[{"date_created":"2020-01-30T10:31:42Z","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"doi":"10.1242/jcs.233387","article_type":"original","isi":1,"status":"public","external_id":{"isi":["000473327900017"],"pmid":["31076515"]},"volume":132,"publication_status":"published","author":[{"full_name":"Sahgal, Pranshu","first_name":"Pranshu","last_name":"Sahgal"},{"orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H"},{"full_name":"Icha, Jaroslav","last_name":"Icha","first_name":"Jaroslav"},{"first_name":"Ilkka","last_name":"Paatero","full_name":"Paatero, Ilkka"},{"last_name":"Hamidi","first_name":"Hellyeh","full_name":"Hamidi, Hellyeh"},{"last_name":"Arjonen","first_name":"Antti","full_name":"Arjonen, Antti"},{"first_name":"Mika","last_name":"Pietilä","full_name":"Pietilä, Mika"},{"full_name":"Rokka, Anne","last_name":"Rokka","first_name":"Anne"},{"full_name":"Ivaska, Johanna","first_name":"Johanna","last_name":"Ivaska"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-06-07T00:00:00Z","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1242/jcs.233387","open_access":"1"}],"month":"06","intvolume":"       132","issue":"11","title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","day":"07","pmid":1,"department":[{"_id":"MiSi"}],"date_updated":"2023-09-06T15:01:00Z","type":"journal_article","citation":{"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).","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.","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.” <i>Journal of Cell Science</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/jcs.233387\">https://doi.org/10.1242/jcs.233387</a>.","ieee":"P. Sahgal <i>et al.</i>, “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” <i>Journal of Cell Science</i>, vol. 132, no. 11. The Company of Biologists, 2019.","ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. <i>Journal of Cell Science</i>. 2019;132(11). doi:<a href=\"https://doi.org/10.1242/jcs.233387\">10.1242/jcs.233387</a>","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. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.233387\">https://doi.org/10.1242/jcs.233387</a>","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” <i>Journal of Cell Science</i>, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/jcs.233387\">10.1242/jcs.233387</a>."},"quality_controlled":"1","_id":"7420","publication":"Journal of Cell Science","article_number":"jcs233387","publisher":"The Company of Biologists","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2019","oa":1},{"isi":1,"status":"public","external_id":{"isi":["000468200800004"],"pmid":["30576024"]},"publication_status":"published","volume":28,"author":[{"last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rodrigues","first_name":"Nicolas","full_name":"Rodrigues, Nicolas"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"},{"last_name":"Kirkpatrick","first_name":"Mark","full_name":"Kirkpatrick, Mark"}],"date_created":"2020-01-30T10:33:05Z","doi":"10.1111/mec.14990","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"article_type":"original","page":"1877-1889","abstract":[{"lang":"eng","text":"X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes."}],"oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-04-01T00:00:00Z","date_updated":"2023-09-06T15:00:13Z","department":[{"_id":"BeVi"}],"type":"journal_article","month":"04","intvolume":"        28","issue":"8","title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","day":"01","pmid":1,"language":[{"iso":"eng"}],"publisher":"Wiley","article_processing_charge":"No","year":"2019","citation":{"ista":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 28(8), 1877–1889.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889.","chicago":"Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>.","ama":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. 2019;28(8):1877-1889. doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>","ieee":"M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog,” <i>Molecular Ecology</i>, vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.","mla":"Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>, vol. 28, no. 8, Wiley, 2019, pp. 1877–89, doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>.","apa":"Toups, M. A., Rodrigues, N., Perrin, N., &#38; Kirkpatrick, M. (2019). A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>"},"_id":"7421","quality_controlled":"1","publication":"Molecular Ecology"},{"status":"public","external_id":{"arxiv":["1708.09364"],"isi":["000458109300009"]},"isi":1,"author":[{"last_name":"Sokolowski","first_name":"Thomas R","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joris","last_name":"Paijmans","full_name":"Paijmans, Joris"},{"full_name":"Bossen, Laurens","first_name":"Laurens","last_name":"Bossen"},{"full_name":"Miedema, Thomas","first_name":"Thomas","last_name":"Miedema"},{"first_name":"Martijn","last_name":"Wehrens","full_name":"Wehrens, Martijn"},{"last_name":"Becker","first_name":"Nils B.","full_name":"Becker, Nils B."},{"last_name":"Kaizu","first_name":"Kazunari","full_name":"Kaizu, Kazunari"},{"full_name":"Takahashi, Koichi","last_name":"Takahashi","first_name":"Koichi"},{"first_name":"Marileen","last_name":"Dogterom","full_name":"Dogterom, Marileen"},{"last_name":"ten Wolde","first_name":"Pieter Rein","full_name":"ten Wolde, Pieter Rein"}],"volume":150,"publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"doi":"10.1063/1.5064867","date_created":"2020-01-30T10:34:36Z","article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-02-07T00:00:00Z","department":[{"_id":"GaTk"}],"date_updated":"2023-09-06T14:59:28Z","type":"journal_article","intvolume":"       150","month":"02","day":"07","issue":"5","title":"eGFRD in all dimensions","article_processing_charge":"No","arxiv":1,"language":[{"iso":"eng"}],"publisher":"AIP Publishing","oa":1,"year":"2019","citation":{"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.","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.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2019. <a href=\"https://doi.org/10.1063/1.5064867\">https://doi.org/10.1063/1.5064867</a>.","ieee":"T. R. Sokolowski <i>et al.</i>, “eGFRD in all dimensions,” <i>The Journal of Chemical Physics</i>, vol. 150, no. 5. AIP Publishing, 2019.","ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. <i>The Journal of Chemical Physics</i>. 2019;150(5). doi:<a href=\"https://doi.org/10.1063/1.5064867\">10.1063/1.5064867</a>","mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” <i>The Journal of Chemical Physics</i>, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:<a href=\"https://doi.org/10.1063/1.5064867\">10.1063/1.5064867</a>.","apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5064867\">https://doi.org/10.1063/1.5064867</a>"},"publication":"The Journal of Chemical Physics","article_number":"054108","_id":"7422","quality_controlled":"1"},{"day":"01","title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","issue":"1","month":"02","intvolume":"        55","type":"journal_article","date_updated":"2023-09-06T14:58:39Z","department":[{"_id":"LaEr"}],"publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","_id":"7423","quality_controlled":"1","citation":{"mla":"Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:<a href=\"https://doi.org/10.1214/18-aihp888\">10.1214/18-aihp888</a>.","apa":"Akemann, G., Checinski, T., Liu, D., &#38; Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-aihp888\">https://doi.org/10.1214/18-aihp888</a>","ama":"Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>. 