-14T12:47:42Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000485663900001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.7554/eLife.42766","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["2050084X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6868","status":"public","title":"HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons","ddc":["570"],"intvolume":" 8","oa_version":"Published Version","file":[{"checksum":"c350b7861ef0fb537cae8a3232aec016","date_created":"2019-09-16T13:14:33Z","date_updated":"2020-07-14T12:47:42Z","file_id":"6880","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4008137,"access_level":"open_access","file_name":"2019_eLife_Byczkowicz.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control electrical rhythmicity and excitability in the heart and brain, but the function of HCN channels at the subcellular level in axons remains poorly understood. Here, we show that the action potential conduction velocity in both myelinated and unmyelinated central axons can be bidirectionally modulated by a HCN channel blocker, cyclic adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar mossy fiber boutons show that HCN channels ensure reliable high-frequency firing and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration 13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2 channels control conduction velocity primarily by altering the resting membrane potential\r\nand are associated with significant metabolic costs. These results suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity to finely tune energy consumption and temporal delays across axons in the brain."}],"publication":"eLife","citation":{"chicago":"Byczkowicz, Niklas, Abdelmoneim Eshra, Jacqueline-Claire Montanaro-Punzengruber, Andrea Trevisiol, Johannes Hirrlinger, Maarten Hp Kole, Ryuichi Shigemoto, and Stefan Hallermann. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42766.","mla":"Byczkowicz, Niklas, et al. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” ELife, vol. 8, e42766, eLife Sciences Publications, 2019, doi:10.7554/eLife.42766.","short":"N. Byczkowicz, A. Eshra, J.-C. Montanaro-Punzengruber, A. Trevisiol, J. Hirrlinger, M.H. Kole, R. Shigemoto, S. Hallermann, ELife 8 (2019).","ista":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, Trevisiol A, Hirrlinger J, Kole MH, Shigemoto R, Hallermann S. 2019. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 8, e42766.","apa":"Byczkowicz, N., Eshra, A., Montanaro-Punzengruber, J.-C., Trevisiol, A., Hirrlinger, J., Kole, M. H., … Hallermann, S. (2019). HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42766","ieee":"N. Byczkowicz et al., “HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons,” eLife, vol. 8. eLife Sciences Publications, 2019.","ama":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, et al. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 2019;8. doi:10.7554/eLife.42766"},"article_type":"original","date_published":"2019-09-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","has_accepted_license":"1"},{"volume":146,"date_updated":"2023-08-30T06:19:04Z","date_created":"2019-09-22T22:00:36Z","author":[{"full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu","first_name":"Qiang"},{"last_name":"Gallemi","first_name":"Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal"},{"full_name":"Pospíšil, Jiří","last_name":"Pospíšil","first_name":"Jiří"},{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"publisher":"The Company of Biologists","department":[{"_id":"EvBe"}],"publication_status":"published","pmid":1,"year":"2019","acknowledgement":"We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738).","ec_funded":1,"article_number":"dev175919","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1242/dev.175919","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1242/dev.175919","open_access":"1"}],"external_id":{"isi":["000486297400011"],"pmid":["31391194"]},"oa":1,"publication_identifier":{"eissn":["14779129"]},"month":"09","oa_version":"Published Version","intvolume":" 146","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis","status":"public","_id":"6897","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"17","abstract":[{"lang":"eng","text":"The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins."}],"type":"journal_article","date_published":"2019-09-12T00:00:00Z","article_type":"original","citation":{"ista":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919.","ieee":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” Development, vol. 146, no. 17. The Company of Biologists, 2019.","apa":"Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., & Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. The Company of Biologists. https://doi.org/10.1242/dev.175919","ama":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 2019;146(17). doi:10.1242/dev.175919","chicago":"Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.175919.","mla":"Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” Development, vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:10.1242/dev.175919.","short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019)."},"publication":"Development","article_processing_charge":"No","day":"12","scopus_import":"1"},{"month":"12","publication_identifier":{"issn":["00068993"],"eissn":["18726240"]},"external_id":{"pmid":["31521639"],"isi":["000491646600033"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.brainres.2019.146458","language":[{"iso":"eng"}],"article_number":"146458","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"Elsevier","author":[{"id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","first_name":"Bárbara","last_name":"Oliveira","full_name":"Oliveira, Bárbara"},{"full_name":"Yahya, Aysan Çerağ","first_name":"Aysan Çerağ","last_name":"Yahya","id":"365A65F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"date_updated":"2023-08-30T06:19:49Z","date_created":"2019-09-22T22:00:35Z","volume":1724,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Brain Research","citation":{"ista":"Oliveira B, Yahya AÇ, Novarino G. 2019. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. 1724, 146458.","ieee":"B. Oliveira, A. Ç. Yahya, and G. Novarino, “Modeling cell-cell interactions in the brain using cerebral organoids,” Brain Research, vol. 1724. Elsevier, 2019.","apa":"Oliveira, B., Yahya, A. Ç., & Novarino, G. (2019). Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. Elsevier. https://doi.org/10.1016/j.brainres.2019.146458","ama":"Oliveira B, Yahya AÇ, Novarino G. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. 2019;1724. doi:10.1016/j.brainres.2019.146458","chicago":"Oliveira, Bárbara, Aysan Çerağ Yahya, and Gaia Novarino. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” Brain Research. Elsevier, 2019. https://doi.org/10.1016/j.brainres.2019.146458.","mla":"Oliveira, Bárbara, et al. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” Brain Research, vol. 1724, 146458, Elsevier, 2019, doi:10.1016/j.brainres.2019.146458.","short":"B. Oliveira, A.Ç. Yahya, G. Novarino, Brain Research 1724 (2019)."},"article_type":"original","date_published":"2019-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Until recently, a great amount of brain studies have been conducted in human post mortem tissues, cell lines and model organisms. These researches provided useful insights regarding cell-cell interactions occurring in the brain. However, such approaches suffer from technical limitations and inaccurate modeling of the tissue 3D cytoarchitecture. Importantly, they might lack a human genetic background essential for disease modeling. With the development of protocols to generate human cerebral organoids, we are now closer to reproducing the early stages of human brain development in vitro. As a result, more relevant cell-cell interaction studies can be conducted.\r\n\r\nIn this review, we discuss the advantages of 3D cultures over 2D in modulating brain cell-cell interactions during physiological and pathological development, as well as the progress made in developing organoids in which neurons, macroglia, microglia and vascularization are present. Finally, we debate the limitations of those models and possible future directions."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6896","title":"Modeling cell-cell interactions in the brain using cerebral organoids","status":"public","intvolume":" 1724","oa_version":"None"},{"date_created":"2021-07-27T14:09:11Z","date_updated":"2023-08-30T06:20:21Z","oa_version":"Published Version","author":[{"first_name":"Olga","last_name":"Sigalova","full_name":"Sigalova, Olga"},{"full_name":"Chaplin, Andrei","first_name":"Andrei","last_name":"Chaplin"},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"first_name":"Pavel","last_name":"Shelyakin","full_name":"Shelyakin, Pavel"},{"full_name":"Filaretov, Vsevolod","last_name":"Filaretov","first_name":"Vsevolod"},{"first_name":"Evgeny","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny"},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"status":"public","title":"Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"year":"2019","_id":"9731","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb)"}],"type":"research_data_reference","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808772.v1","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808772.v1","open_access":"1"}],"citation":{"mla":"Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1.","short":"O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1.","ama":"Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1","ista":"Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808772.v1.","ieee":"O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1"},"oa":1,"month":"09","day":"12","article_processing_charge":"No"},{"oa_version":"Published Version","date_created":"2021-08-06T07:59:56Z","date_updated":"2023-08-30T06:20:21Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","year":"2019","_id":"9783","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb)"}],"type":"research_data_reference","doi":"10.6084/m9.figshare.9808760.v1","date_published":"2019-09-12T00:00:00Z","citation":{"short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1","ieee":"O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808760.v1"}],"article_processing_charge":"No","day":"12","month":"09"},{"article_processing_charge":"No","day":"12","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808850.v1"}],"citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 20 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808850.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 20 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808850.v1.","ieee":"O. M. Sigalova et al., “Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808850.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808850.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808850.v1"},"oa":1,"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808850.v1","type":"research_data_reference","abstract":[{"lang":"eng","text":"Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb)"}],"_id":"9897","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"full_name":"Chaplin, Andrei V.","last_name":"Chaplin","first_name":"Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","last_name":"Shelyakin"},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"oa_version":"Published Version","date_updated":"2023-08-30T06:20:21Z","date_created":"2021-08-12T07:58:15Z"},{"type":"research_data_reference","abstract":[{"text":"Distribution of OGs with mosaic phyletic patterns across species (complete genomes only). (CSV 7 kb)","lang":"eng"}],"year":"2019","_id":"9890","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"status":"public","title":"Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"oa_version":"Published Version","date_updated":"2023-08-30T06:20:21Z","date_created":"2021-08-11T14:26:40Z","article_processing_charge":"No","day":"12","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808802.v1"}],"oa":1,"citation":{"ieee":"O. M. Sigalova et al., “Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808802.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808802.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808802.v1","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808802.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808802.v1."},"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808802.v1"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9892","year":"2019","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V","full_name":"Chaplin, Andrei V"},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"oa_version":"Published Version","date_created":"2021-08-12T07:11:53Z","date_updated":"2023-08-30T06:20:21Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Distribution of OGs with mosaic phyletic patterns across species (all genomes). (CSV 10 kb)"}],"oa":1,"citation":{"mla":"Sigalova, Olga M., et al. Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808814.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808814.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808814.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808814.v1.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808814.v1","ieee":"O. M. Sigalova et al., “Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808814.v1"}],"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808814.v1","article_processing_charge":"No","month":"09","day":"12"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808820.v1","open_access":"1"}],"citation":{"ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808820.v1.","ieee":"O. M. Sigalova et al., “Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808820.v1","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808820.v1","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808820.v1.","mla":"Sigalova, Olga M., et al. Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808820.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"doi":"10.6084/m9.figshare.9808820.v1","date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","month":"09","day":"12","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"status":"public","title":"Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","year":"2019","_id":"9893","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-08-12T07:20:10Z","date_updated":"2023-08-30T06:20:21Z","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","last_name":"Bochkareva"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A."},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Summary of peripheral genesa phyletic patterns and tree concordance. (CSV 26 kb)"}]},{"type":"research_data_reference","abstract":[{"text":"Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 kb)","lang":"eng"}],"title":"Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9894","year":"2019","date_created":"2021-08-12T07:25:07Z","date_updated":"2023-08-30T06:20:21Z","oa_version":"Published Version","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","last_name":"Bochkareva"},{"full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","last_name":"Shelyakin"},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"month":"09","day":"12","article_processing_charge":"No","citation":{"mla":"Sigalova, Olga M., et al. Additional File 18 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808826.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 18 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808826.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808826.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808826.v1.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808826.v1","ieee":"O. M. Sigalova et al., “Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808826.v1","open_access":"1"}],"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808826.v1"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Additional information on proteins from OG1. (CSV 30 kb)"}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","year":"2019","_id":"9895","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-08-12T07:44:52Z","date_updated":"2023-08-30T06:20:21Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"article_processing_charge":"No","day":"12","month":"09","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808835.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808835.v1.","ieee":"O. M. Sigalova et al., “Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808835.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808835.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808835.v1"},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808835.v1","open_access":"1"}],"oa":1,"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808835.v1"},{"abstract":[{"text":"Summary of the analysed genomes. (CSV 24 kb)","lang":"eng"}],"type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"author":[{"full_name":"Sigalova, Olga M.","first_name":"Olga M.","last_name":"Sigalova"},{"full_name":"Chaplin, Andrei V.","last_name":"Chaplin","first_name":"Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"oa_version":"Published Version","date_updated":"2023-08-30T06:20:21Z","date_created":"2021-08-12T07:50:53Z","_id":"9896","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","article_processing_charge":"No","month":"09","day":"02","doi":"10.6084/m9.figshare.9808841.v1","date_published":"2019-09-02T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808841.v1"}],"citation":{"ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808841.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808841.v1.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808841.v1","ieee":"O. M. Sigalova et al., “Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808841.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808841.v1."},"oa":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000485216800009"],"pmid":["31511517"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-019-12068-x","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"month":"09","pmid":1,"year":"2019","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"first_name":"Dorothee","last_name":"Bornhorst","full_name":"Bornhorst, Dorothee"},{"full_name":"Xia, Peng","last_name":"Xia","first_name":"Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nakajima","first_name":"Hiroyuki","full_name":"Nakajima, Hiroyuki"},{"full_name":"Dingare, Chaitanya","first_name":"Chaitanya","last_name":"Dingare"},{"full_name":"Herzog, Wiebke","last_name":"Herzog","first_name":"Wiebke"},{"first_name":"Virginie","last_name":"Lecaudey","full_name":"Lecaudey, Virginie"},{"full_name":"Mochizuki, Naoki","last_name":"Mochizuki","first_name":"Naoki"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Yelon, Deborah","first_name":"Deborah","last_name":"Yelon"},{"full_name":"Abdelilah-Seyfried, Salim","first_name":"Salim","last_name":"Abdelilah-Seyfried"}],"volume":10,"date_created":"2019-09-22T22:00:37Z","date_updated":"2023-08-30T06:21:23Z","file_date_updated":"2020-07-14T12:47:44Z","citation":{"chicago":"Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications. Nature Publishing Group, 2019. https://doi.org/10.1038/s41467-019-12068-x.","short":"D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113.","mla":"Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:10.1038/s41467-019-12068-x.","ieee":"D. Bornhorst et al., “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” Nature communications, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019.","apa":"Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-019-12068-x","ista":"Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113.","ama":"Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 2019;10(1):4113. doi:10.1038/s41467-019-12068-x"},"publication":"Nature communications","page":"4113","date_published":"2019-09-11T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"11","_id":"6899","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","status":"public","ddc":["570"],"file":[{"relation":"main_file","file_id":"6926","checksum":"62c2512712e16d27c1797d318d14ba9f","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T11:18:50Z","access_level":"open_access","file_name":"2019_Nature_Bornhorst.pdf","content_type":"application/pdf","file_size":3905793,"creator":"kschuh"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed."}]},{"file_date_updated":"2020-07-14T12:47:44Z","article_number":"710","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","last_name":"Bochkareva"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"related_material":{"record":[{"id":"9731","relation":"research_data","status":"public"},{"id":"9783","relation":"research_data","status":"public"},{"id":"9890","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9892"},{"id":"9893","status":"public","relation":"research_data"},{"id":"9894","relation":"research_data","status":"public"},{"id":"9895","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9896"},{"id":"9897","relation":"research_data","status":"public"},{"id":"9898","status":"public","relation":"research_data"},{"id":"9899","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9900"},{"id":"9901","relation":"research_data","status":"public"}]},"date_updated":"2023-08-30T06:20:22Z","date_created":"2019-09-22T22:00:36Z","volume":20,"year":"2019","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"FyKo"}],"month":"09","publication_identifier":{"eissn":["14712164"]},"doi":"10.1186/s12864-019-6059-5","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000485256100001"]},"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"file_name":"2019_BioMed_Sigalova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4157175,"creator":"kschuh","relation":"main_file","file_id":"6924","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T10:33:17Z","checksum":"b798773c5823012d31c812c9f7975da2"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6898","ddc":["570"],"title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","intvolume":" 20","day":"12","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-12T00:00:00Z","publication":"BMC Genomics","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics. BioMed Central, 2019. https://doi.org/10.1186/s12864-019-6059-5.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics, vol. 20, no. 1, 710, BioMed Central, 2019, doi:10.1186/s12864-019-6059-5.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-019-6059-5","ieee":"O. M. Sigalova et al., “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” BMC Genomics, vol. 20, no. 1. BioMed Central, 2019.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5"}},{"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2019.09.003","isi":1,"quality_controlled":"1","project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000489132500002"],"pmid":["31541740"]},"month":"10","publication_identifier":{"issn":["1674-2052","1752-9867"]},"date_created":"2019-09-30T10:00:40Z","date_updated":"2023-08-30T06:55:02Z","volume":12,"author":[{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","last_name":"Artner","full_name":"Artner, Christina"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Cell Press","year":"2019","pmid":1,"date_published":"2019-10-07T00:00:00Z","article_type":"original","page":"1312-1314","publication":"Molecular Plant","citation":{"short":"C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314.","mla":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant, vol. 12, no. 10, Cell Press, 2019, pp. 1312–14, doi:10.1016/j.molp.2019.09.003.","chicago":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant. Cell Press, 2019. https://doi.org/10.1016/j.molp.2019.09.003.","ama":"Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 2019;12(10):1312-1314. doi:10.1016/j.molp.2019.09.003","ieee":"C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth regulation,” Molecular Plant, vol. 12, no. 10. Cell Press, pp. 1312–1314, 2019.","apa":"Artner, C., & Benková, E. (2019). Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2019.09.003","ista":"Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 12(10), 1312–1314."},"day":"07","article_processing_charge":"No","scopus_import":"1","oa_version":"None","status":"public","title":"Ethylene and cytokinin - partners in root growth regulation","intvolume":" 12","_id":"6920","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"10","type":"journal_article"},{"oa":1,"citation":{"ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808859.v1.","ieee":"O. M. Sigalova et al., “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808859.v1","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808859.v1","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1.","mla":"Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808859.v1"}],"doi":"10.6084/m9.figshare.9808859.v1","date_published":"2019-09-12T00:00:00Z","day":"12","month":"09","article_processing_charge":"No","status":"public","title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9898","year":"2019","date_updated":"2023-08-30T06:20:22Z","date_created":"2021-08-12T08:10:23Z","oa_version":"Published Version","author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A."},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb)"}]},{"abstract":[{"lang":"eng","text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-12T10:54:03Z","date_updated":"2023-08-30T06:20:22Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A."},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"status":"public","title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","_id":"9901","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"12","month":"09","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808907.v1","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808907.v1","open_access":"1"}],"citation":{"ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808907.v1.","ieee":"O. M. Sigalova et al., “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1.","mla":"Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"oa":1},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)"}],"title":"Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","year":"2019","_id":"9899","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-30T06:20:22Z","date_created":"2021-08-12T08:18:09Z","oa_version":"Published Version","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"month":"09","day":"12","article_processing_charge":"No","oa":1,"citation":{"mla":"Sigalova, Olga M., et al. Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808865.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808865.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808865.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808865.v1.","ieee":"O. M. Sigalova et al., “Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808865.v1"},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808865.v1","open_access":"1"}],"doi":"10.6084/m9.figshare.9808865.v1","date_published":"2019-09-12T00:00:00Z"},{"abstract":[{"text":"Pan-genome statistics by species. (CSV 3 kb)","lang":"eng"}],"type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"oa_version":"Published Version","date_created":"2021-08-12T08:44:49Z","date_updated":"2023-08-30T06:20:22Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9900","year":"2019","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","article_processing_charge":"No","day":"12","month":"09","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808886.v1","oa":1,"citation":{"short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808886.v1","ieee":"O. M. Sigalova et al., “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808886.v1."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808886.v1","open_access":"1"}]},{"abstract":[{"text":"A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n","lang":"eng"}],"issue":"11","type":"journal_article","file":[{"date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-08T13:07:44Z","checksum":"6c9fbbd5ea8ce10ae93e55ad560a7bf9","file_id":"6937","relation":"main_file","creator":"jrybicki","file_size":1682718,"content_type":"application/pdf","file_name":"ecog.04444.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["577"],"status":"public","title":"What can observational data reveal about metacommunity processes?","intvolume":" 42","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6936","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","page":"1877-1886","publication":"Ecography","citation":{"chicago":"Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444.","short":"O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.","mla":"Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444.","apa":"Ovaskainen, O., Rybicki, J., & Abrego, N. (2019). What can observational data reveal about metacommunity processes? Ecography. Wiley. https://doi.org/10.1111/ecog.04444","ieee":"O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal about metacommunity processes?,” Ecography, vol. 42, no. 11. Wiley, pp. 1877–1886, 2019.","ista":"Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal about metacommunity processes? Ecography. 42(11), 1877–1886.","ama":"Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444"},"file_date_updated":"2020-07-14T12:47:45Z","ec_funded":1,"date_updated":"2023-08-30T06:57:25Z","date_created":"2019-10-08T13:01:24Z","volume":42,"author":[{"full_name":"Ovaskainen, Otso","last_name":"Ovaskainen","first_name":"Otso"},{"full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646"},{"full_name":"Abrego, Nerea","last_name":"Abrego","first_name":"Nerea"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Wiley","year":"2019","month":"11","publication_identifier":{"issn":["0906-7590"],"eissn":["1600-0587"]},"language":[{"iso":"eng"}],"doi":"10.1111/ecog.04444","isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000486348700001"]},"oa":1},{"month":"11","publication_identifier":{"eissn":["1521-1878"]},"language":[{"iso":"eng"}],"doi":"10.1002/bies.201900151","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000489502000001"]},"file_date_updated":"2020-07-14T12:47:42Z","article_number":"1900151","date_created":"2019-09-07T14:40:03Z","date_updated":"2023-08-30T06:56:26Z","volume":41,"author":[{"last_name":"Giese","first_name":"B","full_name":"Giese, B"},{"first_name":"J L","last_name":"Friess","full_name":"Friess, J L"},{"full_name":"Schetelig, M F ","first_name":"M F ","last_name":"Schetelig"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Philip","last_name":"Messer","full_name":"Messer, Philip"},{"first_name":"Florence","last_name":"Debarre","full_name":"Debarre, Florence"},{"last_name":"Meimberg","first_name":"H","full_name":"Meimberg, H"},{"full_name":"Windbichler, N","last_name":"Windbichler","first_name":"N"},{"first_name":"C","last_name":"Boete","full_name":"Boete, C"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","publication":"BioEssays","citation":{"mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151.","ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151"},"abstract":[{"text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2019_BioEssays_Giese.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":193248,"file_id":"6939","relation":"main_file","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-10-11T06:59:26Z","checksum":"8cc7551bff70b2658f8d5630f228ee12"}],"title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","status":"public","ddc":["570"],"intvolume":" 41","_id":"6857","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa_version":"None","intvolume":" 105","title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging","status":"public","_id":"6890","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods."}],"type":"book_chapter","date_published":"2019-08-27T00:00:00Z","page":"117-159","citation":{"chicago":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159.","mla":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008.","apa":"Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function (Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008","ieee":"M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in Complementary Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159.","ista":"Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.","ama":"Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008"},"publication":"Complementary Strategies to Study Virus Structure and Function","article_processing_charge":"No","day":"27","series_title":"Advances in Virus Research","scopus_import":"1","volume":105,"date_updated":"2023-08-30T06:56:00Z","date_created":"2019-09-18T08:15:37Z","author":[{"full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"editor":[{"full_name":"Rey, Félix A.","first_name":"Félix A.","last_name":"Rey"}],"department":[{"_id":"FlSc"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","language":[{"iso":"eng"}],"doi":"10.1016/bs.aivir.2019.07.008","quality_controlled":"1","isi":1,"external_id":{"pmid":[" 31522703"],"isi":["000501594500006"]},"publication_identifier":{"issn":["0065-3527"],"isbn":["9780128184561"]},"month":"08"},{"article_number":"100601","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2019","acknowledgement":"We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1 - 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021 Joint Project “Strongly interacting systems in confined geometries” is gratefully acknowledged.","volume":123,"date_updated":"2023-08-30T06:57:53Z","date_created":"2019-10-14T06:31:13Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-form-of-magnetism-found/","description":"News auf IST Website","relation":"press_release"}]},"author":[{"full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Defenu, Nicolò","first_name":"Nicolò","last_name":"Defenu"},{"first_name":"István","last_name":"Nándori","full_name":"Nándori, István"},{"last_name":"Salasnich","first_name":"Luca","full_name":"Salasnich, Luca"},{"full_name":"Trombettoni, Andrea","last_name":"Trombettoni","first_name":"Andrea"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"09","project":[{"_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.06253","open_access":"1"}],"external_id":{"arxiv":["1907.06253"],"isi":["000483587200004"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.123.100601","type":"journal_article","issue":"10","abstract":[{"text":"We study the effect of a linear tunneling coupling between two-dimensional systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the one-body correlation functions are algebraically decaying and the other with\r\nexponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law\r\ndecay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent. We provide a picture of the phase diagram using a renormalization group approach.","lang":"eng"}],"intvolume":" 123","title":"Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6940","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"06","article_type":"original","citation":{"chicago":"Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601.","short":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019).","mla":"Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American Physical Society, 2019, doi:10.1103/physrevlett.123.100601.","ieee":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models,” Physical Review Letters, vol. 123, no. 10. American Physical Society, 2019.","apa":"Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019). Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601","ista":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 123(10), 100601.","ama":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 2019;123(10). doi:10.1103/physrevlett.123.100601"},"publication":"Physical Review Letters","date_published":"2019-09-06T00:00:00Z"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000491128800062"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1126/sciadv.aaw6490","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23752548"]},"month":"09","year":"2019","publisher":"American Association for the Advancement of Science","department":[{"_id":"LeSa"}],"publication_status":"published","author":[{"first_name":"Chao","last_name":"Qi","full_name":"Qi, Chao"},{"full_name":"Minin, Giulio Di","first_name":"Giulio Di","last_name":"Minin"},{"full_name":"Vercellino, Irene","first_name":"Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449"},{"first_name":"Anton","last_name":"Wutz","full_name":"Wutz, Anton"},{"first_name":"Volodymyr M.","last_name":"Korkhov","full_name":"Korkhov, Volodymyr M."}],"volume":5,"date_created":"2019-09-29T22:00:45Z","date_updated":"2023-08-30T06:55:31Z","article_number":"eaaw6490","file_date_updated":"2020-07-14T12:47:44Z","citation":{"short":"C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (2019).","mla":"Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490.","chicago":"Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw6490.","ama":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw6490","ieee":"C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","apa":"Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019). Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490","ista":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490."},"publication":"Science Advances","date_published":"2019-09-18T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18","_id":"6919","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 5","status":"public","ddc":["570"],"title":"Structural basis of sterol recognition by human hedgehog receptor PTCH1","file":[{"checksum":"b2256c9117655bc15f621ba0babf219f","date_created":"2019-10-02T11:13:54Z","date_updated":"2020-07-14T12:47:44Z","file_id":"6928","relation":"main_file","creator":"kschuh","file_size":1236101,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_AAAS_Qi.