[{"department":[{"_id":"SyCr"}],"title":"Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion","publist_id":"3538","author":[{"last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"first_name":"Anne","full_name":"Andersen, Anne","last_name":"Andersen"},{"full_name":"Boomsma, Jacobus","last_name":"Boomsma","first_name":"Jacobus"},{"first_name":"David","last_name":"Nash","full_name":"Nash, David"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:41:27Z","citation":{"chicago":"Ugelvig, Line V, Anne Andersen, Jacobus Boomsma, and David Nash. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05592.x.","ista":"Ugelvig LV, Andersen A, Boomsma J, Nash D. 2012. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 21(13), 3224–3236.","mla":"Ugelvig, Line V., et al. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology, vol. 21, no. 13, Wiley-Blackwell, 2012, pp. 3224–36, doi:10.1111/j.1365-294X.2012.05592.x.","ama":"Ugelvig LV, Andersen A, Boomsma J, Nash D. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 2012;21(13):3224-3236. doi:10.1111/j.1365-294X.2012.05592.x","apa":"Ugelvig, L. V., Andersen, A., Boomsma, J., & Nash, D. (2012). Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05592.x","ieee":"L. V. Ugelvig, A. Andersen, J. Boomsma, and D. Nash, “Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion,” Molecular Ecology, vol. 21, no. 13. Wiley-Blackwell, pp. 3224–3236, 2012.","short":"L.V. Ugelvig, A. Andersen, J. Boomsma, D. Nash, Molecular Ecology 21 (2012) 3224–3236."},"status":"public","type":"journal_article","_id":"3156","volume":21,"date_published":"2012-07-01T00:00:00Z","doi":"10.1111/j.1365-294X.2012.05592.x","issue":"13","date_created":"2018-12-11T12:01:43Z","page":"3224 - 3236","day":"01","publication":"Molecular Ecology","language":[{"iso":"eng"}],"year":"2012","publication_status":"published","month":"07","intvolume":" 21","publisher":"Wiley-Blackwell","scopus_import":1,"quality_controlled":"1","oa_version":"None","acknowledgement":"The work was financed by the Danish National Science Research Foundation via a grant to the Centre for Social Evolution.\r\nWe thank four anonymous reviewers for useful comments on the manuscript, J. Bergsten, P. Bina, B. Carlsson, M. Johannesson and A.E. Lomborg for providing additional wingtip samples, A. Illum for assistance in the field, and in particular P.S. Nielsen for mediating the contact to the collectors and the Swedish authorities. Collection was made possible through a permit by the Åtgärdsprogrammet, supported by the Swedish Environmental Protection Agency.","abstract":[{"text":"Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km.","lang":"eng"}]},{"date_created":"2018-12-11T12:01:44Z","doi":"10.1016/j.ejcb.2012.04.002","date_published":"2012-11-01T00:00:00Z","page":"923 - 929","publication":"European Journal of Cell Biology","day":"01","year":"2012","oa":1,"publisher":"Elsevier","quality_controlled":"1","title":"Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo","external_id":{"pmid":["22658956"]},"author":[{"first_name":"Hannah","full_name":"Schachtner, Hannah","last_name":"Schachtner"},{"first_name":"Ang","last_name":"Li","full_name":"Li, Ang"},{"last_name":"Stevenson","full_name":"Stevenson, David","first_name":"David"},{"first_name":"Simon","full_name":"Calaminus, Simon","last_name":"Calaminus"},{"first_name":"Steven","full_name":"Thomas, Steven","last_name":"Thomas"},{"first_name":"Steve","full_name":"Watson, Steve","last_name":"Watson"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Wedlich Söldner, Roland","last_name":"Wedlich Söldner","first_name":"Roland"},{"first_name":"Douglas","last_name":"Strathdee","full_name":"Strathdee, Douglas"},{"first_name":"Laura","last_name":"Machesky","full_name":"Machesky, Laura"}],"publist_id":"3534","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K. Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell Biology 91 (2012) 923–929.","ieee":"H. Schachtner et al., “Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo,” European Journal of Cell Biology, vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.","apa":"Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S., … Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2012.04.002","ama":"Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 2012;91(11-12):923-929. doi:10.1016/j.ejcb.2012.04.002","mla":"Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology, vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:10.1016/j.ejcb.2012.04.002.","ista":"Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK, Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 91(11–12), 923–929.","chicago":"Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas, Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ejcb.2012.04.002."