[{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"01","department":[{"_id":"ToBo"}],"page":"117 - 123","title":"Oct4 kinetics predict cell lineage patterning in the early mammalian embryo","_id":"3429","volume":13,"publication":"Nature Cell Biology","language":[{"iso":"eng"}],"doi":"10.1038/ncb2154","year":"2011","publication_status":"published","acknowledgement":"This work was supported by the Beckman Institute and Biological Imaging Center at the California Institute of Technology and by the NHGRI Center of Excellence in Genomic Science grant P50HG004071.","citation":{"ieee":"N. Plachta, M. T. Bollenbach, S. Pease, S. Fraser, and P. Pantazis, “Oct4 kinetics predict cell lineage patterning in the early mammalian embryo,” <i>Nature Cell Biology</i>, vol. 13, no. 2. Nature Publishing Group, pp. 117–123, 2011.","ama":"Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. <i>Nature Cell Biology</i>. 2011;13(2):117-123. doi:<a href=\"https://doi.org/10.1038/ncb2154\">10.1038/ncb2154</a>","chicago":"Plachta, Nicolas, Mark Tobias Bollenbach, Shirley Pease, Scott Fraser, and Periklis Pantazis. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early Mammalian Embryo.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/ncb2154\">https://doi.org/10.1038/ncb2154</a>.","apa":"Plachta, N., Bollenbach, M. T., Pease, S., Fraser, S., &#38; Pantazis, P. (2011). Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2154\">https://doi.org/10.1038/ncb2154</a>","mla":"Plachta, Nicolas, et al. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early Mammalian Embryo.” <i>Nature Cell Biology</i>, vol. 13, no. 2, Nature Publishing Group, 2011, pp. 117–23, doi:<a href=\"https://doi.org/10.1038/ncb2154\">10.1038/ncb2154</a>.","ista":"Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. 2011. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology. 13(2), 117–123.","short":"N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell Biology 13 (2011) 117–123."},"date_updated":"2021-01-12T07:43:24Z","date_created":"2018-12-11T12:03:17Z","intvolume":"        13","issue":"2","author":[{"full_name":"Plachta, Nicolas","first_name":"Nicolas","last_name":"Plachta"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"},{"last_name":"Pease","first_name":"Shirley","full_name":"Pease, Shirley"},{"first_name":"Scott","full_name":"Fraser, Scott","last_name":"Fraser"},{"last_name":"Pantazis","first_name":"Periklis","full_name":"Pantazis, Periklis"}],"publisher":"Nature Publishing Group","date_published":"2011-01-23T00:00:00Z","abstract":[{"text":"Transcription factors are central to sustaining pluripotency, yet little is known about transcription factor dynamics in defining pluripotency in the early mammalian embryo. Here, we establish a fluorescence decay after photoactivation (FDAP) assay to quantitatively study the kinetic behaviour of Oct4, a key transcription factor controlling pre-implantation development in the mouse embryo. FDAP measurements reveal that each cell in a developing embryo shows one of two distinct Oct4 kinetics, before there are any morphologically distinguishable differences or outward signs of lineage patterning. The differences revealed by FDAP are due to differences in the accessibility of Oct4 to its DNA binding sites in the nucleus. Lineage tracing of the cells in the two distinct sub-populations demonstrates that the Oct4 kinetics predict lineages of the early embryo. Cells with slower Oct4 kinetics are more likely to give rise to the pluripotent cell lineage that contributes to the inner cell mass. Those with faster Oct4 kinetics contribute mostly to the extra-embryonic lineage. Our findings identify Oct4 kinetics, rather than differences in total transcription factor expression levels, as a predictive measure of developmental cell lineage patterning in the early mouse embryo.","lang":"eng"}],"oa_version":"None","publist_id":"2971","day":"23","type":"journal_article","scopus_import":1,"status":"public"},{"date_created":"2018-12-11T12:03:41Z","quality_controlled":"1","publisher":"Springer","abstract":[{"lang":"eng","text":"Cell migration on two-dimensional (2D) substrates follows entirely different rules than cell migration in three-dimensional (3D) environments. This is especially relevant for leukocytes that are able to migrate in the absence of adhesion receptors within the confined geometry of artificial 3D extracellular matrix scaffolds and within the interstitial space in vivo. Here, we describe in detail a simple and economical protocol to visualize dendritic cell migration in 3D collagen scaffolds along chemotactic gradients. This method can be adapted to other cell types and may serve as a physiologically relevant paradigm for the directed locomotion of most amoeboid cells."}],"day":"17","status":"public","type":"journal_article","main_file_link":[{"url":"https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf","open_access":"1"}],"article_type":"original","month":"05","page":"149 - 165","department":[{"_id":"MiSi"}],"volume":769,"language":[{"iso":"eng"}],"year":"2011","date_updated":"2021-01-12T07:43:55Z","intvolume":"       769","author":[{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Tim","full_name":"Lämmermann, Tim","last_name":"Lämmermann"}],"date_published":"2011-05-17T00:00:00Z","oa_version":"Published Version","publist_id":"2882","alternative_title":["Methods in Molecular Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell Migration","_id":"3505","title":"In vitro analysis of chemotactic leukocyte migration in 3D environments","article_processing_charge":"No","doi":"10.1007/978-1-61779-207-6_11","publication_status":"published","oa":1,"citation":{"ieee":"M. K. Sixt and T. Lämmermann, “In vitro analysis of chemotactic leukocyte migration in 3D environments,” <i>Cell Migration</i>, vol. 769. Springer, pp. 149–165, 2011.","ama":"Sixt MK, Lämmermann T. In vitro analysis of chemotactic leukocyte migration in 3D environments. <i>Cell Migration</i>. 2011;769:149-165. doi:<a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">10.1007/978-1-61779-207-6_11</a>","chicago":"Sixt, Michael K, and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” <i>Cell Migration</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">https://doi.org/10.1007/978-1-61779-207-6_11</a>.","short":"M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165.","ista":"Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 769, 149–165.","apa":"Sixt, M. K., &#38; Lämmermann, T. (2011). In vitro analysis of chemotactic leukocyte migration in 3D environments. <i>Cell Migration</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">https://doi.org/10.1007/978-1-61779-207-6_11</a>","mla":"Sixt, Michael K., and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” <i>Cell Migration</i>, vol. 769, Springer, 2011, pp. 149–65, doi:<a href=\"https://doi.org/10.1007/978-1-61779-207-6_11\">10.1007/978-1-61779-207-6_11</a>."