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"9"},{"language":[{"iso":"eng"}],"doi":"10.3389/fimmu.2019.02153","quality_controlled":"1","isi":1,"external_id":{"pmid":["31616407"],"isi":["000487187000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["1664-3224"]},"month":"09","volume":10,"date_updated":"2023-08-30T07:18:23Z","date_created":"2019-11-04T15:50:06Z","author":[{"full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","first_name":"Réka K","last_name":"Kelemen"},{"full_name":"Rajakaruna, H","last_name":"Rajakaruna","first_name":"H"},{"first_name":"IA","last_name":"Cockburn","full_name":"Cockburn, IA"},{"first_name":"VV","last_name":"Ganusov","full_name":"Ganusov, VV"}],"publisher":"Frontiers","department":[{"_id":"BeVi"}],"publication_status":"published","pmid":1,"year":"2019","file_date_updated":"2020-07-14T12:47:46Z","article_number":"2153","date_published":"2019-09-20T00:00:00Z","article_type":"original","citation":{"chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153.","short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019).","mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers, 2019.","ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153.","ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153"},"publication":"Frontiers in Immunology","article_processing_charge":"No","has_accepted_license":"1","day":"20","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6984","date_created":"2019-11-04T15:54:00Z","date_updated":"2020-07-14T12:47:46Z","checksum":"68d1708f7aa412544159b498ef17a6b9","file_name":"2019_FrontiersImmonology_Kelemen.pdf","access_level":"open_access","file_size":2083061,"content_type":"application/pdf","creator":"dernst"}],"intvolume":" 10","ddc":["570"],"title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","status":"public","_id":"6983","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","issue":"5","abstract":[{"text":"We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to fJournal of the ACM. 2019;66(5). doi:10.1145/3339471","apa":"Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471","ieee":"C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM, 2019.","ista":"Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32.","short":"C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).","mla":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM, vol. 66, no. 5, 32, ACM, 2019, doi:10.1145/3339471.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3339471."},"publication":"Journal of the ACM","date_published":"2019-09-01T00:00:00Z","article_number":"32","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","year":"2019","volume":66,"date_updated":"2023-08-30T07:07:23Z","date_created":"2019-10-24T17:12:48Z","author":[{"last_name":"Lenzen","first_name":"Christoph","full_name":"Lenzen, Christoph"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel"}],"publication_identifier":{"issn":["0004-5411"]},"month":"09","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000496514100001"],"arxiv":["1705.06173"]},"language":[{"iso":"eng"}],"doi":"10.1145/3339471"},{"doi":"10.1007/978-3-030-30281-8_7","conference":{"name":"QEST: Quantitative Evaluation of Systems","end_date":"2019-09-12","start_date":"2019-09-10","location":"Glasgow, United Kingdom"},"language":[{"iso":"eng"}],"external_id":{"isi":["000679281300007"],"arxiv":["1906.08178"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08178"}],"oa":1,"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9783030302801"],"issn":["0302-9743"],"eisbn":["9783030302818"]},"month":"09","author":[{"full_name":"Ashok, Pranav","last_name":"Ashok","first_name":"Pranav"},{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Jan","last_name":"Křetínský","full_name":"Křetínský, Jan"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"},{"first_name":"Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor"}],"volume":11785,"date_created":"2019-10-14T06:57:49Z","date_updated":"2023-08-30T06:59:36Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"ChLa"}],"publication_status":"published","date_published":"2019-09-04T00:00:00Z","citation":{"ama":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy representation by decision trees with linear classifiers. In: 16th International Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature; 2019:109-128. doi:10.1007/978-3-030-30281-8_7","ista":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019. Strategy representation by decision trees with linear classifiers. 16th International Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11785, 109–128.","ieee":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman, “Strategy representation by decision trees with linear classifiers,” in 16th International Conference on Quantitative Evaluation of Systems, Glasgow, United Kingdom, 2019, vol. 11785, pp. 109–128.","apa":"Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., & Toman, V. (2019). Strategy representation by decision trees with linear classifiers. In 16th International Conference on Quantitative Evaluation of Systems (Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7","mla":"Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear Classifiers.” 16th International Conference on Quantitative Evaluation of Systems, vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7.","short":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman, in:, 16th International Conference on Quantitative Evaluation of Systems, Springer Nature, 2019, pp. 109–128.","chicago":"Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear Classifiers.” In 16th International Conference on Quantitative Evaluation of Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7."},"publication":"16th International Conference on Quantitative Evaluation of Systems","page":"109-128","article_processing_charge":"No","day":"04","scopus_import":"1","oa_version":"Preprint","_id":"6942","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 11785","title":"Strategy representation by decision trees with linear classifiers","status":"public","abstract":[{"text":"Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of 𝜔 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"]},{"year":"2019","publisher":"Elsevier","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"full_name":"Schmickler, C.H.","first_name":"C.H.","last_name":"Schmickler"},{"full_name":"Hammer, H.-W.","first_name":"H.-W.","last_name":"Hammer"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"volume":798,"date_created":"2019-10-18T18:33:32Z","date_updated":"2023-08-30T07:06:42Z","article_number":"135016","file_date_updated":"2020-07-14T12:47:46Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000494939000086"],"arxiv":["1904.00913"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.physletb.2019.135016","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0370-2693"]},"month":"11","_id":"6955","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 798","title":"Universal physics of bound states of a few charged particles","status":"public","ddc":["530"],"oa_version":"Published Version","file":[{"file_name":"2019_PhysicsLettersB_Schmickler.pdf","access_level":"open_access","file_size":528362,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6974","date_created":"2019-10-25T12:47:04Z","date_updated":"2020-07-14T12:47:46Z","checksum":"d27f983b34ea7dafdf356afbf9472fbf"}],"type":"journal_article","abstract":[{"text":"We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential.","lang":"eng"}],"citation":{"apa":"Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics of bound states of a few charged particles. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2019.135016","ieee":"C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound states of a few charged particles,” Physics Letters B, vol. 798. Elsevier, 2019.","ista":"Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016.","ama":"Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016","chicago":"Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier, 2019. https://doi.org/10.1016/j.physletb.2019.135016.","short":"C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).","mla":"Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016."},"publication":"Physics Letters B","article_type":"original","date_published":"2019-11-10T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"10"},{"file_date_updated":"2020-07-14T12:47:47Z","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"last_name":"Cousin","first_name":"Michael A.","full_name":"Cousin, Michael A."}],"date_updated":"2023-08-30T07:21:50Z","date_created":"2019-11-12T14:37:08Z","volume":151,"year":"2019","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"SiHi"}],"month":"12","publication_identifier":{"eissn":["1471-4159"],"issn":["0022-3042"]},"doi":"10.1111/jnc.14862","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000490703100001"],"pmid":["31479508"]},"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"text":"Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes.","lang":"eng"}],"issue":"5","type":"journal_article","file":[{"relation":"main_file","file_id":"7452","checksum":"ec1fb2aebb874009bc309adaada6e1d7","date_created":"2020-02-05T10:30:02Z","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","file_name":"2019_JournNeurochemistry_Cheung.pdf","file_size":4334962,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"7005","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","ddc":["570"],"status":"public","intvolume":" 151","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","publication":"Journal of Neurochemistry","citation":{"chicago":"Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14862.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:10.1111/jnc.14862.","ieee":"G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.","apa":"Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862","ista":"Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 151(5), 570–583.","ama":"Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862"},"article_type":"original","page":"570-583"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7000","ddc":["510","515","518"],"title":"Convergence analysis of projection method for variational inequalities","status":"public","intvolume":" 38","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps.","lang":"eng"}],"issue":"4","publication":"Computational and Applied Mathematics","citation":{"mla":"Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161, Springer Nature, 2019, doi:10.1007/s40314-019-0955-9.","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9.","ama":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 2019;38(4). doi:10.1007/s40314-019-0955-9","ista":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 38(4), 161.","apa":"Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9","ieee":"Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” Computational and Applied Mathematics, vol. 38, no. 4. Springer Nature, 2019."},"article_type":"original","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"VlKo"}],"author":[{"full_name":"Shehu, Yekini","first_name":"Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139"},{"last_name":"Iyiola","first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S."},{"last_name":"Li","first_name":"Xiao-Huan","full_name":"Li, Xiao-Huan"},{"first_name":"Qiao-Li","last_name":"Dong","full_name":"Dong, Qiao-Li"}],"date_updated":"2023-08-30T07:20:32Z","date_created":"2019-11-12T12:41:44Z","volume":38,"article_number":"161","ec_funded":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s40314-019-0955-9"}],"external_id":{"isi":["000488973100005"],"arxiv":["2101.09081"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"doi":"10.1007/s40314-019-0955-9","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]}},{"month":"12","publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"external_id":{"isi":["000497966900007"],"pmid":["31582855"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41580-019-0172-9","language":[{"iso":"eng"}],"year":"2019","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MiSi"}],"author":[{"full_name":"Yamada, KM","last_name":"Yamada","first_name":"KM"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"date_updated":"2023-08-30T07:22:20Z","date_created":"2019-11-12T14:54:42Z","volume":20,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Nature Reviews Molecular Cell Biology","citation":{"ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752.","apa":"Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9","ieee":"K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.","ama":"Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9","chicago":"Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9.","mla":"Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:10.1038/s41580-019-0172-9.","short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752."},"article_type":"review","page":"738–752","date_published":"2019-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration."}],"issue":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7009","title":"Mechanisms of 3D cell migration","status":"public","intvolume":" 20","oa_version":"None"},{"abstract":[{"lang":"eng","text":"Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth."}],"issue":"10","type":"journal_article","oa_version":"None","title":"Platelets in host defense: Experimental and clinical insights","status":"public","intvolume":" 40","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6988","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","article_type":"review","page":"922-938","publication":"Trends in Immunology","citation":{"ama":"Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004","apa":"Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host defense: Experimental and clinical insights. Trends in Immunology. Cell Press. https://doi.org/10.1016/j.it.2019.08.004","ieee":"L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press, pp. 922–938, 2019.","ista":"Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 40(10), 922–938.","short":"L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.","mla":"Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp. 922–38, doi:10.1016/j.it.2019.08.004.","chicago":"Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell Press, 2019. https://doi.org/10.1016/j.it.2019.08.004."},"ec_funded":1,"date_updated":"2023-08-30T07:19:23Z","date_created":"2019-11-04T16:27:36Z","volume":40,"author":[{"last_name":"Nicolai","first_name":"Leo","full_name":"Nicolai, Leo"},{"full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","first_name":"Florian R","last_name":"Gärtner"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"}],"year":"2019","pmid":1,"month":"10","publication_identifier":{"issn":["1471-4906"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.it.2019.08.004","isi":1,"quality_controlled":"1","project":[{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"external_id":{"pmid":["31601520"],"isi":["000493292100005"]}},{"oa_version":"None","_id":"7002","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Optimal multiple importance sampling","status":"public","intvolume":" 38","abstract":[{"text":"Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2019-07-01T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"ista":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. 2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4), 37.","ieee":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","apa":"Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., & Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323009","ama":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323009","chicago":"Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.","mla":"Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009.","short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019)."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Ivo","last_name":"Kondapaneni","full_name":"Kondapaneni, Ivo"},{"last_name":"Vevoda","first_name":"Petr","full_name":"Vevoda, Petr"},{"first_name":"Pascal","last_name":"Grittmann","full_name":"Grittmann, Pascal"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"full_name":"Slusallek, Philipp","last_name":"Slusallek","first_name":"Philipp"},{"last_name":"Křivánek","first_name":"Jaroslav","full_name":"Křivánek, Jaroslav"}],"date_created":"2019-11-12T13:05:40Z","date_updated":"2023-08-30T07:21:25Z","volume":38,"year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"ec_funded":1,"article_number":"37","doi":"10.1145/3306346.3323009","language":[{"iso":"eng"}],"external_id":{"isi":["000475740600011"]},"isi":1,"quality_controlled":"1","project":[{"name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"}],"month":"07","publication_identifier":{"issn":["0730-0301"]}},{"date_published":"2019-10-01T00:00:00Z","article_type":"original","page":"102401","publication":"Physical Review Fluids","citation":{"chicago":"Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids. American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.","mla":"Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.","ieee":"N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American Physical Society, p. 102401, 2019.","apa":"Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401.","ama":"Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","status":"public","intvolume":" 4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6978","abstract":[{"lang":"eng","text":"In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence."}],"issue":"10","type":"journal_article","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.4.102401","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1810.02211","open_access":"1"}],"external_id":{"arxiv":["1810.02211"],"isi":["000493510400001"]},"month":"10","date_created":"2019-11-04T10:04:01Z","date_updated":"2023-08-30T07:20:03Z","volume":4,"author":[{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"last_name":"Dogra","first_name":"Akshunna","full_name":"Dogra, Akshunna"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"year":"2019"},{"article_processing_charge":"No","has_accepted_license":"1","day":"27","scopus_import":"1","date_published":"2019-11-27T00:00:00Z","citation":{"chicago":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004.","short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.","mla":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004.","ieee":"M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” Cell Systems, vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019.","apa":"Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2019.10.004","ista":"Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3.","ama":"Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3. doi:10.1016/j.cels.2019.10.004"},"publication":"Cell Systems","page":"423-433.e1-e3","article_type":"original","issue":"5","abstract":[{"text":"Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information.","lang":"eng"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":4238460,"creator":"dernst","access_level":"open_access","file_name":"2019_CellSystems_Lukacisin.pdf","checksum":"7a11d6c2f9523d65b049512d61733178","date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-15T10:57:42Z","relation":"main_file","file_id":"7027"}],"oa_version":"Published Version","_id":"7026","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","ddc":["570"],"status":"public","publication_identifier":{"issn":["2405-4712"]},"month":"11","doi":"10.1016/j.cels.2019.10.004","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000499495400003"]},"oa":1,"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:48Z","author":[{"last_name":"Lukacisin","first_name":"Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin"},{"first_name":"Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"}],"volume":9,"date_created":"2019-11-15T10:51:42Z","date_updated":"2023-08-30T07:24:58Z","year":"2019","publisher":"Cell Press","department":[{"_id":"ToBo"}],"publication_status":"published"},{"scopus_import":"1","day":"29","article_processing_charge":"No","publication":"Combinatorica","citation":{"chicago":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica. Springer Nature, 2019. https://doi.org/10.1007/s00493-019-3905-7.","short":"R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279.","mla":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica, vol. 39, no. 6, Springer Nature, 2019, pp. 1267–79, doi:10.1007/s00493-019-3905-7.","ieee":"R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4,” Combinatorica, vol. 39, no. 6. Springer Nature, pp. 1267–1279, 2019.","apa":"Fulek, R., & Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-019-3905-7","ista":"Fulek R, Kynčl J. 2019. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 39(6), 1267–1279.","ama":"Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 2019;39(6):1267-1279. doi:10.1007/s00493-019-3905-7"},"article_type":"original","page":"1267-1279","date_published":"2019-10-29T00:00:00Z","type":"journal_article","abstract":[{"text":"We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus.","lang":"eng"}],"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7034","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","status":"public","intvolume":" 39","oa_version":"Preprint","month":"10","publication_identifier":{"eissn":["1439-6912"],"issn":["0209-9683"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.00508"}],"oa":1,"external_id":{"arxiv":["1709.00508"],"isi":["000493267200003"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"doi":"10.1007/s00493-019-3905-7","language":[{"iso":"eng"}],"ec_funded":1,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"date_updated":"2023-08-30T07:26:25Z","date_created":"2019-11-18T14:29:50Z","volume":39},{"_id":"7032","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","title":"Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators","status":"public","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"IEEE","author":[{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"full_name":"Kuamri, Madhuri","first_name":"Madhuri","last_name":"Kuamri"},{"last_name":"Schwefel","first_name":"Harald G. L.","full_name":"Schwefel, Harald G. L."}],"date_created":"2019-11-18T13:58:22Z","date_updated":"2023-08-30T07:26:01Z","oa_version":"None","article_number":"8873300","type":"conference","abstract":[{"lang":"eng","text":"Optical frequency combs (OFCs) are light sources whose spectra consists of equally spaced frequency lines in the optical domain [1]. They have great potential for improving high-capacity data transfer, all-optical atomic clocks, spectroscopy, and high-precision measurements [2]."}],"publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","citation":{"ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. 2019. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 8873300.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, and H. G. L. Schwefel, “Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators,” in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 2019.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kuamri, M., & Schwefel, H. G. L. (2019). Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Munich, Germany: IEEE. https://doi.org/10.1109/cleoe-eqec.2019.8873300","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE; 2019. doi:10.1109/cleoe-eqec.2019.8873300","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kuamri, and Harald G. L. Schwefel. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8873300.","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8873300, IEEE, 2019, doi:10.1109/cleoe-eqec.2019.8873300.","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, IEEE, 2019."},"external_id":{"isi":["000630002701617"]},"isi":1,"quality_controlled":"1","conference":{"location":"Munich, Germany","start_date":"2019-06-23","end_date":"2019-06-27","name":"CLEO: Conference on Lasers and Electro-Optics Europe"},"doi":"10.1109/cleoe-eqec.2019.8873300","date_published":"2019-10-17T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","day":"17","month":"10","publication_identifier":{"isbn":["9781728104690"]},"article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":6467393,"creator":"dernst","file_name":"2019_ScientificReports_Maes.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T07:49:52Z","checksum":"9ab397ed9c1c454b34bffb8cc863d734","relation":"main_file","file_id":"7096"}],"_id":"7095","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","ddc":["570"],"status":"public","intvolume":" 9","day":"12","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-12T00:00:00Z","publication":"Scientific Reports","citation":{"chicago":"Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-53049-w.","mla":"Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports, vol. 9, 16565, Springer Nature, 2019, doi:10.1038/s41598-019-53049-w.","short":"M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019).","ista":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 9, 16565.","apa":"Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., & Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-53049-w","ieee":"M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells, “Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,” Scientific Reports, vol. 9. Springer Nature, 2019.","ama":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 2019;9. doi:10.1038/s41598-019-53049-w"},"article_type":"original","file_date_updated":"2020-07-14T12:47:49Z","article_number":"16565","author":[{"full_name":"Maes, Margaret E","last_name":"Maes","first_name":"Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grosser, J. A.","last_name":"Grosser","first_name":"J. A."},{"full_name":"Fehrman, R. L.","first_name":"R. L.","last_name":"Fehrman"},{"full_name":"Schlamp, C. L.","last_name":"Schlamp","first_name":"C. L."},{"last_name":"Nickells","first_name":"R. W.","full_name":"Nickells, R. W."}],"date_created":"2019-11-25T07:45:17Z","date_updated":"2023-08-30T07:26:54Z","volume":9,"year":"2019","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"SaSi"}],"month":"11","publication_identifier":{"eissn":["2045-2322"]},"doi":"10.1038/s41598-019-53049-w","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000495857600019"],"pmid":["31719602"]},"isi":1,"quality_controlled":"1"},{"issue":"1","abstract":[{"lang":"eng","text":"Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway."}],"type":"journal_article","file":[{"checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","date_created":"2019-11-25T07:58:05Z","date_updated":"2020-07-14T12:47:49Z","relation":"main_file","file_id":"7098","file_size":2626069,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_CommunicBiology_Nagano.pdf"}],"oa_version":"Published Version","_id":"7097","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 2","status":"public","title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2019-11-15T00:00:00Z","citation":{"short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019).","mla":"Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology, vol. 2, no. 1, 419, Springer Nature, 2019, doi:10.1038/s42003-019-0670-5.","chicago":"Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0670-5.","ama":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2019;2(1). doi:10.1038/s42003-019-0670-5","apa":"Nagano, M., Toshima, J. Y., Siekhaus, D. E., & Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0670-5","ieee":"M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” Communications Biology, vol. 2, no. 1. Springer Nature, 2019.","ista":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2(1), 419."},"publication":"Communications Biology","article_type":"original","file_date_updated":"2020-07-14T12:47:49Z","article_number":"419","author":[{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"last_name":"Toshima","first_name":"Junko Y.","full_name":"Toshima, Junko Y."},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"volume":2,"date_updated":"2023-08-30T07:27:55Z","date_created":"2019-11-25T07:55:01Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"DaSi"}],"publication_status":"published","publication_identifier":{"issn":["2399-3642"]},"month":"11","doi":"10.1038/s42003-019-0670-5","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000496767800005"]},"quality_controlled":"1","isi":1},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20","page":"781-794.e4","article_type":"original","citation":{"apa":"Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild, M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.013","ieee":"Y. Kasugai et al., “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” Neuron, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019.","ista":"Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4.","ama":"Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 2019;104(4):781-794.e4. doi:10.1016/j.neuron.2019.08.013","chicago":"Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.013.","short":"Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.","mla":"Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:10.1016/j.neuron.2019.08.013."},"publication":"Neuron","date_published":"2019-11-20T00:00:00Z","type":"journal_article","issue":"4","intvolume":" 104","title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","status":"public","ddc":["571","599"],"_id":"7099","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","publication_identifier":{"issn":["0896-6273"]},"month":"11","quality_controlled":"1","isi":1,"external_id":{"pmid":["31543297"],"isi":["000497963500017"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.013"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.08.013","department":[{"_id":"RySh"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript.","year":"2019","volume":104,"date_created":"2019-11-25T08:02:39Z","date_updated":"2023-08-30T07:28:22Z","author":[{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"first_name":"Elisabeth","last_name":"Vogel","full_name":"Vogel, Elisabeth"},{"full_name":"Hörtnagl, Heide","last_name":"Hörtnagl","first_name":"Heide"},{"last_name":"Schönherr","first_name":"Sabine","full_name":"Schönherr, Sabine"},{"full_name":"Paradiso, Enrica","last_name":"Paradiso","first_name":"Enrica"},{"last_name":"Hauschild","first_name":"Markus","full_name":"Hauschild, Markus"},{"full_name":"Göbel, Georg","first_name":"Georg","last_name":"Göbel"},{"full_name":"Milenkovic, Ivan","first_name":"Ivan","last_name":"Milenkovic"},{"full_name":"Peterschmitt, Yvan","first_name":"Yvan","last_name":"Peterschmitt"},{"first_name":"Ramon","last_name":"Tasan","full_name":"Tasan, Ramon"},{"first_name":"Günther","last_name":"Sperk","full_name":"Sperk, Günther"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"first_name":"Werner","last_name":"Sieghart","full_name":"Sieghart, Werner"},{"last_name":"Singewald","first_name":"Nicolas","full_name":"Singewald, Nicolas"},{"last_name":"Lüthi","first_name":"Andreas","full_name":"Lüthi, Andreas"},{"first_name":"Francesco","last_name":"Ferraguti","full_name":"Ferraguti, Francesco"}]},{"publisher":"AAAS","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2019","volume":364,"date_updated":"2023-09-05T11:51:09Z","date_created":"2019-05-14T13:07:47Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/"}]},"author":[{"last_name":"Telley","first_name":"L","full_name":"Telley, L"},{"last_name":"Agirman","first_name":"G","full_name":"Agirman, G"},{"first_name":"J","last_name":"Prados","full_name":"Prados, J"},{"last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"full_name":"Fièvre, S","first_name":"S","last_name":"Fièvre"},{"first_name":"P","last_name":"Oberst","full_name":"Oberst, P"},{"full_name":"Bartolini, G","first_name":"G","last_name":"Bartolini"},{"full_name":"Vitali, I","first_name":"I","last_name":"Vitali"},{"full_name":"Cadilhac, C","last_name":"Cadilhac","first_name":"C"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Nguyen, L","first_name":"L","last_name":"Nguyen"},{"first_name":"A","last_name":"Dayer","full_name":"Dayer, A"},{"first_name":"D","last_name":"Jabaudon","full_name":"Jabaudon, D"}],"article_number":"eaav2522","ec_funded":1,"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf"}],"external_id":{"isi":["000467631800034"],"pmid":["31073041"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.aav2522","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"05","intvolume":" 364","title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6455","oa_version":"Published Version","type":"journal_article","issue":"6440","abstract":[{"text":"During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity.","lang":"eng"}],"article_type":"original","citation":{"short":"L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini, I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science 364 (2019).","mla":"Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:10.1126/science.aav2522.","chicago":"Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini, et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science. AAAS, 2019. https://doi.org/10.1126/science.aav2522.","ama":"Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 2019;364(6440). doi:10.1126/science.aav2522","apa":"Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., … Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. AAAS. https://doi.org/10.1126/science.aav2522","ieee":"L. Telley et al., “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” Science, vol. 364, no. 6440. AAAS, 2019.","ista":"Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 364(6440), eaav2522."},"publication":"Science","date_published":"2019-05-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10"},{"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1021/jacs.9b01394","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000469292300004"],"pmid":["31017419 "]},"ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","volume":141,"date_updated":"2023-09-05T12:03:45Z","date_created":"2019-06-25T11:53:35Z","author":[{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu"},{"full_name":"Kuster, Beatrice","last_name":"Kuster","first_name":"Beatrice"},{"first_name":"Maximilian","last_name":"Schuster","full_name":"Schuster, Maximilian"},{"full_name":"Dobrozhan, Oleksandr","last_name":"Dobrozhan","first_name":"Oleksandr"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"},{"last_name":"Kovalenko","first_name":"Maksym V.","full_name":"Kovalenko, Maksym V."}],"department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2019","article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1","date_published":"2019-04-19T00:00:00Z","page":"8025-8029","article_type":"original","citation":{"ieee":"M. Ibáñez et al., “Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion,” Journal of the American Chemical Society, vol. 141, no. 20. American Chemical Society, pp. 8025–8029, 2019.","apa":"Ibáñez, M., Hasler, R., Genç, A., Liu, Y., Kuster, B., Schuster, M., … Kovalenko, M. V. (2019). Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b01394","ista":"Ibáñez M, Hasler R, Genç A, Liu Y, Kuster B, Schuster M, Dobrozhan O, Cadavid D, Arbiol J, Cabot A, Kovalenko MV. 2019. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 141(20), 8025–8029.","ama":"Ibáñez M, Hasler R, Genç A, et al. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 2019;141(20):8025-8029. doi:10.1021/jacs.9b01394","chicago":"Ibáñez, Maria, Roger Hasler, Aziz Genç, Yu Liu, Beatrice Kuster, Maximilian Schuster, Oleksandr Dobrozhan, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b01394.","short":"M. Ibáñez, R. Hasler, A. Genç, Y. Liu, B. Kuster, M. Schuster, O. Dobrozhan, D. Cadavid, J. Arbiol, A. Cabot, M.V. Kovalenko, Journal of the American Chemical Society 141 (2019) 8025–8029.","mla":"Ibáñez, Maria, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society, vol. 141, no. 20, American Chemical Society, 2019, pp. 8025–29, doi:10.1021/jacs.9b01394."},"publication":"Journal of the American Chemical Society","issue":"20","abstract":[{"lang":"eng","text":"The bottom-up assembly of colloidal nanocrystals is a versatile methodology to produce composite nanomaterials with precisely tuned electronic properties. Beyond the synthetic control over crystal domain size, shape, crystal phase, and composition, solution-processed nanocrystals allow exquisite surface engineering. This provides additional means to modulate the nanomaterial characteristics and particularly its electronic transport properties. For instance, inorganic surface ligands can be used to tune the type and concentration of majority carriers or to modify the electronic band structure. Herein, we report the thermoelectric properties of SnTe nanocomposites obtained from the consolidation of surface-engineered SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to (i) converge the light and heavy bands through partial Cd alloying and (ii) generate CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge, the highest thermoelectric figure of merit reported for solution-processed SnTe."}],"type":"journal_article","file":[{"date_updated":"2020-07-14T12:47:34Z","date_created":"2019-06-25T11:59:00Z","checksum":"34d7ec837869cc6a07996b54f75696b7","file_id":"6587","relation":"main_file","creator":"cpetz","file_size":6234004,"content_type":"application/pdf","file_name":"JACS_April2019.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 141","ddc":["540"],"status":"public","title":"Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6586"},{"article_type":"original","publication":"Physical Review B","citation":{"ista":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 99(9), 094205.","ieee":"P. T. Dumitrescu, A. Goremykina, S. A. Parameswaran, M. Serbyn, and R. Vasseur, “Kosterlitz-Thouless scaling at many-body localization phase transitions,” Physical Review B, vol. 99, no. 9. American Physical Society, 2019.","apa":"Dumitrescu, P. T., Goremykina, A., Parameswaran, S. A., Serbyn, M., & Vasseur, R. (2019). Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.99.094205","ama":"Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 2019;99(9). doi:10.1103/physrevb.99.094205","chicago":"Dumitrescu, Philipp T., Anna Goremykina, Siddharth A. Parameswaran, Maksym Serbyn, and Romain Vasseur. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.99.094205.","mla":"Dumitrescu, Philipp T., et al. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B, vol. 99, no. 9, 094205, American Physical Society, 2019, doi:10.1103/physrevb.99.094205.","short":"P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019)."