--- _id: '751' abstract: - lang: eng text: The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components. article_processing_charge: No author: - first_name: Yutaka full_name: Matsubayashi, Yutaka last_name: Matsubayashi - first_name: Adam full_name: Louani, Adam last_name: Louani - first_name: Anca full_name: Dragu, Anca last_name: Dragu - first_name: Besaiz full_name: Sanchez Sanchez, Besaiz last_name: Sanchez Sanchez - first_name: Eduardo full_name: Serna Morales, Eduardo last_name: Serna Morales - first_name: Lawrence full_name: Yolland, Lawrence last_name: Yolland - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Gema full_name: Vizcay, Gema last_name: Vizcay - first_name: Roland full_name: Fleck, Roland last_name: Fleck - first_name: John full_name: Heddleston, John last_name: Heddleston - first_name: Teng full_name: Chew, Teng last_name: Chew - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Brian full_name: Stramer, Brian last_name: Stramer citation: ama: Matsubayashi Y, Louani A, Dragu A, et al. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 2017;27(22):3526-3534e.4. doi:10.1016/j.cub.2017.10.001 apa: Matsubayashi, Y., Louani, A., Dragu, A., Sanchez Sanchez, B., Serna Morales, E., Yolland, L., … Stramer, B. (2017). A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.10.001 chicago: Matsubayashi, Yutaka, Adam Louani, Anca Dragu, Besaiz Sanchez Sanchez, Eduardo Serna Morales, Lawrence Yolland, Attila György, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.10.001. ieee: Y. Matsubayashi et al., “A moving source of matrix components is essential for De Novo basement membrane formation,” Current Biology, vol. 27, no. 22. Cell Press, p. 3526–3534e.4, 2017. ista: Matsubayashi Y, Louani A, Dragu A, Sanchez Sanchez B, Serna Morales E, Yolland L, György A, Vizcay G, Fleck R, Heddleston J, Chew T, Siekhaus DE, Stramer B. 2017. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 27(22), 3526–3534e.4. mla: Matsubayashi, Yutaka, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology, vol. 27, no. 22, Cell Press, 2017, p. 3526–3534e.4, doi:10.1016/j.cub.2017.10.001. short: Y. Matsubayashi, A. Louani, A. Dragu, B. Sanchez Sanchez, E. Serna Morales, L. Yolland, A. György, G. Vizcay, R. Fleck, J. Heddleston, T. Chew, D.E. Siekhaus, B. Stramer, Current Biology 27 (2017) 3526–3534e.4. date_created: 2018-12-11T11:48:18Z date_published: 2017-11-09T00:00:00Z date_updated: 2023-09-27T12:25:31Z day: '09' ddc: - '570' - '576' department: - _id: DaSi doi: 10.1016/j.cub.2017.10.001 external_id: isi: - '000415815800031' file: - access_level: open_access checksum: 264cf6c6c3551486ba5ea786850e000a content_type: application/pdf creator: system date_created: 2018-12-12T10:09:45Z date_updated: 2020-07-14T12:47:59Z file_id: '4770' file_name: IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf file_size: 4770657 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 3526 - 3534e.4 publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press publist_id: '6905' pubrep_id: '875' quality_controlled: '1' scopus_import: '1' status: public title: A moving source of matrix components is essential for De Novo basement membrane formation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 27 year: '2017' ... --- _id: '7725' abstract: - lang: eng text: Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is plausible. Existing studies on the adaptation of plasticity typically focus on single traits and a few populations, while theory about interactions among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale (for example, multiple populations) perspective is required. We present data from a landscape scale, replicated, multi-trait experiment using a classic predator–prey system centred on the water flea Daphnia pulex. We find predator regime-driven differences in genetic variation of multivariate plasticity. These differences are associated with strong divergent selection linked to a predation regime. Our findings are evidence for local adaptation of plasticity, suggesting that responses of populations to environmental variation depend on the conditions in which they evolved in the past. article_processing_charge: No article_type: original author: - first_name: Julia full_name: Reger, Julia last_name: Reger - first_name: Martin I. full_name: Lind, Martin I. last_name: Lind - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Andrew P. full_name: Beckerman, Andrew P. last_name: Beckerman citation: ama: Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2017;2:100-107. doi:10.1038/s41559-017-0373-6 apa: Reger, J., Lind, M. I., Robinson, M. R., & Beckerman, A. P. (2017). Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0373-6 chicago: Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution. Springer Nature, 2017. https://doi.org/10.1038/s41559-017-0373-6. ieee: J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives local adaptation of phenotypic plasticity,” Nature Ecology & Evolution, vol. 2. Springer Nature, pp. 100–107, 2017. ista: Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2, 100–107. mla: Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology & Evolution, vol. 2, Springer Nature, 2017, pp. 100–07, doi:10.1038/s41559-017-0373-6. short: J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology & Evolution 2 (2017) 100–107. date_created: 2020-04-30T10:46:02Z date_published: 2017-11-27T00:00:00Z date_updated: 2021-01-12T08:15:07Z day: '27' doi: 10.1038/s41559-017-0373-6 extern: '1' intvolume: ' 2' language: - iso: eng month: '11' oa_version: None page: 100-107 publication: Nature Ecology & Evolution publication_identifier: issn: - 2397-334X publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Predation drives local adaptation of phenotypic plasticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2017' ... --- _id: '7727' abstract: - lang: eng text: Genes of the major histocompatibility complex (MHC) have been shown to influence social signalling and mate preferences in many species, including humans. First observations suggest that MHC signalling may also affect female fertility. To test this hypothesis, we exposed 191 female horses (Equus caballus) to either an MHC-similar or an MHC-dissimilar stimulus male around the time of ovulation and conception. A within-subject experimental design controlled for non-MHC-linked male characteristics, and instrumental insemination with semen of other males (n = 106) controlled for potential confounding effects of semen or embryo characteristics. We found that females were more likely to become pregnant if exposed to an MHC-dissimilar than to an MHC-similar male, while overall genetic distance to the stimulus males (based on microsatellite markers on 20 chromosomes) had no effect. Our results demonstrate that early pregnancy failures can be due to maternal life-history decisions (cryptic female choice) influenced by MHC-linked social signalling. article_number: '20171824' article_processing_charge: No article_type: original author: - first_name: D. full_name: Burger, D. last_name: Burger - first_name: S. full_name: Thomas, S. last_name: Thomas - first_name: H. full_name: Aepli, H. last_name: Aepli - first_name: M. full_name: Dreyer, M. last_name: Dreyer - first_name: G. full_name: Fabre, G. last_name: Fabre - first_name: E. full_name: Marti, E. last_name: Marti - first_name: H. full_name: Sieme, H. last_name: Sieme - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: C. full_name: Wedekind, C. last_name: Wedekind citation: ama: 'Burger D, Thomas S, Aepli H, et al. Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. 2017;284(1868). doi:10.1098/rspb.2017.1824' apa: 'Burger, D., Thomas, S., Aepli, H., Dreyer, M., Fabre, G., Marti, E., … Wedekind, C. (2017). Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2017.1824' chicago: 'Burger, D., S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, Matthew Richard Robinson, and C. Wedekind. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2017. https://doi.org/10.1098/rspb.2017.1824.' ieee: 'D. Burger et al., “Major histocompatibility complex-linked social signalling affects female fertility,” Proceedings of the Royal Society B: Biological Sciences, vol. 284, no. 1868. The Royal Society, 2017.' ista: 'Burger D, Thomas S, Aepli H, Dreyer M, Fabre G, Marti E, Sieme H, Robinson MR, Wedekind C. 2017. Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. 284(1868), 20171824.' mla: 'Burger, D., et al. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences, vol. 284, no. 1868, 20171824, The Royal Society, 2017, doi:10.1098/rspb.2017.1824.' short: 'D. Burger, S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, M.R. Robinson, C. Wedekind, Proceedings of the Royal Society B: Biological Sciences 284 (2017).' date_created: 2020-04-30T10:46:43Z date_published: 2017-12-06T00:00:00Z date_updated: 2021-01-12T08:15:08Z day: '06' doi: 10.1098/rspb.2017.1824 extern: '1' external_id: pmid: - '29212724' intvolume: ' 284' issue: '1868' language: - iso: eng month: '12' oa_version: None pmid: 1 publication: 'Proceedings of the Royal Society B: Biological Sciences' publication_identifier: issn: - 0962-8452 - 1471-2954 publication_status: published publisher: The Royal Society quality_controlled: '1' status: public title: Major histocompatibility complex-linked social signalling affects female fertility type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 284 year: '2017' ... --- _id: '7728' abstract: - lang: eng text: 'Meta-analyses of genome-wide association studies, which dominate genetic discovery, are based on data from diverse historical time periods and populations. Genetic scores derived from genome-wide association studies explain only a fraction of the heritability estimates obtained from whole-genome studies on single populations, known as the ‘hidden heritability’ puzzle. Using seven sampling populations (n = 35,062), we test whether hidden heritability is attributed to heterogeneity across sampling populations and time, showing that estimates are substantially smaller across populations compared with within populations. We show that the hidden heritability varies substantially: from zero for height to 20% for body mass index, 37% for education, 40% for age at first birth and up to 75% for number of children. Simulations demonstrate that our results are more likely to reflect heterogeneity in phenotypic measurement or gene–environment interactions than genetic heterogeneity. These findings have substantial implications for genetic discovery, suggesting that large homogenous datasets are required for behavioural phenotypes and that gene–environment interaction may be a central challenge for genetic discovery.' article_processing_charge: No article_type: original author: - first_name: Felix C. full_name: Tropf, Felix C. last_name: Tropf - first_name: S. Hong full_name: Lee, S. Hong last_name: Lee - first_name: Renske M. full_name: Verweij, Renske M. last_name: Verweij - first_name: Gert full_name: Stulp, Gert last_name: Stulp - first_name: Peter J. full_name: van der Most, Peter J. last_name: van der Most - first_name: Ronald full_name: de Vlaming, Ronald last_name: de Vlaming - first_name: Andrew full_name: Bakshi, Andrew last_name: Bakshi - first_name: Daniel A. full_name: Briley, Daniel A. last_name: Briley - first_name: Charles full_name: Rahal, Charles last_name: Rahal - first_name: Robert full_name: Hellpap, Robert last_name: Hellpap - first_name: Anastasia N. full_name: Iliadou, Anastasia N. last_name: Iliadou - first_name: Tõnu full_name: Esko, Tõnu last_name: Esko - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Sarah E. full_name: Medland, Sarah E. last_name: Medland - first_name: Nicholas G. full_name: Martin, Nicholas G. last_name: Martin - first_name: Nicola full_name: Barban, Nicola last_name: Barban - first_name: Harold full_name: Snieder, Harold last_name: Snieder - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Melinda C. full_name: Mills, Melinda C. last_name: Mills citation: ama: Tropf FC, Lee SH, Verweij RM, et al. Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. 2017;1(10):757-765. doi:10.1038/s41562-017-0195-1 apa: Tropf, F. C., Lee, S. H., Verweij, R. M., Stulp, G., van der Most, P. J., de Vlaming, R., … Mills, M. C. (2017). Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-017-0195-1 chicago: Tropf, Felix C., S. Hong Lee, Renske M. Verweij, Gert Stulp, Peter J. van der Most, Ronald de Vlaming, Andrew Bakshi, et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” Nature Human Behaviour. Springer Nature, 2017. https://doi.org/10.1038/s41562-017-0195-1. ieee: F. C. Tropf et al., “Hidden heritability due to heterogeneity across seven populations,” Nature Human Behaviour, vol. 1, no. 10. Springer Nature, pp. 757–765, 2017. ista: Tropf FC, Lee SH, Verweij RM, Stulp G, van der Most PJ, de Vlaming R, Bakshi A, Briley DA, Rahal C, Hellpap R, Iliadou AN, Esko T, Metspalu A, Medland SE, Martin NG, Barban N, Snieder H, Robinson MR, Mills MC. 2017. Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. 