}},{"date_updated":"2021-01-12T07:51:45Z","date_created":"2018-12-11T12:04:49Z","intvolume":"        55","date_published":"2011-03-16T00:00:00Z","publisher":"Springer","author":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Harald Janovjak","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"},{"full_name":"Isacoff, Ehud Y","first_name":"Ehud","last_name":"Isacoff"}],"quality_controlled":0,"publist_id":"2504","abstract":[{"text":"Small photochromic molecules are widespread in nature and serve as switches for a plethora of light-controlled processes. In a typical photoreceptor, the different geometries and polarities of the photochrome isomers are tightly coupled to functionally relevant conformational changes in the proteins. The past decade has seen extensive efforts to mimic nature and create proteins controlled by synthetic photochromes in the laboratory. Here, we discuss the role of molecular modeling to gain a structural understanding of photochromes and to design light-controlled peptides and proteins. We address several fundamental questions: What are the molecular structures of photochromes, particularly for metastable isomers that cannot be addressed experimentally? How are the structures of bistable photoisomers coupled to the conformational states of peptides and proteins? Can we design light-controlled proteins rapidly and reliably? After an introduction to the principles of molecular modeling, we answer these questions by examining systems that range from the size of isolated photochromes, to that of peptides and large cell surface receptors, each from its unique computational perspective.","lang":"eng"}],"status":"public","type":"book_chapter","extern":1,"day":"16","month":"03","page":"233 - 266","doi":"10.1007/978-1-61779-031-7_13","year":"2011","publication_status":"published","volume":55,"_id":"3724","title":"Structure-based design of light-controlled proteins","publication":"Photosensitive Molecules for the Control of Biological Function","citation":{"short":"H.L. Janovjak, E. Isacoff, in:, Photosensitive Molecules for the Control of Biological Function, Springer, 2011, pp. 233–266.","ista":"Janovjak HL, Isacoff E. 2011.Structure-based design of light-controlled proteins. In: Photosensitive Molecules for the Control of Biological Function. vol. 55, 233–266.","apa":"Janovjak, H. L., &#38; Isacoff, E. (2011). Structure-based design of light-controlled proteins. In <i>Photosensitive Molecules for the Control of Biological Function</i> (Vol. 55, pp. 233–266). Springer. <a href=\"https://doi.org/10.1007/978-1-61779-031-7_13\">https://doi.org/10.1007/978-1-61779-031-7_13</a>","mla":"Janovjak, Harald L., and Ehud Isacoff. “Structure-Based Design of Light-Controlled Proteins.” <i>Photosensitive Molecules for the Control of Biological Function</i>, vol. 55, Springer, 2011, pp. 233–66, doi:<a href=\"https://doi.org/10.1007/978-1-61779-031-7_13\">10.1007/978-1-61779-031-7_13</a>.","chicago":"Janovjak, Harald L, and Ehud Isacoff. “Structure-Based Design of Light-Controlled Proteins.” In <i>Photosensitive Molecules for the Control of Biological Function</i>, 55:233–66. Springer, 2011. <a href=\"https://doi.org/10.1007/978-1-61779-031-7_13\">https://doi.org/10.1007/978-1-61779-031-7_13</a>.","ama":"Janovjak HL, Isacoff E. Structure-based design of light-controlled proteins. In: <i>Photosensitive Molecules for the Control of Biological Function</i>. Vol 55. Springer; 2011:233-266. doi:<a href=\"https://doi.org/10.1007/978-1-61779-031-7_13\">10.1007/978-1-61779-031-7_13</a>","ieee":"H. L. Janovjak and E. Isacoff, “Structure-based design of light-controlled proteins,” in <i>Photosensitive Molecules for the Control of Biological Function</i>, vol. 55, Springer, 2011, pp. 233–266."}},{"status":"public","type":"journal_article","extern":"1","day":"01","oa_version":"None","publist_id":"2457","abstract":[{"lang":"eng","text":"The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon and Orinoco basins, covering an area of approximately 7 million km2. Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present-day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male-mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male-mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's Fs tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene."}],"date_published":"2011-04-01T00:00:00Z","publisher":"Wiley","author":[{"full_name":"Hollatz, Claudia","first_name":"Claudia","last_name":"Hollatz"},{"last_name":"Vilaça","full_name":"Vilaça, Sibelle","first_name":"Sibelle"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo"},{"first_name":"Míriam","full_name":"Marmontel, Míriam","last_name":"Marmontel"},{"last_name":"Baker","first_name":"Cyndi","full_name":"Baker, Cyndi"},{"full_name":"Santos, Fabrício","first_name":"Fabrício","last_name":"Santos"}],"issue":"4","date_updated":"2021-01-12T07:52:05Z","date_created":"2018-12-11T12:05:04Z","intvolume":"       102","citation":{"chicago":"Hollatz, Claudia, Sibelle Vilaça, Rodrigo A Fernandes Redondo, Míriam Marmontel, Cyndi Baker, and Fabrício Santos. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” <i>Biological Journal of the Linnean Society</i>. Wiley, 2011. <a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">https://doi.org/10.1111/j.1095-8312.2011.01616.x</a>.","ieee":"C. Hollatz, S. Vilaça, R. A. Fernandes Redondo, M. Marmontel, C. Baker, and F. Santos, “The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis),” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 4. Wiley, pp. 812–827, 2011.","ama":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). <i>Biological Journal of the Linnean Society</i>. 2011;102(4):812-827. doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">10.1111/j.1095-8312.2011.01616.x</a>","mla":"Hollatz, Claudia, et al. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 4, Wiley, 2011, pp. 812–27, doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">10.1111/j.1095-8312.2011.01616.x</a>.","apa":"Hollatz, C., Vilaça, S., Fernandes Redondo, R. A., Marmontel, M., Baker, C., &#38; Santos, F. (2011). The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). <i>Biological Journal of the Linnean Society</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">https://doi.org/10.1111/j.1095-8312.2011.01616.x</a>","short":"C. Hollatz, S. Vilaça, R.A. Fernandes Redondo, M. Marmontel, C. Baker, F. Santos, Biological Journal of the Linnean Society 102 (2011) 812–827.","ista":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. 2011. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. 102(4), 812–827."},"language":[{"iso":"eng"}],"doi":"10.1111/j.1095-8312.2011.01616.x","year":"2011","publication_status":"published","_id":"3770","volume":102,"article_processing_charge":"No","title":"The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)","publication":"Biological Journal of the Linnean Society","page":"812 - 827","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"issue":"3","intvolume":"       102","date_created":"2018-12-11T12:05:05Z","date_updated":"2021-01-12T07:52:05Z","date_published":"2011-02-10T00:00:00Z","publisher":"Wiley-Blackwell","quality_controlled":"1","author":[{"last_name":"Pavan","first_name":"Ana","full_name":"Pavan, Ana"},{"last_name":"Martins","first_name":"Felipe","full_name":"Martins, Felipe"},{"first_name":"Fabrício","full_name":"Santos, Fabrício","last_name":"Santos"},{"last_name":"Ditchfield","full_name":"Ditchfield, Albert","first_name":"Albert"},{"last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2456","oa_version":"None","abstract":[{"text":"The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages.","lang":"eng"}],"type":"journal_article","status":"public","scopus_import":1,"day":"10","month":"02","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"527 - 539","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2011","doi":"10.1111/j.1095-8312.2010.01601.x","language":[{"iso":"eng"}],"volume":102,"_id":"3771","title":"Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.","publication":"Biological Journal of the Linnean Society","citation":{"ista":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. 2011. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 102(3), 527–539.","short":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 527–539.","mla":"Pavan, Ana, et al. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 3, Wiley-Blackwell, 2011, pp. 527–39, doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">10.1111/j.1095-8312.2010.01601.x</a>.","apa":"Pavan, A., Martins, F., Santos, F., Ditchfield, A., &#38; Fernandes Redondo, R. A. (2011). Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. <i>Biological Journal of the Linnean Society</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">https://doi.org/10.1111/j.1095-8312.2010.01601.x</a>","ieee":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, and R. A. Fernandes Redondo, “Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.,” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539, 2011.","ama":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. <i>Biological Journal of the Linnean Society</i>. 