},"date_published":"2019-03-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","status":"public","title":"Kosterlitz-Thouless scaling at many-body localization phase transitions","intvolume":" 99","_id":"6174","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We propose a scaling theory for the many-body localization (MBL) phase transition in one dimension, building on the idea that it proceeds via a “quantum avalanche.” We argue that the critical properties can be captured at a coarse-grained level by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological grounds, we identify the scaling variables as the density of thermal regions and the length scale that controls the decay of typical matrix elements. Within this KT picture, the MBL phase is a line of fixed points that terminates at the delocalization transition. We discuss two possible scenarios distinguished by the distribution of rare, fractal thermal inclusions within the MBL phase. In the first scenario, these regions have a stretched exponential distribution in the MBL phase. In the second scenario, the near-critical MBL phase hosts rare thermal regions that are power-law-distributed in size. This points to the existence of a second transition within the MBL phase, at which these power laws change to the stretched exponential form expected at strong disorder. We numerically simulate two different phenomenological RGs previously proposed to describe the MBL transition. Both RGs display a universal power-law length distribution of thermal regions at the transition with a critical exponent αc=2, and continuously varying exponents in the MBL phase consistent with the KT picture.","lang":"eng"}],"issue":"9","isi":1,"quality_controlled":"1","external_id":{"isi":["000462883200001"],"arxiv":["1811.03103"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.03103","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.99.094205","month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","year":"2019","date_updated":"2023-09-05T12:11:13Z","date_created":"2019-03-25T07:32:08Z","volume":99,"author":[{"full_name":"Dumitrescu, Philipp T.","first_name":"Philipp T.","last_name":"Dumitrescu"},{"full_name":"Goremykina, Anna","last_name":"Goremykina","first_name":"Anna"},{"last_name":"Parameswaran","first_name":"Siddharth A.","full_name":"Parameswaran, Siddharth A."},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"last_name":"Vasseur","first_name":"Romain","full_name":"Vasseur, Romain"}],"article_number":"094205"},{"date_published":"2019-06-01T00:00:00Z","publication":"Plant Physiology","citation":{"ieee":"J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.","ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377.","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377."},"article_type":"original","page":"757-766","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","_id":"6366","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","intvolume":" 180","abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"issue":"2","type":"journal_article","doi":"10.1104/pp.18.01377","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["31000634"],"isi":["000470086100019"]},"main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"isi":1,"quality_controlled":"1","month":"06","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"author":[{"full_name":"Bellstaedt, Julia","first_name":"Julia","last_name":"Bellstaedt"},{"full_name":"Trenner, Jana","last_name":"Trenner","first_name":"Jana"},{"full_name":"Lippmann, Rebecca","last_name":"Lippmann","first_name":"Rebecca"},{"last_name":"Poeschl","first_name":"Yvonne","full_name":"Poeschl, Yvonne"},{"full_name":"Zhang, Xixi","last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Quint, Marcel","last_name":"Quint","first_name":"Marcel"},{"full_name":"Delker, Carolin","last_name":"Delker","first_name":"Carolin"}],"date_created":"2019-04-30T15:24:22Z","date_updated":"2023-09-05T12:25:19Z","volume":180,"year":"2019","pmid":1,"publication_status":"published","publisher":"ASPB","department":[{"_id":"JiFr"}]},{"ec_funded":1,"volume":147,"date_updated":"2023-09-05T12:22:21Z","date_created":"2019-11-04T16:10:50Z","author":[{"id":"42A24CCC-F248-11E8-B48F-1D18A9856A87","first_name":"Penghui","last_name":"Li","full_name":"Li, Penghui"}],"department":[{"_id":"TaHa"}],"publisher":"AMS","publication_status":"published","year":"2019","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1090/proc/14586","project":[{"name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.07039"}],"oa":1,"external_id":{"arxiv":["1810.07039"],"isi":["000488621700004"]},"issue":"11","abstract":[{"lang":"eng","text":"Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. "}],"type":"journal_article","oa_version":"Preprint","intvolume":" 147","title":"A colimit of traces of reflection groups","status":"public","_id":"6986","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","page":"4597-4604","article_type":"original","citation":{"ama":"Li P. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586","apa":"Li, P. (2019). A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586","ieee":"P. Li, “A colimit of traces of reflection groups,” Proceedings of the American Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019.","ista":"Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604.","short":"P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604.","mla":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604, doi:10.1090/proc/14586.","chicago":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586."},"publication":"Proceedings of the American Mathematical Society"},{"page":"159-172.e7","citation":{"short":"G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7.","mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:10.1016/j.neuron.2019.01.051.","chicago":"Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.051.","ama":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 2019;102(1):159-172.e7. doi:10.1016/j.neuron.2019.01.051","ieee":"G. Ortiz-Álvarez et al., “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” Neuron, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.","apa":"Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.051","ista":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7."},"publication":"Neuron","date_published":"2019-04-03T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03","intvolume":" 102","title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","ddc":["570"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6454","file":[{"relation":"main_file","file_id":"6457","checksum":"1fb6e195c583eb0c5cabf26f69ff6675","date_created":"2019-05-15T09:28:41Z","date_updated":"2020-07-14T12:47:30Z","access_level":"open_access","file_name":"2019_Neuron_Ortiz.pdf","file_size":7288572,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells."}],"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.01.051","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"month":"04","publisher":"Elsevier","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2019","volume":102,"date_created":"2019-05-14T13:06:30Z","date_updated":"2023-09-05T13:02:21Z","author":[{"last_name":"Ortiz-Álvarez","first_name":"G","full_name":"Ortiz-Álvarez, G"},{"full_name":"Daclin, M","first_name":"M","last_name":"Daclin"},{"last_name":"Shihavuddin","first_name":"A","full_name":"Shihavuddin, A"},{"full_name":"Lansade, P","last_name":"Lansade","first_name":"P"},{"full_name":"Fortoul, A","first_name":"A","last_name":"Fortoul"},{"full_name":"Faucourt, M","first_name":"M","last_name":"Faucourt"},{"first_name":"S","last_name":"Clavreul","full_name":"Clavreul, S"},{"full_name":"Lalioti, ME","last_name":"Lalioti","first_name":"ME"},{"full_name":"Taraviras, S","first_name":"S","last_name":"Taraviras"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Livet, J","first_name":"J","last_name":"Livet"},{"full_name":"Meunier, A","last_name":"Meunier","first_name":"A"},{"full_name":"Genovesio, A","last_name":"Genovesio","first_name":"A"},{"full_name":"Spassky, N","last_name":"Spassky","first_name":"N"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z"},{"issue":"20","type":"journal_article","oa_version":"None","_id":"6979","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal","intvolume":" 29","day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-21T00:00:00Z","publication":"Current Biology","citation":{"mla":"Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology, vol. 29, no. 20, Cell Press, 2019, pp. R1091–93, doi:10.1016/j.cub.2019.08.068.","short":"A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.","chicago":"Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology. Cell Press, 2019. https://doi.org/10.1016/j.cub.2019.08.068.","ama":"Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 2019;29(20):R1091-R1093. doi:10.1016/j.cub.2019.08.068","ista":"Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 29(20), R1091–R1093.","apa":"Kopf, A., & Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.08.068","ieee":"A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal,” Current Biology, vol. 29, no. 20. Cell Press, pp. R1091–R1093, 2019."},"article_type":"original","page":"R1091-R1093","author":[{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"date_created":"2019-11-04T15:18:29Z","date_updated":"2023-09-05T12:43:43Z","volume":29,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Cell Press","month":"10","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"doi":"10.1016/j.cub.2019.08.068","language":[{"iso":"eng"}],"external_id":{"pmid":["31639357"],"isi":["000491286200016"]},"quality_controlled":"1","isi":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6980","intvolume":" 38","title":"Tissue rheology in embryonic organization","status":"public","ddc":["570"],"file":[{"access_level":"open_access","file_name":"2019_Embo_Petridou.pdf","file_size":847356,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6981","checksum":"76f7f4e79ab6d850c30017a69726fd85","date_created":"2019-11-04T15:30:08Z","date_updated":"2020-07-14T12:47:46Z"}],"oa_version":"Published Version","type":"journal_article","issue":"20","abstract":[{"lang":"eng","text":"Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development."}],"citation":{"ama":"Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497","apa":"Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497","ieee":"N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,” The EMBO Journal, vol. 38, no. 20. EMBO, 2019.","ista":"Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497.","short":"N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).","mla":"Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal, vol. 38, no. 20, e102497, EMBO, 2019, doi:10.15252/embj.2019102497.","chicago":"Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal. EMBO, 2019. https://doi.org/10.15252/embj.2019102497."},"publication":"The EMBO Journal","article_type":"review","date_published":"2019-10-15T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"15","pmid":1,"year":"2019","department":[{"_id":"CaHe"}],"publisher":"EMBO","publication_status":"published","author":[{"last_name":"Petridou","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Petridou, Nicoletta"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"volume":38,"date_created":"2019-11-04T15:24:29Z","date_updated":"2023-09-05T13:04:13Z","article_number":"e102497","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31512749"],"isi":["000485561900001"]},"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"name":"Tissue material properties in embryonic development","call_identifier":"FWF","grant_number":"V00736","_id":"2693FD8C-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.15252/embj.2019102497","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"month":"10"},{"department":[{"_id":"ChLa"}],"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","publication_status":"published","year":"2019","volume":41,"date_created":"2019-06-11T14:05:59Z","date_updated":"2023-09-05T13:18:09Z","author":[{"first_name":"Yongqin","last_name":"Xian","full_name":"Xian, Yongqin"},{"orcid":"0000-0002-4561-241X","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"},{"full_name":"Schiele, Bernt","last_name":"Schiele","first_name":"Bernt"},{"full_name":"Akata, Zeynep","last_name":"Akata","first_name":"Zeynep"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1707.00600"],"isi":["000480343900015"]},"main_file_link":[{"url":"https://arxiv.org/abs/1707.00600","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1109/tpami.2018.2857768","publication_identifier":{"eissn":["1939-3539"],"issn":["0162-8828"]},"month":"09","intvolume":" 41","title":"Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6554","oa_version":"Preprint","type":"journal_article","issue":"9","abstract":[{"text":"Due to the importance of zero-shot learning, i.e. classifying images where there is a lack of labeled training data, the number of proposed approaches has recently increased steadily. We argue that it is time to take a step back and to analyze the status quo of the area. The purpose of this paper is three-fold. First, given the fact that there is no agreed upon zero-shot learning benchmark, we first define a new benchmark by unifying both the evaluation protocols and data splits of publicly available datasets used for this task. This is an important contribution as published results are often not comparable and sometimes even flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset which we make publicly available both in terms of image features and the images themselves. Second, we compare and analyze a significant number of the state-of-the-art methods in depth, both in the classic zero-shot setting but also in the more realistic generalized zero-shot setting. Finally, we discuss in detail the limitations of the current status of the area which can be taken as a basis for advancing it.","lang":"eng"}],"page":"2251 - 2265","article_type":"original","citation":{"ista":"Xian Y, Lampert C, Schiele B, Akata Z. 2019. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 41(9), 2251–2265.","ieee":"Y. Xian, C. Lampert, B. Schiele, and Z. Akata, “Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9. Institute of Electrical and Electronics Engineers (IEEE), pp. 2251–2265, 2019.","apa":"Xian, Y., Lampert, C., Schiele, B., & Akata, Z. (2019). Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/tpami.2018.2857768","ama":"Xian Y, Lampert C, Schiele B, Akata Z. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2019;41(9):2251-2265. doi:10.1109/tpami.2018.2857768","chicago":"Xian, Yongqin, Christoph Lampert, Bernt Schiele, and Zeynep Akata. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE), 2019. https://doi.org/10.1109/tpami.2018.2857768.","mla":"Xian, Yongqin, et al. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9, Institute of Electrical and Electronics Engineers (IEEE), 2019, pp. 2251–65, doi:10.1109/tpami.2018.2857768.","short":"Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis and Machine Intelligence 41 (2019) 2251–2265."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","date_published":"2019-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6259","title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","ddc":["580"],"status":"public","intvolume":" 568","oa_version":"Submitted Version","file":[{"file_id":"8751","relation":"main_file","date_updated":"2020-11-13T07:37:41Z","date_created":"2020-11-13T07:37:41Z","success":1,"checksum":"6b84ab602a34382cf0340a37a1378c75","file_name":"2019_Nature _Cao_accepted.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4321328}],"scopus_import":"1","day":"11","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature","citation":{"ista":"Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243.","ieee":"M. Cao et al., “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” Nature, vol. 568. Springer Nature, pp. 240–243, 2019.","apa":"Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1069-7","ama":"Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 2019;568:240-243. doi:10.1038/s41586-019-1069-7","chicago":"Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1069-7.","mla":"Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature, vol. 568, Springer Nature, 2019, pp. 240–43, doi:10.1038/s41586-019-1069-7.","short":"M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243."},"article_type":"original","page":"240-243","date_published":"2019-04-11T00:00:00Z","file_date_updated":"2020-11-13T07:37:41Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","author":[{"full_name":"Cao, Min","first_name":"Min","last_name":"Cao"},{"last_name":"Chen","first_name":"Rong","full_name":"Chen, Rong"},{"full_name":"Li, Pan","first_name":"Pan","last_name":"Li"},{"full_name":"Yu, Yongqiang","last_name":"Yu","first_name":"Yongqiang"},{"last_name":"Zheng","first_name":"Rui","full_name":"Zheng, Rui"},{"full_name":"Ge, Danfeng","first_name":"Danfeng","last_name":"Ge"},{"full_name":"Zheng, Wei","first_name":"Wei","last_name":"Zheng"},{"full_name":"Wang, Xuhui","last_name":"Wang","first_name":"Xuhui"},{"last_name":"Gu","first_name":"Yangtao","full_name":"Gu, Yangtao"},{"full_name":"Gelová, Zuzana","last_name":"Gelová","first_name":"Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Zhang, Heng","last_name":"Zhang","first_name":"Heng"},{"last_name":"Liu","first_name":"Renyi","full_name":"Liu, Renyi"},{"full_name":"He, Jun","first_name":"Jun","last_name":"He"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/"}]},"date_created":"2019-04-09T08:37:05Z","date_updated":"2023-09-05T14:58:41Z","volume":568,"month":"04","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"oa":1,"external_id":{"pmid":["30944466"],"isi":["000464412700050"]},"isi":1,"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"doi":"10.1038/s41586-019-1069-7","language":[{"iso":"eng"}]},{"file":[{"content_type":"application/pdf","file_size":19317348,"creator":"dernst","access_level":"open_access","file_name":"2019_RESULTS_McDougall.pdf","checksum":"7f43e1e3706d15061475c5c57efc2786","date_created":"2020-05-14T10:09:30Z","date_updated":"2020-07-14T12:47:46Z","relation":"main_file","file_id":"7829"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6987","intvolume":" 68","status":"public","ddc":["570"],"title":"Emergence of embryo shape during cleavage divisions","abstract":[{"lang":"eng","text":"Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern."}],"type":"book_chapter","alternative_title":["RESULTS"],"date_published":"2019-10-10T00:00:00Z","citation":{"ama":"McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154. doi:10.1007/978-3-030-23459-1_6","apa":"McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski (Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol. 68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6","ieee":"A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.","ista":"McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154.","short":"A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.","mla":"McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:10.1007/978-3-030-23459-1_6.","chicago":"McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6."