1(10), 757–765. mla: Tropf, Felix C., et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” Nature Human Behaviour, vol. 1, no. 10, Springer Nature, 2017, pp. 757–65, doi:10.1038/s41562-017-0195-1. short: F.C. Tropf, S.H. Lee, R.M. Verweij, G. Stulp, P.J. van der Most, R. de Vlaming, A. Bakshi, D.A. Briley, C. Rahal, R. Hellpap, A.N. Iliadou, T. Esko, A. Metspalu, S.E. Medland, N.G. Martin, N. Barban, H. Snieder, M.R. Robinson, M.C. Mills, Nature Human Behaviour 1 (2017) 757–765. date_created: 2020-04-30T10:47:02Z date_published: 2017-09-11T00:00:00Z date_updated: 2021-01-12T08:15:08Z day: '11' doi: 10.1038/s41562-017-0195-1 extern: '1' intvolume: ' 1' issue: '10' language: - iso: eng month: '09' oa_version: None page: 757-765 publication: Nature Human Behaviour publication_identifier: issn: - 2397-3374 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Hidden heritability due to heterogeneity across seven populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2017' ... --- _id: '7729' abstract: - lang: eng text: Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000 participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs for complete inbreeding; P<0.001). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data. article_processing_charge: No article_type: original author: - first_name: Loic full_name: Yengo, Loic last_name: Yengo - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Bruce S. full_name: Weir, Bruce S. last_name: Weir - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 2017;114(32):8602-8607. doi:10.1073/pnas.1621096114 apa: Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., & Visscher, P. M. (2017). Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1621096114 chicago: Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621096114. ieee: L. Yengo et al., “Detection and quantification of inbreeding depression for complex traits from SNP data,” Proceedings of the National Academy of Sciences, vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607, 2017. ista: Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607. mla: Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences, vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07, doi:10.1073/pnas.1621096114. short: L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher, Proceedings of the National Academy of Sciences 114 (2017) 8602–8607. date_created: 2020-04-30T10:47:19Z date_published: 2017-08-08T00:00:00Z date_updated: 2021-01-12T08:15:09Z day: '08' doi: 10.1073/pnas.1621096114 extern: '1' intvolume: ' 114' issue: '32' language: - iso: eng month: '08' oa_version: None page: 8602-8607 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - relation: other url: https://doi.org/10.1073/pnas.1718598115 status: public title: Detection and quantification of inbreeding depression for complex traits from SNP data type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '7731' abstract: - lang: eng text: 'Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n = 625) and skin (n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).' article_processing_charge: No article_type: original author: - first_name: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Gerhard full_name: Moser, Gerhard last_name: Moser - first_name: Jian full_name: Zeng, Jian last_name: Zeng - first_name: Sandra full_name: Beleza, Sandra last_name: Beleza - first_name: Gregory S. full_name: Barsh, Gregory S. last_name: Barsh - first_name: Hua full_name: Tang, Hua last_name: Tang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Lloyd-Jones LR, Robinson MR, Moser G, et al. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 2017;206(2):1113-1126. doi:10.1534/genetics.116.193383 apa: Lloyd-Jones, L. R., Robinson, M. R., Moser, G., Zeng, J., Beleza, S., Barsh, G. S., … Visscher, P. M. (2017). Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193383 chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Gerhard Moser, Jian Zeng, Sandra Beleza, Gregory S. Barsh, Hua Tang, and Peter M. Visscher. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193383. ieee: L. R. Lloyd-Jones et al., “Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models,” Genetics, vol. 206, no. 2. Genetics Society of America, pp. 1113–1126, 2017. ista: Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, Tang H, Visscher PM. 2017. Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics. 206(2), 1113–1126. mla: Lloyd-Jones, Luke R., et al. “Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics, vol. 206, no. 2, Genetics Society of America, 2017, pp. 1113–26, doi:10.1534/genetics.116.193383. short: L.R. Lloyd-Jones, M.R. Robinson, G. Moser, J. Zeng, S. Beleza, G.S. Barsh, H. Tang, P.M. Visscher, Genetics 206 (2017) 1113–1126. date_created: 2020-04-30T10:47:50Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:15:10Z day: '01' doi: 10.1534/genetics.116.193383 extern: '1' intvolume: ' 206' issue: '2' language: - iso: eng month: '06' oa_version: None page: 1113-1126 publication: Genetics publication_identifier: issn: - 0016-6731 - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 206 year: '2017' ... --- _id: '7733' abstract: - lang: eng text: "Sections\r\nPDFPDF\r\nTools\r\nShare\r\nAbstract\r\nBackground: Gene discovery has provided remarkable biological insights into amyotrophic lateral sclerosis (ALS). One challenge for clinical application of genetic testing is critical evaluation of the significance of reported variants.\r\nMethods: We use whole exome sequencing (WES) to develop a clinically relevant approach to identify a subset of ALS patients harboring likely pathogenic mutations. In parallel, we assess if DNA methylation can be used to screen for pathogenicity of novel variants since a methylation signature has been shown to associate with the pathogenic C9orf72 expansion, but has not been explored for other ALS mutations. Australian patients identified with ALS‐relevant variants were cross‐checked with population databases and case reports to critically assess whether they were “likely causal,” “uncertain significance,” or “unlikely causal.”\r\nResults: Published ALS variants were identified in >10% of patients; however, in only 3% of patients (4/120) could these be confidently considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential DNA methylation signature in these mutation carriers.