2019;55(1):441-479. doi:<a href=\"https://doi.org/10.1214/18-aihp888\">10.1214/18-aihp888</a>","ieee":"G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.","chicago":"Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-aihp888\">https://doi.org/10.1214/18-aihp888</a>.","short":"G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479.","ista":"Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479."},"oa":1,"year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Institute of Mathematical Statistics","arxiv":1,"article_type":"original","doi":"10.1214/18-aihp888","publication_identifier":{"issn":["0246-0203"]},"date_created":"2020-01-30T10:36:50Z","author":[{"first_name":"Gernot","last_name":"Akemann","full_name":"Akemann, Gernot"},{"last_name":"Checinski","first_name":"Tomasz","full_name":"Checinski, Tomasz"},{"last_name":"Liu","first_name":"Dangzheng","full_name":"Liu, Dangzheng","id":"2F947E34-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Strahov","first_name":"Eugene","full_name":"Strahov, Eugene"}],"publication_status":"published","volume":55,"status":"public","external_id":{"arxiv":["1704.05224"],"isi":["000456070200013"]},"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-02-01T00:00:00Z","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1704.05224","open_access":"1"}],"page":"441-479","abstract":[{"text":"We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors.","lang":"eng"}]},{"article_processing_charge":"No","language":[{"iso":"eng"}],"arxiv":1,"publisher":"EMS Press","oa":1,"year":"2019","citation":{"ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.","chicago":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” <i>Documenta Mathematica</i>. EMS Press, 2019. <a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">https://doi.org/10.25537/dm.2019v24.1135-1177</a>.","ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. <i>Documenta Mathematica</i>. 2019;24:1135-1177. doi:<a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">10.25537/dm.2019v24.1135-1177</a>","ieee":"T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” <i>Documenta Mathematica</i>, vol. 24. EMS Press, pp. 1135–1177, 2019.","apa":"Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. <i>Documenta Mathematica</i>. EMS Press. <a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">https://doi.org/10.25537/dm.2019v24.1135-1177</a>","mla":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” <i>Documenta Mathematica</i>, vol. 24, EMS Press, 2019, pp. 1135–77, doi:<a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">10.25537/dm.2019v24.1135-1177</a>."},"publication":"Documenta Mathematica","quality_controlled":"1","_id":"7436","has_accepted_license":"1","date_updated":"2023-10-17T07:42:21Z","department":[{"_id":"TaHa"}],"type":"journal_article","month":"05","intvolume":"        24","day":"20","title":"On derived equivalences of k3 surfaces in positive characteristic","ddc":["510"],"page":"1135-1177","abstract":[{"text":"For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:58Z","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2019-05-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000517806400019"],"arxiv":["1809.08970"]},"status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"author":[{"first_name":"Tanya K","last_name":"Srivastava","id":"4D046628-F248-11E8-B48F-1D18A9856A87","full_name":"Srivastava, Tanya K"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_size":469730,"date_updated":"2020-07-14T12:47:58Z","file_id":"7438","checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","file_name":"2019_DocumMath_Srivastava.pdf","date_created":"2020-02-03T06:26:12Z"}],"scopus_import":"1","publication_status":"published","volume":24,"doi":"10.25537/dm.2019v24.1135-1177","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"date_created":"2020-02-02T23:01:06Z","article_type":"original"},{"date_created":"2020-02-02T23:01:06Z","publication_identifier":{"isbn":["9781510886988"]},"isi":1,"external_id":{"arxiv":["1810.07766"],"isi":["000684034307036"]},"status":"public","scopus_import":"1","publication_status":"published","volume":"2019-June","author":[{"full_name":"Yu, Chen","last_name":"Yu","first_name":"Chen"},{"last_name":"Tang","first_name":"Hanlin","full_name":"Tang, Hanlin"},{"full_name":"Renggli, Cedric","first_name":"Cedric","last_name":"Renggli"},{"full_name":"Kassing, Simon","first_name":"Simon","last_name":"Kassing"},{"full_name":"Singla, Ankit","first_name":"Ankit","last_name":"Singla"},{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","first_name":"Ce","full_name":"Zhang, Ce"},{"first_name":"Ji","last_name":"Liu","full_name":"Liu, Ji"}],"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-06-01T00:00:00Z","page":"12481-12512","abstract":[{"text":"Most of today's distributed machine learning systems assume reliable networks: whenever two machines exchange information (e.g., gradients or models), the network should guarantee the delivery of the message. At the same time, recent work exhibits the impressive tolerance of machine learning algorithms to errors or noise arising from relaxed communication or synchronization. In this paper, we connect these two trends, and consider the following question: Can we design machine learning systems that are tolerant to network unreliability during training? With this motivation, we focus on a theoretical problem of independent interest-given a standard distributed parameter server architecture, if every communication between the worker and the server has a non-zero probability p of being dropped, does there exist an algorithm that still converges, and at what speed? The technical contribution of this paper is a novel theoretical analysis proving that distributed learning over unreliable network can achieve comparable convergence rate to centralized or distributed learning over reliable networks. Further, we prove that the influence of the packet drop rate diminishes with the growth of the number of parameter servers. We map this theoretical result onto a real-world scenario, training deep neural networks over an unreliable network layer, and conduct network simulation to validate the system improvement by allowing the networks to be unreliable.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1810.07766","open_access":"1"}],"month":"06","title":"Distributed learning over unreliable networks","day":"01","date_updated":"2023-09-06T15:21:48Z","department":[{"_id":"DaAl"}],"type":"conference","citation":{"ama":"Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks. In: <i>36th International Conference on Machine Learning, ICML 2019</i>. Vol 2019-June. IMLS; 2019:12481-12512.","ieee":"C. Yu <i>et al.