},"issue":"11-12","volume":91,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 91","month":"11","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment.","lang":"eng"}],"department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T07:41:27Z","status":"public","type":"journal_article","_id":"3158"},{"title":"Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components","article_processing_charge":"No","publist_id":"3417","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"full_name":"Peters, Jan","last_name":"Peters","first_name":"Jan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 7(1), 31–41.","chicago":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing. Springer, 2012. https://doi.org/10.1007/s11554-010-0168-3.","ieee":"C. Lampert and J. Peters, “Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components,” Journal of Real-Time Image Processing, vol. 7, no. 1. Springer, pp. 31–41, 2012.","short":"C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.","ama":"Lampert C, Peters J. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 2012;7(1):31-41. doi:10.1007/s11554-010-0168-3","apa":"Lampert, C., & Peters, J. (2012). Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. Springer. https://doi.org/10.1007/s11554-010-0168-3","mla":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:10.1007/s11554-010-0168-3."},"date_created":"2018-12-11T12:02:15Z","date_published":"2012-03-01T00:00:00Z","doi":"10.1007/s11554-010-0168-3","page":"31 - 41","publication":"Journal of Real-Time Image Processing","day":"01","year":"2012","has_accepted_license":"1","oa":1,"publisher":"Springer","quality_controlled":"1","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:46:04Z","ddc":["000"],"date_updated":"2022-05-24T08:05:40Z","status":"public","article_type":"original","type":"journal_article","_id":"3248","issue":"1","volume":7,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-12T10:52:25Z","file_name":"2012_Springer_Lampert.pdf","creator":"kschuh","date_updated":"2020-07-14T12:46:04Z","file_size":2933187,"checksum":"241be47ea50e81a283bcf4c45b07e8cc","file_id":"5958","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1861-8219"],"issn":["1861-8200"]},"intvolume":" 7","month":"03","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz.","lang":"eng"}]},{"_id":"3247","type":"journal_article","status":"public","date_updated":"2021-01-12T07:42:05Z","citation":{"ista":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 13(1), 293–298.","chicago":"Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5.","apa":"Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5","ama":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298. doi:10.1007/s10592-011-0262-5","ieee":"S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics, vol. 13, no. 1. Springer, pp. 293–298, 2012.","short":"S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298.","mla":"Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:10.1007/s10592-011-0262-5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3420","author":[{"first_name":"Sibelle","last_name":"Vilaça","full_name":"Vilaça, Sibelle"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A"},{"full_name":"Lins, Lívia","last_name":"Lins","first_name":"Lívia"},{"last_name":"Santos","full_name":"Santos, Fabrício","first_name":"Fabrício"}],"title":"Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)","department":[{"_id":"JoBo"}],"abstract":[{"text":"The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species.","lang":"eng"}],"oa_version":"None","acknowledgement":"The present study received grants from FAPEMIG, CNPq, Petrobras Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all ethical guidelines and legal requirements of Brazil for sampling and studying an endangered species.\r\nWe thank the Specialist Work Group for the Conservation of Brazilian Merganser for valuable discussions and opinions on this manuscript. We also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing the samples from Argentina, Bradley C. Livezey for sending copies of his papers, and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly improved this manuscript.","quality_controlled":"1","scopus_import":1,"publisher":"Springer","month":"02","intvolume":" 13","publication_status":"published","year":"2012","day":"01","publication":"Conservation Genetics","language":[{"iso":"eng"}],"page":"293 - 298","doi":"10.1007/s10592-011-0262-5","issue":"1","date_published":"2012-02-01T00:00:00Z","volume":13,"date_created":"2018-12-11T12:02:15Z"},{"scopus_import":1,"quality_controlled":"1","publisher":"Cell Press","intvolume":" 22","month":"01","abstract":[{"text":"How cells orchestrate their behavior during collective migration is a long-standing question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated mechanosensitive response that promotes cell polarization and movement persistence during the collective mesendoderm migration in gastrulation.","lang":"eng"}],"oa_version":"None","page":"3 - 4","date_created":"2018-12-11T12:02:14Z","date_published":"2012-01-17T00:00:00Z","doi":"10.1016/j.devcel.2011.12.018","issue":"1","volume":22,"year":"2012","publication_status":"published","publication":"Developmental Cell","language":[{"iso":"eng"}],"day":"17","type":"journal_article","status":"public","_id":"3245","publist_id":"3426","author":[{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"title":"Spurred by resistance mechanosensation in collective migration","department":[{"_id":"CaHe"}],"citation":{"ama":"Behrndt M, Heisenberg C-PJ. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 2012;22(1):3-4. doi:10.1016/j.devcel.2011.12.018","apa":"Behrndt, M., & Heisenberg, C.-P. J. (2012). Spurred by resistance mechanosensation in collective migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.12.018","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Spurred by resistance mechanosensation in collective migration,” Developmental Cell, vol. 22, no. 1. Cell Press, pp. 3–4, 2012.","short":"M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 22 (2012) 3–4.","mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell, vol. 22, no. 1, Cell Press, 2012, pp. 3–4, doi:10.1016/j.devcel.2011.12.018.","ista":"Behrndt M, Heisenberg C-PJ. 2012. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 22(1), 3–4.","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2011.12.018."},"date_updated":"2021-01-12T07:42:05Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"article_number":"041903","author":[{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Walczak","full_name":"Walczak, Aleksandra","first_name":"Aleksandra"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"}],"publist_id":"3386","title":"Optimizing information flow in small genetic networks. III. A self-interacting gene","citation":{"ama":"Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903","apa":"Tkačik, G., Walczak, A., & Bialek, W. (2012). Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.85.041903","short":"G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012).","ieee":"G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks. III. A self-interacting gene,” Physical Review E statistical nonlinear and soft matter physics , vol. 85, no. 4. American Institute of Physics, 2012.","mla":"Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 85, no. 4, 041903, American Institute of Physics, 2012, doi:10.1103/PhysRevE.85.041903.","ista":"Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 85(4), 041903.","chicago":"Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2012. https://doi.org/10.1103/PhysRevE.85.041903."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"American Institute of Physics","acknowledgement":"We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W. M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania.","date_created":"2018-12-11T12:02:20Z","doi":"10.1103/PhysRevE.85.041903","date_published":"2012-04-01T00:00:00Z","year":"2012","publication":" Physical Review E statistical nonlinear and soft matter physics ","day":"01","type":"journal_article","status":"public","_id":"3262","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T07:42:14Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1112.5026"}],"scopus_import":1,"intvolume":" 85","month":"04","abstract":[{"lang":"eng","text":"Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point."}],"oa_version":"Preprint","volume":85,"issue":"4","publication_status":"published","language":[{"iso":"eng"}]},{"publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"416 - 426","doi":"10.1016/j.dam.2011.10.026","date_published":"2012-03-01T00:00:00Z","date_created":"2018-12-11T12:02:18Z","year":"2012","day":"01","publication":"Discrete Applied Mathematics","publist_id":"3397","author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"external_id":{"arxiv":["1005.2305"]},"title":"Generalized roof duality and bisubmodular functions","citation":{"chicago":"Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2011.10.026.","ista":"Kolmogorov V. 2012. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 160(4–5), 416–426.","mla":"Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics, vol. 160, no. 4–5, Elsevier, 2012, pp. 416–26, doi:10.1016/j.dam.2011.10.026.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 416–426.","ieee":"V. Kolmogorov, “Generalized roof duality and bisubmodular functions,” Discrete Applied Mathematics, vol. 160, no. 4–5. Elsevier, pp. 416–426, 2012.","apa":"Kolmogorov, V. (2012). Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2011.10.026","ama":"Kolmogorov V. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 2012;160(4-5):416-426. doi:10.1016/j.dam.2011.10.026"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1005.2305","open_access":"1"}],"month":"03","intvolume":" 160","abstract":[{"text":"Consider a convex relaxation f̂ of a pseudo-Boolean function f. We say that the relaxation is totally half-integral if f̂(x) is a polyhedral function with half-integral extreme points x, and this property is preserved after adding an arbitrary combination of constraints of the form x i=x j, x i=1-x j, and x i=γ where γ∈{0,1,1/2} is a constant. A well-known example is the roof duality relaxation for quadratic pseudo-Boolean functions f. We argue that total half-integrality is a natural requirement for generalizations of roof duality to arbitrary pseudo-Boolean functions. Our contributions are as follows. First, we provide a complete characterization of totally half-integral relaxations f̂ by establishing a one-to-one correspondence with bisubmodular functions. Second, we give a new characterization of bisubmodular functions. Finally, we show some relationships between general totally half-integral relaxations and relaxations based on the roof duality. On the conceptual level, our results show that bisubmodular functions provide a natural generalization of the roof duality approach to higher-order terms. This can be viewed as a non-submodular analogue of the fact that submodular functions generalize the s-t minimum cut problem with non-negative weights to higher-order terms.","lang":"eng"}],"oa_version":"Preprint","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2934"}]},"volume":160,"issue":"4-5","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"3257","department":[{"_id":"VlKo"}],"date_updated":"2023-02-23T11:04:49Z"},{"language":[{"iso":"eng"}],"publication":"Life on Earth and other planetary bodies","day":"01","publication_status":"published","year":"2012","date_created":"2018-12-11T12:02:25Z","date_published":"2012-01-01T00:00:00Z","volume":24,"doi":"10.1007/978-94-007-4966-5_22","page":"387 - 405","oa_version":"None","abstract":[{"text":"The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons.","lang":"eng"}],"intvolume":" 24","month":"01","quality_controlled":"1","publisher":"Springer","alternative_title":["Cellular Origin, Life in Extreme Habitats and Astrobiology"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:20Z","citation":{"chicago":"Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” In Life on Earth and Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22.","ista":"de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and other planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol. 24, 387–405.","mla":"de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22.","short":"H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, Springer, 2012, pp. 387–405.","ieee":"H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be anticipated in the exploration of the solar system?,” in Life on Earth and other planetary bodies, vol. 24, Springer, 2012, pp. 387–405.","ama":"de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and Other Planetary Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22","apa":"de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity be anticipated in the exploration of the solar system? In Life on Earth and other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22"},"department":[{"_id":"NiBa"}],"title":"Can the evolution of multicellularity be anticipated in the exploration of the solar system?","author":[{"orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold","last_name":"de Vladar","first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chela Flores","full_name":"Chela Flores, Julian","first_name":"Julian"}],"publist_id":"3369","_id":"3277","status":"public","type":"book_chapter"},{"acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)","quality_controlled":"1","publisher":"Springer","year":"2012","day":"04","page":"369 - 382","date_published":"2012-05-04T00:00:00Z","doi":"10.1007/978-3-642-28914-9_21","date_created":"2018-12-11T12:02:25Z","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"citation":{"mla":"Jain, Abhishek, et al. Hardness Preserving Constructions of Pseudorandom Functions. Vol. 7194, Springer, 2012, pp. 369–82, doi:10.1007/978-3-642-28914-9_21.","ieee":"A. Jain, K. Z. Pietrzak, and A. Tentes, “Hardness preserving constructions of pseudorandom functions,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 369–382.","short":"A. Jain, K.Z. Pietrzak, A. Tentes, in:, Springer, 2012, pp. 369–382.","apa":"Jain, A., Pietrzak, K. Z., & Tentes, A. (2012). Hardness preserving constructions of pseudorandom functions (Vol. 7194, pp. 369–382). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_21","ama":"Jain A, Pietrzak KZ, Tentes A. Hardness preserving constructions of pseudorandom functions. In: Vol 7194. Springer; 2012:369-382. doi:10.1007/978-3-642-28914-9_21","chicago":"Jain, Abhishek, Krzysztof Z Pietrzak, and Aris Tentes. “Hardness Preserving Constructions of Pseudorandom Functions,” 7194:369–82. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_21.","ista":"Jain A, Pietrzak KZ, Tentes A. 2012. Hardness preserving constructions of pseudorandom functions. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 369–382."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3367","author":[{"full_name":"Jain, Abhishek","last_name":"Jain","first_name":"Abhishek"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"last_name":"Tentes","full_name":"Tentes, Aris","first_name":"Aris"}],"title":"Hardness preserving constructions of pseudorandom functions","abstract":[{"lang":"eng","text":"We show a hardness-preserving construction of a PRF from any length doubling PRG which improves upon known constructions whenever we can put a non-trivial upper bound q on the number of queries to the PRF. Our construction requires only O(logq) invocations to the underlying PRG with each query. In comparison, the number of invocations by the best previous hardness-preserving construction (GGM using Levin's trick) is logarithmic in the hardness of the PRG. For example, starting from an exponentially secure PRG {0,1} n → {0,1} 2n, we get a PRF which is exponentially secure if queried at most q = exp(√n)times and where each invocation of the PRF requires Θ(√n) queries to the underlying PRG. This is much less than the Θ(n) required by known constructions. \r\n"}],"oa_version":"None","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"http://www.iacr.org/archive/tcc2012/tcc2012-index.html"}],"month":"05","intvolume":" 7194","publication_status":"published","language":[{"iso":"eng"}],"volume":7194,"ec_funded":1,"_id":"3279","type":"conference","conference":{"name":"TCC: Theory of Cryptography Conference","location":"Taormina, Sicily, Italy","end_date":"2012-03-21","start_date":"2012-03-19"},"status":"public","date_updated":"2021-01-12T07:42:21Z","department":[{"_id":"KrPi"}]},{"publication_status":"published","year":"2012","language":[{"iso":"eng"}],"publication":" Engineering Analysis with Boundary Elements","day":"01","page":"960 - 967","date_created":"2018-12-11T12:02:24Z","volume":36,"doi":"10.1016/j.enganabound.2011.12.014","issue":"6","date_published":"2012-06-01T00:00:00Z","abstract":[{"text":"A boundary element model of a tunnel running through horizontally layered soil with anisotropic material properties is presented. Since there is no analytical fundamental solution for wave propagation inside a layered orthotropic medium in 3D, the fundamental displacements and stresses have to be calculated numerically. In our model this is done in the Fourier domain with respect to space and time. The assumption of a straight tunnel with infinite extension in the x direction makes it possible to decouple the system for every wave number kx, leading to a 2.5D-problem, which is suited for parallel computation. The special form of the fundamental solution, resulting from our Fourier ansatz, and the fact, that the calculation of the boundary integral equation is performed in the Fourier domain, enhances the stability and efficiency of the numerical calculations.","lang":"eng"}],"acknowledgement":"This work was supported by the Austrian Federal Ministry of Transport, Innovation and Technology under the Grant Bmvit-isb2 and the FFG under the project Pr. Nr. 809089.","oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","intvolume":" 36","month":"06","date_updated":"2021-01-12T07:42:19Z","citation":{"ieee":"G. Rieckh, W. Kreuzer, H. Waubke, and P. Balazs, “A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil,” Engineering Analysis with Boundary Elements, vol. 36, no. 6. Elsevier, pp. 960–967, 2012.","short":"G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs, Engineering Analysis with Boundary Elements 36 (2012) 960–967.","ama":"Rieckh G, Kreuzer W, Waubke H, Balazs P. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 2012;36(6):960-967. doi:10.1016/j.enganabound.2011.12.014","apa":"Rieckh, G., Kreuzer, W., Waubke, H., & Balazs, P. (2012). A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. Elsevier. https://doi.org/10.1016/j.enganabound.2011.12.014","mla":"Rieckh, Georg, et al. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements, vol. 36, no. 6, Elsevier, 2012, pp. 960–67, doi:10.1016/j.enganabound.2011.12.014.","ista":"Rieckh G, Kreuzer W, Waubke H, Balazs P. 2012. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 36(6), 960–967.","chicago":"Rieckh, Georg, Wolfgang Kreuzer, Holger Waubke, and Peter Balazs. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements. Elsevier, 2012. https://doi.org/10.1016/j.enganabound.2011.12.014."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","last_name":"Rieckh","full_name":"Rieckh, Georg"},{"first_name":"Wolfgang","last_name":"Kreuzer","full_name":"Kreuzer, Wolfgang"},{"first_name":"Holger","last_name":"Waubke","full_name":"Waubke, Holger"},{"full_name":"Balazs, Peter","last_name":"Balazs","first_name":"Peter"}],"publist_id":"3372","title":"A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil","department":[{"_id":"GaTk"}],"_id":"3274","type":"journal_article","status":"public"}]