--- _id: '1019' abstract: - lang: eng text: As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline. article_processing_charge: No author: - first_name: Eliza full_name: Argyridou, Eliza last_name: Argyridou - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Annabella full_name: Königer, Annabella last_name: Königer - first_name: John full_name: Parsch, John last_name: Parsch citation: ama: Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 2017;119(1):27-34. doi:10.1038/hdy.2017.12 apa: Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12 chicago: Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12. ieee: E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,” Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017. ista: Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 119(1), 27–34. mla: Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1, Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12. short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34. date_created: 2018-12-11T11:49:43Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-09-22T09:41:21Z day: '01' department: - _id: BeVi doi: 10.1038/hdy.2017.12 external_id: isi: - '000405397800004' intvolume: ' 119' isi: 1 issue: '1' language: - iso: eng month: '07' oa_version: None page: 27 - 34 publication: Heredity publication_identifier: issn: - 0018067X publication_status: published publisher: Nature Publishing Group publist_id: '6374' quality_controlled: '1' related_material: record: - id: '9861' relation: research_data status: public scopus_import: '1' status: public title: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 119 year: '2017' ... --- _id: '9861' abstract: - lang: eng text: As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline. article_processing_charge: No author: - first_name: Eliza full_name: Argyridou, Eliza last_name: Argyridou - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Annabella full_name: Königer, Annabella last_name: Königer - first_name: John full_name: Parsch, John last_name: Parsch citation: ama: 'Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. 2017. doi:10.5061/dryad.02f6r' apa: 'Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Dryad. https://doi.org/10.5061/dryad.02f6r' chicago: 'Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Dryad, 2017. https://doi.org/10.5061/dryad.02f6r.' ieee: 'E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.” Dryad, 2017.' ista: 'Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster, Dryad, 10.5061/dryad.02f6r.' mla: 'Argyridou, Eliza, et al. Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster. Dryad, 2017, doi:10.5061/dryad.02f6r.' short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017). date_created: 2021-08-10T08:12:52Z date_published: 2017-02-14T00:00:00Z date_updated: 2023-09-22T09:41:20Z day: '14' department: - _id: BeVi doi: 10.5061/dryad.02f6r main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.02f6r month: '02' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1019' relation: used_in_publication status: public status: public title: 'Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '1006' abstract: - lang: eng text: 'Background: The phenomenon of immune priming, i.e. enhanced protection following a secondary exposure to a pathogen, has now been demonstrated in a wide range of invertebrate species. Despite accumulating phenotypic evidence, knowledge of its mechanistic underpinnings is currently very limited. Here we used the system of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus thuringiensis (Bt) to further our molecular understanding of the oral immune priming phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants) of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon later challenge exposure, using a whole-transcriptome sequencing approach. Results: Whereas gene expression of individuals primed with the orally non-pathogenic strain showed minor changes to controls, we found that priming with the pathogenic strain induced regulation of a large set of distinct genes, many of which are known immune candidates. Intriguingly, the immune repertoire activated upon priming and subsequent challenge qualitatively differed from the one mounted upon infection with Bt without previous priming. Moreover, a large subset of priming-specific genes showed an inverse regulation compared to their regulation upon challenge only. Conclusions: Our data demonstrate that gene expression upon infection is strongly affected by previous immune priming. We hypothesise that this shift in gene expression indicates activation of a more targeted and efficient response towards a previously encountered pathogen, in anticipation of potential secondary encounter.' article_processing_charge: No author: - first_name: Jenny full_name: Greenwood, Jenny last_name: Greenwood - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Sarah full_name: Behrens, Sarah last_name: Behrens - first_name: Daniela full_name: Essar, Daniela last_name: Essar - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: Greenwood J, Milutinovic B, Peuß R, et al. Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. 2017;18(1):329. doi:10.1186/s12864-017-3705-7 apa: Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-017-3705-7 chicago: Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics. BioMed Central, 2017. https://doi.org/10.1186/s12864-017-3705-7. ieee: J. Greenwood et al., “Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,” BMC Genomics, vol. 18, no. 1. BioMed Central, p. 329, 2017. ista: Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics. 18(1), 329. mla: Greenwood, Jenny, et al. “Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics, vol. 18, no. 1, BioMed Central, 2017, p. 329, doi:10.1186/s12864-017-3705-7. short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, BMC Genomics 18 (2017) 329. date_created: 2018-12-11T11:49:39Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-22T09:47:44Z day: '26' ddc: - '570' department: - _id: SyCr doi: 10.1186/s12864-017-3705-7 external_id: isi: - '000400625200004' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:46Z date_updated: 2018-12-12T10:16:46Z file_id: '5236' file_name: IST-2017-814-v1+1_s12864-017-3705-7.pdf file_size: 2379672 relation: main_file file_date_updated: 2018-12-12T10:16:46Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '04' oa: 1 oa_version: Published Version page: '329' publication: BMC Genomics publication_identifier: issn: - '14712164' publication_status: published publisher: BioMed Central publist_id: '6392' pubrep_id: '814' quality_controlled: '1' related_material: record: - id: '9859' relation: research_data status: public - id: '9860' relation: research_data status: public scopus_import: '1' status: public title: Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae 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: 18 year: '2017' ... --- _id: '1011' abstract: - lang: eng text: Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly equivalent, are standard models for interprocedural analysis. Yet RSMs are more convenient as they (a) explicitly model function calls and returns, and (b) specify many natural parameters for algorithmic analysis, e.g., the number of entries and exits. We consider a general framework where RSM transitions are labeled from a semiring and path properties are algebraic with semiring operations, which can model, e.g., interprocedural reachability and dataflow analysis problems. Our main contributions are new algorithms for several fundamental problems. As compared to a direct translation of RSMs to PDSs and the best-known existing bounds of PDSs, our analysis algorithm improves the complexity for finite-height semirings (that subsumes reachability and standard dataflow properties). We further consider the problem of extracting distance values from the representation structures computed by our algorithm, and give efficient algorithms that distinguish the complexity of a one-time preprocessing from the complexity of each individual query. Another advantage of our algorithm is that our improvements carry over to the concurrent setting, where we improve the bestknown complexity for the context-bounded analysis of concurrent RSMs. Finally, we provide a prototype implementation that gives a significant speed-up on several benchmarks from the SLAM/SDV project. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Samarth full_name: Mishra, Samarth last_name: Mishra - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. Faster algorithms for weighted recursive state machines. In: Yang H, ed. Vol 10201. Springer; 2017:287-313. doi:10.1007/978-3-662-54434-1_11' apa: 'Chatterjee, K., Kragl, B., Mishra, S., & Pavlogiannis, A. (2017). Faster algorithms for weighted recursive state machines. In H. Yang (Ed.) (Vol. 10201, pp. 287–313). Presented at the ESOP: European Symposium on Programming, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54434-1_11' chicago: Chatterjee, Krishnendu, Bernhard Kragl, Samarth Mishra, and Andreas Pavlogiannis. “Faster Algorithms for Weighted Recursive State Machines.” edited by Hongseok Yang, 10201:287–313. Springer, 2017. https://doi.org/10.1007/978-3-662-54434-1_11. ieee: 'K. Chatterjee, B. Kragl, S. Mishra, and A. Pavlogiannis, “Faster algorithms for weighted recursive state machines,” presented at the ESOP: European Symposium on Programming, Uppsala, Sweden, 2017, vol. 10201, pp. 287–313.' ista: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. 2017. Faster algorithms for weighted recursive state machines. ESOP: European Symposium on Programming, LNCS, vol. 10201, 287–313.' mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Weighted Recursive State Machines. Edited by Hongseok Yang, vol. 10201, Springer, 2017, pp. 287–313, doi:10.1007/978-3-662-54434-1_11. short: K. Chatterjee, B. Kragl, S. Mishra, A. Pavlogiannis, in:, H. Yang (Ed.), Springer, 2017, pp. 287–313. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'ESOP: European Symposium on Programming' start_date: 2017-04-22 date_created: 2018-12-11T11:49:41Z date_published: 2017-03-19T00:00:00Z date_updated: 2023-09-22T09:44:50Z day: '19' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-662-54434-1_11 ec_funded: 1 editor: - first_name: Hongseok full_name: Yang, Hongseok last_name: Yang external_id: isi: - '000681702400011' intvolume: ' 10201' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1701.04914 month: '03' oa: 1 oa_version: Submitted Version page: 287 - 313 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _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: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6384' quality_controlled: '1' scopus_import: '1' status: public title: Faster algorithms for weighted recursive state machines type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10201 year: '2017' ... --- _id: '1004' abstract: - lang: eng text: The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment. article_processing_charge: No author: - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 2017;45:82-89. doi:10.1016/j.gde.2017.03.010 apa: Ötvös, K., & Benková, E. (2017). Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2017.03.010 chicago: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development. Elsevier, 2017. https://doi.org/10.1016/j.gde.2017.03.010. ieee: K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” Current Opinion in Genetics & Development, vol. 45. Elsevier, pp. 82–89, 2017. ista: Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 45, 82–89. mla: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development, vol. 45, Elsevier, 2017, pp. 82–89, doi:10.1016/j.gde.2017.03.010. short: K. Ötvös, E. Benková, Current Opinion in Genetics & Development 45 (2017) 82–89. date_created: 2018-12-11T11:49:38Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-09-22T09:48:15Z day: '01' ddc: - '575' department: - _id: EvBe doi: 10.1016/j.gde.2017.03.010 external_id: isi: - '000404880400013' pmid: - '28391060' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-04-17T08:00:36Z date_updated: 2019-04-17T08:00:36Z file_id: '6336' file_name: Otvos_Benkova_CurOpDevBiol_2017.pdf file_size: 364133 relation: main_file success: 1 file_date_updated: 2019-04-17T08:00:36Z has_accepted_license: '1' intvolume: ' 45' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '08' oa: 1 oa_version: Submitted Version page: 82 - 89 pmid: 1 project: - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development publication: Current Opinion in Genetics & Development publication_identifier: issn: - 0959437X publication_status: published publisher: Elsevier publist_id: '6394' pubrep_id: '1017' quality_controlled: '1' scopus_import: '1' status: public title: Spatiotemporal mechanisms of root branching tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 45 year: '2017' ... --- _id: '1010' abstract: - lang: eng text: 'We prove a local law in the bulk of the spectrum for random Gram matrices XX∗, a generalization of sample covariance matrices, where X is a large matrix with independent, centered entries with arbitrary variances. The limiting eigenvalue density that generalizes the Marchenko-Pastur law is determined by solving a system of nonlinear equations. Our entrywise and averaged local laws are on the optimal scale with the optimal error bounds. They hold both in the square case (hard edge) and in the properly rectangular case (soft edge). In the latter case we also establish a macroscopic gap away from zero in the spectrum of XX∗. ' article_number: '25' article_processing_charge: No author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Alt J, Erdös L, Krüger TH. Local law for random Gram matrices. Electronic Journal of Probability. 2017;22. doi:10.1214/17-EJP42 apa: Alt, J., Erdös, L., & Krüger, T. H. (2017). Local law for random Gram matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-EJP42 chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Law for Random Gram Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-EJP42. ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local law for random Gram matrices,” Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics, 2017. ista: Alt J, Erdös L, Krüger TH. 2017. Local law for random Gram matrices. Electronic Journal of Probability. 22, 25. mla: Alt, Johannes, et al. “Local Law for Random Gram Matrices.” Electronic Journal of Probability, vol. 22, 25, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP42. short: J. Alt, L. Erdös, T.H. Krüger, Electronic Journal of Probability 22 (2017). date_created: 2018-12-11T11:49:40Z date_published: 2017-03-08T00:00:00Z date_updated: 2023-09-22T09:45:23Z day: '08' ddc: - '510' - '539' department: - _id: LaEr doi: 10.1214/17-EJP42 ec_funded: 1 external_id: arxiv: - '1606.07353' isi: - '000396611900025' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:13:39Z date_updated: 2018-12-12T10:13:39Z file_id: '5024' file_name: IST-2017-807-v1+1_euclid.ejp.1488942016.pdf file_size: 639384 relation: main_file file_date_updated: 2018-12-12T10:13:39Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Journal of Probability publication_identifier: issn: - '10836489' publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6386' pubrep_id: '807' quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: '1' status: public title: Local law for random Gram matrices 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: 22 year: '2017' ... --- _id: '1009' abstract: - lang: eng text: A standard objective in partially-observable Markov decision processes (POMDPs) is to find a policy that maximizes the expected discounted-sum payoff. However, such policies may still permit unlikely but highly undesirable outcomes, which is problematic especially in safety-critical applications. Recently, there has been a surge of interest in POMDPs where the goal is to maximize the probability to ensure that the payoff is at least a given threshold, but these approaches do not consider any optimization beyond satisfying this threshold constraint. In this work we go beyond both the “expectation” and “threshold” approaches and consider a “guaranteed payoff optimization (GPO)” problem for POMDPs, where we are given a threshold t and the objective is to find a policy σ such that a) each possible outcome of σ yields a discounted-sum payoff of at least t, and b) the expected discounted-sum payoff of σ is optimal (or near-optimal) among all policies satisfying a). We present a practical approach to tackle the GPO problem and evaluate it on standard POMDP benchmarks. acknowledgement: 'he research leading to these results was supported by the Austrian Science Fund (FWF) NFN Grant no. S11407-N23 (RiSE/SHiNE); two ERC Starting grants (279307: Graph Games, 279499: inVEST); the Vienna Science and Tech- nology Fund (WWTF) through project ICT15-003; and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734].' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny - first_name: Guillermo full_name: Pérez, Guillermo last_name: Pérez - first_name: Jean full_name: Raskin, Jean last_name: Raskin - first_name: Djordje full_name: Zikelic, Djordje last_name: Zikelic citation: ama: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. Optimizing expectation with guarantees in POMDPs. In: Proceedings of the 31st AAAI Conference on Artificial Intelligence. Vol 5. AAAI Press; 2017:3725-3732.' apa: 'Chatterjee, K., Novotný, P., Pérez, G., Raskin, J., & Zikelic, D. (2017). Optimizing expectation with guarantees in POMDPs. In Proceedings of the 31st AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3725–3732). San Francisco, CA, United States: AAAI Press.' chicago: Chatterjee, Krishnendu, Petr Novotný, Guillermo Pérez, Jean Raskin, and Djordje Zikelic. “Optimizing Expectation with Guarantees in POMDPs.” In Proceedings of the 31st AAAI Conference on Artificial Intelligence, 5:3725–32. AAAI Press, 2017. ieee: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, and D. Zikelic, “Optimizing expectation with guarantees in POMDPs,” in Proceedings of the 31st AAAI Conference on Artificial Intelligence, San Francisco, CA, United States, 2017, vol. 5, pp. 3725–3732. ista: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. 2017. Optimizing expectation with guarantees in POMDPs. Proceedings of the 31st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 5, 3725–3732.' mla: Chatterjee, Krishnendu, et al. “Optimizing Expectation with Guarantees in POMDPs.” Proceedings of the 31st AAAI Conference on Artificial Intelligence, vol. 5, AAAI Press, 2017, pp. 3725–32. short: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, D. Zikelic, in:, Proceedings of the 31st AAAI Conference on Artificial Intelligence, AAAI Press, 2017, pp. 3725–3732. conference: end_date: 2017-02-10 location: San Francisco, CA, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2017-02-04 date_created: 2018-12-11T11:49:40Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-22T09:46:41Z day: '01' department: - _id: KrCh ec_funded: 1 external_id: isi: - '000485630703107' intvolume: ' 5' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/download/14354/14092 month: '01' oa: 1 oa_version: Submitted Version page: 3725 - 3732 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Proceedings of the 31st AAAI Conference on Artificial Intelligence publication_status: published publisher: AAAI Press publist_id: '6387' quality_controlled: '1' scopus_import: '1' status: public title: Optimizing expectation with guarantees in POMDPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 5 year: '2017' ... --- _id: '9859' abstract: - lang: eng text: 'Lists of all differentially expressed genes in the different priming-challenge treatments (compared to the fully naïve control; xlsx file). Relevant columns include the following: sample_1 and sample_2 – treatment groups being compared; Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change) – log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated compared with sample 2, positive means sample 2 upregulated compared with sample 1; cuffdiff test_statistic – test statistic of differential expression test; p_value – p-value of differential expression test; q_value (FDR correction) – adjusted P-value of differential expression test. (XLSX 598 kb)' article_processing_charge: No author: - first_name: Jenny full_name: Greenwood, Jenny last_name: Greenwood - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Sarah full_name: Behrens, Sarah last_name: Behrens - first_name: Daniela full_name: Essar, Daniela last_name: Essar - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d1.v1' apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1' chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature, 2017. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1.' ieee: 'J. Greenwood et al., “Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.” Springer Nature, 2017.' ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae, Springer Nature, 10.6084/m9.figshare.c.3756974_d1.v1.' mla: 'Greenwood, Jenny, et al. Additional File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d1.v1.' short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (2017). date_created: 2021-08-10T07:59:02Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-22T09:47:44Z day: '26' department: - _id: SyCr doi: 10.6084/m9.figshare.c.3756974_d1.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1 month: '04' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '1006' relation: used_in_publication status: public status: public title: 'Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9860' article_processing_charge: No author: - first_name: Jenny full_name: Greenwood, Jenny last_name: Greenwood - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Sarah full_name: Behrens, Sarah last_name: Behrens - first_name: Daniela full_name: Essar, Daniela last_name: Essar - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d5.v1' apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel, P., … Kurtz, J. (2017). Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1' chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature, 2017. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1.' ieee: 'J. Greenwood et al., “Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.” Springer Nature, 2017.' ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg H, Kurtz J. 2017. Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae, Springer Nature, 10.6084/m9.figshare.c.3756974_d5.v1.' mla: 'Greenwood, Jenny, et al. Additional File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d5.v1.' short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (2017). date_created: 2021-08-10T08:07:12Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-22T09:47:44Z day: '26' department: - _id: SyCr doi: 10.6084/m9.figshare.c.3756974_d5.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1 month: '04' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '1006' relation: used_in_publication status: public status: public title: 'Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '1002' abstract: - lang: eng text: " We present an interactive design system to create functional mechanical \ objects. Our computational approach allows novice users to retarget an existing mechanical template to a user-specified input shape. Our proposed representation for a mechanical template encodes a parameterized mechanism, mechanical constraints that ensure a physically valid configuration, spatial relationships of mechanical parts to the user-provided shape, and functional constraints that specify an intended functionality. We provide an intuitive interface and optimization-in-the-loop approach for finding a valid configuration of the mechanism and the shape to ensure that higher-level functional goals are met. Our algorithm interactively optimizes the mechanism while the user manipulates the placement of mechanical components and the shape. Our system allows users to efficiently explore various design choices and to synthesize customized mechanical objects that can be fabricated with rapid prototyping technologies. We demonstrate the efficacy of our approach by retargeting various mechanical templates to different shapes and fabricating the resulting functional mechanical objects.\r\n" alternative_title: - ACM Transactions on Graphics article_number: '81' article_processing_charge: No author: - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Duygu full_name: Ceylan, Duygu last_name: Ceylan - first_name: Wilmot full_name: Li, Wilmot last_name: Li - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. Functionality-aware retargeting of mechanisms to 3D shapes. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073710' apa: 'Zhang, R., Auzinger, T., Ceylan, D., Li, W., & Bickel, B. (2017). Functionality-aware retargeting of mechanisms to 3D shapes (Vol. 36). Presented at the SIGGRAPH: Computer Graphics and Interactive Techniques, Los Angeles, CA, United States : ACM. https://doi.org/10.1145/3072959.3073710' chicago: Zhang, Ran, Thomas Auzinger, Duygu Ceylan, Wilmot Li, and Bernd Bickel. “Functionality-Aware Retargeting of Mechanisms to 3D Shapes,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073710. ieee: 'R. Zhang, T. Auzinger, D. Ceylan, W. Li, and B. Bickel, “Functionality-aware retargeting of mechanisms to 3D shapes,” presented at the SIGGRAPH: Computer Graphics and Interactive Techniques, Los Angeles, CA, United States , 2017, vol. 36, no. 4.' ista: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. 2017. Functionality-aware retargeting of mechanisms to 3D shapes. SIGGRAPH: Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 81.' mla: Zhang, Ran, et al. Functionality-Aware Retargeting of Mechanisms to 3D Shapes. Vol. 36, no. 4, 81, ACM, 2017, doi:10.1145/3072959.3073710. short: R. Zhang, T. Auzinger, D. Ceylan, W. Li, B. Bickel, in:, ACM, 2017. conference: end_date: 2017-08-03 location: 'Los Angeles, CA, United States ' name: 'SIGGRAPH: Computer Graphics and Interactive Techniques' start_date: 2017-07-30 date_created: 2018-12-11T11:49:38Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-22T09:49:31Z day: '01' ddc: - '003' - '004' department: - _id: BeBi doi: 10.1145/3072959.3073710 ec_funded: 1 external_id: isi: - '000406432100049' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:09:05Z date_updated: 2018-12-12T10:09:05Z file_id: '4728' file_name: IST-2018-1050-v1+1_MechRet.pdf file_size: 25463895 relation: main_file file_date_updated: 2018-12-12T10:09:05Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '4' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '6396' pubrep_id: '1050' quality_controlled: '1' related_material: record: - id: '8386' relation: dissertation_contains status: public scopus_import: '1' status: public title: Functionality-aware retargeting of mechanisms to 3D shapes type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 36 year: '2017' ... --- _id: '1001' abstract: - lang: eng text: We present a computational approach for designing CurveUps, curvy shells that form from an initially flat state. They consist of small rigid tiles that are tightly held together by two pre-stretched elastic sheets attached to them. Our method allows the realization of smooth, doubly curved surfaces that can be fabricated as a flat piece. Once released, the restoring forces of the pre-stretched sheets support the object to take shape in 3D. CurveUps are structurally stable in their target configuration. The design process starts with a target surface. Our method generates a tile layout in 2D and optimizes the distribution, shape, and attachment areas of the tiles to obtain a configuration that is fabricable and in which the curved up state closely matches the target. Our approach is based on an efficient approximate model and a local optimization strategy for an otherwise intractable nonlinear optimization problem. We demonstrate the effectiveness of our approach for a wide range of shapes, all realized as physical prototypes. alternative_title: - ACM Transactions on Graphics article_number: '64' article_processing_charge: No author: - first_name: Ruslan full_name: Guseinov, Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 - first_name: Eder full_name: Miguel, Eder last_name: Miguel - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Guseinov R, Miguel E, Bickel B. CurveUps: Shaping objects from flat plates with tension-actuated curvature. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073709' apa: 'Guseinov, R., Miguel, E., & Bickel, B. (2017). CurveUps: Shaping objects from flat plates with tension-actuated curvature (Vol. 36). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/3072959.3073709' chicago: 'Guseinov, Ruslan, Eder Miguel, and Bernd Bickel. “CurveUps: Shaping Objects from Flat Plates with Tension-Actuated Curvature,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073709.' ieee: 'R. Guseinov, E. Miguel, and B. Bickel, “CurveUps: Shaping objects from flat plates with tension-actuated curvature,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2017, vol. 36, no. 4.' ista: 'Guseinov R, Miguel E, Bickel B. 2017. CurveUps: Shaping objects from flat plates with tension-actuated curvature. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 64.' mla: 'Guseinov, Ruslan, et al. CurveUps: Shaping Objects from Flat Plates with Tension-Actuated Curvature. Vol. 36, no. 4, 64, ACM, 2017, doi:10.1145/3072959.3073709.' short: R. Guseinov, E. Miguel, B. Bickel, in:, ACM, 2017. conference: end_date: 2017-08-25 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2017-08-19 date_created: 2018-12-11T11:49:38Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-22T09:49:58Z day: '01' ddc: - '003' - '004' department: - _id: BeBi doi: 10.1145/3072959.3073709 ec_funded: 1 external_id: isi: - '000406432100032' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:10:24Z date_updated: 2018-12-12T10:10:24Z file_id: '4811' file_name: IST-2018-1053-v1+1_CurveUp.pdf file_size: 36159696 relation: main_file file_date_updated: 2018-12-12T10:10:24Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '4' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version project: - _id: 25082902-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '645599' name: Soft-bodied intelligence for Manipulation - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_status: published publisher: ACM publist_id: '6397' pubrep_id: '1053' quality_controlled: '1' related_material: record: - id: '8366' relation: dissertation_contains status: public status: public title: 'CurveUps: Shaping objects from flat plates with tension-actuated curvature' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 36 year: '2017' ... --- _id: '1003' abstract: - lang: eng text: Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globally optimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstraction-refinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under- and an overapproximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. Our experimental results demonstrate the efficiency of the methodology. article_processing_charge: No author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Shibashis full_name: Guha, Shibashis last_name: Guha - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: 'Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning about network games. In: AAAI Press; 2017:70-76. doi:10.24963/ijcai.2017/11' apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). An abstraction-refinement methodology for reasoning about network games (pp. 70–76). Presented at the IJCAI: International Joint Conference on Artificial Intelligence , Melbourne, Australia: AAAI Press. https://doi.org/10.24963/ijcai.2017/11' chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement Methodology for Reasoning about Network Games,” 70–76. AAAI Press, 2017. https://doi.org/10.24963/ijcai.2017/11. ieee: 'G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology for reasoning about network games,” presented at the IJCAI: International Joint Conference on Artificial Intelligence , Melbourne, Australia, 2017, pp. 70–76.' ista: 'Avni G, Guha S, Kupferman O. 2017. An abstraction-refinement methodology for reasoning about network games. IJCAI: International Joint Conference on Artificial Intelligence , 70–76.' mla: Avni, Guy, et al. An Abstraction-Refinement Methodology for Reasoning about Network Games. AAAI Press, 2017, pp. 70–76, doi:10.24963/ijcai.2017/11. short: G. Avni, S. Guha, O. Kupferman, in:, AAAI Press, 2017, pp. 70–76. conference: end_date: 2017-08-25 location: Melbourne, Australia name: 'IJCAI: International Joint Conference on Artificial Intelligence ' start_date: 2017-08-19 date_created: 2018-12-11T11:49:38Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T09:49:00Z day: '30' ddc: - '004' department: - _id: ToHe doi: 10.24963/ijcai.2017/11 external_id: isi: - '000764137500011' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:58Z date_updated: 2018-12-12T10:16:58Z file_id: '5249' file_name: IST-2017-818-v1+1_allIJCAI_CR.pdf file_size: 365172 relation: main_file file_date_updated: 2018-12-12T10:16:58Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 70 - 76 project: - _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 publication_identifier: issn: - '10450823' publication_status: published publisher: AAAI Press publist_id: '6395' pubrep_id: '818' quality_controlled: '1' related_material: record: - id: '6006' relation: later_version status: public scopus_import: '1' status: public title: An abstraction-refinement methodology for reasoning about network games type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '1000' abstract: - lang: eng text: 'We study probabilistic models of natural images and extend the autoregressive family of PixelCNN models by incorporating latent variables. Subsequently, we describe two new generative image models that exploit different image transformations as latent variables: a quantized grayscale view of the image or a multi-resolution image pyramid. The proposed models tackle two known shortcomings of existing PixelCNN models: 1) their tendency to focus on low-level image details, while largely ignoring high-level image information, such as object shapes, and 2) their computationally costly procedure for image sampling. We experimentally demonstrate benefits of our LatentPixelCNN models, in particular showing that they produce much more realistically looking image samples than previous state-of-the-art probabilistic models. ' acknowledgement: We thank Tim Salimans for spotting a mistake in our preliminary arXiv manuscript. This work was funded by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036. article_processing_charge: No author: - first_name: Alexander full_name: Kolesnikov, Alexander id: 2D157DB6-F248-11E8-B48F-1D18A9856A87 last_name: Kolesnikov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Kolesnikov A, Lampert C. PixelCNN models with auxiliary variables for natural image modeling. In: 34th International Conference on Machine Learning. Vol 70. JMLR; 2017:1905-1914.' apa: 'Kolesnikov, A., & Lampert, C. (2017). PixelCNN models with auxiliary variables for natural image modeling. In 34th International Conference on Machine Learning (Vol. 70, pp. 1905–1914). Sydney, Australia: JMLR.' chicago: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary Variables for Natural Image Modeling.” In 34th International Conference on Machine Learning, 70:1905–14. JMLR, 2017. ieee: A. Kolesnikov and C. Lampert, “PixelCNN models with auxiliary variables for natural image modeling,” in 34th International Conference on Machine Learning, Sydney, Australia, 2017, vol. 70, pp. 1905–1914. ista: 'Kolesnikov A, Lampert C. 2017. PixelCNN models with auxiliary variables for natural image modeling. 34th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 70, 1905–1914.' mla: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary Variables for Natural Image Modeling.” 34th International Conference on Machine Learning, vol. 70, JMLR, 2017, pp. 1905–14. short: A. Kolesnikov, C. Lampert, in:, 34th International Conference on Machine Learning, JMLR, 2017, pp. 1905–1914. conference: end_date: 2017-08-11 location: Sydney, Australia name: 'ICML: International Conference on Machine Learning' start_date: 2017-08-06 date_created: 2018-12-11T11:49:37Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-09-22T09:50:41Z day: '01' department: - _id: ChLa ec_funded: 1 external_id: arxiv: - '1612.08185' isi: - '000683309501102' has_accepted_license: '1' intvolume: ' 70' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.08185 month: '08' oa: 1 oa_version: Submitted Version page: 1905 - 1914 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: 34th International Conference on Machine Learning publication_identifier: isbn: - 978-151085514-4 publication_status: published publisher: JMLR publist_id: '6398' quality_controlled: '1' scopus_import: '1' status: public title: PixelCNN models with auxiliary variables for natural image modeling type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 70 year: '2017' ... --- _id: '998' abstract: - lang: eng text: 'A major open problem on the road to artificial intelligence is the development of incrementally learning systems that learn about more and more concepts over time from a stream of data. In this work, we introduce a new training strategy, iCaRL, that allows learning in such a class-incremental way: only the training data for a small number of classes has to be present at the same time and new classes can be added progressively. iCaRL learns strong classifiers and a data representation simultaneously. This distinguishes it from earlier works that were fundamentally limited to fixed data representations and therefore incompatible with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period of time where other strategies quickly fail. ' article_processing_charge: No author: - first_name: Sylvestre Alvise full_name: Rebuffi, Sylvestre Alvise last_name: Rebuffi - first_name: Alexander full_name: Kolesnikov, Alexander id: 2D157DB6-F248-11E8-B48F-1D18A9856A87 last_name: Kolesnikov - first_name: Georg full_name: Sperl, Georg id: 4DD40360-F248-11E8-B48F-1D18A9856A87 last_name: Sperl - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. iCaRL: Incremental classifier and representation learning. In: Vol 2017. IEEE; 2017:5533-5542. doi:10.1109/CVPR.2017.587' apa: 'Rebuffi, S. A., Kolesnikov, A., Sperl, G., & Lampert, C. (2017). iCaRL: Incremental classifier and representation learning (Vol. 2017, pp. 5533–5542). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.587' chicago: 'Rebuffi, Sylvestre Alvise, Alexander Kolesnikov, Georg Sperl, and Christoph Lampert. “ICaRL: Incremental Classifier and Representation Learning,” 2017:5533–42. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.587.' ieee: 'S. A. Rebuffi, A. Kolesnikov, G. Sperl, and C. Lampert, “iCaRL: Incremental classifier and representation learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 5533–5542.' ista: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. 2017. iCaRL: Incremental classifier and representation learning. CVPR: Computer Vision and Pattern Recognition vol. 2017, 5533–5542.' mla: 'Rebuffi, Sylvestre Alvise, et al. ICaRL: Incremental Classifier and Representation Learning. Vol. 2017, IEEE, 2017, pp. 5533–42, doi:10.1109/CVPR.2017.587.' short: S.A. Rebuffi, A. Kolesnikov, G. Sperl, C. Lampert, in:, IEEE, 2017, pp. 5533–5542. conference: end_date: 2017-07-26 location: Honolulu, HA, United States name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2017-07-21 date_created: 2018-12-11T11:49:37Z date_published: 2017-04-14T00:00:00Z date_updated: 2023-09-22T09:51:58Z day: '14' department: - _id: ChLa - _id: ChWo doi: 10.1109/CVPR.2017.587 ec_funded: 1 external_id: isi: - '000418371405066' intvolume: ' 2017' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.07725 month: '04' oa: 1 oa_version: Submitted Version page: 5533 - 5542 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: isbn: - 978-153860457-1 publication_status: published publisher: IEEE publist_id: '6400' quality_controlled: '1' scopus_import: '1' status: public title: 'iCaRL: Incremental classifier and representation learning' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2017 year: '2017' ... --- _id: '990' abstract: - lang: eng text: Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations. article_processing_charge: No author: - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252 apa: Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252 chicago: Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252. ieee: H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” Evolution; International Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017. ista: Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 71(6), 1478–1493. mla: Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:10.1111/evo.13252. short: H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493. date_created: 2018-12-11T11:49:34Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-22T09:55:13Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1111/evo.13252 ec_funded: 1 external_id: isi: - '000403014800005' pmid: - '28419447' file: - access_level: open_access checksum: 6d4c38cb1347fd43620d1736c6df5c79 content_type: application/pdf creator: dernst date_created: 2019-04-17T07:37:04Z date_updated: 2020-07-14T12:48:18Z file_id: '6329' file_name: 2017_Evolution_Sachdeva_supplement.pdf file_size: 625260 relation: main_file - access_level: open_access checksum: f1d90dd8831b44baf49b4dd176f263af content_type: application/pdf creator: dernst date_created: 2019-04-17T07:37:04Z date_updated: 2020-07-14T12:48:18Z file_id: '6330' file_name: 2017_Evolution_Sachdeva_article.pdf file_size: 520110 relation: main_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' intvolume: ' 71' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: '1478 - 1493 ' pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Evolution; International Journal of Organic Evolution publication_identifier: issn: - '00143820' publication_status: published publisher: Wiley-Blackwell publist_id: '6409' pubrep_id: '977' quality_controlled: '1' scopus_import: '1' status: public title: Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 71 year: '2017' ... --- _id: '988' abstract: - lang: eng text: The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement. article_processing_charge: No author: - first_name: Gaurav full_name: Nanda, Gaurav last_name: Nanda - first_name: Juan L full_name: Aguilera Servin, Juan L id: 2A67C376-F248-11E8-B48F-1D18A9856A87 last_name: Aguilera Servin orcid: 0000-0002-2862-8372 - first_name: Péter full_name: Rakyta, Péter last_name: Rakyta - first_name: Andor full_name: Kormányos, Andor last_name: Kormányos - first_name: Reinhold full_name: Kleiner, Reinhold last_name: Kleiner - first_name: Dieter full_name: Koelle, Dieter last_name: Koelle - first_name: Kazuo full_name: Watanabe, Kazuo last_name: Watanabe - first_name: Takashi full_name: Taniguchi, Takashi last_name: Taniguchi - first_name: Lieven full_name: Vandersypen, Lieven last_name: Vandersypen - first_name: Srijit full_name: Goswami, Srijit last_name: Goswami citation: ama: Nanda G, Aguilera Servin JL, Rakyta P, et al. Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. 