2011;102(3):527-539. doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">10.1111/j.1095-8312.2010.01601.x</a>","chicago":"Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” <i>Biological Journal of the Linnean Society</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">https://doi.org/10.1111/j.1095-8312.2010.01601.x</a>."}},{"date_updated":"2021-01-12T07:52:08Z","date_created":"2018-12-11T12:05:07Z","intvolume":"       106","issue":"2","external_id":{"pmid":["20502479"]},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"publisher":"Nature Publishing Group","date_published":"2011-02-01T00:00:00Z","oa_version":"Submitted Version","publist_id":"2449","day":"01","status":"public","type":"journal_article","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/","open_access":"1"}],"month":"02","pmid":1,"page":"205 - 206","department":[{"_id":"NiBa"}],"_id":"3778","title":"Estimating linkage disequilibria","volume":106,"publication":"Heredity","language":[{"iso":"eng"}],"doi":"10.1038/hdy.2010.67","publication_status":"published","year":"2011","oa":1,"citation":{"ieee":"N. H. Barton, “Estimating linkage disequilibria,” <i>Heredity</i>, vol. 106, no. 2. Nature Publishing Group, pp. 205–206, 2011.","ama":"Barton NH. Estimating linkage disequilibria. <i>Heredity</i>. 2011;106(2):205-206. doi:<a href=\"https://doi.org/10.1038/hdy.2010.67\">10.1038/hdy.2010.67</a>","chicago":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” <i>Heredity</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/hdy.2010.67\">https://doi.org/10.1038/hdy.2010.67</a>.","apa":"Barton, N. H. (2011). Estimating linkage disequilibria. <i>Heredity</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/hdy.2010.67\">https://doi.org/10.1038/hdy.2010.67</a>","mla":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” <i>Heredity</i>, vol. 106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:<a href=\"https://doi.org/10.1038/hdy.2010.67\">10.1038/hdy.2010.67</a>.","short":"N.H. Barton, Heredity 106 (2011) 205–206.","ista":"Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206."}},{"author":[{"last_name":"Fasy","id":"F65D502E-E68D-11E9-9252-C644099818F6","full_name":"Fasy, Brittany Terese","first_name":"Brittany Terese"}],"quality_controlled":"1","publisher":"Szegedi Tudományegyetem","date_published":"2011-01-01T00:00:00Z","date_updated":"2021-01-12T07:52:09Z","date_created":"2018-12-11T12:05:08Z","intvolume":"        77","issue":"1-2","day":"01","status":"public","type":"journal_article","abstract":[{"lang":"eng","text":"We bound the difference in length of two curves in terms of their total curvatures and the Fréchet distance. The bound is independent of the dimension of the ambient Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and it generalizes a result by Fáry and Chakerian."}],"oa_version":"None","publist_id":"2446","page":"359 - 367","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","acknowledgement":"Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.","citation":{"ama":"Fasy BT. The difference in length of curves in R^n. <i>Acta Sci Math (Szeged)</i>. 2011;77(1-2):359-367.","ieee":"B. T. Fasy, “The difference in length of curves in R^n,” <i>Acta Sci. Math. (Szeged)</i>, vol. 77, no. 1–2. Szegedi Tudományegyetem, pp. 359–367, 2011.","chicago":"Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” <i>Acta Sci. Math. (Szeged)</i>. Szegedi Tudományegyetem, 2011.","mla":"Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” <i>Acta Sci. Math. (Szeged)</i>, vol. 77, no. 1–2, Szegedi Tudományegyetem, 2011, pp. 359–67.","apa":"Fasy, B. T. (2011). The difference in length of curves in R^n. <i>Acta Sci. Math. (Szeged)</i>. Szegedi Tudományegyetem.","short":"B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367.","ista":"Fasy BT. 2011. The difference in length of curves in R^n. Acta Sci. Math. (Szeged). 77(1–2), 359–367."},"_id":"3781","title":"The difference in length of curves in R^n","volume":77,"publication":"Acta Sci. Math. (Szeged)","language":[{"iso":"eng"}],"year":"2011","publication_status":"published"},{"oa_version":"Published Version","publist_id":"2443","scopus_import":1,"issue":"2","date_updated":"2021-01-12T07:52:10Z","intvolume":"        91","date_published":"2011-03-01T00:00:00Z","author":[{"orcid":"0000-0002-0343-8329","last_name":"Palero","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","full_name":"Palero, Ferran","first_name":"Ferran"},{"first_name":"Guillermo","full_name":"Guerao, Guillermo","last_name":"Guerao"},{"full_name":"Clark, Paul","first_name":"Paul","last_name":"Clark"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"}],"doi":"10.1017/S0025315410000287","publication_status":"published","publication":"Journal of the Marine Biological Association of the United Kingdom","_id":"3784","title":"Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description","article_processing_charge":"No","citation":{"short":"F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492.","ista":"Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 91(2), 485–492.","apa":"Palero, F., Guerao, G., Clark, P., &#38; Abello, P. (2011). Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. <i>Journal of the Marine Biological Association of the United Kingdom</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0025315410000287\">https://doi.org/10.1017/S0025315410000287</a>","mla":"Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” <i>Journal of the Marine Biological Association of the United Kingdom</i>, vol. 91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:<a href=\"https://doi.org/10.1017/S0025315410000287\">10.1017/S0025315410000287</a>.","ama":"Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. <i>Journal of the Marine Biological Association of the United Kingdom</i>. 2011;91(2):485-492. doi:<a href=\"https://doi.org/10.1017/S0025315410000287\">10.1017/S0025315410000287</a>","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description,” <i>Journal of the Marine Biological Association of the United Kingdom</i>, vol. 91, no. 2. Cambridge University Press, pp. 485–492, 2011.","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” <i>Journal of the Marine Biological Association of the United Kingdom</i>. Cambridge University Press, 2011. <a href=\"https://doi.org/10.1017/S0025315410000287\">https://doi.org/10.1017/S0025315410000287</a>."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus.","lang":"eng"}],"type":"journal_article","status":"public","day":"01","date_created":"2018-12-11T12:05:09Z","quality_controlled":"1","publisher":"Cambridge University Press","language":[{"iso":"eng"}],"year":"2011","volume":91,"main_file_link":[{"open_access":"1","url":"https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf"}],"article_type":"original","month":"03","page":"485 - 492","department":[{"_id":"NiBa"}]},{"abstract":[{"lang":"eng","text":"During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes."}],"publist_id":"2436","oa_version":"None","day":"01","alternative_title":["Current Topics in Developmental Biology"],"status":"public","scopus_import":"1","type":"book_chapter","date_created":"2018-12-11T12:05:11Z","intvolume":"        95","date_updated":"2021-01-12T07:52:13Z","editor":[{"first_name":"Michel","full_name":"Labouesse, Michel","last_name":"Labouesse"}],"author":[{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"quality_controlled":"1","publisher":"Elsevier","date_published":"2011-01-01T00:00:00Z","_id":"3791","volume":95,"title":"Cell sorting in development","article_processing_charge":"No","publication":"Forces and Tension in Development","year":"2011","publication_status":"published","doi":"10.1016/B978-0-12-385065-2.00006-2","language":[{"iso":"eng"}],"citation":{"ieee":"G. Krens and C.