</i>, “Distributed learning over unreliable networks,” in <i>36th International Conference on Machine Learning, ICML 2019</i>, Long Beach, CA, United States, 2019, vol. 2019–June, pp. 12481–12512.","mla":"Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” <i>36th International Conference on Machine Learning, ICML 2019</i>, vol. 2019–June, IMLS, 2019, pp. 12481–512.","apa":"Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., … Liu, J. (2019). Distributed learning over unreliable networks. In <i>36th International Conference on Machine Learning, ICML 2019</i> (Vol. 2019–June, pp. 12481–12512). Long Beach, CA, United States: IMLS.","ista":"Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu J. 2019. Distributed learning over unreliable networks. 36th International Conference on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning vol. 2019–June, 12481–12512.","short":"C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang, J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS, 2019, pp. 12481–12512.","chicago":"Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.” In <i>36th International Conference on Machine Learning, ICML 2019</i>, 2019–June:12481–512. IMLS, 2019."},"_id":"7437","quality_controlled":"1","publication":"36th International Conference on Machine Learning, ICML 2019","arxiv":1,"language":[{"iso":"eng"}],"publisher":"IMLS","article_processing_charge":"No","year":"2019","conference":{"start_date":"2019-06-10","name":"ICML: International Conference on Machine Learning","end_date":"2019-06-15","location":"Long Beach, CA, United States"},"oa":1},{"date_published":"2019-06-03T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:58Z","ddc":["530"],"abstract":[{"text":"We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition.","lang":"eng"}],"article_type":"original","doi":"10.22331/q-2019-06-03-150","publication_identifier":{"issn":["2521-327X"]},"date_created":"2020-02-05T09:57:57Z","author":[{"full_name":"Vukics, A.","last_name":"Vukics","first_name":"A."},{"full_name":"Dombi, A.","last_name":"Dombi","first_name":"A."},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"last_name":"Domokos","first_name":"P.","full_name":"Domokos, P."}],"file":[{"date_created":"2020-02-11T09:25:23Z","file_name":"2019_Quantum_Vukics.pdf","checksum":"26b9ba8f0155d183f1ee55295934a17f","file_id":"7483","file_size":5805248,"date_updated":"2020-07-14T12:47:58Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication_status":"published","volume":3,"status":"public","external_id":{"arxiv":["1809.09737"],"isi":["000469987500004"]},"isi":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"150","publication":"Quantum","quality_controlled":"1","_id":"7451","citation":{"short":"A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019).","ista":"Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 3, 150.","chicago":"Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. <a href=\"https://doi.org/10.22331/q-2019-06-03-150\">https://doi.org/10.22331/q-2019-06-03-150</a>.","ieee":"A. Vukics, A. Dombi, J. M. Fink, and P. Domokos, “Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition,” <i>Quantum</i>, vol. 3. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019.","ama":"Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. <i>Quantum</i>. 2019;3. doi:<a href=\"https://doi.org/10.22331/q-2019-06-03-150\">10.22331/q-2019-06-03-150</a>","apa":"Vukics, A., Dombi, A., Fink, J. M., &#38; Domokos, P. (2019). Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/q-2019-06-03-150\">https://doi.org/10.22331/q-2019-06-03-150</a>","mla":"Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” <i>Quantum</i>, vol. 3, 150, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019, doi:<a href=\"https://doi.org/10.22331/q-2019-06-03-150\">10.22331/q-2019-06-03-150</a>."},"oa":1,"year":"2019","article_processing_charge":"No","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","day":"03","title":"Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition","intvolume":"         3","month":"06","type":"journal_article","date_updated":"2023-09-07T14:57:39Z","has_accepted_license":"1","department":[{"_id":"JoFi"}]},{"publication":"Computing and Software Science","_id":"7453","quality_controlled":"1","citation":{"chicago":"Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius Mikučionis. “Continuous-Time Models for System Design and Analysis.” In <i>Computing and Software Science</i>, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77. LNCS. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">https://doi.org/10.1007/978-3-319-91908-9_22</a>.","ista":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time models for system design and analysis. In: Computing and Software Science. Lecture Notes in Computer Science, vol. 10000, 452–477.","short":"R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B. Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature, 2019, pp. 452–477.","mla":"Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.” <i>Computing and Software Science</i>, edited by Bernhard Steffen and Gerhard Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:<a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">10.1007/978-3-319-91908-9_22</a>.","apa":"Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., &#38; Mikučionis, M. (2019). Continuous-time models for system design and analysis. In B. Steffen &#38; G. Woeginger (Eds.), <i>Computing and Software Science</i> (Vol. 10000, pp. 452–477). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">https://doi.org/10.1007/978-3-319-91908-9_22</a>","ama":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time models for system design and analysis. In: Steffen B, Woeginger G, eds. <i>Computing and Software Science</i>. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:<a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">10.1007/978-3-319-91908-9_22</a>","ieee":"R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time models for system design and analysis,” in <i>Computing and Software Science</i>, vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477."},"oa":1,"year":"2019","project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"article_processing_charge":"No","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS, funded by the Danish National Research Foundation and the National Science Foundation, China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant LASSO.","publisher":"Springer Nature","language":[{"iso":"eng"}],"day":"05","title":"Continuous-time models for system design and analysis","intvolume":"     10000","month":"10","type":"book_chapter","date_updated":"2022-09-06T08:25:52Z","department":[{"_id":"ToHe"}],"alternative_title":["Lecture Notes in Computer Science"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-10-05T00:00:00Z","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1007/978-3-319-91908-9_22","open_access":"1"}],"page":"452-477","abstract":[{"lang":"eng","text":"We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement."}],"doi":"10.1007/978-3-319-91908-9_22","publication_identifier":{"eisbn":["9783319919089"],"eissn":["0302-9743"],"issn":["1611-3349"],"isbn":["9783319919072"]},"date_created":"2020-02-05T10:51:44Z","author":[{"full_name":"Alur, Rajeev","first_name":"Rajeev","last_name":"Alur"},{"last_name":"Giacobbe","first_name":"Mirco","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Larsen, Kim G.","first_name":"Kim G.","last_name":"Larsen"},{"first_name":"Marius","last_name":"Mikučionis","full_name":"Mikučionis, Marius"}],"scopus_import":"1","publication_status":"published","volume":10000,"series_title":"LNCS","status":"public","editor":[{"first_name":"Bernhard","last_name":"Steffen","full_name":"Steffen, Bernhard"},{"full_name":"Woeginger, Gerhard","last_name":"Woeginger","first_name":"Gerhard"}]},{"author":[{"full_name":"Vadla, Samba Siva","first_name":"Samba Siva","last_name":"Vadla"},{"first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815"},{"full_name":"John, Subish","last_name":"John","first_name":"Subish"},{"first_name":"Gabriel","last_name":"Caruntu","full_name":"Caruntu, Gabriel"},{"full_name":"Roy, Somnath C.","last_name":"Roy","first_name":"Somnath C."}],"type":"journal_article","publication_status":"published","volume":159,"status":"public","date_updated":"2023-02-23T13:08:31Z","day":"15","article_type":"original","title":"Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites","doi":"10.1016/j.scriptamat.2018.09.003","intvolume":"       159","month":"01","publication_identifier":{"issn":["1359-6462"]},"date_created":"2020-02-05T14:19:17Z","page":"33-36","extern":"1","abstract":[{"text":"We report the fabrication of BaTiO3-Ni magnetoelectric nanocomposites comprising of BaTiO3 nanotubes surrounded by Ni matrix. BaTiO3 nanotubes obtained from the hydrothermal transformation of TiO2 have both inner and outer surfaces, which facilitates greater magnetoelectric coupling with the surrounding Ni matrix. The magnetoelectric coupling was studied by measuring the piezoelectric behavior in the presence of an in-plane direct magnetic field. A higher magnetoelectric voltage coefficient of 110 mV/cm·Oe was obtained, because of better coupling between Ni and BaTiO3 through the walls of the nanotubes. Such nanocomposite developed directly on Ti substrate may lead to efficient fabrication of magnetoelectric devices.","lang":"eng"}],"year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Elsevier","publication":"Scripta Materialia","_id":"7459","date_published":"2019-01-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"mla":"Vadla, Samba Siva, et al. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.” <i>Scripta Materialia</i>, vol. 159, Elsevier, 2019, pp. 33–36, doi:<a href=\"https://doi.org/10.1016/j.scriptamat.2018.09.003\">10.1016/j.scriptamat.2018.09.003</a>.","apa":"Vadla, S. S., Costanzo, T., John, S., Caruntu, G., &#38; Roy, S. C. (2019). Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. <i>Scripta Materialia</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scriptamat.2018.09.003\">https://doi.org/10.1016/j.scriptamat.2018.09.003</a>","ama":"Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. <i>Scripta Materialia</i>. 2019;159:33-36. doi:<a href=\"https://doi.org/10.1016/j.scriptamat.2018.09.003\">10.1016/j.scriptamat.2018.09.003</a>","ieee":"S. S. Vadla, T. Costanzo, S. John, G. Caruntu, and S. C. Roy, “Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites,” <i>Scripta Materialia</i>, vol. 159. Elsevier, pp. 33–36, 2019.","chicago":"Vadla, Samba Siva, Tommaso Costanzo, Subish John, Gabriel Caruntu, and Somnath C. Roy. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.” <i>Scripta Materialia</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.scriptamat.2018.09.003\">https://doi.org/10.1016/j.scriptamat.2018.09.003</a>.","ista":"Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. 2019. Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 159, 33–36.","short":"S.S. Vadla, T. Costanzo, S. John, G. Caruntu, S.C. Roy, Scripta Materialia 159 (2019) 33–36."},"oa_version":"None"},{"month":"06","title":"Map inference via block-coordinate Frank-Wolfe algorithm","day":"01","department":[{"_id":"VlKo"}],"ec_funded":1,"date_updated":"2023-09-07T14:54:24Z","type":"conference","citation":{"chicago":"Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, Vol. 2019–June. IEEE, 2019. <a href=\"https://doi.org/10.1109/CVPR.2019.01140\">https://doi.org/10.1109/CVPR.2019.01140</a>.","ista":"Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2019–June, 11138–11147.","short":"P. Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2019.","mla":"Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, vol. 2019–June, 11138–11147, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/CVPR.2019.01140\">10.1109/CVPR.2019.01140</a>.","apa":"Swoboda, P., &#38; Kolmogorov, V. (2019). Map inference via block-coordinate Frank-Wolfe algorithm. In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i> (Vol. 2019–June). Long Beach, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2019.01140\">https://doi.org/10.1109/CVPR.2019.01140</a>","ieee":"P. Swoboda and V. Kolmogorov, “Map inference via block-coordinate Frank-Wolfe algorithm,” in <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, Long Beach, CA, United States, 2019, vol. 2019–June.","ama":"Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm. In: <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>. Vol 2019-June. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/CVPR.2019.01140\">10.1109/CVPR.2019.01140</a>"},"quality_controlled":"1","_id":"7468","publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","article_number":"11138-11147","language":[{"iso":"eng"}],"publisher":"IEEE","arxiv":1,"article_processing_charge":"No","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"year":"2019","oa":1,"conference":{"start_date":"2019-06-15","name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2019-06-20","location":"Long Beach, CA, United States"},"date_created":"2020-02-09T23:00:52Z","publication_identifier":{"isbn":["9781728132938"],"issn":["10636919"]},"doi":"10.1109/CVPR.2019.01140","isi":1,"external_id":{"arxiv":["1806.05049"],"isi":["000542649304076"]},"status":"public","volume":"2019-June","publication_status":"published","scopus_import":"1","author":[{"last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"oa_version":"Preprint","date_published":"2019-06-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems."}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.05049","open_access":"1"}]},{"publication":"Nature Cell Biology","_id":"7476","quality_controlled":"1","citation":{"chicago":"Andersen, Marianne Stemann, Edouard B Hannezo, Svetlana Ulyanchenko, Soline Estrach, Yasuko Antoku, Sabrina Pisano, Kim E. Boonekamp, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” <i>Nature Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41556-019-0362-x\">https://doi.org/10.1038/s41556-019-0362-x</a>.","short":"M.S. Andersen, E.B. Hannezo, S. Ulyanchenko, S. Estrach, Y. Antoku, S. Pisano, K.E. Boonekamp, S. Sendrup, M. Maimets, M.T. Pedersen, J.V. Johansen, D.L. Clement, C.C. Feral, B.D. Simons, K.B. Jensen, Nature Cell Biology 21 (2019) 924–932.","ista":"Andersen MS, Hannezo EB, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons BD, Jensen KB. 2019. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. 21(8), 924–932.","apa":"Andersen, M. S., Hannezo, E. B., Ulyanchenko, S., Estrach, S., Antoku, Y., Pisano, S., … Jensen, K. B. (2019). Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-019-0362-x\">https://doi.org/10.1038/s41556-019-0362-x</a>","mla":"Andersen, Marianne Stemann, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” <i>Nature Cell Biology</i>, vol. 21, no. 8, Springer Nature, 2019, pp. 924–32, doi:<a href=\"https://doi.org/10.1038/s41556-019-0362-x\">10.1038/s41556-019-0362-x</a>.","ama":"Andersen MS, Hannezo EB, Ulyanchenko S, et al. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. <i>Nature Cell Biology</i>. 2019;21(8):924-932. doi:<a href=\"https://doi.org/10.1038/s41556-019-0362-x\">10.1038/s41556-019-0362-x</a>","ieee":"M. S. Andersen <i>et al.</i>, “Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states,” <i>Nature Cell Biology</i>, vol. 21, no. 8. Springer Nature, pp. 924–932, 2019."},"oa":1,"extern":"1","year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Springer Nature","pmid":1,"day":"01","title":"Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states","issue":"8","month":"08","intvolume":"        21","type":"journal_article","date_updated":"2021-01-12T08:13:47Z","date_published":"2019-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978139/","open_access":"1"}],"page":"924-932","abstract":[{"lang":"eng","text":"The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent maintenance remain poorly understood. Here, we apply large-scale quantitative fate mapping to define the patterns of cell fate behaviour during SG development and maintenance. We show that the SG develops from a defined number of lineage-restricted progenitors that undergo a programme of independent and stochastic cell fate decisions. Following an expansion phase, equipotent progenitors transition into a phase of homeostatic turnover, which is correlated with changes in the mechanical properties of the stroma and spatial restrictions on gland size. Expression of the oncogene KrasG12D results in a release from these constraints and unbridled gland expansion. Quantitative clonal fate analysis reveals that, during this phase, the primary effect of the Kras oncogene is to drive a constant fate bias with little effect on cell division rates. These findings provide insight into the developmental programme of the SG, as well as the mechanisms that drive tumour progression and gland dysfunction."}],"article_type":"original","doi":"10.1038/s41556-019-0362-x","publication_identifier":{"issn":["1465-7392","1476-4679"]},"date_created":"2020-02-11T08:43:49Z","author":[{"last_name":"Andersen","first_name":"Marianne Stemann","full_name":"Andersen, Marianne Stemann"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ulyanchenko, Svetlana","last_name":"Ulyanchenko","first_name":"Svetlana"},{"last_name":"Estrach","first_name":"Soline","full_name":"Estrach, Soline"},{"full_name":"Antoku, Yasuko","last_name":"Antoku","first_name":"Yasuko"},{"full_name":"Pisano, Sabrina","last_name":"Pisano","first_name":"Sabrina"},{"first_name":"Kim E.","last_name":"Boonekamp","full_name":"Boonekamp, Kim E."},{"full_name":"Sendrup, Sarah","first_name":"Sarah","last_name":"Sendrup"},{"full_name":"Maimets, Martti","first_name":"Martti","last_name":"Maimets"},{"last_name":"Pedersen","first_name":"Marianne Terndrup","full_name":"Pedersen, Marianne Terndrup"},{"last_name":"Johansen","first_name":"Jens V.","full_name":"Johansen, Jens V."},{"full_name":"Clement, Ditte L.","last_name":"Clement","first_name":"Ditte L."},{"full_name":"Feral, Chloe C.","last_name":"Feral","first_name":"Chloe C."},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"last_name":"Jensen","first_name":"Kim B.","full_name":"Jensen, Kim B."}],"publication_status":"published","volume":21,"external_id":{"pmid":["31358966"]},"status":"public"},{"publication_identifier":{"issn":["15505499"],"isbn":["9781728148038"]},"doi":"10.1109/ICCV.2019.00144","date_created":"2020-02-11T09:06:57Z","author":[{"last_name":"Bui Thi Mai","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"volume":"2019-October","scopus_import":"1","file":[{"relation":"main_file","file_size":735768,"date_updated":"2020-07-14T12:47:59Z","access_level":"open_access","creator":"bphuong","content_type":"application/pdf","file_id":"7480","date_created":"2020-02-11T09:06:39Z","file_name":"main.pdf","checksum":"7b77fb5c2d27c4c37a7612ba46a66117"}],"publication_status":"published","external_id":{"isi":["000531438101047"]},"status":"public","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-10-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:59Z","oa_version":"Submitted Version","ddc":["000"],"abstract":[{"text":"Multi-exit architectures, in which a stack of processing layers is interleaved with early output layers, allow the processing of a test example to stop early and thus save computation time and/or energy.  In this work, we propose a new training procedure for multi-exit architectures based on the principle of knowledge distillation. The method encourage searly exits to mimic later, more accurate exits, by matching their output probabilities.\r\nExperiments  on  CIFAR100  and  ImageNet  show  that distillation-based training significantly improves the accuracy of early exits while maintaining state-of-the-art accuracy  for  late  ones.   The  method  is  particularly  beneficial when  training  data  is  limited  and  it  allows  a  straightforward extension to semi-supervised learning,i.e. making use of unlabeled data at training time. Moreover, it takes only afew lines to implement and incurs almost no computational overhead at training time, and none at all at test time.","lang":"eng"}],"page":"1355-1364","day":"01","title":"Distillation-based training for multi-exit architectures","month":"10","type":"conference","department":[{"_id":"ChLa"}],"ec_funded":1,"date_updated":"2023-09-08T11:11:12Z","has_accepted_license":"1","publication":"IEEE International Conference on Computer Vision","_id":"7479","quality_controlled":"1","citation":{"mla":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” <i>IEEE International Conference on Computer Vision</i>, vol. 2019–October, IEEE, 2019, pp. 1355–64, doi:<a href=\"https://doi.org/10.1109/ICCV.2019.00144\">10.1109/ICCV.2019.00144</a>.","apa":"Phuong, M., &#38; Lampert, C. (2019). Distillation-based training for multi-exit architectures. In <i>IEEE International Conference on Computer Vision</i> (Vol. 2019–October, pp. 1355–1364). Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2019.00144\">https://doi.org/10.1109/ICCV.2019.00144</a>","ieee":"M. Phuong and C. Lampert, “Distillation-based training for multi-exit architectures,” in <i>IEEE International Conference on Computer Vision</i>, Seoul, Korea, 2019, vol. 2019–October, pp. 1355–1364.","ama":"Phuong M, Lampert C. Distillation-based training for multi-exit architectures. In: <i>IEEE International Conference on Computer Vision</i>. Vol 2019-October. IEEE; 2019:1355-1364. doi:<a href=\"https://doi.org/10.1109/ICCV.2019.00144\">10.1109/ICCV.2019.00144</a>","chicago":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” In <i>IEEE International Conference on Computer Vision</i>, 2019–October:1355–64. IEEE, 2019. <a href=\"https://doi.org/10.1109/ICCV.2019.00144\">https://doi.org/10.1109/ICCV.2019.00144</a>.","short":"M. Phuong, C. Lampert, in:, IEEE International Conference on Computer Vision, IEEE, 2019, pp. 1355–1364.","ista":"Phuong M, Lampert C. 2019. Distillation-based training for multi-exit architectures. IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision vol. 2019–October, 1355–1364."