\r\nConclusions: The use of WES in a typical ALS clinic demonstrates a critical approach to variant assessment with the capability to combine cohorts to enhance the largely unknown genetic basis of ALS." article_processing_charge: No article_type: original author: - first_name: Fleur C. full_name: Garton, Fleur C. last_name: Garton - first_name: Beben full_name: Benyamin, Beben last_name: Benyamin - first_name: Qiongyi full_name: Zhao, Qiongyi last_name: Zhao - first_name: Zhijun full_name: Liu, Zhijun last_name: Liu - first_name: Jacob full_name: Gratten, Jacob last_name: Gratten - first_name: Anjali K. full_name: Henders, Anjali K. last_name: Henders - first_name: Zong-Hong full_name: Zhang, Zong-Hong last_name: Zhang - first_name: Janette full_name: Edson, Janette last_name: Edson - first_name: Sarah full_name: Furlong, Sarah last_name: Furlong - first_name: Sarah full_name: Morgan, Sarah last_name: Morgan - first_name: Susan full_name: Heggie, Susan last_name: Heggie - first_name: Kathryn full_name: Thorpe, Kathryn last_name: Thorpe - first_name: Casey full_name: Pfluger, Casey last_name: Pfluger - first_name: Karen A. full_name: Mather, Karen A. last_name: Mather - first_name: Perminder S. full_name: Sachdev, Perminder S. last_name: Sachdev - first_name: Allan F. full_name: McRae, Allan F. last_name: McRae - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Sonia full_name: Shah, Sonia last_name: Shah - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Marie full_name: Mangelsdorf, Marie last_name: Mangelsdorf - first_name: Robert D. full_name: Henderson, Robert D. last_name: Henderson - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Pamela A. full_name: McCombe, Pamela A. last_name: McCombe citation: ama: Garton FC, Benyamin B, Zhao Q, et al. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 2017;5(4):418-428. doi:10.1002/mgg3.302 apa: Garton, F. C., Benyamin, B., Zhao, Q., Liu, Z., Gratten, J., Henders, A. K., … McCombe, P. A. (2017). Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. Wiley. https://doi.org/10.1002/mgg3.302 chicago: Garton, Fleur C., Beben Benyamin, Qiongyi Zhao, Zhijun Liu, Jacob Gratten, Anjali K. Henders, Zong-Hong Zhang, et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine. Wiley, 2017. https://doi.org/10.1002/mgg3.302. ieee: F. C. Garton et al., “Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort,” Molecular Genetics & Genomic Medicine, vol. 5, no. 4. Wiley, pp. 418–428, 2017. ista: Garton FC, Benyamin B, Zhao Q, Liu Z, Gratten J, Henders AK, Zhang Z-H, Edson J, Furlong S, Morgan S, Heggie S, Thorpe K, Pfluger C, Mather KA, Sachdev PS, McRae AF, Robinson MR, Shah S, Visscher PM, Mangelsdorf M, Henderson RD, Wray NR, McCombe PA. 2017. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine. 5(4), 418–428. mla: Garton, Fleur C., et al. “Whole Exome Sequencing and DNA Methylation Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics & Genomic Medicine, vol. 5, no. 4, Wiley, 2017, pp. 418–28, doi:10.1002/mgg3.302. short: F.C. Garton, B. Benyamin, Q. Zhao, Z. Liu, J. Gratten, A.K. Henders, Z.-H. Zhang, J. Edson, S. Furlong, S. Morgan, S. Heggie, K. Thorpe, C. Pfluger, K.A. Mather, P.S. Sachdev, A.F. McRae, M.R. Robinson, S. Shah, P.M. Visscher, M. Mangelsdorf, R.D. Henderson, N.R. Wray, P.A. McCombe, Molecular Genetics & Genomic Medicine 5 (2017) 418–428. date_created: 2020-04-30T10:48:25Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:15:10Z day: '01' doi: 10.1002/mgg3.302 extern: '1' intvolume: ' 5' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/mgg3.302 month: '07' oa: 1 oa_version: Published Version page: 418-428 publication: Molecular Genetics & Genomic Medicine publication_identifier: issn: - 2324-9269 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2017' ... --- _id: '7755' abstract: - lang: eng text: We give a bird's-eye view of the plastic deformation of crystals aimed at the statistical physics community, as well as a broad introduction to the statistical theories of forced rigid systems aimed at the plasticity community. Memory effects in magnets, spin glasses, charge density waves, and dilute colloidal suspensions are discussed in relation to the onset of plastic yielding in crystals. Dislocation avalanches and complex dislocation tangles are discussed via a brief introduction to the renormalization group and scaling. Analogies to emergent scale invariance in fracture, jamming, coarsening, and a variety of depinning transitions are explored. Dislocation dynamics in crystals challenge nonequilibrium statistical physics. Statistical physics provides both cautionary tales of subtle memory effects in nonequilibrium systems and systematic tools designed to address complex scale-invariant behavior on multiple length scales and timescales. article_processing_charge: No article_type: original author: - first_name: James P. full_name: Sethna, James P. last_name: Sethna - first_name: Matthew K. full_name: Bierbaum, Matthew K. last_name: Bierbaum - first_name: Karin A. full_name: Dahmen, Karin A. last_name: Dahmen - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Julia R. full_name: Greer, Julia R. last_name: Greer - first_name: Lorien X. full_name: Hayden, Lorien X. last_name: Hayden - first_name: Jaron P. full_name: Kent-Dobias, Jaron P. last_name: Kent-Dobias - first_name: Edward D. full_name: Lee, Edward D. last_name: Lee - first_name: Danilo B. full_name: Liarte, Danilo B. last_name: Liarte - first_name: Xiaoyue full_name: Ni, Xiaoyue last_name: Ni - first_name: Katherine N. full_name: Quinn, Katherine N. last_name: Quinn - first_name: Archishman full_name: Raju, Archishman last_name: Raju - first_name: D. Zeb full_name: Rocklin, D. Zeb last_name: Rocklin - first_name: Ashivni full_name: Shekhawat, Ashivni last_name: Shekhawat - first_name: Stefano full_name: Zapperi, Stefano last_name: Zapperi citation: ama: 'Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 2017;47:217-246. doi:10.1146/annurev-matsci-070115-032036' apa: 'Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J. R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. Annual Reviews. https://doi.org/10.1146/annurev-matsci-070115-032036' chicago: 'Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich, Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research. Annual Reviews, 2017. https://doi.org/10.1146/annurev-matsci-070115-032036.' ieee: 'J. P. Sethna et al., “Deformation of crystals: Connections with statistical physics,” Annual Review of Materials Research, vol. 47. Annual Reviews, pp. 217–246, 2017.' ista: 'Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi S. 2017. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 47, 217–246.' mla: 'Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research, vol. 47, Annual Reviews, 2017, pp. 217–46, doi:10.1146/annurev-matsci-070115-032036.' short: J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X. Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z. Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017) 217–246. date_created: 2020-04-30T11:38:24Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:15:18Z day: '01' doi: 10.1146/annurev-matsci-070115-032036 extern: '1' intvolume: ' 47' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1146/annurev-matsci-070115-032036 month: '07' oa: 1 oa_version: Published Version page: 217-246 publication: Annual Review of Materials Research publication_identifier: issn: - 1531-7331 - 1545-4118 publication_status: published publisher: Annual Reviews quality_controlled: '1' status: public title: 'Deformation of crystals: Connections with statistical physics' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2017' ... --- _id: '7756' abstract: - lang: eng text: We study the shear jamming of athermal frictionless soft spheres, and find that in the thermodynamic limit, a shear-jammed state exists with different elastic properties from the isotropically-jammed state. For example, shear-jammed states can have a non-zero residual shear stress in the thermodynamic limit that arises from long-range stress-stress correlations. As a result, the ratio of the shear and bulk moduli, which in isotropically-jammed systems vanishes as the jamming transition is approached from above, instead approaches a constant. Despite these striking differences, we argue that in a deeper sense, the shear jamming and isotropic jamming transitions actually have the same symmetry, and that the differences can be fully understood by rotating the six-dimensional basis of the elastic modulus tensor. article_processing_charge: No article_type: original author: - first_name: Marco full_name: Baity-Jesi, Marco last_name: Baity-Jesi - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel - first_name: James P. full_name: Sethna, James P. last_name: Sethna citation: ama: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 2017;167(3-4):735-748. doi:10.1007/s10955-016-1703-9 apa: Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., & Sethna, J. P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-016-1703-9 chicago: Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel, and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics. Springer Nature, 2017. https://doi.org/10.1007/s10955-016-1703-9. ieee: M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent SO(3) symmetry of the frictionless shear jamming transition,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017. ista: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 167(3–4), 735–748. mla: Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer Nature, 2017, pp. 735–48, doi:10.1007/s10955-016-1703-9. short: M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal of Statistical Physics 167 (2017) 735–748. date_created: 2020-04-30T11:38:38Z date_published: 2017-01-03T00:00:00Z date_updated: 2021-01-12T08:15:19Z day: '03' doi: 10.1007/s10955-016-1703-9 extern: '1' intvolume: ' 167' issue: 3-4 language: - iso: eng month: '01' oa_version: None page: 735-748 publication: Journal of Statistical Physics publication_identifier: issn: - 0022-4715 - 1572-9613 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Emergent SO(3) symmetry of the frictionless shear jamming transition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 167 year: '2017' ... --- _id: '7757' abstract: - lang: eng text: Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks. article_processing_charge: No article_type: original author: - first_name: Jason W. full_name: Rocks, Jason W. last_name: Rocks - first_name: Nidhi full_name: Pashine, Nidhi last_name: Pashine - first_name: Irmgard full_name: Bischofberger, Irmgard last_name: Bischofberger - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 2017;114(10):2520-2525. doi:10.1073/pnas.1612139114 apa: Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2017). Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612139114 chicago: Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1612139114. ieee: J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” Proceedings of the National Academy of Sciences, vol. 114, no. 10. Proceedings of the National Academy of Sciences, pp. 2520–2525, 2017. ista: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 114(10), 2520–2525. mla: Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences, vol. 114, no. 10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:10.1073/pnas.1612139114. short: J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel, Proceedings of the National Academy of Sciences 114 (2017) 2520–2525. date_created: 2020-04-30T11:38:53Z date_published: 2017-03-07T00:00:00Z date_updated: 2021-01-12T08:15:19Z day: '07' doi: 10.1073/pnas.1612139114 extern: '1' intvolume: ' 114' issue: '10' language: - iso: eng month: '03' oa_version: None page: 2520-2525 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Designing allostery-inspired response in mechanical networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '7758' abstract: - lang: eng text: Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles. article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner citation: ama: Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 2017;114(2):257-262. doi:10.1073/pnas.1608838114 apa: Goodrich, C. P., & Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1608838114 chicago: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1608838114. ieee: C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” Proceedings of the National Academy of Sciences, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017. ista: Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262. mla: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:10.1073/pnas.1608838114. short: C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262. date_created: 2020-04-30T11:39:09Z date_published: 2017-01-10T00:00:00Z date_updated: 2021-01-12T08:15:20Z day: '10' doi: 10.1073/pnas.1608838114 extern: '1' intvolume: ' 114' issue: '2' language: - iso: eng month: '01' oa_version: None page: 257-262 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Using active colloids as machines to weave and braid on the micrometer scale type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '459' abstract: - lang: eng text: The social insects bees, wasps, ants, and termites are species-rich, occur in many habitats, and often constitute a large part of the biomass. Many are also invasive, including species of termites, the red imported fire ant, and the Argentine ant. While invasive social insects have been a problem in Southern Europe for some time, Central Europa was free