-P. J. Heisenberg, “Cell sorting in development,” in <i>Forces and Tension in Development</i>, vol. 95, M. Labouesse, Ed. Elsevier, 2011, pp. 189–213.","ama":"Krens G, Heisenberg C-PJ. Cell sorting in development. In: Labouesse M, ed. <i>Forces and Tension in Development</i>. Vol 95. Elsevier; 2011:189-213. doi:<a href=\"https://doi.org/10.1016/B978-0-12-385065-2.00006-2\">10.1016/B978-0-12-385065-2.00006-2</a>","chicago":"Krens, Gabriel, and Carl-Philipp J Heisenberg. “Cell Sorting in Development.” In <i>Forces and Tension in Development</i>, edited by Michel Labouesse, 95:189–213. Elsevier, 2011. <a href=\"https://doi.org/10.1016/B978-0-12-385065-2.00006-2\">https://doi.org/10.1016/B978-0-12-385065-2.00006-2</a>.","ista":"Krens G, Heisenberg C-PJ. 2011.Cell sorting in development. In: Forces and Tension in Development. Current Topics in Developmental Biology, vol. 95, 189–213.","short":"G. Krens, C.-P.J. Heisenberg, in:, M. Labouesse (Ed.), Forces and Tension in Development, Elsevier, 2011, pp. 189–213.","mla":"Krens, Gabriel, and Carl-Philipp J. Heisenberg. “Cell Sorting in Development.” <i>Forces and Tension in Development</i>, edited by Michel Labouesse, vol. 95, Elsevier, 2011, pp. 189–213, doi:<a href=\"https://doi.org/10.1016/B978-0-12-385065-2.00006-2\">10.1016/B978-0-12-385065-2.00006-2</a>.","apa":"Krens, G., &#38; Heisenberg, C.-P. J. (2011). Cell sorting in development. In M. Labouesse (Ed.), <i>Forces and Tension in Development</i> (Vol. 95, pp. 189–213). Elsevier. <a href=\"https://doi.org/10.1016/B978-0-12-385065-2.00006-2\">https://doi.org/10.1016/B978-0-12-385065-2.00006-2</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","department":[{"_id":"CaHe"}],"page":"189 - 213"},{"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T12:05:13Z","status":"public","type":"book_chapter","day":"03","file_date_updated":"2020-07-14T12:46:16Z","has_accepted_license":"1","ddc":["000"],"abstract":[{"lang":"eng","text":"We address the problem of covering ℝ n with congruent balls, while minimizing the number of balls that contain an average point. Considering the 1-parameter family of lattices defined by stretching or compressing the integer grid in diagonal direction, we give a closed formula for the covering density that depends on the distortion parameter. We observe that our family contains the thinnest lattice coverings in dimensions 2 to 5. We also consider the problem of packing congruent balls in ℝ n , for which we give a closed formula for the packing density as well. Again we observe that our family contains optimal configurations, this time densest packings in dimensions 2 and 3."}],"department":[{"_id":"HeEd"}],"page":"20 - 35","month":"05","language":[{"iso":"eng"}],"year":"2011","volume":6570,"date_published":"2011-05-03T00:00:00Z","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299"}],"editor":[{"first_name":"Cristian","full_name":"Calude, Cristian","last_name":"Calude"},{"full_name":"Rozenberg, Grzegorz","first_name":"Grzegorz","last_name":"Rozenberg"},{"last_name":"Salomaa","first_name":"Arto","full_name":"Salomaa, Arto"}],"date_updated":"2021-01-12T07:52:15Z","intvolume":"      6570","alternative_title":["LNCS"],"oa_version":"Submitted Version","pubrep_id":"539","publist_id":"2427","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” In <i>Rainbow of Computer Science</i>, edited by Cristian Calude, Grzegorz Rozenberg, and Arto Salomaa, 6570:20–35. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-19391-0_2\">https://doi.org/10.1007/978-3-642-19391-0_2</a>.","ama":"Edelsbrunner H, Kerber M. Covering and packing with spheres by diagonal distortion in R^n. In: Calude C, Rozenberg G, Salomaa A, eds. <i>Rainbow of Computer Science</i>. Vol 6570. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer; 2011:20-35. doi:<a href=\"https://doi.org/10.1007/978-3-642-19391-0_2\">10.1007/978-3-642-19391-0_2</a>","ieee":"H. Edelsbrunner and M. Kerber, “Covering and packing with spheres by diagonal distortion in R^n,” in <i>Rainbow of Computer Science</i>, vol. 6570, C. Calude, G. Rozenberg, and A. Salomaa, Eds. Springer, 2011, pp. 20–35.","ista":"Edelsbrunner H, Kerber M. 2011.Covering and packing with spheres by diagonal distortion in R^n. In: Rainbow of Computer Science. LNCS, vol. 6570, 20–35.","short":"H. Edelsbrunner, M. Kerber, in:, C. Calude, G. Rozenberg, A. Salomaa (Eds.), Rainbow of Computer Science, Springer, 2011, pp. 20–35.","apa":"Edelsbrunner, H., &#38; Kerber, M. (2011). Covering and packing with spheres by diagonal distortion in R^n. In C. Calude, G. Rozenberg, &#38; A. Salomaa (Eds.), <i>Rainbow of Computer Science</i> (Vol. 6570, pp. 20–35). Springer. <a href=\"https://doi.org/10.1007/978-3-642-19391-0_2\">https://doi.org/10.1007/978-3-642-19391-0_2</a>","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” <i>Rainbow of Computer Science</i>, edited by Cristian Calude et al., vol. 6570, Springer, 2011, pp. 20–35, doi:<a href=\"https://doi.org/10.1007/978-3-642-19391-0_2\">10.1007/978-3-642-19391-0_2</a>."},"oa":1,"series_title":"Dedicated to Hermann Maurer on the Occasion of His 70th Birthday","doi":"10.1007/978-3-642-19391-0_2","publication_status":"published","file":[{"access_level":"open_access","content_type":"application/pdf","file_id":"4640","file_name":"IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf","creator":"system","file_size":436875,"checksum":"aaf22b4d7bd4277ffe8db532119cf474","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-12T10:07:42Z","relation":"main_file"}],"_id":"3796","publication":"Rainbow of Computer Science","title":"Covering and packing with spheres by diagonal distortion in R^n"},{"abstract":[{"text":"We present a detailed study of the local density of states (LDOS) associated with the surface-state band near a step edge of the strong topological insulator Bi2Te3 and reveal a one-dimensional bound state that runs parallel to the step edge and is bound to it at some characteristic distance. This bound state is clearly observed in the bulk gap region, while it becomes entangled with the oscillations of the warped surface band at high energy, and with the valence-band states near the Dirac point. We obtain excellent fits to theoretical predictions [Alpichshev, 2011] that properly incorporate the three-dimensional nature of the problem to the surface state. Fitting the data at different energies, we can recalculate the LDOS originating from the Dirac band without the contribution of the bulk bands or incoherent tunneling effects. ","lang":"eng"}],"day":"21","extern":"1","status":"public","type":"journal_article","date_created":"2018-12-11T11:46:10Z","quality_controlled":"1","publisher":"American Physical Society","external_id":{"arxiv":["1003.2233"]},"volume":84,"year":"2011","language":[{"iso":"eng"}],"month":"07","article_type":"original","main_file_link":[{"url":"https://arxiv.org/abs/1003.2233","open_access":"1"}],"publist_id":"7443","oa_version":"Preprint","intvolume":"        84","date_updated":"2021-01-12T07:52:44Z","issue":"4","author":[{"orcid":"0000-0002-7183-5203","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"},{"first_name":"J G","full_name":"Analytis, J G","last_name":"Analytis"},{"full_name":"Chu, J H","first_name":"J H","last_name":"Chu"},{"full_name":"Fisher, I R","first_name":"I R","last_name":"Fisher"},{"first_name":"A","full_name":"Kapitulnik, A","last_name":"Kapitulnik"}],"date_published":"2011-07-21T00:00:00Z","title":"STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3","_id":"386","publication":"Physical Review B - Condensed Matter and Materials Physics","article_processing_charge":"No","publication_status":"published","doi":"10.1103/PhysRevB.84.041104","oa":1,"citation":{"mla":"Alpichshev, Zhanybek, et al. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 84, no. 4, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevB.84.041104\">10.1103/PhysRevB.84.041104</a>.","apa":"Alpichshev, Z., Analytis, J. G., Chu, J. H., Fisher, I. R., &#38; Kapitulnik, A. (2011). STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.84.041104\">https://doi.org/10.1103/PhysRevB.84.041104</a>","ista":"Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. 2011. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. 84(4).","short":"Z. Alpichshev, J.G. Analytis, J.H. Chu, I.R. Fisher, A. Kapitulnik, Physical Review B - Condensed Matter and Materials Physics 84 (2011).","chicago":"Alpichshev, Zhanybek, J G Analytis, J H Chu, I R Fisher, and A Kapitulnik. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevB.84.041104\">https://doi.org/10.1103/PhysRevB.84.041104</a>.","ieee":"Z. Alpichshev, J. G. Analytis, J. H. Chu, I. R. Fisher, and A. Kapitulnik, “STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 84, no. 4. American Physical Society, 2011.","ama":"Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2011;84(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.84.041104\">10.1103/PhysRevB.84.041104</a>"},"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"05","page":"1 - 13","department":[{"_id":"HeEd"}],"publication":"Journal of Experimental Algorithmics","_id":"3965","volume":16,"title":"Computing elevation maxima by searching the Gauss sphere","publication_status":"published","year":"2011","doi":"10.1145/1963190.1970375","language":[{"iso":"eng"}],"citation":{"ieee":"B. Wang, H. Edelsbrunner, and D. Morozov, “Computing elevation maxima by searching the Gauss sphere,” <i>Journal of Experimental Algorithmics</i>, vol. 16, no. 2.2. ACM, pp. 1–13, 2011.","ama":"Wang B, Edelsbrunner H, Morozov D. Computing elevation maxima by searching the Gauss sphere. <i>Journal of Experimental Algorithmics</i>. 2011;16(2.2):1-13. doi:<a href=\"https://doi.org/10.1145/1963190.1970375\">10.1145/1963190.1970375</a>","chicago":"Wang, Bei, Herbert Edelsbrunner, and Dmitriy Morozov. “Computing Elevation Maxima by Searching the Gauss Sphere.” <i>Journal of Experimental Algorithmics</i>. ACM, 2011. <a href=\"https://doi.org/10.1145/1963190.1970375\">https://doi.org/10.1145/1963190.1970375</a>.","mla":"Wang, Bei, et al. “Computing Elevation Maxima by Searching the Gauss Sphere.” <i>Journal of Experimental Algorithmics</i>, vol. 16, no. 2.2, ACM, 2011, pp. 1–13, doi:<a href=\"https://doi.org/10.1145/1963190.1970375\">10.1145/1963190.1970375</a>.","apa":"Wang, B., Edelsbrunner, H., &#38; Morozov, D. (2011). Computing elevation maxima by searching the Gauss sphere. <i>Journal of Experimental Algorithmics</i>. ACM. <a href=\"https://doi.org/10.1145/1963190.1970375\">https://doi.org/10.1145/1963190.1970375</a>","short":"B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics 16 (2011) 1–13.","ista":"Wang B, Edelsbrunner H, Morozov D. 2011. Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. 16(2.2), 1–13."},"date_created":"2018-12-11T12:06:09Z","intvolume":"        16","date_updated":"2021-01-12T07:53:31Z","issue":"2.2","author":[{"first_name":"Bei","full_name":"Wang, Bei","last_name":"Wang"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Dmitriy","full_name":"Morozov, Dmitriy","last_name":"Morozov"}],"publisher":"ACM","quality_controlled":"1","date_published":"2011-05-01T00:00:00Z","abstract":[{"text":"The elevation function on a smoothly embedded 2-manifold in R-3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in identifying coarse docking configurations for protein pairs. Transporting the concept from the smooth to the piecewise linear category, this paper describes an algorithm for finding all local maxima. While its worst-case running time is the same as of the algorithm used in prior work, its performance in practice is orders of magnitudes superior. We cast light on this improvement by relating the running time to the total absolute Gaussian curvature of the 2-manifold.","lang":"eng"}],"publist_id":"2161","oa_version":"None","day":"01","status":"public","type":"journal_article","scopus_import":1},{"publication_status":"published","year":"2011","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.6398-10.2011","_id":"469","title":"Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor","publication":"European Journal of Neuroscience","volume":31,"citation":{"ista":"Vyleta N, Smith S. 2011. Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor. European Journal of Neuroscience. 31(12), 4593–4606.","short":"N. Vyleta, S. Smith, European Journal of Neuroscience 31 (2011) 4593–4606.","mla":"Vyleta, Nicholas, and Stephen Smith. “Spontaneous Glutamate Release Is Independent of Calcium Influx and Tonically Activated by the Calcium-Sensing Receptor.” <i>European Journal of Neuroscience</i>, vol. 31, no. 12, Wiley-Blackwell, 2011, pp. 4593–606, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.6398-10.2011\">10.1523/JNEUROSCI.6398-10.2011</a>.","apa":"Vyleta, N., &#38; Smith, S. (2011). Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1523/JNEUROSCI.6398-10.2011\">https://doi.org/10.1523/JNEUROSCI.6398-10.2011</a>","ama":"Vyleta N, Smith S. Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor. <i>European Journal of Neuroscience</i>. 2011;31(12):4593-4606. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.6398-10.2011\">10.1523/JNEUROSCI.6398-10.2011</a>","ieee":"N. Vyleta and S. Smith, “Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor,” <i>European Journal of Neuroscience</i>, vol. 31, no. 12. Wiley-Blackwell, pp. 4593–4606, 2011.","chicago":"Vyleta, Nicholas, and Stephen Smith. “Spontaneous Glutamate Release Is Independent of Calcium Influx and Tonically Activated by the Calcium-Sensing Receptor.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1523/JNEUROSCI.6398-10.2011\">https://doi.org/10.1523/JNEUROSCI.6398-10.2011</a>."},"oa":1,"month":"03","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097128/"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"PeJo"}],"page":"4593 - 4606","publist_id":"7353","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Spontaneous release of glutamate is important for maintaining synaptic strength and controlling spike timing in the brain. Mechanisms regulating spontaneous exocytosis remain poorly understood. Extracellular calcium concentration ([Ca2+]o) regulates Ca2+ entry through voltage-activated calcium channels (VACCs) and consequently is a pivotal determinant of action potential-evoked vesicle fusion. Extracellular Ca 2+ also enhances spontaneous release, but via unknown mechanisms. Here we report that external Ca2+ triggers spontaneous glutamate release more weakly than evoked release in mouse neocortical neurons. Blockade of VACCs has no effect on the spontaneous release rate or its dependence on [Ca2+]o. Intracellular [Ca2+] slowly increases in a minority of neurons following increases in [Ca2+]o. Furthermore, the enhancement of spontaneous release by extracellular calcium is insensitive to chelation of intracellular calcium by BAPTA. Activation of the calcium-sensing receptor (CaSR), a G-protein-coupled receptor present in nerve terminals, by several specific agonists increased spontaneous glutamate release. The frequency of spontaneous synaptic transmission was decreased in CaSR mutant neurons. The concentration-effect relationship for extracellular calcium regulation of spontaneous release was well described by a combination of CaSR-dependent and CaSR-independent mechanisms. Overall these results indicate that extracellular Ca2+ does not trigger spontaneous glutamate release by simply increasing calcium influx but stimulates CaSR and thereby promotes resting spontaneous glutamate release. "}],"scopus_import":1,"status":"public","type":"journal_article","day":"23","issue":"12","date_created":"2018-12-11T11:46:39Z","intvolume":"        