},"oa":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9418"}]},"conference":{"start_date":"2019-10-27","name":"ICCV: International Conference on Computer Vision","end_date":"2019-11-02","location":"Seoul, Korea"},"year":"2019","article_processing_charge":"No","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publisher":"IEEE"},{"publication_identifier":{"isbn":["9780128132517"],"eisbn":["9780128132524"]},"month":"02","doi":"10.1016/B978-0-12-809633-8.90721-0","date_created":"2020-02-23T23:00:36Z","day":"06","title":"Social immunity","status":"public","external_id":{"isi":["000248989500026"]},"department":[{"_id":"SyCr"}],"editor":[{"full_name":"Choe, Jae","last_name":"Choe","first_name":"Jae"}],"date_updated":"2023-09-08T11:12:04Z","isi":1,"edition":"2","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer"},{"orcid":"0000-0002-8696-6978","full_name":"Kutzer, Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer","first_name":"Megan"}],"type":"book_chapter","publication_status":"published","scopus_import":"1","oa_version":"None","citation":{"ieee":"S. Cremer and M. Kutzer, “Social immunity,” in <i>Encyclopedia of Animal Behavior</i>, 2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.","ama":"Cremer S, Kutzer M. Social immunity. In: Choe J, ed. <i>Encyclopedia of Animal Behavior</i>. 2nd ed. Elsevier; 2019:747-755. doi:<a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">10.1016/B978-0-12-809633-8.90721-0</a>","apa":"Cremer, S., &#38; Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), <i>Encyclopedia of Animal Behavior</i> (2nd ed., pp. 747–755). Elsevier. <a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">https://doi.org/10.1016/B978-0-12-809633-8.90721-0</a>","mla":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” <i>Encyclopedia of Animal Behavior</i>, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:<a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">10.1016/B978-0-12-809633-8.90721-0</a>.","short":"S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior, 2nd ed., Elsevier, 2019, pp. 747–755.","ista":"Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior. , 747–755.","chicago":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In <i>Encyclopedia of Animal Behavior</i>, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. <a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">https://doi.org/10.1016/B978-0-12-809633-8.90721-0</a>."},"publication":"Encyclopedia of Animal Behavior","_id":"7513","date_published":"2019-02-06T00:00:00Z","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","publisher":"Elsevier","language":[{"iso":"eng"}],"year":"2019","abstract":[{"lang":"eng","text":"Social insects (i.e., ants, termites and the social bees and wasps) protect their colonies from disease using a combination of individual immunity and collectively performed defenses, termed social immunity. The first line of social immune defense is sanitary care, which is performed by colony members to protect their pathogen-exposed nestmates from developing an infection. If sanitary care fails and an infection becomes established, a second line of social immune defense is deployed to stop disease transmission within the colony and to protect the valuable queens, which together with the males are the reproductive individuals of the colony. Insect colonies are separated into these reproductive individuals and the sterile worker force, forming a superorganismal reproductive unit reminiscent of the differentiated germline and soma in a multicellular organism. Ultimately, the social immune response preserves the germline of the superorganism insect colony and increases overall fitness of the colony in case of disease. "}],"page":"747-755"},{"date_created":"2020-02-26T08:46:40Z","month":"10","title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","day":"08","ec_funded":1,"department":[{"_id":"RoSe"}],"date_updated":"2023-09-07T13:12:41Z","status":"public","scopus_import":1,"type":"preprint","publication_status":"draft","author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","first_name":"Andreas","last_name":"Deuchert"},{"last_name":"Mayer","first_name":"Simon","full_name":"Mayer, Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"oa_version":"Preprint","citation":{"ista":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372, .","short":"A. Deuchert, S. Mayer, R. Seiringer, ArXiv:1910.03372 (n.d.).","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv:1910.03372</i>. ArXiv, n.d.","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” <i>arXiv:1910.03372</i>. ArXiv.","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv:191003372</i>.","apa":"Deuchert, A., Mayer, S., &#38; Seiringer, R. (n.d.). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv:1910.03372</i>. ArXiv.","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv:1910.03372</i>, ArXiv."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7524","date_published":"2019-10-08T00:00:00Z","publication":"arXiv:1910.03372","publisher":"ArXiv","language":[{"iso":"eng"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"year":"2019","abstract":[{"lang":"eng","text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$ and inverse temperature $\\beta$ differs from the one of the non-interacting system by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$. Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ = \\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho \\ll 1$ and if $\\beta \\rho \\gtrsim 1$."}],"page":"61","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.03372"}],"oa":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"7790"},{"status":"public","relation":"dissertation_contains","id":"7514"}]}},{"date_created":"2020-02-28T10:03:24Z","publication_identifier":{"issn":["1049-5258"]},"volume":32,"publication_status":"published","author":[{"first_name":"Chris","last_name":"Wendler","full_name":"Wendler, Chris"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Püschel, Markus","last_name":"Püschel","first_name":"Markus"}],"isi":1,"external_id":{"isi":["000534424300084"],"arxiv":["1909.02253"]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-12-01T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs.","lang":"eng"}],"page":"927-938","main_file_link":[{"open_access":"1","url":"http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks"}],"title":"Powerset convolutional neural networks","day":"01","intvolume":"        32","month":"12","type":"conference","department":[{"_id":"DaAl"}],"ec_funded":1,"date_updated":"2023-09-08T11:13:52Z","_id":"7542","quality_controlled":"1","citation":{"mla":"Wendler, Chris, et al. <i>Powerset Convolutional Neural Networks</i>. Vol. 32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.","apa":"Wendler, C., Alistarh, D.