of invasive ant species until recently because most ants are adapted to warmer climates. Only in the 1990s, did Lasius neglectus, a close relative of the common black garden ant, arrive in Germany. First described in 1990 based on individuals collected in Budapest, the species has since been detected for example in France, Germany, Spain, England, and Kyrgyzstan. The species is spread with soil during construction work or plantings, and L. neglectus therefore is often found in parks and botanical gardens. Another invasive ant now spreading in southern Germany is Formica fuscocinerea, which occurs along rivers, including in the sandy floodplains of the river Isar. As is typical of pioneer species, F. fuscocinerea quickly becomes extremely abundant and therefore causes problems for example on playgrounds in Munich. All invasive ant species are characterized by cooperation across nests, leading to strongly interconnected, very large super-colonies. The resulting dominance results in the extinction of native ant species as well as other arthropod species and thus in the reduction of biodiversity. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Cremer S. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. 2017;46:105-116.' apa: 'Cremer, S. (2017). Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. Verlag Dr. Friedrich Pfeil.' chicago: 'Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” Rundgespräche Forum Ökologie. Verlag Dr. Friedrich Pfeil, 2017.' ieee: 'S. Cremer, “Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern,” Rundgespräche Forum Ökologie, vol. 46. Verlag Dr. Friedrich Pfeil, pp. 105–116, 2017.' ista: 'Cremer S. 2017. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. 46, 105–116.' mla: 'Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” Rundgespräche Forum Ökologie, vol. 46, Verlag Dr. Friedrich Pfeil, 2017, pp. 105–16.' short: S. Cremer, Rundgespräche Forum Ökologie 46 (2017) 105–116. date_created: 2018-12-11T11:46:35Z date_published: 2017-04-04T00:00:00Z date_updated: 2023-10-17T12:28:13Z day: '04' ddc: - '592' department: - _id: SyCr file: - access_level: open_access checksum: 4919baf9050415ca151fe22497379f78 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:52Z date_updated: 2020-07-14T12:46:32Z file_id: '5175' file_name: IST-2018-962-v1+1_044676698_07_Cremer__Invasive_Ameisen_in_Europa_...__BY-ND_.pdf file_size: 1711131 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 46' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '04' oa: 1 oa_version: Published Version page: 105 - 116 publication: Rundgespräche Forum Ökologie publication_identifier: issn: - 2366-2875 publication_status: published publisher: Verlag Dr. Friedrich Pfeil publist_id: '7362' pubrep_id: '962' quality_controlled: '1' status: public title: 'Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern' tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2017' ... --- _id: '463' abstract: - lang: eng text: We investigate transient behaviors induced by magnetic fields on the dynamics of the flow of a ferrofluid in the gap between two concentric, independently rotating cylinders. Without applying any magnetic fields, we uncover emergence of flow states constituted by a combination of a localized spiral state (SPIl) in the top and bottom of the annulus and different multi-cell flow states (SPI2v, SPI3v) with toroidally closed vortices in the interior of the bulk (SPIl+2v = SPIl + SPI2v and SPIl+3v = SPIl + SPI3v). However, when a magnetic field is presented, we observe the transient behaviors between multi-cell states passing through two critical thresholds in a strength of an axial (transverse) magnetic field. Before the first critical threshold of a magnetic field strength, multi-stable states with different number of cells could be observed. After the first critical threshold, we find the transient behavior between the three- and two-cell flow states. For more strength of magnetic field or after the second critical threshold, we discover that multi-cell states are disappeared and a localized spiral state remains to be stimulated. The studied transient behavior could be understood by the investigation of various quantities including a modal kinetic energy, a mode amplitude of the radial velocity, wavenumber, angular momentum, and torque. In addition, the emergence of new flow states and the transient behavior between their states in ferrofluidic flows indicate that richer and potentially controllable dynamics through magnetic fields could be possible in ferrofluic flow. article_number: '113112' article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Soorok full_name: Ryu, Soorok last_name: Ryu citation: ama: Altmeyer S, Do Y, Ryu S. Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. 2017;27(11). doi:10.1063/1.5002771 apa: Altmeyer, S., Do, Y., & Ryu, S. (2017). Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. AIP Publishing. https://doi.org/10.1063/1.5002771 chicago: Altmeyer, Sebastian, Younghae Do, and Soorok Ryu. “Transient Behavior between Multi-Cell Flow States in Ferrofluidic Taylor-Couette Flow.” Chaos. AIP Publishing, 2017. https://doi.org/10.1063/1.5002771. ieee: S. Altmeyer, Y. Do, and S. Ryu, “Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow,” Chaos, vol. 27, no. 11. AIP Publishing, 2017. ista: Altmeyer S, Do Y, Ryu S. 2017. Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. 27(11), 113112. mla: Altmeyer, Sebastian, et al. “Transient Behavior between Multi-Cell Flow States in Ferrofluidic Taylor-Couette Flow.” Chaos, vol. 27, no. 11, 113112, AIP Publishing, 2017, doi:10.1063/1.5002771. short: S. Altmeyer, Y. Do, S. Ryu, Chaos 27 (2017). date_created: 2018-12-11T11:46:37Z date_published: 2017-11-01T00:00:00Z date_updated: 2024-02-28T13:02:12Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.1063/1.5002771 file: - access_level: open_access checksum: 0731f9d416760c1062db258ca51f8bdc content_type: application/pdf creator: dernst date_created: 2019-10-24T15:14:30Z date_updated: 2020-07-14T12:46:32Z file_id: '6970' file_name: 2017_Chaos_Altmeyer.pdf file_size: 7714020 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 27' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Chaos publication_identifier: issn: - '10541500' publication_status: published publisher: AIP Publishing publist_id: '7358' quality_controlled: '1' scopus_import: '1' status: public title: Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2017' ... --- _id: '464' abstract: - lang: eng text: The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years. article_number: '26' article_processing_charge: No arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017 apa: Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017 chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017. ieee: K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017. ista: Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26. mla: Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017. short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017). date_created: 2018-12-11T11:46:37Z date_published: 2017-09-26T00:00:00Z date_updated: 2025-06-02T08:53:41Z day: '26' ddc: - '004' department: - _id: KrCh doi: 10.23638/LMCS-13(3:26)2017 ec_funded: 1 external_id: arxiv: - '1410.0833' file: - access_level: open_access checksum: 12d469ae69b80361333d7dead965cf5d content_type: application/pdf creator: system date_created: 2018-12-12T10:13:27Z date_updated: 2020-07-14T12:46:32Z file_id: '5010' file_name: IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf file_size: 582940 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Logical Methods in Computer Science publication_identifier: issn: - 1860-5974 publication_status: published publisher: International Federation of Computational Logic publist_id: '7357' pubrep_id: '956' quality_controlled: '1' related_material: record: - id: '1661' relation: earlier_version status: public scopus_import: '1' status: public title: Improved algorithms for parity and Streett objectives tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '465' abstract: - lang: eng text: 'The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Jan full_name: Otop, Jan last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017 apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017. ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017. ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3). mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017. short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017). date_created: 2018-12-11T11:46:37Z date_published: 2017-09-13T00:00:00Z date_updated: 2023-02-23T12:26:25Z day: '13' ddc: - '004' department: - _id: KrCh - _id: ToHe doi: 10.23638/LMCS-13(3:23)2017 ec_funded: 1 file: - access_level: open_access checksum: 08041379ba408d40664f449eb5907a8f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:37Z date_updated: 2020-07-14T12:46:33Z file_id: '5090' file_name: IST-2015-321-v1+1_main.pdf file_size: 279071 relation: main_file - access_level: open_access checksum: 08041379ba408d40664f449eb5907a8f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:38Z date_updated: 2020-07-14T12:46:33Z file_id: '5091' file_name: IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf file_size: 279071 relation: main_file file_date_updated: 2020-07-14T12:46:33Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Logical Methods in Computer Science publication_identifier: issn: - '18605974' publication_status: published publisher: International Federation of Computational Logic publist_id: '7356' pubrep_id: '955' quality_controlled: '1' related_material: record: - id: '1610' relation: earlier_version status: public - id: '5438' relation: earlier_version status: public scopus_import: 1 status: public title: Edit distance for pushdown automata tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '466' abstract: - lang: eng text: 'We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. ' article_number: '15' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Křetínská, Zuzana last_name: Křetínská - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017 apa: Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017 chicago: Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017. ieee: K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017. ista: Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15. mla: Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017. short: K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017). date_created: 2018-12-11T11:46:38Z date_published: 2017-07-03T00:00:00Z date_updated: 2023-02-23T12:26:16Z day: '03' ddc: - '004' department: - _id: KrCh doi: 10.23638/LMCS-13(2:15)2017 ec_funded: 1 file: - access_level: open_access checksum: bfa405385ec6229ad5ead89ab5751639 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:32Z date_updated: 2020-07-14T12:46:33Z file_id: '5354' file_name: IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf file_size: 511832 relation: main_file file_date_updated: 2020-07-14T12:46:33Z has_accepted_license: '1' intvolume: ' 13' issue: '2' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2590DB08-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '701309' name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020) publication: Logical Methods in Computer Science publication_identifier: issn: - '18605974' publication_status: published publisher: International Federation of Computational Logic publist_id: '7355' pubrep_id: '957' quality_controlled: '1' related_material: record: - id: '1657' relation: earlier_version status: public - id: '5429' relation: earlier_version status: public - id: '5435' relation: earlier_version status: public scopus_import: 1 status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '467' abstract: - lang: eng text: Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties. article_number: '31' arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769 apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017. ista: Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31. mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769. short: K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017). date_created: 2018-12-11T11:46:38Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-02-23T12:26:19Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1145/3152769 ec_funded: 1 external_id: arxiv: - '1606.03598' intvolume: ' 18' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.03598 month: '12' oa: 1 oa_version: Preprint project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ACM Transactions on Computational Logic (TOCL) publication_identifier: issn: - '15293785' publication_status: published publisher: ACM publist_id: '7354' quality_controlled: '1' related_material: record: - id: '1656' relation: earlier_version status: public - id: '5415' relation: earlier_version status: public - id: '5436' relation: earlier_version status: public scopus_import: 1 status: public title: Nested weighted automata type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2017' ... --- _id: '470' abstract: - lang: eng text: This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios. acknowledged_ssus: - _id: ScienComp article_number: '103' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678 apa: Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678 chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678. ieee: S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017. ista: Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103. mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678. short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017). date_created: 2018-12-11T11:46:39Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-02-23T12:20:26Z day: '01' ddc: - '006' department: - _id: ChWo doi: 10.1145/3072959.3073678 ec_funded: 1 file: - access_level: open_access checksum: 82a3b2bfeee4ddef16ecc21675d1a48a content_type: application/pdf creator: wojtan date_created: 2020-01-24T09:32:35Z date_updated: 2020-07-14T12:46:34Z file_id: '7359' file_name: wavepackets_final.pdf file_size: 13131683 relation: main_file file_date_updated: 2020-07-14T12:46:34Z has_accepted_license: '1' intvolume: ' 36' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: ACM Transactions on Graphics publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '7350' quality_controlled: '1' scopus_import: 1 status: public title: Water wave packets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ... --- _id: '471' abstract: - lang: eng text: 'We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. ' article_number: '12' author: - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 2017;18(2). doi:10.1145/3060139 apa: Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2017). Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3060139 chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139. ieee: P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2. ACM, 2017. ista: Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 18(2), 12. mla: Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2, 12, ACM, 2017, doi:10.1145/3060139. short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017). date_created: 2018-12-11T11:46:39Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-02-21T16:48:11Z day: '01' department: - _id: ToHe doi: 10.1145/3060139 ec_funded: 1 intvolume: ' 18' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.05739 month: '05' oa: 1 oa_version: Submitted Version project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ACM Transactions on Computational Logic (TOCL) publication_identifier: issn: - '15293785' publication_status: published publisher: ACM publist_id: '7349' quality_controlled: '1' related_material: record: - id: '1234' relation: earlier_version status: public scopus_import: 1 status: public title: Faster statistical model checking for unbounded temporal properties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2017' ... --- _id: '472' abstract: - lang: eng text: α-Synuclein is a presynaptic protein the function of which has yet to be identified, but its neuronal content increases in patients of synucleinopa-thies including Parkinson’s disease. Chronic overexpression of α-synuclein reportedly expresses various phenotypes of synaptic dysfunction, but the primary target of its toxicity has not been determined. To investigate this, we acutely loaded human recombinant α-synuclein or its pathological mutants in their monomeric forms into the calyces of Held presynaptic terminals in slices from auditorily mature and immature rats of either sex. Membrane capacitance measurements revealed significant and specific inhibitory effects of WT monomeric α-synuclein on vesicle endocytosis throughout development. However, the α-synuclein A53T mutant affected vesicle endocytosis only at immature calyces, where as the A30P mutant had no effect throughout. The endocytic impairment by WTα-synuclein was rescued by intraterminal coloading of the microtubule (MT) polymerization blocker nocodazole. Furthermore, it was reversibly rescued by presynaptically loaded photostatin-1, a pho-toswitcheable inhibitor of MT polymerization, inalight-wavelength-dependent manner. Incontrast, endocyticinhibition by the A53T mutant at immature calyces was not rescued by nocodazole. Functionally, presynaptically loaded WT α-synuclein had no effect on basal synaptic transmission evoked at a low frequency, but significantly attenuated exocytosis and impaired the fidelity of neurotransmission during prolonged high-frequency stimulation. We conclude that monomeric WTα-synuclein primarily inhibits vesicle endocytosis via MT overassembly, thereby impairing high-frequency neurotransmission. author: - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Zachari full_name: Taoufiq, Zachari last_name: Taoufiq - first_name: Oliver full_name: Thorn Seshold, Oliver last_name: Thorn Seshold - first_name: Dirk full_name: Trauner, Dirk last_name: Trauner - first_name: Masato full_name: Hasegawa, Masato last_name: Hasegawa - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 2017;37(25):6043-6052. doi:10.1523/JNEUROSCI.0179-17.2017 apa: Eguchi, K., Taoufiq, Z., Thorn Seshold, O., Trauner, D., Hasegawa, M., & Takahashi, T. (2017). Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1523/JNEUROSCI.0179-17.2017 chicago: Eguchi, Kohgaku, Zachari Taoufiq, Oliver Thorn Seshold, Dirk Trauner, Masato Hasegawa, and Tomoyuki Takahashi. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1523/JNEUROSCI.0179-17.2017. ieee: K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, and T. Takahashi, “Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held,” European Journal of Neuroscience, vol. 37, no. 25. Wiley-Blackwell, pp. 6043–6052, 2017. ista: Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. 2017. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 37(25), 6043–6052. mla: Eguchi, Kohgaku, et al. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience, vol. 37, no. 25, Wiley-Blackwell, 2017, pp. 6043–52, doi:10.1523/JNEUROSCI.0179-17.2017. short: K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, T. Takahashi, European Journal of Neuroscience 37 (2017) 6043–6052. date_created: 2018-12-11T11:46:40Z date_published: 2017-06-21T00:00:00Z date_updated: 2021-01-12T08:00:51Z day: '21' doi: 10.1523/JNEUROSCI.0179-17.2017 extern: '1' intvolume: ' 37' issue: '25' language: - iso: eng month: '06' oa_version: None page: 6043 - 6052 publication: European Journal of Neuroscience publication_identifier: issn: - '02706474' publication_status: published publisher: Wiley-Blackwell publist_id: '7348' quality_controlled: '1' status: public title: Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2017' ...