31","date_updated":"2021-01-12T08:00:49Z","date_published":"2011-03-23T00:00:00Z","author":[{"first_name":"Nicholas","full_name":"Vyleta, Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","last_name":"Vyleta"},{"first_name":"Stephen","full_name":"Smith, Stephen","last_name":"Smith"}],"quality_controlled":"1","publisher":"Wiley-Blackwell"},{"month":"01","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"volume":2011,"year":"2011","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:45Z","quality_controlled":"1","publisher":"Hindawi Publishing Corporation","abstract":[{"lang":"eng","text":"BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. "}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"ddc":["005"],"has_accepted_license":"1","day":"01","file_date_updated":"2020-07-14T12:46:35Z","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"490","title":"BioSig: The free and open source software library for biomedical signal processing","publication":"Computational Intelligence and Neuroscience","publication_status":"published","file":[{"checksum":"8263bbf255171f2054f43f3db5f53b6e","creator":"system","file_size":2863551,"date_updated":"2020-07-14T12:46:35Z","relation":"main_file","date_created":"2018-12-12T10:07:44Z","access_level":"open_access","content_type":"application/pdf","file_id":"4642","file_name":"IST-2018-947-v1+1_2011_Schloegl_BioSig.pdf"}],"doi":"10.1155/2011/935364","oa":1,"citation":{"ama":"Schlögl A, Vidaurre C, Sander T. BioSig: The free and open source software library for biomedical signal processing. <i>Computational Intelligence and Neuroscience</i>. 2011;2011. doi:<a href=\"https://doi.org/10.1155/2011/935364\">10.1155/2011/935364</a>","ieee":"A. Schlögl, C. Vidaurre, and T. Sander, “BioSig: The free and open source software library for biomedical signal processing,” <i>Computational Intelligence and Neuroscience</i>, vol. 2011. Hindawi Publishing Corporation, 2011.","chicago":"Schlögl, Alois, Carmen Vidaurre, and Tilmann Sander. “BioSig: The Free and Open Source Software Library for Biomedical Signal Processing.” <i>Computational Intelligence and Neuroscience</i>. Hindawi Publishing Corporation, 2011. <a href=\"https://doi.org/10.1155/2011/935364\">https://doi.org/10.1155/2011/935364</a>.","ista":"Schlögl A, Vidaurre C, Sander T. 2011. BioSig: The free and open source software library for biomedical signal processing. Computational Intelligence and Neuroscience. 2011, 935364.","short":"A. Schlögl, C. Vidaurre, T. Sander, Computational Intelligence and Neuroscience 2011 (2011).","apa":"Schlögl, A., Vidaurre, C., &#38; Sander, T. (2011). BioSig: The free and open source software library for biomedical signal processing. <i>Computational Intelligence and Neuroscience</i>. Hindawi Publishing Corporation. <a href=\"https://doi.org/10.1155/2011/935364\">https://doi.org/10.1155/2011/935364</a>","mla":"Schlögl, Alois, et al. “BioSig: The Free and Open Source Software Library for Biomedical Signal Processing.” <i>Computational Intelligence and Neuroscience</i>, vol. 2011, 935364, Hindawi Publishing Corporation, 2011, doi:<a href=\"https://doi.org/10.1155/2011/935364\">10.1155/2011/935364</a>."},"article_number":"935364","intvolume":"      2011","date_updated":"2021-01-12T08:01:02Z","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"last_name":"Vidaurre","full_name":"Vidaurre, Carmen","first_name":"Carmen"},{"last_name":"Sander","full_name":"Sander, Tilmann","first_name":"Tilmann"}],"date_published":"2011-01-01T00:00:00Z","publist_id":"7330","pubrep_id":"947","oa_version":"Published Version","scopus_import":1},{"author":[{"id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander","first_name":"Alexander","last_name":"Eichner"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"publisher":"American Association for the Advancement of Science","quality_controlled":"1","date_published":"2011-11-08T00:00:00Z","date_updated":"2021-01-12T08:01:02Z","date_created":"2018-12-11T11:46:46Z","intvolume":"         4","issue":"198","day":"08","type":"journal_article","scopus_import":1,"status":"public","abstract":[{"text":"In their search for antigens, lymphocytes continuously shuttle among blood vessels, lymph vessels, and lymphatic tissues. Chemokines mediate entry of lymphocytes into lymphatic tissues, and sphingosine 1-phosphate (S1P) promotes localization of lymphocytes to the vasculature. Both signals are sensed through G protein-coupled receptors (GPCRs). Most GPCRs undergo ligand-dependent homologous receptor desensitization, a process that decreases their signaling output after previous exposure to high ligand concentration. Such desensitization can explain why lymphocytes do not take an intermediate position between two signals but rather oscillate between them. The desensitization of S1P receptor 1 (S1PR1) is mediated by GPCR kinase 2 (GRK2). Deletion of GRK2 in lymphocytes compromises desensitization by high vascular S1P concentrations, thereby reducing responsiveness to the chemokine signal and trapping the cells in the vascular compartment. The desensitization kinetics of S1PR1 allows lymphocytes to dynamically shuttle between vasculature and lymphatic tissue, although the positional information in both compartments is static.","lang":"eng"}],"oa_version":"None","publist_id":"7329","department":[{"_id":"MiSi"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"11","citation":{"apa":"Eichner, A., &#38; Sixt, M. K. (2011). Setting the clock for recirculating lymphocytes. <i>Science Signaling</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scisignal.2002617\">https://doi.org/10.1126/scisignal.2002617</a>","mla":"Eichner, Alexander, and Michael K. Sixt. “Setting the Clock for Recirculating Lymphocytes.” <i>Science Signaling</i>, vol. 4, no. 198, pe43, American Association for the Advancement of Science, 2011, doi:<a href=\"https://doi.org/10.1126/scisignal.2002617\">10.1126/scisignal.2002617</a>.","ista":"Eichner A, Sixt MK. 2011. Setting the clock for recirculating lymphocytes. Science Signaling. 4(198), pe43.","short":"A. Eichner, M.K. Sixt, Science Signaling 4 (2011).","ama":"Eichner A, Sixt MK. Setting the clock for recirculating lymphocytes. <i>Science Signaling</i>. 2011;4(198). doi:<a href=\"https://doi.org/10.1126/scisignal.2002617\">10.1126/scisignal.2002617</a>","ieee":"A. Eichner and M. K. Sixt, “Setting the clock for recirculating lymphocytes,” <i>Science Signaling</i>, vol. 4, no. 198. American Association for the Advancement of Science, 2011.","chicago":"Eichner, Alexander, and Michael K Sixt. “Setting the Clock for Recirculating Lymphocytes.” <i>Science Signaling</i>. American Association for the Advancement of Science, 2011. <a href=\"https://doi.org/10.1126/scisignal.2002617\">https://doi.org/10.1126/scisignal.2002617</a>."},"article_number":"pe43","_id":"491","title":"Setting the clock for recirculating lymphocytes","volume":4,"publication":"Science Signaling","language":[{"iso":"eng"}],"doi":"10.1126/scisignal.2002617","year":"2011","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","doi":"10.1038/emboj.2011.301","publication":"EMBO Journal","_id":"518","title":"CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells","article_processing_charge":"No","citation":{"mla":"Schraivogel, Daniel, et al. “CAMTA1 Is a Novel Tumour Suppressor Regulated by MiR-9/9 * in Glioblastoma Stem Cells.” <i>EMBO Journal</i>, vol. 30, no. 20, Wiley-Blackwell, 2011, pp. 4309–22, doi:<a href=\"https://doi.org/10.1038/emboj.2011.301\">10.1038/emboj.2011.301</a>.","apa":"Schraivogel, D., Weinmann, L., Beier, D., Tabatabai, G., Eichner, A., Zhu, J., … Meister, G. (2011). CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2011.301\">https://doi.org/10.1038/emboj.2011.301</a>","short":"D. Schraivogel, L. Weinmann, D. Beier, G. Tabatabai, A. Eichner, J. Zhu, M. Anton, M.K. Sixt, M. Weller, C. Beier, G. Meister, EMBO Journal 30 (2011) 4309–4322.","ista":"Schraivogel D, Weinmann L, Beier D, Tabatabai G, Eichner A, Zhu J, Anton M, Sixt MK, Weller M, Beier C, Meister G. 2011. CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells. EMBO Journal. 