-A., &#38; Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada: Neural Information Processing Systems Foundation.","ieee":"C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.","ama":"Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks. In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.","chicago":"Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation, 2019.","ista":"Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks. NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.","short":"C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing Systems Foundation, 2019, pp. 927–938."},"year":"2019","oa":1,"conference":{"location":"Vancouver, Canada","name":"NIPS: Conference on Neural Information Processing Systems","end_date":"2019-12-14","start_date":"2019-12-08"},"publisher":"Neural Information Processing Systems Foundation","language":[{"iso":"eng"}],"arxiv":1,"article_processing_charge":"No","project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"type":"journal_article","date_updated":"2021-01-12T08:14:07Z","title":"Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans","issue":"11","day":"01","pmid":1,"month":"11","intvolume":"         9","extern":"1","year":"2019","publisher":"Genetics Society of America","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","_id":"7547","publication":"G3: Genes, Genomes, Genetics","citation":{"ama":"Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. <i>G3: Genes, Genomes, Genetics</i>. 2019;9(11):3703-3714. doi:<a href=\"https://doi.org/10.1534/g3.119.400654\">10.1534/g3.119.400654</a>","ieee":"J. Cohn <i>et al.</i>, “Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” <i>G3: Genes, Genomes, Genetics</i>, vol. 9, no. 11. Genetics Society of America, pp. 3703–3714, 2019.","apa":"Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H. R., &#38; Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/g3.119.400654\">https://doi.org/10.1534/g3.119.400654</a>","mla":"Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” <i>G3: Genes, Genomes, Genetics</i>, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14, doi:<a href=\"https://doi.org/10.1534/g3.119.400654\">10.1534/g3.119.400654</a>.","ista":"Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT. 2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. 9(11), 3703–3714.","short":"J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T. Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.","chicago":"Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono, H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2019. <a href=\"https://doi.org/10.1534/g3.119.400654\">https://doi.org/10.1534/g3.119.400654</a>."},"publication_status":"published","volume":9,"author":[{"first_name":"Jesse","last_name":"Cohn","full_name":"Cohn, Jesse"},{"first_name":"Vivek","last_name":"Dwivedi","full_name":"Dwivedi, Vivek"},{"full_name":"Valperga, Giulio","first_name":"Giulio","last_name":"Valperga"},{"first_name":"Nicole","last_name":"Zarate","full_name":"Zarate, Nicole"},{"first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"},{"first_name":"H. Robert","last_name":"Horvitz","full_name":"Horvitz, H. Robert"},{"full_name":"Pierce, Jonathan T.","last_name":"Pierce","first_name":"Jonathan T."}],"external_id":{"pmid":["31519744"]},"status":"public","article_type":"original","date_created":"2020-02-28T10:44:27Z","doi":"10.1534/g3.119.400654","publication_identifier":{"issn":["2160-1836"]},"page":"3703-3714","abstract":[{"text":"The BH3-only family of proteins is key for initiating apoptosis in a variety of contexts, and may also contribute to non-apoptotic cellular processes. Historically, the nematode Caenorhabditis elegans has provided a powerful system for studying and identifying conserved regulators of BH3-only proteins. In C. elegans, the BH3-only protein egl-1 is expressed during development to cell-autonomously trigger most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed after development in the sensory neuron pair URX without inducing apoptosis. We used genetic screening and epistasis analysis to determine that its transcription is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family proteins are also expressed in the adult nervous system of mammals, we suggest that studying egl-1 expression in URX may shed light on mechanisms that regulate conserved family members in higher organisms.","lang":"eng"}],"date_published":"2019-11-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"extern":"1","abstract":[{"text":"Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils is a well-established hallmark of Alzheimer’s disease, the complex mechanisms linking this process to neurodegeneration are still incompletely understood. The nematode worm C. elegans is a valuable model organism through which to study these mechanisms because of its simple nervous system and its relatively short lifespan. Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study the toxic effects of the overexpression of Aβ in the muscle or nervous systems. However, the wide variety of effects associated with the tissue-level overexpression of Aβ makes it difficult to single out and study specific cellular mechanisms related to the onset of Alzheimer’s disease. Here, to better understand how to investigate the early events affecting neuronal signalling, we created a C. elegans model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural assays, we found that the Aβ42-expressing animals displayed a subtle modulation of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG neurons in young Aβ42-expressing nematodes were activated more strongly than in control animals, and that neuronal activation remained intact until old age. Taken together, our results suggest that Aβ42-expression in this very subtle model of AD is sufficient to modulate the behavioural response but not strong enough to generate significant neurotoxicity, suggesting that slightly more aggressive perturbations will enable effectively studies of the links between the modulation of a physiological response and its associated neurotoxicity.","lang":"eng"}],"year":"2019","language":[{"iso":"eng"}],"publisher":"Public Library of Science","article_processing_charge":"No","quality_controlled":"1","_id":"7548","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-05-31T00:00:00Z","article_number":"e0217746","publication":"PLOS ONE","citation":{"ieee":"T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo, “Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response,” <i>PLOS ONE</i>, vol. 14, no. 5. Public Library of Science, 2019.","ama":"Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. <i>PLOS ONE</i>. 2019;14(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0217746\">10.1371/journal.pone.0217746</a>","mla":"Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” <i>PLOS ONE</i>, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pone.0217746\">10.1371/journal.pone.0217746</a>.","apa":"Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., &#38; Vendruscolo, M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. <i>PLOS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0217746\">https://doi.org/10.1371/journal.pone.0217746</a>","ista":"Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. 