},"publication":"Evo-Devo: Non-model species in cell and developmental biology","page":"127-154","article_processing_charge":"No","has_accepted_license":"1","day":"10","scopus_import":"1","author":[{"first_name":"Alex","last_name":"McDougall","full_name":"McDougall, Alex"},{"first_name":"Janet","last_name":"Chenevert","full_name":"Chenevert, Janet"},{"id":"33280250-F248-11E8-B48F-1D18A9856A87","last_name":"Godard","first_name":"Benoit G","full_name":"Godard, Benoit G"},{"last_name":"Dumollard","first_name":"Remi","full_name":"Dumollard, Remi"}],"volume":68,"date_created":"2019-11-04T16:20:19Z","date_updated":"2023-09-05T15:01:12Z","pmid":1,"year":"2019","editor":[{"last_name":"Tworzydlo","first_name":"Waclaw","full_name":"Tworzydlo, Waclaw"},{"full_name":"Bilinski, Szczepan M.","first_name":"Szczepan M.","last_name":"Bilinski"}],"department":[{"_id":"CaHe"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2020-07-14T12:47:46Z","doi":"10.1007/978-3-030-23459-1_6","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["31598855"]},"quality_controlled":"1","publication_identifier":{"issn":["0080-1844"],"isbn":["9783030234584","9783030234591"],"eissn":["1861-0412"]},"month":"10"},{"year":"2019","department":[{"_id":"JuFi"}],"publisher":"SIAM","publication_status":"published","author":[{"first_name":"Gero","last_name":"Friesecke","full_name":"Friesecke, Gero"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","first_name":"Michael","last_name":"Kniely","full_name":"Kniely, Michael"}],"volume":17,"date_updated":"2023-09-05T15:05:45Z","date_created":"2019-08-04T21:59:21Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"oa":1,"external_id":{"isi":["000487931800002"],"arxiv":["1808.04200"]},"quality_controlled":"1","isi":1,"doi":"10.1137/18M1207272","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15403467"],"issn":["15403459"]},"month":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6762","intvolume":" 17","status":"public","title":"New optimal control problems in density functional theory motivated by photovoltaics","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size.","lang":"eng"}],"citation":{"short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.","chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272.","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272","apa":"Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947."},"publication":"Multiscale Modeling and Simulation","page":"926-947","date_published":"2019-07-16T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"16"},{"type":"journal_article","abstract":[{"lang":"eng","text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10874","intvolume":" 5","title":"Modular invariants for genus 3 hyperelliptic curves","status":"public","oa_version":"Preprint","scopus_import":"1","keyword":["Algebra and Number Theory"],"article_processing_charge":"No","day":"02","citation":{"chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6.","mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9.","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6"},"publication":"Research in Number Theory","article_type":"original","date_published":"2019-01-02T00:00:00Z","article_number":"9","acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","year":"2019","publisher":"Springer Nature","department":[{"_id":"TiBr"}],"publication_status":"published","author":[{"full_name":"Ionica, Sorina","first_name":"Sorina","last_name":"Ionica"},{"last_name":"Kılıçer","first_name":"Pınar","full_name":"Kılıçer, Pınar"},{"full_name":"Lauter, Kristin","last_name":"Lauter","first_name":"Kristin"},{"full_name":"Lorenzo García, Elisa","first_name":"Elisa","last_name":"Lorenzo García"},{"full_name":"Manzateanu, Maria-Adelina","id":"be8d652e-a908-11ec-82a4-e2867729459c","last_name":"Manzateanu","first_name":"Maria-Adelina"},{"first_name":"Maike","last_name":"Massierer","full_name":"Massierer, Maike"},{"full_name":"Vincent, Christelle","last_name":"Vincent","first_name":"Christelle"}],"volume":5,"date_updated":"2023-09-05T15:39:31Z","date_created":"2022-03-18T12:09:48Z","publication_identifier":{"issn":["2522-0160"],"eissn":["2363-9555"]},"month":"01","oa":1,"external_id":{"arxiv":["1807.08986"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.08986"}],"quality_controlled":"1","doi":"10.1007/s40993-018-0146-6","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics."}],"issue":"1","_id":"7100","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","status":"public","ddc":["510"],"intvolume":" 372","file":[{"content_type":"application/pdf","file_size":884469,"creator":"dernst","file_name":"2019_CommMathPhys_Jeblick.pdf","access_level":"open_access","date_created":"2019-11-25T08:11:11Z","date_updated":"2020-07-14T12:47:49Z","checksum":"cd283b475dd739e04655315abd46f528","relation":"main_file","file_id":"7101"}],"oa_version":"Published Version","scopus_import":"1","day":"08","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Communications in Mathematical Physics","citation":{"chicago":"Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x.","short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","mla":"Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.","ieee":"M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.","apa":"Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x","ista":"Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.","ama":"Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69. doi:10.1007/s00220-019-03599-x"},"article_type":"original","page":"1-69","date_published":"2019-11-08T00:00:00Z","file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"acknowledgement":"OA fund by IST Austria","year":"2019","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","author":[{"full_name":"Jeblick, Maximilian","last_name":"Jeblick","first_name":"Maximilian"},{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold","full_name":"Leopold, Nikolai K"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"date_updated":"2023-09-06T10:47:43Z","date_created":"2019-11-25T08:08:02Z","volume":372,"month":"11","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"external_id":{"isi":["000495193700002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"doi":"10.1007/s00220-019-03599-x","language":[{"iso":"eng"}]},{"file":[{"relation":"main_file","file_id":"8660","date_created":"2020-10-14T08:54:49Z","date_updated":"2020-10-14T08:54:49Z","checksum":"94e0426856aad9a9bd0135d5436efbf1","success":1,"file_name":"2019_NaturePlants_Skokan_accepted.pdf","access_level":"open_access","file_size":1980851,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","_id":"7106","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["580"],"status":"public","title":"PIN-driven auxin transport emerged early in streptophyte evolution","intvolume":" 5","abstract":[{"text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2019-11-01T00:00:00Z","publication":"Nature Plants","citation":{"chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5.","short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","ieee":"R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5"},"article_type":"original","page":"1114-1119","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"last_name":"Medvecká","first_name":"Eva","full_name":"Medvecká, Eva"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"full_name":"Müller, Karel","first_name":"Karel","last_name":"Müller"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"full_name":"Karady, Michal","last_name":"Karady","first_name":"Michal"},{"first_name":"Yuzhou","last_name":"Zhang","full_name":"Zhang, Yuzhou"},{"first_name":"Dorina P.","last_name":"Janacek","full_name":"Janacek, Dorina P."},{"full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z.","last_name":"Hammes"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"date_created":"2019-11-25T09:08:04Z","date_updated":"2023-09-06T11:09:49Z","volume":5,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","file_date_updated":"2020-10-14T08:54:49Z","ec_funded":1,"doi":"10.1038/s41477-019-0542-5","language":[{"iso":"eng"}],"external_id":{"pmid":["31712756"],"isi":["000496526100010"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"month":"11","publication_identifier":{"issn":["2055-0278"]}},{"author":[{"last_name":"Yolland","first_name":"Lawrence","full_name":"Yolland, Lawrence"},{"first_name":"Mubarik","last_name":"Burki","full_name":"Burki, Mubarik"},{"full_name":"Marcotti, Stefania","last_name":"Marcotti","first_name":"Stefania"},{"last_name":"Luchici","first_name":"Andrei","full_name":"Luchici, Andrei"},{"last_name":"Kenny","first_name":"Fiona N.","full_name":"Kenny, Fiona N."},{"full_name":"Davis, John Robert","last_name":"Davis","first_name":"John Robert"},{"first_name":"Eduardo","last_name":"Serna-Morales","full_name":"Serna-Morales, Eduardo"},{"full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","first_name":"Jan"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"last_name":"Davidson","first_name":"Andrew","full_name":"Davidson, Andrew"},{"full_name":"Wood, Will","first_name":"Will","last_name":"Wood"},{"full_name":"Schumacher, Linus J.","last_name":"Schumacher","first_name":"Linus J."},{"full_name":"Endres, Robert G.","last_name":"Endres","first_name":"Robert G."},{"full_name":"Miodownik, Mark","first_name":"Mark","last_name":"Miodownik"},{"full_name":"Stramer, Brian M.","last_name":"Stramer","first_name":"Brian M."}],"date_updated":"2023-09-06T11:08:52Z","date_created":"2019-11-25T08:55:00Z","volume":21,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","month":"11","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"doi":"10.1038/s41556-019-0411-5","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"isi":1,"quality_controlled":"1","abstract":[{"text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7105","status":"public","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","intvolume":" 21","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","publication":"Nature Cell Biology","citation":{"ieee":"L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5."},"article_type":"original","page":"1370-1381"},{"year":"2019","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","author":[{"full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"full_name":"Ničković, Dejan","last_name":"Ničković","first_name":"Dejan"},{"full_name":"Pnueli, Amir","last_name":"Pnueli","first_name":"Amir"}],"date_created":"2019-11-26T10:22:32Z","date_updated":"2023-09-06T11:11:56Z","volume":66,"article_number":"19","external_id":{"isi":["000495406300005"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"doi":"10.1145/3286976","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["0004-5411"]},"_id":"7109","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"From real-time logic to timed automata","status":"public","intvolume":" 66","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We show how to construct temporal testers for the logic MITL, a prominent linear-time logic for real-time systems. A temporal tester is a transducer that inputs a signal holding the Boolean value of atomic propositions and outputs the truth value of a formula along time. Here we consider testers over continuous-time Boolean signals that use clock variables to enforce duration constraints, as in timed automata. We first rewrite the MITL formula into a “simple” formula using a limited set of temporal modalities. We then build testers for these specific modalities and show how to compose testers for simple formulae into complex ones. Temporal testers can be turned into acceptors, yielding a compositional translation from MITL to timed automata. This construction is much simpler than previously known and remains asymptotically optimal. It supports both past and future operators and can easily be extended."}],"issue":"3","publication":"Journal of the ACM","citation":{"short":"T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).","mla":"Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976.","chicago":"Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976.","ama":"Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata. Journal of the ACM. 2019;66(3). doi:10.1145/3286976","ieee":"T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","apa":"Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976","ista":"Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19."},"article_type":"original","date_published":"2019-05-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"type":"journal_article","abstract":[{"text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable.","lang":"eng"}],"issue":"3","_id":"7108","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Shellability is NP-complete","status":"public","intvolume":" 66","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Journal of the ACM","citation":{"ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019).","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024."},"article_type":"original","date_published":"2019-06-01T00:00:00Z","article_number":"21","year":"2019","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"ACM","author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"full_name":"Patak, Pavel","first_name":"Pavel","last_name":"Patak","id":"B593B804-1035-11EA-B4F1-947645A5BB83"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"184"}]},"date_updated":"2023-09-06T11:10:58Z","date_created":"2019-11-26T10:13:59Z","volume":66,"month":"06","publication_identifier":{"issn":["0004-5411"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1711.08436.pdf"}],"external_id":{"isi":["000495406300007"],"arxiv":["1711.08436"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1145/3314024","language":[{"iso":"eng"}]},{"volume":11773,"date_created":"2019-12-04T16:07:50Z","date_updated":"2023-09-06T11:18:08Z","author":[{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin"}],"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030313036","9783030313043"],"eissn":["1611-3349"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-31304-3_9","conference":{"location":"Trieste, Italy","start_date":"2019-09-18","end_date":"2019-09-20","name":"CMSB: Computational Methods in Systems Biology"},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000557875100009"]},"abstract":[{"lang":"eng","text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","intvolume":" 11773","status":"public","title":"Transient memory in gene regulation","_id":"7147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"17","scopus_import":"1","date_published":"2019-09-17T00:00:00Z","page":"155-187","citation":{"ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019). Transient memory in gene regulation. In 17th International Conference on Computational Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. https://doi.org/10.1007/978-3-030-31304-3_9","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: 17th International Conference on Computational Methods in Systems Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference on Computational Methods in Systems Biology, 11773:155–87. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31304-3_9.","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International Conference on Computational Methods in Systems Biology, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9.","short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187."},"publication":"17th International Conference on Computational Methods in Systems Biology"},{"oa_version":"Preprint","_id":"7136","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Strong chain rules for min-entropy under few bits spoiled","status":"public","abstract":[{"lang":"eng","text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240.","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: 2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019.","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In 2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240."},"day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Skórski, Maciej","last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"date_created":"2019-11-28T10:19:21Z","date_updated":"2023-09-06T11:15:41Z","year":"2019","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","article_number":"8849240","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2019-07-12","start_date":"2019-07-07","location":"Paris, France"},"doi":"10.1109/isit.2019.8849240","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.08476"}],"external_id":{"isi":["000489100301043"],"arxiv":["1702.08476"]},"isi":1,"quality_controlled":"1","month":"07","publication_identifier":{"isbn":["9781538692912"]}},{"date_created":"2019-11-26T15:07:49Z","date_updated":"2023-09-06T11:14:55Z","oa_version":"None","author":[{"last_name":"Khirirat","first_name":"Sarit","full_name":"Khirirat, Sarit"},{"full_name":"Johansson, Mikael","first_name":"Mikael","last_name":"Johansson"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"}],"status":"public","publication_status":"published","title":"Gradient compression for communication-limited convex optimization","department":[{"_id":"DaAl"}],"publisher":"IEEE","year":"2019","_id":"7122","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Data-rich applications in machine-learning and control have motivated an intense research on large-scale optimization. Novel algorithms have been proposed and shown to have optimal convergence rates in terms of iteration counts. However, their practical performance is severely degraded by the cost of exchanging high-dimensional gradient vectors between computing nodes. Several gradient compression heuristics have recently been proposed to reduce communications, but few theoretical results exist that quantify how they impact algorithm convergence. This paper establishes and strengthens the convergence guarantees for gradient descent under a family of gradient compression techniques. For convex optimization problems, we derive admissible step sizes and quantify both the number of iterations and the number of bits that need to be exchanged to reach a target accuracy. Finally, we validate the performance of different gradient compression techniques in simulations. The numerical results highlight the properties of different gradient compression algorithms and confirm that fast convergence with limited information exchange is possible."}],"article_number":"8619625","type":"conference","language":[{"iso":"eng"}],"conference":{"end_date":"2018-12-19","start_date":"2018-12-17","location":"Miami Beach, FL, United States","name":"CDC: Conference on Decision and Control"},"doi":"10.1109/cdc.2018.8619625","date_published":"2019-01-21T00:00:00Z","quality_controlled":"1","isi":1,"publication":"2018 IEEE Conference on Decision and Control","citation":{"ama":"Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited convex optimization. In: 2018 IEEE Conference on Decision and Control. IEEE; 2019. doi:10.1109/cdc.2018.8619625","apa":"Khirirat, S., Johansson, M., & Alistarh, D.-A. (2019). Gradient compression for communication-limited convex optimization. In 2018 IEEE Conference on Decision and Control. Miami Beach, FL, United States: IEEE. https://doi.org/10.1109/cdc.2018.8619625","ieee":"S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited convex optimization,” in 2018 IEEE Conference on Decision and Control, Miami Beach, FL, United States, 2019.","ista":"Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference on Decision and Control, 8619625.","short":"S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision and Control, IEEE, 2019.","mla":"Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex Optimization.” 2018 IEEE Conference on Decision and Control, 8619625, IEEE, 2019, doi:10.1109/cdc.2018.8619625.","chicago":"Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression for Communication-Limited Convex Optimization.” In 2018 IEEE Conference on Decision and Control. IEEE, 2019. https://doi.org/10.1109/cdc.2018.8619625."