30(20), 4309–4322.","ieee":"D. Schraivogel <i>et al.</i>, “CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells,” <i>EMBO Journal</i>, vol. 30, no. 20. Wiley-Blackwell, pp. 4309–4322, 2011.","ama":"Schraivogel D, Weinmann L, Beier D, et al. CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells. <i>EMBO Journal</i>. 2011;30(20):4309-4322. doi:<a href=\"https://doi.org/10.1038/emboj.2011.301\">10.1038/emboj.2011.301</a>","chicago":"Schraivogel, Daniel, Lasse Weinmann, Dagmar Beier, Ghazaleh Tabatabai, Alexander Eichner, Jia Zhu, Martina Anton, et al. “CAMTA1 Is a Novel Tumour Suppressor Regulated by MiR-9/9 * in Glioblastoma Stem Cells.” <i>EMBO Journal</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1038/emboj.2011.301\">https://doi.org/10.1038/emboj.2011.301</a>."},"oa":1,"issue":"20","intvolume":"        30","date_updated":"2021-01-12T08:01:19Z","date_published":"2011-10-19T00:00:00Z","author":[{"first_name":"Daniel","full_name":"Schraivogel, Daniel","last_name":"Schraivogel"},{"last_name":"Weinmann","first_name":"Lasse","full_name":"Weinmann, Lasse"},{"full_name":"Beier, Dagmar","first_name":"Dagmar","last_name":"Beier"},{"last_name":"Tabatabai","first_name":"Ghazaleh","full_name":"Tabatabai, Ghazaleh"},{"id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander","first_name":"Alexander","last_name":"Eichner"},{"last_name":"Zhu","full_name":"Zhu, Jia","first_name":"Jia"},{"last_name":"Anton","full_name":"Anton, Martina","first_name":"Martina"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"last_name":"Weller","full_name":"Weller, Michael","first_name":"Michael"},{"full_name":"Beier, Christoph","first_name":"Christoph","last_name":"Beier"},{"last_name":"Meister","first_name":"Gunter","full_name":"Meister, Gunter"}],"publist_id":"7301","oa_version":"Submitted Version","scopus_import":1,"month":"10","article_type":"original","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199389/"}],"page":"4309 - 4322","department":[{"_id":"MiSi"}],"pmid":1,"year":"2011","language":[{"iso":"eng"}],"volume":30,"date_created":"2018-12-11T11:46:55Z","publisher":"Wiley-Blackwell","quality_controlled":"1","external_id":{"pmid":["21857646"]},"abstract":[{"lang":"eng","text":"Cancer stem cells or cancer initiating cells are believed to contribute to cancer recurrence after therapy. MicroRNAs (miRNAs) are short RNA molecules with fundamental roles in gene regulation. The role of miRNAs in cancer stem cells is only poorly understood. Here, we report miRNA expression profiles of glioblastoma stem cell-containing CD133 + cell populations. We find that miR-9, miR-9 * (referred to as miR-9/9 *), miR-17 and miR-106b are highly abundant in CD133 + cells. Furthermore, inhibition of miR-9/9 * or miR-17 leads to reduced neurosphere formation and stimulates cell differentiation. Calmodulin-binding transcription activator 1 (CAMTA1) is a putative transcription factor, which induces the expression of the anti-proliferative cardiac hormone natriuretic peptide A (NPPA). We identify CAMTA1 as an miR-9/9 * and miR-17 target. CAMTA1 expression leads to reduced neurosphere formation and tumour growth in nude mice, suggesting that CAMTA1 can function as tumour suppressor. Consistently, CAMTA1 and NPPA expression correlate with patient survival. Our findings could provide a basis for novel strategies of glioblastoma therapy."}],"status":"public","type":"journal_article","day":"19"},{"volume":39,"language":[{"iso":"eng"}],"year":"2011","page":"297 - 331","department":[{"_id":"ToHe"}],"main_file_link":[{"url":"https://infoscience.epfl.ch/record/178042/files/art3A10.10072Fs10703-011-0131-3.pdf","open_access":"1"}],"article_type":"original","month":"12","day":"01","status":"public","type":"journal_article","abstract":[{"text":"Software transactional memories (STM) are described in the literature with assumptions of sequentially consistent program execution and atomicity of high level operations like read, write, and abort. However, in a realistic setting, processors use relaxed memory models to optimize hardware performance. Moreover, the atomicity of operations depends on the underlying hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We describe RML, a simple language for expressing concurrent programs. We develop a semantics of RML parametrized by a relaxed memory model. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm restricted to two threads and two variables, and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the restricted STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order for two threads and two variables. Finally, we extend the verification results for DSTM and TL2 to an arbitrary number of threads and variables by manually proving that the structural properties of STMs are satisfied at the hardware level of atomicity under the considered relaxed memory models.","lang":"eng"}],"ddc":["000"],"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:47:00Z","oa":1,"citation":{"chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Verification of STM on Relaxed Memory Models.” <i>Formal Methods in System Design</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10703-011-0131-3\">https://doi.org/10.1007/s10703-011-0131-3</a>.","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Verification of STM on relaxed memory models,” <i>Formal Methods in System Design</i>, vol. 39, no. 3. Springer, pp. 297–331, 2011.","ama":"Guerraoui R, Henzinger TA, Singh V. Verification of STM on relaxed memory models. <i>Formal Methods in System Design</i>. 2011;39(3):297-331. doi:<a href=\"https://doi.org/10.1007/s10703-011-0131-3\">10.1007/s10703-011-0131-3</a>","apa":"Guerraoui, R., Henzinger, T. A., &#38; Singh, V. (2011). Verification of STM on relaxed memory models. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-011-0131-3\">https://doi.org/10.1007/s10703-011-0131-3</a>","mla":"Guerraoui, Rachid, et al. “Verification of STM on Relaxed Memory Models.” <i>Formal Methods in System Design</i>, vol. 39, no. 3, Springer, 2011, pp. 297–331, doi:<a href=\"https://doi.org/10.1007/s10703-011-0131-3\">10.1007/s10703-011-0131-3</a>.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, Formal Methods in System Design 39 (2011) 297–331.","ista":"Guerraoui R, Henzinger TA, Singh V. 2011. Verification of STM on relaxed memory models. Formal Methods in System Design. 39(3), 297–331."},"_id":"531","publication":"Formal Methods in System Design","title":"Verification of STM on relaxed memory models","article_processing_charge":"No","doi":"10.1007/s10703-011-0131-3","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"oa_version":"Published Version","publist_id":"7288","author":[{"last_name":"Guerraoui","first_name":"Rachid","full_name":"Guerraoui, Rachid"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","full_name":"Singh, Vasu","first_name":"Vasu","last_name":"Singh"}],"date_published":"2011-12-01T00:00:00Z","date_updated":"2021-01-12T08:01:27Z","intvolume":"        39","issue":"3"},{"ddc":["000","004"],"has_accepted_license":"1","abstract":[{"text":"Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is ̃O(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the ̃O(n·m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of O(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m > n4/3 an earlier bound of O(min(m1.5, m·n2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n2), which is an improvement over earlier bounds for m > n4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.","lang":"eng"}],"status":"public","type":"technical_report","file_date_updated":"2020-07-14T12:46:39Z","day":"11","related_material":{"record":[{"status":"public","id":"3165","relation":"later_version"}]},"date_created":"2018-12-12T11:38:59Z","publisher":"IST Austria","year":"2011","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"month":"07","department":[{"_id":"KrCh"}],"page":"20","pubrep_id":"15","oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"date_updated":"2023-02-23T11:15:12Z","date_published":"2011-07-11T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"file":[{"date_created":"2018-12-12T11:53:43Z","relation":"main_file","date_updated":"2020-07-14T12:46:39Z","file_size":388665,"creator":"system","checksum":"0b354264229045d982332fd2cb5b9a26","file_name":"IST-2011-0009_IST-2011-0009.pdf","file_id":"5504","content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","doi":"10.15479/AT:IST-2011-0009","_id":"5379","title":"An O(n2) time algorithm for alternating Büchi games","article_processing_charge":"No","citation":{"ama":"Chatterjee K, Henzinger MH. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">10.15479/AT:IST-2011-0009</a>","ieee":"K. Chatterjee and M. H. Henzinger, <i>An O(n2) time algorithm for alternating Büchi games</i>. IST Austria, 2011.","chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">https://doi.org/10.15479/AT:IST-2011-0009</a>.","ista":"Chatterjee K, Henzinger MH. 2011. An O(n2) time algorithm for alternating Büchi games, IST Austria, 20p.","short":"K. Chatterjee, M.H. Henzinger, An O(N2) Time Algorithm for Alternating Büchi Games, IST Austria, 2011.","apa":"Chatterjee, K., &#38; Henzinger, M. H. (2011). <i>An O(n2) time algorithm for alternating Büchi games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">https://doi.org/10.15479/AT:IST-2011-0009</a>","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">10.15479/AT:IST-2011-0009</a>."},"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"abstract":[{"lang":"eng","text":"We consider 2-player games played on a finite state space for an infinite number of rounds.  The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. We study concurrent games with ω-regular winning conditions specified as parity objectives.  We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). We study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies.  In terms of precision, strategies can be deterministic, uniform, finite-precision or infinite-precision;  and in terms of memory, strategies can be memoryless, finite-memory or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies.  We show that the winning sets can be computed in O(n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. While this complexity is the same as for the simpler class of turn-based parity games, where in each state only one of the two players has a choice of moves, our algorithms,that are obtained by characterization of the winning sets as μ-calculus formulas, are considerably more involved than those for turn-based games."}],"oa_version":"Published Version","has_accepted_license":"1","pubrep_id":"16","ddc":["000"],"related_material":{"record":[{"relation":"later_version","id":"3338","status":"public"}]},"alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:39Z","day":"11","status":"public","type":"technical_report","date_updated":"2023-02-23T11:22:53Z","date_created":"2018-12-12T11:39:00Z","publisher":"IST Austria","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"date_published":"2011-07-11T00:00:00Z","publication_identifier":{"issn":["2664-1690"]},"_id":"5380","title":"Bounded rationality in concurrent parity games","language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2011-0008","file":[{"file_size":500399,"creator":"system","checksum":"0fd38186409be819a911c4990fa79d1f","relation":"main_file","date_created":"2018-12-12T11:54:22Z","date_updated":"2020-07-14T12:46:39Z","access_level":"open_access","file_name":"IST-2011-0008_IST-2011-0008.pdf","file_id":"5544","content_type":"application/pdf"}],"publication_status":"published","year":"2011","oa":1,"citation":{"apa":"Chatterjee, K. (2011). <i>Bounded rationality in concurrent parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">https://doi.org/10.15479/AT:IST-2011-0008</a>","mla":"Chatterjee, Krishnendu. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">10.15479/AT:IST-2011-0008</a>.","short":"K. Chatterjee, Bounded Rationality in Concurrent Parity Games, IST Austria, 2011.","ista":"Chatterjee K. 2011. Bounded rationality in concurrent parity games, IST Austria, 53p.","ieee":"K. Chatterjee, <i>Bounded rationality in concurrent parity games</i>. IST Austria, 2011.","ama":"Chatterjee K. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">10.15479/AT:IST-2011-0008</a>","chicago":"Chatterjee, Krishnendu. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">https://doi.org/10.15479/AT:IST-2011-0008</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","department":[{"_id":"KrCh"}],"page":"53"},{"date_updated":"2023-02-23T11:05:48Z","date_created":"2018-12-12T11:39:00Z","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"publisher":"IST Austria","date_published":"2011-07-05T00:00:00Z","abstract":[{"lang":"eng","text":"In two-player finite-state stochastic games of partial obser- vation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distri- bution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or pos- itively (i.e., with positive probability), no matter the strategy of the second player.\r\n\r\nWe classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two- sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization.\r\n\r\nOur main results for pure strategies are as follows: (1) For one-sided games with player 2 perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strate- gies are not sufficient, and present an exponential upper bound on mem- ory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algo- rithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 perfect observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and posi- tive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence re- sult exhibit serious flaws in previous results in the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed."}],"oa_version":"Published Version","has_accepted_license":"1","ddc":["000","005"],"pubrep_id":"17","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"relation":"later_version","status":"public","id":"1903"},{"relation":"later_version","status":"public","id":"2211"},{"id":"2955","status":"public","relation":"later_version"}]},"file_date_updated":"2020-07-14T12:46:39Z","day":"05","type":"technical_report","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","page":"43","department":[{"_id":"KrCh"}],"publication_identifier":{"issn":["2664-1690"]},"title":"Partial-observation stochastic games: How to win when belief fails","_id":"5381","language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2011-0007","year":"2011","publication_status":"published","file":[{"file_name":"IST-2011-0007_IST-2011-0007.pdf","content_type":"application/pdf","file_id":"5488","access_level":"open_access","date_created":"2018-12-12T11:53:27Z","relation":"main_file","date_updated":"2020-07-14T12:46:39Z","checksum":"06bf6dfc97f6006e3fd0e9a3f31bc961","file_size":574055,"creator":"system"}],"oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">https://doi.org/10.15479/AT:IST-2011-0007</a>.","ieee":"K. Chatterjee and L. Doyen, <i>Partial-observation stochastic games: How to win when belief fails</i>. IST Austria, 2011.","ama":"Chatterjee K, Doyen L. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">10.15479/AT:IST-2011-0007</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">10.15479/AT:IST-2011-0007</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Partial-observation stochastic games: How to win when belief fails</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">https://doi.org/10.15479/AT:IST-2011-0007</a>","ista":"Chatterjee K, Doyen L. 2011. Partial-observation stochastic games: How to win when belief fails, IST Austria, 43p.","short":"K. Chatterjee, L. Doyen, Partial-Observation Stochastic Games: How to Win When Belief Fails, IST Austria, 2011."}}]