14(5), e0217746.","short":"T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo, PLOS ONE 14 (2019).","chicago":"Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson, Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” <i>PLOS ONE</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pone.0217746\">https://doi.org/10.1371/journal.pone.0217746</a>."},"oa_version":"Published Version","type":"journal_article","publication_status":"published","volume":14,"author":[{"last_name":"Sinnige","first_name":"Tessa","full_name":"Sinnige, Tessa"},{"full_name":"Ciryam, Prashanth","first_name":"Prashanth","last_name":"Ciryam"},{"last_name":"Casford","first_name":"Samuel","full_name":"Casford, Samuel"},{"first_name":"Christopher M.","last_name":"Dobson","full_name":"Dobson, Christopher M."},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"}],"date_updated":"2021-01-12T08:14:08Z","status":"public","issue":"5","article_type":"original","title":"Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response","day":"31","date_created":"2020-02-28T10:45:13Z","doi":"10.1371/journal.pone.0217746","month":"05","intvolume":"        14","publication_identifier":{"issn":["1932-6203"]}},{"citation":{"mla":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.","apa":"Portinale, L., &#38; Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho.","ama":"Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. 2019;28(2):425-447.","ieee":"L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.","chicago":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho, 2019.","ista":"Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447.","short":"L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447."},"publication":"Advances in Mathematical Sciences and Applications","quality_controlled":"1","_id":"7550","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"article_processing_charge":"No","arxiv":1,"acknowledgement":"This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375.","publisher":"Gakko Tosho","language":[{"iso":"eng"}],"oa":1,"year":"2019","intvolume":"        28","month":"10","day":"22","issue":"2","title":"Penalization via global functionals of optimal-control problems for dissipative evolution","date_updated":"2022-06-17T07:52:41Z","department":[{"_id":"JaMa"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-10-22T00:00:00Z","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1910.10050","open_access":"1"}],"page":"425-447","abstract":[{"text":"We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. ","lang":"eng"}],"publication_identifier":{"issn":["1343-4373"]},"date_created":"2020-02-28T10:54:41Z","article_type":"original","external_id":{"arxiv":["1910.10050"]},"status":"public","author":[{"last_name":"Portinale","first_name":"Lorenzo","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stefanelli, Ulisse","first_name":"Ulisse","last_name":"Stefanelli"}],"publication_status":"published","volume":28},{"language":[{"iso":"eng"}],"arxiv":1,"publisher":"ArXiv","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","page":"5","year":"2019","abstract":[{"text":"There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. ","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1912.08579","open_access":"1"}],"oa":1,"citation":{"ama":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. <i>arXiv:191208579</i>.","ieee":"W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” <i>arXiv:1912.08579</i>. ArXiv.","mla":"Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv:1912.08579</i>, ArXiv.","apa":"Bialek, W., Gregor, T., &#38; Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. <i>arXiv:1912.08579</i>. ArXiv.","ista":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, .","short":"W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).","chicago":"Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv:1912.08579</i>. ArXiv, n.d."},"oa_version":"Preprint","_id":"7552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-12-18T00:00:00Z","publication":"arXiv:1912.08579","date_updated":"2021-01-12T08:14:09Z","department":[{"_id":"GaTk"}],"external_id":{"arxiv":["1912.08579"]},"status":"public","type":"preprint","publication_status":"submitted","author":[{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"date_created":"2020-02-28T10:57:08Z","month":"12","title":"Action at a distance in transcriptional regulation","day":"18"},{"_id":"7576","quality_controlled":"1","publication":"EPiC Series in Computing","citation":{"short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61.","ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In <i>EPiC Series in Computing</i>, 61:41–61. EasyChair Publications, 2019. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>.","ieee":"F. Immler <i>et al.</i>, “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in <i>EPiC Series in Computing</i>, Montreal, Canada, 2019, vol. 61, pp. 41–61.","ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: <i>EPiC Series in Computing</i>. Vol 61. EasyChair Publications; 2019:41-61. doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>","mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” <i>EPiC Series in Computing</i>, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>.","apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In <i>EPiC Series in Computing</i> (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>"},"year":"2019","oa":1,"conference":{"end_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","location":"Montreal, Canada","start_date":"2019-04-15"},"publisher":"EasyChair Publications","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","day":"25","month":"05","intvolume":"        61","type":"conference","department":[{"_id":"ToHe"}],"has_accepted_license":"1","date_updated":"2021-01-12T08:14:17Z","date_published":"2019-05-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:48:00Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools."}],"page":"41-61","ddc":["000"],"date_created":"2020-03-08T23:00:49Z","publication_identifier":{"eissn":["23987340"]},"doi":"10.29007/m75b","volume":61,"scopus_import":1,"publication_status":"published","file":[{"relation":"main_file","date_updated":"2020-07-14T12:48:00Z","file_size":1934830,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"7617","date_created":"2020-03-24T07:36:36Z","file_name":"2019_ARCH19_Immler.pdf","checksum":"9138977a06fcd6a95976eb4bca875f0c"}],"author":[{"full_name":"Immler, Fabian","first_name":"Fabian","last_name":"Immler"},{"full_name":"Althoff, Matthias","last_name":"Althoff","first_name":"Matthias"},{"first_name":"Luis","last_name":"Benet","full_name":"Benet, Luis"},{"last_name":"Chapoutot","first_name":"Alexandre","full_name":"Chapoutot, Alexandre"},{"full_name":"Chen, Xin","last_name":"Chen","first_name":"Xin"},{"full_name":"Forets, Marcelo","first_name":"Marcelo","last_name":"Forets"},{"first_name":"Luca","last_name":"Geretti","full_name":"Geretti, Luca"},{"last_name":"Kochdumper","first_name":"Niklas","full_name":"Kochdumper, Niklas"},{"last_name":"Sanders","first_name":"David P.","full_name":"Sanders, David P."},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian"}],"status":"public"}]