},"external_id":{"isi":["000458114800023"]},"day":"21","month":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9781538613955"],"issn":["0743-1546"]},"scopus_import":"1"},{"day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-25T00:00:00Z","article_type":"original","page":"1632-1641","publication":"Nature Ecology & Evolution","citation":{"short":"B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641.","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:10.1038/s41559-019-1050-8.","chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution. Springer Nature, 2019. https://doi.org/10.1038/s41559-019-1050-8.","ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 2019;3(12):1632-1641. doi:10.1038/s41559-019-1050-8","apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-019-1050-8","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” Nature Ecology & Evolution, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019.","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 3(12), 1632–1641."},"abstract":[{"text":"Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity.","lang":"eng"}],"issue":"12","type":"journal_article","oa_version":"None","status":"public","title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","intvolume":" 3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7146","month":"11","publication_identifier":{"issn":["2397-334X"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41559-019-1050-8","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000500728800009"]},"ec_funded":1,"date_updated":"2023-09-06T11:18:59Z","date_created":"2019-12-04T16:05:25Z","volume":3,"author":[{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Springer Nature","year":"2019"},{"publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"month":"12","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41422-019-0254-4","open_access":"1"}],"oa":1,"external_id":{"pmid":["31745287"],"isi":["000500749600001"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41422-019-0254-4","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2019","volume":29,"date_created":"2019-12-02T12:30:48Z","date_updated":"2023-09-06T11:20:58Z","author":[{"full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","first_name":"Scott A"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"965-966","article_type":"original","citation":{"short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.","apa":"Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966."},"publication":"Cell Research","date_published":"2019-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content."}],"intvolume":" 29","title":"Defying gravity: a plant's quest for moisture","status":"public","_id":"7143","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version"},{"date_published":"2019-12-01T00:00:00Z","article_type":"original","citation":{"mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108, Springer Nature, 2019, doi:10.1038/s41534-019-0220-5.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5.","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 2019;5. doi:10.1038/s41534-019-0220-5","ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” npj Quantum Information, vol. 5. Springer Nature, 2019.","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5"},"publication":"npj Quantum Information","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":1580132,"creator":"dernst","file_name":"2019_NPJ_Rueda.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-09T08:25:06Z","checksum":"13e0ea1d4f9b5f5710780d9473364f58","relation":"main_file","file_id":"7157"}],"oa_version":"Published Version","intvolume":" 5","status":"public","title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","ddc":["530"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7156","abstract":[{"lang":"eng","text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41534-019-0220-5","project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","call_identifier":"H2020"},{"name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000502996200003"],"arxiv":["1909.01470"]},"publication_identifier":{"issn":["2056-6387"]},"month":"12","volume":5,"date_updated":"2023-09-06T11:22:39Z","date_created":"2019-12-09T08:18:56Z","author":[{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease","full_name":"Hease, William J"},{"last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"department":[{"_id":"JoFi"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","article_number":"108"},{"publisher":"The Company of Biologists","department":[{"_id":"AnKi"}],"publication_status":"published","pmid":1,"year":"2019","volume":146,"date_updated":"2023-09-06T11:26:36Z","date_created":"2019-12-10T14:39:50Z","author":[{"full_name":"Guerrero, Pilar","last_name":"Guerrero","first_name":"Pilar"},{"last_name":"Perez-Carrasco","first_name":"Ruben","full_name":"Perez-Carrasco, Ruben"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P"},{"first_name":"David","last_name":"Page","full_name":"Page, David"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"first_name":"Karen M.","last_name":"Page","full_name":"Page, Karen M."}],"article_number":"dev176297","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","project":[{"call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000507575700004"],"pmid":["31784457"]},"language":[{"iso":"eng"}],"doi":"10.1242/dev.176297","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"month":"12","intvolume":" 146","ddc":["570"],"status":"public","title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7165","file":[{"file_name":"2019_Development_Guerrero.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7797881,"creator":"dernst","relation":"main_file","file_id":"7177","date_created":"2019-12-13T07:34:06Z","date_updated":"2020-07-14T12:47:50Z","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a"}],"oa_version":"Published Version","type":"journal_article","issue":"23","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"article_type":"original","citation":{"ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297","ieee":"P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019.","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297","chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019)."},"publication":"Development","date_published":"2019-12-04T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"04"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","citation":{"mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” 19th International Conference on Runtime Verification, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17.","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.","chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In 19th International Conference on Runtime Verification, 11757:292–309. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17.","ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: 19th International Conference on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17","ista":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In 19th International Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in 19th International Conference on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309."},"publication":"19th International Conference on Runtime Verification","page":"292-309","abstract":[{"lang":"eng","text":"Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. "}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7159","intvolume":" 11757","status":"public","title":"Shape expressions for specifying and extracting signal features","publication_identifier":{"isbn":["9783030320782","9783030320799"],"issn":["0302-9743"]},"month":"10","doi":"10.1007/978-3-030-32079-9_17","conference":{"name":"RV: Runtime Verification","location":"Porto, Portugal","start_date":"2019-10-08","end_date":"2019-10-11"},"language":[{"iso":"eng"}],"external_id":{"isi":["000570006300017"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"isi":1,"quality_controlled":"1","author":[{"full_name":"Ničković, Dejan","first_name":"Dejan","last_name":"Ničković"},{"full_name":"Qin, Xin","first_name":"Xin","last_name":"Qin"},{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"},{"full_name":"Mateis, Cristinel","first_name":"Cristinel","last_name":"Mateis"},{"first_name":"Jyotirmoy","last_name":"Deshmukh","full_name":"Deshmukh, Jyotirmoy"}],"volume":11757,"date_created":"2019-12-09T08:47:55Z","date_updated":"2023-09-06T11:24:10Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published"},{"author":[{"first_name":"Tomás","last_name":"Brázdil","full_name":"Brázdil, Tomás"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Kucera","first_name":"Antonín","full_name":"Kucera, Antonín"},{"full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velan","first_name":"Dominik","full_name":"Velan, Dominik"}],"volume":11781,"date_updated":"2023-09-06T12:40:58Z","date_created":"2019-12-15T23:00:44Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"issn":["03029743"],"isbn":["9783030317836"],"eissn":["16113349"]},"month":"10","doi":"10.1007/978-3-030-31784-3_27","conference":{"name":"ATVA: Automated TEchnology for Verification and Analysis","end_date":"2019-10-31","location":"Taipei, Taiwan","start_date":"2019-10-28"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.11010","open_access":"1"}],"external_id":{"isi":["000723515700027"],"arxiv":["1907.11010"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"abstract":[{"text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2).","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"7183","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 11781","title":"Deciding fast termination for probabilistic VASS with nondeterminism","status":"public","article_processing_charge":"No","day":"21","scopus_import":"1","date_published":"2019-10-21T00:00:00Z","citation":{"chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27.","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27"},"publication":"International Symposium on Automated Technology for Verification and Analysis","page":"462-478"},{"status":"public","title":"Systematic Y2H screening reveals extensive effector-complex formation","ddc":["580"],"intvolume":" 10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7182","file":[{"access_level":"open_access","file_name":"2019_FrontiersPlant_Alcantara.pdf","creator":"dernst","content_type":"application/pdf","file_size":1532505,"file_id":"7185","relation":"main_file","checksum":"995aa838aec2064d93550de82b40bbd1","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:58:43Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome."}],"issue":"11","article_type":"original","publication":"Frontiers in Plant Science","citation":{"apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437","ieee":"A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019).","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437."},"date_published":"2019-11-14T00:00:00Z","scopus_import":"1","day":"14","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Frontiers","year":"2019","pmid":1,"date_updated":"2023-09-06T14:33:46Z","date_created":"2019-12-15T23:00:43Z","volume":10,"author":[{"full_name":"Alcântara, André","first_name":"André","last_name":"Alcântara"},{"full_name":"Bosch, Jason","first_name":"Jason","last_name":"Bosch"},{"full_name":"Nazari, Fahimeh","first_name":"Fahimeh","last_name":"Nazari"},{"full_name":"Hoffmann, Gesa","first_name":"Gesa","last_name":"Hoffmann"},{"last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"full_name":"Uhse, Simon","first_name":"Simon","last_name":"Uhse"},{"full_name":"Darino, Martin A.","last_name":"Darino","first_name":"Martin A."},{"full_name":"Olukayode, Toluwase","first_name":"Toluwase","last_name":"Olukayode"},{"full_name":"Reumann, Daniel","last_name":"Reumann","first_name":"Daniel"},{"first_name":"Laura","last_name":"Baggaley","full_name":"Baggaley, Laura"},{"full_name":"Djamei, Armin","first_name":"Armin","last_name":"Djamei"}],"article_number":"1437","file_date_updated":"2020-07-14T12:47:52Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31803201"],"isi":["000499821700001"]},"language":[{"iso":"eng"}],"doi":"10.3389/fpls.2019.01437","month":"11","publication_identifier":{"eissn":["1664462X"]}},{"date_created":"2019-12-15T23:00:43Z","date_updated":"2023-09-06T14:08:21Z","volume":10,"author":[{"first_name":"Katarzyna","last_name":"Retzer","full_name":"Retzer, Katarzyna"},{"full_name":"Akhmanova, Maria","first_name":"Maria","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162"},{"last_name":"Konstantinova","first_name":"Nataliia","full_name":"Konstantinova, Nataliia"},{"first_name":"Kateřina","last_name":"Malínská","full_name":"Malínská, Kateřina"},{"last_name":"Leitner","first_name":"Johannes","full_name":"Leitner, Johannes"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"}],"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Springer Nature","year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:52Z","article_number":"5516","language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-13543-1","quality_controlled":"1","isi":1,"project":[{"_id":"264CBBAC-B435-11E9-9278-68D0E5697425","grant_number":"M02379","call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31797871"],"isi":["000500508100001"]},"oa":1,"month":"12","publication_identifier":{"eissn":["20411723"]},"file":[{"file_name":"2019_NatureComm_Retzer.pdf","access_level":"open_access","file_size":5156533,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7184","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:37:50Z","checksum":"77e8720a8e0f3091b98159f85be40893"}],"oa_version":"Published Version","ddc":["570"],"title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","status":"public","intvolume":" 10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7180","abstract":[{"text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.","lang":"eng"}],"type":"journal_article","date_published":"2019-12-01T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019).","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1.","chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1","ieee":"K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1","ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"year":"2019","pmid":1,"date_updated":"2023-09-06T14:32:52Z","date_created":"2019-12-15T23:00:43Z","volume":37,"author":[{"last_name":"Garriga","first_name":"Edgar","full_name":"Garriga, Edgar"},{"first_name":"Paolo","last_name":"Di Tommaso","full_name":"Di Tommaso, Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"first_name":"Ionas","last_name":"Erb","full_name":"Erb, Ionas"},{"full_name":"Mansouri, Leila","last_name":"Mansouri","first_name":"Leila"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","first_name":"Hafid","last_name":"Laayouni"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Floden, Evan","first_name":"Evan","last_name":"Floden"},{"full_name":"Notredame, Cedric","last_name":"Notredame","first_name":"Cedric"}],"related_material":{"record":[{"id":"13059","relation":"research_data","status":"public"}]},"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"}],"external_id":{"isi":["000500748900021"],"pmid":["31792410"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41587-019-0333-6","month":"12","publication_identifier":{"issn":["10870156"],"eissn":["15461696"]},"status":"public","title":"Large multiple sequence alignments with a root-to-leaf regressive method","intvolume":" 37","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7181","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6.","lang":"eng"}],"issue":"12","article_type":"original","page":"1466-1470","publication":"Nature Biotechnology","citation":{"ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470."},"date_published":"2019-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000508156800001"],"pmid":["31736464"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.51381","month":"11","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"SiHi"}],"year":"2019","pmid":1,"date_created":"2019-12-22T23:00:42Z","date_updated":"2023-09-06T14:38:39Z","volume":8,"author":[{"full_name":"Llorca, Alfredo","first_name":"Alfredo","last_name":"Llorca"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J"},{"last_name":"Wong","first_name":"Fong Kuan","full_name":"Wong, Fong Kuan"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"last_name":"Serafeimidou-Pouliou","first_name":"Eleni","full_name":"Serafeimidou-Pouliou, Eleni"},{"last_name":"Fernández-Otero","first_name":"Marian","full_name":"Fernández-Otero, Marian"},{"last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"full_name":"Arnold, Sebastian J.","first_name":"Sebastian J.","last_name":"Arnold"},{"last_name":"Meyer","first_name":"Martin","full_name":"Meyer, Martin"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"Maravall, Miguel","last_name":"Maravall","first_name":"Miguel"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"article_number":"e51381","file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"article_type":"original","publication":"eLife","citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381"},"date_published":"2019-11-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","status":"public","intvolume":" 8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7202","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2960543,"content_type":"application/pdf","file_name":"2019_eLife_Llorca.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:53Z","date_created":"2020-02-18T15:19:26Z","checksum":"b460ecc33e1a68265e7adea775021f3a","file_id":"7503","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas."}]},{"publication_identifier":{"eissn":["15306860"]},"month":"12","quality_controlled":"1","isi":1,"external_id":{"pmid":["31585509"],"isi":["000507466100054"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1096/fj.201901543R","file_date_updated":"2020-12-06T17:30:09Z","publisher":"FASEB","department":[{"_id":"RySh"}],"publication_status":"published","pmid":1,"year":"2019","volume":33,"date_updated":"2023-09-06T14:34:36Z","date_created":"2019-12-15T23:00:42Z","author":[{"first_name":"Lisa","last_name":"Klotz","full_name":"Klotz, Lisa"},{"last_name":"Wendler","first_name":"Olaf","full_name":"Wendler, Olaf"},{"full_name":"Frischknecht, Renato","first_name":"Renato","last_name":"Frischknecht"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Schulze, Holger","first_name":"Holger","last_name":"Schulze"},{"first_name":"Ralf","last_name":"Enz","full_name":"Enz, Ralf"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"13734-13746","article_type":"original","citation":{"mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R","ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., & Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. FASEB. https://doi.org/10.1096/fj.201901543R","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019."},"publication":"FASEB Journal","date_published":"2019-12-01T00:00:00Z","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity."}],"intvolume":" 33","title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","ddc":["571","599"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7179","file":[{"relation":"main_file","file_id":"8922","date_created":"2020-12-06T17:30:09Z","date_updated":"2020-12-06T17:30:09Z","checksum":"79e3b72481dc32489911121cf3b7d8d0","success":1,"file_name":"Klotz et al 2019 EMBO Reports.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4766789,"creator":"shigemot"}],"oa_version":"Submitted Version"},{"_id":"7201","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"SparCML: High-performance sparse communication for machine learning","oa_version":"Preprint","type":"conference","abstract":[{"text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks.","lang":"eng"}],"citation":{"chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222"},"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","date_published":"2019-11-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"17","year":"2019","publisher":"ACM","department":[{"_id":"DaAl"}],"publication_status":"published","author":[{"full_name":"Renggli, Cedric","last_name":"Renggli","first_name":"Cedric"},{"id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","first_name":"Saleh","last_name":"Ashkboos","full_name":"Ashkboos, Saleh"},{"last_name":"Aghagolzadeh","first_name":"Mehdi","full_name":"Aghagolzadeh, Mehdi"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Hoefler, Torsten","first_name":"Torsten","last_name":"Hoefler"}],"date_created":"2019-12-22T23:00:42Z","date_updated":"2023-09-06T14:37:55Z","article_number":"a11","ec_funded":1,"oa":1,"external_id":{"isi":["000545976800011"],"arxiv":["1802.08021"]},"main_file_link":[{"url":"https://arxiv.org/abs/1802.08021","open_access":"1"}],"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"isi":1,"quality_controlled":"1","doi":"10.1145/3295500.3356222","conference":{"end_date":"2019-11-19","start_date":"2019-11-17","location":"Denver, CO, Unites States","name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["21674329"],"isbn":["9781450362290"],"eissn":["21674337"]},"month":"11"},{"type":"research_data_reference","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"13067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publisher":"Dryad","department":[{"_id":"NiBa"}],"ddc":["570"],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7205"}]},"author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Zuzanna","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"oa_version":"Published Version","date_created":"2023-05-23T16:36:27Z","date_updated":"2023-09-06T14:48:57Z","article_processing_charge":"No","day":"02","month":"12","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"doi":"10.5061/DRYAD.TB2RBNZWK","date_published":"2019-12-02T00:00:00Z"},{"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000511618800007"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s12859-019-3208-4","month":"12","publication_identifier":{"eissn":["14712105"]},"publication_status":"published","publisher":"BMC","department":[{"_id":"DaAl"}],"year":"2019","date_updated":"2023-09-06T14:51:06Z","date_created":"2019-12-29T23:00:46Z","volume":20,"author":[{"full_name":"Aganezov, Sergey","last_name":"Aganezov","first_name":"Sergey"},{"first_name":"Ilya","last_name":"Zban","full_name":"Zban, Ilya"},{"full_name":"Aksenov, Vitalii","first_name":"Vitalii","last_name":"Aksenov","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nikita","last_name":"Alexeev","full_name":"Alexeev, Nikita"},{"last_name":"Schatz","first_name":"Michael C.","full_name":"Schatz, Michael C."}],"article_number":"641","file_date_updated":"2020-07-14T12:47:54Z","article_type":"original","publication":"BMC Bioinformatics","citation":{"ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.","chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4."},"date_published":"2019-12-17T00:00:00Z","scopus_import":"1","day":"17","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"status":"public","title":"Recovering rearranged cancer chromosomes from karyotype graphs","intvolume":" 20","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7214","file":[{"file_id":"7221","relation":"main_file","checksum":"7a30357efdcf8f66587ed495c0927724","date_created":"2020-01-02T16:10:58Z","date_updated":"2020-07-14T12:47:54Z","access_level":"open_access","file_name":"2019_BMCBioinfo_Aganezov.pdf","creator":"dernst","content_type":"application/pdf","file_size":1917374}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.","lang":"eng"}]},{"date_published":"2019-12-03T00:00:00Z","article_type":"review","citation":{"apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109.","ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.","short":"J. Merrin, Bioengineering 6 (2019).","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109."},"publication":"Bioengineering","article_processing_charge":"Yes","has_accepted_license":"1","day":"03","scopus_import":"1","file":[{"relation":"main_file","file_id":"7243","checksum":"80f1499e2a4caccdf3aa54b137fd99a0","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:49:59Z","access_level":"open_access","file_name":"2019_Bioengineering_Merrin.pdf","file_size":2660780,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 6","status":"public","title":"Frontiers in microfluidics, a teaching resource review","ddc":["620"],"_id":"7225","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","abstract":[{"text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3390/bioengineering6040109","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000505590000024"],"pmid":["31816954"]},"oa":1,"publication_identifier":{"eissn":["23065354"]},"month":"12","volume":6,"date_updated":"2023-09-06T14:52:49Z","date_created":"2020-01-05T23:00:45Z","author":[{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NanoFab"}],"publisher":"MDPI","publication_status":"published","pmid":1,"year":"2019","file_date_updated":"2020-07-14T12:47:54Z","article_number":"109"},{"day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2019-08-13T00:00:00Z","page":"317-333","publication":"25th Anniversary of Euro-Par","citation":{"chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333.","mla":"Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in 25th Anniversary of Euro-Par, Göttingen, Germany, 2019, vol. 11725, pp. 317–333.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In 25th Anniversary of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-29400-7_23","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.","ama":"Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: 25th Anniversary of Euro-Par. Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23"},"abstract":[{"lang":"eng","text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.\r\n\r\nIn this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. "}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","status":"public","title":"Scalable FIFO channels for programming via communicating sequential processes","intvolume":" 11725","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7228","month":"08","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9399-4"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-08-30","start_date":"2019-08-26","location":"Göttingen, Germany","name":"Euro-Par: European Conference on Parallel Processing"},"doi":"10.1007/978-3-030-29400-7_23","isi":1,"quality_controlled":"1","external_id":{"isi":["000851061400023"]},"date_updated":"2023-09-06T14:53:59Z","date_created":"2020-01-05T23:00:46Z","volume":11725,"author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Elizarov, Roman","last_name":"Elizarov","first_name":"Roman"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Springer Nature","year":"2019"},{"citation":{"ama":"Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514","ista":"Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference, 8917514.","ieee":"G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale,” in 2019 IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand, 2019.","apa":"Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514","mla":"Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","chicago":"Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019. https://doi.org/10.1109/ITSC.2019.8917514."},"external_id":{"isi":["000521238102050"]},"publication":"2019 IEEE Intelligent Transportation Systems Conference","quality_controlled":"1","isi":1,"date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","conference":{"end_date":"2019-10-30","start_date":"2019-10-27","location":"Auckland, New Zealand","name":"ITSC: Intelligent Transportation Systems Conference"},"language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"isbn":["9781538670248"]},"article_processing_charge":"No","day":"28","month":"11","_id":"7216","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","department":[{"_id":"HeEd"}],"publisher":"IEEE","title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","publication_status":"published","status":"public","author":[{"orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F"},{"last_name":"Cook","first_name":"James","full_name":"Cook, James"},{"full_name":"Fabrikant, Alex","last_name":"Fabrikant","first_name":"Alex"},{"full_name":"Gruteser, Marco","first_name":"Marco","last_name":"Gruteser"}],"oa_version":"None","date_created":"2019-12-29T23:00:47Z","date_updated":"2023-09-06T14:50:28Z","type":"conference","article_number":"8917514","abstract":[{"lang":"eng","text":"We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a \"semisynthetic\" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next."}]},{"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8"},"page":"123-141","date_published":"2019-08-13T00:00:00Z","scopus_import":"1","day":"13","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7231","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","status":"public","intvolume":" 11750","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature."}],"oa":1,"external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11514"}],"isi":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2019-08-27","location":"Amsterdam, The Netherlands","end_date":"2019-08-29"},"doi":"10.1007/978-3-030-29662-9_8","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"author":[{"full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"last_name":"Jiang","first_name":"Yu","full_name":"Jiang, Yu"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:55:15Z","volume":11750},{"author":[{"full_name":"Amin-Wetzel, Niko Paresh","first_name":"Niko Paresh","last_name":"Amin-Wetzel","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425"},{"first_name":"Lisa","last_name":"Neidhardt","full_name":"Neidhardt, Lisa"},{"last_name":"Yan","first_name":"Yahui","full_name":"Yan, Yahui"},{"full_name":"Mayer, Matthias P.","first_name":"Matthias P.","last_name":"Mayer"},{"last_name":"Ron","first_name":"David","full_name":"Ron, David"}],"date_updated":"2023-09-06T14:58:02Z","date_created":"2020-01-19T23:00:39Z","volume":8,"year":"2019","acknowledgement":"We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.","pmid":1,"publication_status":"published","department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications","file_date_updated":"2020-11-19T11:37:41Z","article_number":"e50793","doi":"10.7554/eLife.50793","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31873072"],"isi":["000512303700001"]},"isi":1,"quality_controlled":"1","month":"12","publication_identifier":{"eissn":["2050084X"]},"oa_version":"Published Version","file":[{"date_updated":"2020-11-19T11:37:41Z","date_created":"2020-11-19T11:37:41Z","checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","success":1,"relation":"main_file","file_id":"8777","content_type":"application/pdf","file_size":4817384,"creator":"dernst","file_name":"2019_eLife_AminWetzel.pdf","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7340","title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","ddc":["570"],"status":"public","intvolume":" 8","abstract":[{"text":"Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling.","lang":"eng"}],"type":"journal_article","date_published":"2019-12-24T00:00:00Z","publication":"eLife","citation":{"chicago":"Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","mla":"Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.","ieee":"N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793","ista":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793.","ama":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793"},"article_type":"original","day":"24","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"publication":"The Journal of Chemical Physics","citation":{"ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108.","apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867","ieee":"T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.","mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).","chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867."},"article_type":"original","date_published":"2019-02-07T00:00:00Z","day":"07","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7422","title":"eGFRD in all dimensions","status":"public","intvolume":" 150","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions.","lang":"eng"}],"issue":"5","oa":1,"external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}],"isi":1,"quality_controlled":"1","doi":"10.1063/1.5064867","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"year":"2019","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"GaTk"}],"author":[{"full_name":"Sokolowski, Thomas R","first_name":"Thomas R","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779"},{"first_name":"Joris","last_name":"Paijmans","full_name":"Paijmans, Joris"},{"full_name":"Bossen, Laurens","last_name":"Bossen","first_name":"Laurens"},{"full_name":"Miedema, Thomas","last_name":"Miedema","first_name":"Thomas"},{"last_name":"Wehrens","first_name":"Martijn","full_name":"Wehrens, Martijn"},{"full_name":"Becker, Nils B.","first_name":"Nils B.","last_name":"Becker"},{"full_name":"Kaizu, Kazunari","first_name":"Kazunari","last_name":"Kaizu"},{"full_name":"Takahashi, Koichi","first_name":"Koichi","last_name":"Takahashi"},{"full_name":"Dogterom, Marileen","last_name":"Dogterom","first_name":"Marileen"},{"full_name":"ten Wolde, Pieter Rein","last_name":"ten Wolde","first_name":"Pieter Rein"}],"date_updated":"2023-09-06T14:59:28Z","date_created":"2020-01-30T10:34:36Z","volume":150,"article_number":"054108"},{"status":"public","title":"Extending simple drawings","intvolume":" 11904","_id":"7230","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G."}],"page":"230-243","publication":"27th International Symposium on Graph Drawing and Network Visualization","citation":{"ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18","ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.","apa":"Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18","ista":"Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.","short":"A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.","mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18.","chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18."},"date_published":"2019-11-28T00:00:00Z","scopus_import":"1","day":"28","article_processing_charge":"No","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","year":"2019","date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:56:00Z","volume":11904,"author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","first_name":"Alan M","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M"},{"full_name":"Derka, Martin","last_name":"Derka","first_name":"Martin"},{"full_name":"Parada, Irene","first_name":"Irene","last_name":"Parada"}],"ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.08129"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2019-09-20","start_date":"2019-09-17","location":"Prague, Czech Republic","name":"GD: Graph Drawing and Network Visualization"},"doi":"10.1007/978-3-030-35802-0_18","month":"11","publication_identifier":{"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"],"issn":["0302-9743"]}},{"oa_version":"None","title":"Mixed-time signal temporal logic","status":"public","intvolume":" 11750","_id":"7232","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. "}],"alternative_title":["LNCS"],"type":"conference","date_published":"2019-08-13T00:00:00Z","page":"59-75","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.","short":"T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.","ista":"Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.","apa":"Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4","ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4"},"day":"13","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-06T14:57:17Z","date_created":"2020-01-05T23:00:48Z","volume":11750,"author":[{"full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"first_name":"Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"}],"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","year":"2019","language":[{"iso":"eng"}],"conference":{"name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","location":"Amsterdam, The Netherlands","start_date":"2019-08-27","end_date":"2019-08-29"},"doi":"10.1007/978-3-030-29662-9_4","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"external_id":{"isi":["000611677700004"]},"month":"08","publication_identifier":{"isbn":["978-3-0302-9661-2"],"eissn":["1611-3349"],"issn":["0302-9743"]}},{"article_type":"original","citation":{"ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387","ista":"Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387.","apa":"Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387","ieee":"P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019.","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387.","short":"P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).","chicago":"Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387."},"publication":"Journal of Cell Science","date_published":"2019-06-07T00:00:00Z","article_processing_charge":"No","day":"07","intvolume":" 132","title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7420","oa_version":"Published Version","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic."}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.1242/jcs.233387","open_access":"1"}],"external_id":{"isi":["000473327900017"],"pmid":["31076515"]},"language":[{"iso":"eng"}],"doi":"10.1242/jcs.233387","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"month":"06","department":[{"_id":"MiSi"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"year":"2019","volume":132,"date_updated":"2023-09-06T15:01:00Z","date_created":"2020-01-30T10:31:42Z","author":[{"last_name":"Sahgal","first_name":"Pranshu","full_name":"Sahgal, Pranshu"},{"orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H","full_name":"Alanko, Jonna H"},{"full_name":"Icha, Jaroslav","last_name":"Icha","first_name":"Jaroslav"},{"full_name":"Paatero, Ilkka","last_name":"Paatero","first_name":"Ilkka"},{"first_name":"Hellyeh","last_name":"Hamidi","full_name":"Hamidi, Hellyeh"},{"first_name":"Antti","last_name":"Arjonen","full_name":"Arjonen, Antti"},{"full_name":"Pietilä, Mika","last_name":"Pietilä","first_name":"Mika"},{"full_name":"Rokka, Anne","first_name":"Anne","last_name":"Rokka"},{"full_name":"Ivaska, Johanna","first_name":"Johanna","last_name":"Ivaska"}],"article_number":"jcs233387"}]