2017;17(6):3396-3401. doi:10.1021/acs.nanolett.7b00097 apa: Nanda, G., Aguilera Servin, J. L., Rakyta, P., Kormányos, A., Kleiner, R., Koelle, D., … Goswami, S. (2017). Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b00097 chicago: Nanda, Gaurav, Juan L Aguilera Servin, Péter Rakyta, Andor Kormányos, Reinhold Kleiner, Dieter Koelle, Kazuo Watanabe, Takashi Taniguchi, Lieven Vandersypen, and Srijit Goswami. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b00097. ieee: G. Nanda et al., “Current-phase relation of ballistic graphene Josephson junctions,” Nano Letters, vol. 17, no. 6. American Chemical Society, pp. 3396–3401, 2017. ista: Nanda G, Aguilera Servin JL, Rakyta P, Kormányos A, Kleiner R, Koelle D, Watanabe K, Taniguchi T, Vandersypen L, Goswami S. 2017. Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. 17(6), 3396–3401. mla: Nanda, Gaurav, et al. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.” Nano Letters, vol. 17, no. 6, American Chemical Society, 2017, pp. 3396–401, doi:10.1021/acs.nanolett.7b00097. short: G. Nanda, J.L. Aguilera Servin, P. Rakyta, A. Kormányos, R. Kleiner, D. Koelle, K. Watanabe, T. Taniguchi, L. Vandersypen, S. Goswami, Nano Letters 17 (2017) 3396–3401. date_created: 2018-12-11T11:49:33Z date_published: 2017-05-05T00:00:00Z date_updated: 2023-09-22T09:56:21Z day: '05' ddc: - '621' department: - _id: NanoFab doi: 10.1021/acs.nanolett.7b00097 external_id: isi: - '000403631600011' file: - access_level: open_access checksum: 22021daa90cf13b01becd776838acb7b content_type: application/pdf creator: system date_created: 2018-12-12T10:13:50Z date_updated: 2020-07-14T12:48:18Z file_id: '5037' file_name: IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf file_size: 508638 relation: main_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '6' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 3396 - 3401 publication: Nano Letters publication_identifier: issn: - '15306984' publication_status: published publisher: American Chemical Society publist_id: '6412' pubrep_id: '826' quality_controlled: '1' scopus_import: '1' status: public title: Current-phase relation of ballistic graphene Josephson junctions tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 17 year: '2017' ... --- _id: '993' abstract: - lang: eng text: In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development. article_number: '15140' article_processing_charge: Yes (in subscription journal) author: - first_name: Anna full_name: Levina (Martius), Anna id: 35AF8020-F248-11E8-B48F-1D18A9856A87 last_name: Levina (Martius) - first_name: Viola full_name: Priesemann, Viola last_name: Priesemann citation: ama: Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications. 2017;8. doi:10.1038/ncomms15140 apa: Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140 chicago: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140. ieee: A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140. mla: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140. short: A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017). date_created: 2018-12-11T11:49:35Z date_published: 2017-05-04T00:00:00Z date_updated: 2023-09-22T09:54:07Z day: '04' ddc: - '005' - '571' department: - _id: GaTk - _id: JoCs doi: 10.1038/ncomms15140 ec_funded: 1 external_id: isi: - '000400560700001' file: - access_level: open_access checksum: 9880212f8c4c53404c7c6fbf9023c53a content_type: application/pdf creator: system date_created: 2018-12-12T10:15:05Z date_updated: 2020-07-14T12:48:19Z file_id: '5122' file_name: IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf file_size: 746224 relation: main_file file_date_updated: 2020-07-14T12:48:19Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '05' 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 publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6406' pubrep_id: '819' quality_controlled: '1' scopus_import: '1' status: public title: Subsampling scaling 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: 8 year: '2017' ... --- _id: '995' abstract: - lang: eng text: Recently it was shown that an impurity exchanging orbital angular momentum with a surrounding bath can be described in terms of the angulon quasiparticle [Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor dressed by a many-particle field of boson excitations, and can be formed out of, for example, a molecule or a nonspherical atom in superfluid helium, or out of an electron coupled to lattice phonons or a Bose condensate. Here we develop an approach to the angulon based on the path-integral formalism, which sets the ground for a systematic, perturbative treatment of the angulon problem. The resulting perturbation series can be interpreted in terms of Feynman diagrams, from which, in turn, one can derive a set of diagrammatic rules. These rules extend the machinery of the graphical theory of angular momentum - well known from theoretical atomic spectroscopy - to the case where an environment with an infinite number of degrees of freedom is present. In particular, we show that each diagram can be interpreted as a 'skeleton', which enforces angular momentum conservation, dressed by an additional many-body contribution. This connection between the angulon theory and the graphical theory of angular momentum is particularly important as it allows to systematically and substantially simplify the analytical representation of each diagram. In order to exemplify the technique, we calculate the 1- and 2-loop contributions to the angulon self-energy, the spectral function, and the quasiparticle weight. The diagrammatic theory we develop paves the way to investigate next-to-leading order quantities in a more compact way compared to the variational approaches. article_number: '085410' article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. 2017;96(8). doi:10.1103/PhysRevB.96.085410 apa: Bighin, G., & Lemeshko, M. (2017). Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.085410 chicago: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.085410. ieee: G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 8. American Physical Society, 2017. ista: Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. 96(8), 085410. mla: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 8, 085410, American Physical Society, 2017, doi:10.1103/PhysRevB.96.085410. short: G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 96 (2017). date_created: 2018-12-11T11:49:36Z date_published: 2017-08-07T00:00:00Z date_updated: 2023-09-22T09:53:17Z day: '07' department: - _id: MiLe doi: 10.1103/PhysRevB.96.085410 external_id: isi: - '000407017100009' intvolume: ' 96' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.02616 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - '24699950' publication_status: published publisher: American Physical Society publist_id: '6404' quality_controlled: '1' scopus_import: '1' status: public title: Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 96 year: '2017' ... --- _id: '989' abstract: - lang: eng text: We present a generalized optimal transport model in which the mass-preserving constraint for the L2-Wasserstein distance is relaxed by introducing a source term in the continuity equation. The source term is also incorporated in the path energy by means of its squared L2-norm in time of a functional with linear growth in space. This extension of the original transport model enables local density modulations, which is a desirable feature in applications such as image warping and blending. A key advantage of the use of a functional with linear growth in space is that it allows for singular sources and sinks, which can be supported on points or lines. On a technical level, the L2-norm in time ensures a disintegration of the source in time, which we use to obtain the well-posedness of the model and the existence of geodesic paths. The numerical discretization is based on the proximal splitting approach [18] and selected numerical test cases show the potential of the proposed approach. Furthermore, the approach is applied to the warping and blending of textures. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Martin full_name: Rumpf, Martin last_name: Rumpf - first_name: Stefan full_name: Simon, Stefan last_name: Simon citation: ama: 'Maas J, Rumpf M, Simon S. Transport based image morphing with intensity modulation. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:563-577. doi:10.1007/978-3-319-58771-4_45' apa: 'Maas, J., Rumpf, M., & Simon, S. (2017). Transport based image morphing with intensity modulation. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 563–577). Presented at the SSVM:  Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_45' chicago: Maas, Jan, Martin Rumpf, and Stefan Simon. “Transport Based Image Morphing with Intensity Modulation.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:563–77. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_45. ieee: J. Maas, M. Rumpf, and S. Simon, “Transport based image morphing with intensity modulation,” presented at the SSVM:  Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 563–577. ista: Maas J, Rumpf M, Simon S. 2017. Transport based image morphing with intensity modulation. SSVM:  Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 563–577. mla: Maas, Jan, et al. Transport Based Image Morphing with Intensity Modulation. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 563–77, doi:10.1007/978-3-319-58771-4_45. short: J. Maas, M. Rumpf, S. Simon, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 563–577. conference: end_date: 2017-06-08 location: Kolding, Denmark name: 'SSVM: Scale Space and Variational Methods in Computer Vision' start_date: 2017-06-04 date_created: 2018-12-11T11:49:34Z date_published: 2017-05-18T00:00:00Z date_updated: 2023-09-22T09:55:50Z day: '18' department: - _id: JaMa doi: 10.1007/978-3-319-58771-4_45 editor: - first_name: François full_name: Lauze, François last_name: Lauze - first_name: Yiqiu full_name: Dong, Yiqiu last_name: Dong - first_name: Anders full_name: Bjorholm Dahl, Anders last_name: Bjorholm Dahl external_id: isi: - '000432210900045' intvolume: ' 10302' isi: 1 language: - iso: eng month: '05' oa_version: None page: 563 - 577 publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6410' quality_controlled: '1' scopus_import: '1' status: public title: Transport based image morphing with intensity modulation type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10302 year: '2017' ... --- _id: '994' abstract: - lang: eng text: The formation of vortices is usually considered to be the main mechanism of angular momentum disposal in superfluids. Recently, it was predicted that a superfluid can acquire angular momentum via an alternative, microscopic route -- namely, through interaction with rotating impurities, forming so-called `angulon quasiparticles' [Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to transfer of a small number of angular momentum quanta from the impurity to the superfluid, as opposed to vortex instabilities, where angular momentum is quantized in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules) represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically 3D as well, as opposed to a merely planar rotation which is inherent to vortices. Herein we show that the angulon theory can explain the anomalous broadening of the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities in experiment. article_processing_charge: No author: - first_name: Igor full_name: Cherepanov, Igor id: 339C7E5A-F248-11E8-B48F-1D18A9856A87 last_name: Cherepanov - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Cherepanov I, Lemeshko M. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 2017;1(3). doi:10.1103/PhysRevMaterials.1.035602 apa: Cherepanov, I., & Lemeshko, M. (2017). Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.1.035602 chicago: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials. American Physical Society, 2017. https://doi.org/10.1103/PhysRevMaterials.1.035602. ieee: I. Cherepanov and M. Lemeshko, “Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules,” Physical Review Materials, vol. 1, no. 3. American Physical Society, 2017. ista: Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 1(3). mla: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials, vol. 1, no. 3, American Physical Society, 2017, doi:10.1103/PhysRevMaterials.1.035602. short: I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017). date_created: 2018-12-11T11:49:35Z date_published: 2017-08-08T00:00:00Z date_updated: 2023-09-22T09:53:42Z day: '08' department: - _id: MiLe doi: 10.1103/PhysRevMaterials.1.035602 ec_funded: 1 external_id: isi: - '000416564000004' intvolume: ' 1' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.09220 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Physical Review Materials publication_status: published publisher: American Physical Society publist_id: '6405' quality_controlled: '1' scopus_import: '1' status: public title: Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 1 year: '2017' ... --- _id: '991' abstract: - lang: eng text: Synaptotagmin 7 (Syt7) was originally identified as a slow Ca2+ sensor for lysosome fusion, but its function at fast synapses is controversial. The paper by Luo and Südhof (2017) in this issue of Neuron shows that at the calyx of Held in the auditory brainstem Syt7 triggers asynchronous release during stimulus trains, resulting in reliable and temporally precise high-frequency transmission. Thus, a slow Ca2+ sensor contributes to the fast signaling properties of the calyx synapse. article_processing_charge: No author: - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Chen C, Jonas PM. Synaptotagmins: That’s why so many. Neuron. 2017;94(4):694-696. doi:10.1016/j.neuron.2017.05.011' apa: 'Chen, C., & Jonas, P. M. (2017). Synaptotagmins: That’s why so many. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.05.011' chicago: 'Chen, Chong, and Peter M Jonas. “Synaptotagmins: That’s Why so Many.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.05.011.' ieee: 'C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron, vol. 94, no. 4. Elsevier, pp. 694–696, 2017.' ista: 'Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4), 694–696.' mla: 'Chen, Chong, and Peter M. Jonas. “Synaptotagmins: That’s Why so Many.” Neuron, vol. 94, no. 4, Elsevier, 2017, pp. 694–96, doi:10.1016/j.neuron.2017.05.011.' short: C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696. date_created: 2018-12-11T11:49:34Z date_published: 2017-05-17T00:00:00Z date_updated: 2023-09-22T09:54:37Z day: '17' department: - _id: PeJo doi: 10.1016/j.neuron.2017.05.011 external_id: isi: - '000401415100002' intvolume: ' 94' isi: 1 issue: '4' language: - iso: eng month: '05' oa_version: None page: 694 - 696 publication: Neuron publication_identifier: issn: - '08966273' publication_status: published publisher: Elsevier publist_id: '6408' quality_controlled: '1' scopus_import: '1' status: public title: 'Synaptotagmins: That’s why so many' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 94 year: '2017' ... --- _id: '954' abstract: - lang: eng text: Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for. article_number: e25192 article_processing_charge: Yes author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192 apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192 chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192. ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192. mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192. short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-05-18T00:00:00Z date_updated: 2023-09-22T10:01:17Z day: '18' ddc: - '576' department: - _id: CaGu - _id: NiBa - _id: JoBo doi: 10.7554/eLife.25192 ec_funded: 1 external_id: isi: - '000404024800001' file: - access_level: open_access checksum: 59cdd4400fb41280122d414fea971546 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:49Z date_updated: 2020-07-14T12:48:16Z file_id: '5306' file_name: IST-2017-841-v1+1_elife-25192-v2.pdf file_size: 2441529 relation: main_file - access_level: open_access checksum: b69024880558b858eb8c5d47a92b6377 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:50Z date_updated: 2020-07-14T12:48:16Z file_id: '5307' file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf file_size: 3752660 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '6460' pubrep_id: '841' quality_controlled: '1' scopus_import: '1' status: public title: On the mechanistic nature of epistasis in a canonical cis-regulatory element 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: 6 year: '2017' ... --- _id: '955' abstract: - lang: eng text: 'Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.' article_number: '216' article_processing_charge: Yes (in subscription journal) author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8 apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8 chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8. ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216. mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8. short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-08-09T00:00:00Z date_updated: 2023-09-22T10:00:49Z day: '09' ddc: - '539' - '576' department: - _id: GaTk - _id: NiBa doi: 10.1038/s41467-017-00238-8 ec_funded: 1 external_id: isi: - '000407198800005' file: - access_level: open_access checksum: 29a1b5db458048d3bd5c67e0e2a56818 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:14Z date_updated: 2020-07-14T12:48:16Z file_id: '5064' file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf file_size: 998157 relation: main_file - access_level: open_access checksum: 7b78401e52a576cf3e6bbf8d0abadc17 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:15Z date_updated: 2020-07-14T12:48:16Z file_id: '5065' file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf file_size: 9715993 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '08' 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: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6459' pubrep_id: '864' quality_controlled: '1' related_material: record: - id: '6071' relation: dissertation_contains status: public scopus_import: '1' status: public title: Evolution of new regulatory functions on biophysically realistic fitness landscapes 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: 8 year: '2017' ... --- _id: '962' abstract: - lang: eng text: 'We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Minh full_name: Trinh, Minh last_name: Trinh - first_name: Duc Hiep full_name: Chu, Duc Hiep id: 3598E630-F248-11E8-B48F-1D18A9856A87 last_name: Chu - first_name: Joxan full_name: Jaffar, Joxan last_name: Jaffar citation: ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21' apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21' chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_21. ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 399–418.' ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings. CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.' mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418, doi:10.1007/978-3-319-63390-9_21. short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 399–418. conference: end_date: 2017-07-28 location: Heidelberg, Germany name: 'CAV: Computer Aided Verification' start_date: 2017-07-24 date_created: 2018-12-11T11:49:26Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-22T09:58:02Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-63390-9_21 editor: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Viktor full_name: Kunčak, Viktor last_name: Kunčak external_id: isi: - '000431900900021' intvolume: ' 10427' isi: 1 language: - iso: eng month: '01' oa_version: None page: 399 - 418 project: - _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 publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6443' quality_controlled: '1' scopus_import: '1' status: public title: Model counting for recursively-defined strings type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10427 year: '2017' ... --- _id: '953' abstract: - lang: eng text: 'The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today''s understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.' article_number: '20162864' article_processing_charge: No author: - first_name: Deborah full_name: Charlesworth, Deborah last_name: Charlesworth - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth citation: ama: Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 2017;284(1855). doi:10.1098/rspb.2016.2864 apa: Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864 chicago: Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864. ieee: D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855. Royal Society, The, 2017. ista: Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864. mla: Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864. short: D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-05-31T00:00:00Z date_updated: 2023-09-22T10:01:48Z day: '31' department: - _id: NiBa doi: 10.1098/rspb.2016.2864 external_id: isi: - '000405148800021' pmid: - '28566483' intvolume: ' 284' isi: 1 issue: '1855' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/ month: '05' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '6462' quality_controlled: '1' scopus_import: '1' status: public title: The sources of adaptive evolution type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 284 year: '2017' ... --- _id: '959' abstract: - lang: eng text: In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions. article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419 apa: De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419 chicago: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419. ieee: D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p. 062419, 2017. ista: De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419. mla: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419. short: D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 062419. date_created: 2018-12-11T11:49:25Z date_published: 2017-06-28T00:00:00Z date_updated: 2023-09-22T09:59:01Z day: '28' department: - _id: GaTk doi: 10.1103/PhysRevE.95.062419 ec_funded: 1 external_id: isi: - '000404546400004' intvolume: ' 95' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/pdf/1703.00853.pdf month: '06' oa: 1 oa_version: Submitted Version page: '062419' project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics ' publication_identifier: issn: - '24700045' publication_status: published publisher: American Institute of Physics publist_id: '6446' quality_controlled: '1' scopus_import: '1' status: public title: Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 95 year: '2017' ... --- _id: '956' abstract: - lang: eng text: We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance. article_processing_charge: No author: - first_name: Eric full_name: Carlen, Eric last_name: Carlen - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869. doi:10.1016/j.jfa.2017.05.003 apa: Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003 chicago: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis. Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003. ieee: E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” Journal of Functional Analysis, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017. ista: Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869. mla: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003. short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869. date_created: 2018-12-11T11:49:24Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-22T10:00:18Z day: '01' department: - _id: JaMa doi: 10.1016/j.jfa.2017.05.003 external_id: isi: - '000406082300005' intvolume: ' 273' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.01254 month: '09' oa: 1 oa_version: Submitted Version page: 1810 - 1869 publication: Journal of Functional Analysis publication_identifier: issn: - '00221236' publication_status: published publisher: Academic Press publist_id: '6452' quality_controlled: '1' scopus_import: '1' status: public title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 273 year: '2017' ... --- _id: '952' abstract: - lang: eng text: A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area. article_processing_charge: No author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003' apa: 'Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003' chicago: 'Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.' ieee: 'M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.' ista: 'Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.' mla: 'Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.' short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60. date_created: 2018-12-11T11:49:22Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-22T10:02:21Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2017.03.003 external_id: pmid: - '28411063' file: - access_level: open_access checksum: 9aeff86fa7de69f7a15cf4fc60d57d01 content_type: application/pdf creator: dernst date_created: 2019-04-17T06:39:45Z date_updated: 2020-07-14T12:48:16Z file_id: '6327' file_name: 2017_TheoreticalPopulationBio_Turelli.pdf file_size: 2073856 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 115' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 45 - 60 pmid: 1 publication: Theoretical Population Biology publication_identifier: issn: - '00405809' publication_status: published publisher: Elsevier publist_id: '6463' pubrep_id: '972' quality_controlled: '1' scopus_import: '1' status: public title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2017' ... --- _id: '951' abstract: - lang: eng text: Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo article_number: e2001894 article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894. ieee: T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894. mla: Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017). date_created: 2018-12-11T11:49:22Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:52Z day: '30' ddc: - '576' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894 external_id: isi: - '000402520000012' file: - access_level: open_access checksum: 107d290bd1159ec77b734eb2824b01c8 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:30Z date_updated: 2020-07-14T12:48:16Z file_id: '4691' file_name: IST-2017-843-v1+1_journal.pbio.2001894.pdf file_size: 5541206 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: PLoS Biology publication_identifier: issn: - '15449173' publication_status: published publisher: Public Library of Science publist_id: '6464' pubrep_id: '843' quality_controlled: '1' related_material: record: - id: '9856' relation: research_data status: public - id: '9857' relation: research_data status: public - id: '9858' relation: research_data status: public scopus_import: '1' status: public title: Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti 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: 15 year: '2017' ... --- _id: '947' abstract: - lang: eng text: Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence. article_number: '010401' article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Fabrizio full_name: Capuani, Fabrizio last_name: Capuani - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino citation: ama: De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.010401 apa: De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401 chicago: De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401. ieee: D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017. ista: De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401. mla: De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401. short: D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017). date_created: 2018-12-11T11:49:21Z date_published: 2017-07-10T00:00:00Z date_updated: 2023-09-22T10:03:50Z day: '10' department: - _id: GaTk doi: 10.1103/PhysRevE.96.010401 ec_funded: 1 external_id: isi: - '000405194200002' intvolume: ' 96' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.00219 month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics ' publication_identifier: issn: - '24700045' publication_status: published publisher: American Institute of Physics publist_id: '6470' quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the entropic cost of cellular growth control type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 96 year: '2017' ... --- _id: '9858' article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016. ieee: T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016. mla: Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017). date_created: 2021-08-10T07:47:07Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:51Z day: '30' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894.s016 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '951' relation: used_in_publication status: public status: public title: Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9857' article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015. ieee: T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015. mla: Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017). date_created: 2021-08-10T07:41:52Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:51Z day: '30' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894.s015 month: '05' oa_version: Published Version publisher: 'Public Library of Science ' related_material: record: - id: '951' relation: used_in_publication status: public status: public title: Supporting information concerning observed wMel frequencies and analyses of habitat variables type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9856' article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting Information concerning additional likelihood analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014. ieee: T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting Information concerning additional likelihood analyses and results, Public Library of Science, 10.1371/journal.pbio.2001894.s014. mla: Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017). date_created: 2021-08-10T07:36:04Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:51Z day: '30' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894.s014 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '951' relation: used_in_publication status: public status: public title: Supporting Information concerning additional likelihood analyses and results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '945' abstract: - lang: eng text: While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera. article_processing_charge: Yes (in subscription journal) author: - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190 apa: Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190 chicago: Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2017. https://doi.org/10.1093/molbev/msx190. ieee: A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017. ista: Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649. mla: Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190. short: A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649. date_created: 2018-12-11T11:49:20Z date_published: 2017-07-06T00:00:00Z date_updated: 2023-09-26T15:36:34Z day: '06' ddc: - '570' - '576' department: - _id: BeVi doi: 10.1093/molbev/msx190 external_id: isi: - '000411814800016' file: - access_level: open_access checksum: 009fd68043211d645ceb9d1de28274f2 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:23Z date_updated: 2020-07-14T12:48:15Z file_id: '4810' file_name: IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf file_size: 462863 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '10' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2637 - 2649 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Molecular Biology and Evolution publication_identifier: issn: - '07374038' publication_status: published publisher: Oxford University Press publist_id: '6472' pubrep_id: '848' quality_controlled: '1' scopus_import: '1' status: public title: Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome 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: 34 year: '2017' ... --- _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: '798' abstract: - lang: eng text: Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout. article_number: '1304' article_processing_charge: Yes (in subscription journal) author: - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Mahmoud full_name: Kalaee, Mahmoud last_name: Kalaee - first_name: Paul full_name: Dieterle, Paul last_name: Dieterle - first_name: Oskar full_name: Painter, Oskar last_name: Painter - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01304-x apa: Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., & Fink, J. M. (2017). Mechanical on chip microwave circulator. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01304-x chicago: Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01304-x. ieee: S. Barzanjeh et al., “Mechanical on chip microwave circulator,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304. mla: Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” Nature Communications, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01304-x. short: S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017). date_created: 2018-12-11T11:48:33Z date_published: 2017-10-16T00:00:00Z date_updated: 2023-09-27T12:11:28Z day: '16' ddc: - '539' department: - _id: JoFi doi: 10.1038/s41467-017-01304-x ec_funded: 1 external_id: isi: - '000412999700021' file: - access_level: open_access checksum: b68dafa71d1834c23b742cd9987a3d5f content_type: application/pdf creator: system date_created: 2018-12-12T10:15:25Z date_updated: 2020-07-14T12:48:06Z file_id: '5145' file_name: IST-2017-867-v1+1_s41467-017-01304-x.pdf file_size: 1467696 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics' publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6855' pubrep_id: '867' quality_controlled: '1' scopus_import: '1' status: public title: Mechanical on chip microwave circulator 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: 8 year: '2017' ... --- _id: '791' abstract: - lang: eng text: 'Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between "heavily loaded" balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Jerry full_name: Li, Jerry last_name: Li - first_name: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze orcid: 0000-0001-5634-0731 citation: ama: 'Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority scheduling. In: Proceedings of the ACM Symposium on Principles of Distributed Computing. Vol Part F129314. ACM; 2017:283-292. doi:10.1145/3087801.3087810' apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Nadiradze, G. (2017). The power of choice in priority scheduling. In Proceedings of the ACM Symposium on Principles of Distributed Computing (Vol. Part F129314, pp. 283–292). Washington, WA, USA: ACM. https://doi.org/10.1145/3087801.3087810' chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze. “The Power of Choice in Priority Scheduling.” In Proceedings of the ACM Symposium on Principles of Distributed Computing, Part F129314:283–92. ACM, 2017. https://doi.org/10.1145/3087801.3087810. ieee: D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice in priority scheduling,” in Proceedings of the ACM Symposium on Principles of Distributed Computing, Washington, WA, USA, 2017, vol. Part F129314, pp. 283–292. ista: 'Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292.' mla: Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.” Proceedings of the ACM Symposium on Principles of Distributed Computing, vol. Part F129314, ACM, 2017, pp. 283–92, doi:10.1145/3087801.3087810. short: D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292. conference: end_date: 2017-07-27 location: Washington, WA, USA name: 'PODC: Principles of Distributed Computing' start_date: 2017-07-25 date_created: 2018-12-11T11:48:31Z date_published: 2017-07-26T00:00:00Z date_updated: 2023-09-27T12:17:59Z day: '26' department: - _id: DaAl doi: 10.1145/3087801.3087810 external_id: isi: - '000462995000035' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.04178 month: '07' oa: 1 oa_version: Submitted Version page: 283 - 292 publication: Proceedings of the ACM Symposium on Principles of Distributed Computing publication_identifier: isbn: - 978-145034992-5 publication_status: published publisher: ACM publist_id: '6864' quality_controlled: '1' scopus_import: '1' status: public title: The power of choice in priority scheduling type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: Part F129314 year: '2017' ... --- _id: '792' abstract: - lang: eng text: The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics. article_processing_charge: No author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Kimberly full_name: Short, Kimberly last_name: Short - first_name: Mohammad full_name: Farazmand, Mohammad last_name: Farazmand - first_name: Ashley full_name: Willis, Ashley last_name: Willis - first_name: Predrag full_name: Cvitanović, Predrag last_name: Cvitanović citation: ama: Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 2017;833:274-301. doi:10.1017/jfm.2017.699 apa: Budanur, N. B., Short, K., Farazmand, M., Willis, A., & Cvitanović, P. (2017). Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.699 chicago: Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.699. ieee: N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative periodic orbits form the backbone of turbulent pipe flow,” Journal of Fluid Mechanics, vol. 833. Cambridge University Press, pp. 274–301, 2017. ista: Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833, 274–301. mla: Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” Journal of Fluid Mechanics, vol. 833, Cambridge University Press, 2017, pp. 274–301, doi:10.1017/jfm.2017.699. short: N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of Fluid Mechanics 833 (2017) 274–301. date_created: 2018-12-11T11:48:32Z date_published: 2017-12-25T00:00:00Z date_updated: 2023-09-27T12:17:35Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.699 external_id: isi: - '000414641700001' intvolume: ' 833' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.03720 month: '12' oa: 1 oa_version: Submitted Version page: 274 - 301 project: - _id: 25636330-B435-11E9-9278-68D0E5697425 grant_number: 11-NSF-1070 name: ROOTS Genome-wide Analysis of Root Traits publication: Journal of Fluid Mechanics publication_identifier: issn: - '00221120' publication_status: published publisher: Cambridge University Press publist_id: '6862' quality_controlled: '1' scopus_import: '1' status: public title: Relative periodic orbits form the backbone of turbulent pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 833 year: '2017' ... --- _id: '796' abstract: - lang: eng text: We present the fabrication and characterization of an aluminum transmon qubit on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This process in principle permits the co-fabrication of silicon photonic and mechanical elements, providing a route towards chip-scale integration of electro-opto-mechanical transducers for quantum networking of superconducting microwave quantum circuits. The additional processing steps are compatible with established fabrication techniques for aluminum transmon qubits on silicon. acknowledgement: This work was supported by the AFOSR MURI Quantum Photonic Matter (Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers (Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.J.K. acknowledges the IQIM Postdoctoral Fellowship. article_number: '042603' article_processing_charge: No author: - first_name: Andrew J full_name: Keller, Andrew J last_name: Keller - first_name: Paul full_name: Dieterle, Paul last_name: Dieterle - first_name: Michael full_name: Fang, Michael last_name: Fang - first_name: Brett full_name: Berger, Brett last_name: Berger - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Oskar full_name: Painter, Oskar last_name: Painter citation: ama: Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 2017;111(4). doi:10.1063/1.4994661 apa: Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., & Painter, O. (2017). Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.4994661 chicago: Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” Applied Physics Letters. American Institute of Physics, 2017. https://doi.org/10.1063/1.4994661. ieee: A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter, “Al transmon qubits on silicon on insulator for quantum device integration,” Applied Physics Letters, vol. 111, no. 4. American Institute of Physics, 2017. ista: Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 111(4), 042603. mla: Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” Applied Physics Letters, vol. 111, no. 4, 042603, American Institute of Physics, 2017, doi:10.1063/1.4994661. short: A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied Physics Letters 111 (2017). date_created: 2018-12-11T11:48:33Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-09-27T12:13:36Z day: '01' department: - _id: JoFi doi: 10.1063/1.4994661 external_id: isi: - '000406779700031' intvolume: ' 111' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.10195 month: '07' oa: 1 oa_version: Submitted Version publication: Applied Physics Letters publication_identifier: issn: - '00036951' publication_status: published publisher: American Institute of Physics publist_id: '6857' quality_controlled: '1' scopus_import: '1' status: public title: Al transmon qubits on silicon on insulator for quantum device integration type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 111 year: '2017' ... --- _id: '793' abstract: - lang: eng text: 'Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c > 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). ' article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Hossein full_name: Mojarrad, Hossein last_name: Mojarrad - first_name: Márton full_name: Naszódi, Márton last_name: Naszódi - first_name: József full_name: Solymosi, József last_name: Solymosi - first_name: Sebastian full_name: Stich, Sebastian last_name: Stich - first_name: May full_name: Szedlák, May last_name: Szedlák citation: ama: 'Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 2017;66:28-31. doi:10.1016/j.comgeo.2017.07.002' apa: 'Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., & Szedlák, M. (2017). On the existence of ordinary triangles. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.07.002' chicago: 'Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” Computational Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.07.002.' ieee: 'R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” Computational Geometry: Theory and Applications, vol. 66. Elsevier, pp. 28–31, 2017.' ista: 'Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.' mla: 'Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” Computational Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 28–31, doi:10.1016/j.comgeo.2017.07.002.' short: 'R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31.' date_created: 2018-12-11T11:48:32Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-27T12:15:16Z day: '01' department: - _id: UlWa doi: 10.1016/j.comgeo.2017.07.002 ec_funded: 1 external_id: isi: - '000412039700003' intvolume: ' 66' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1701.08183 month: '01' oa: 1 oa_version: Submitted Version page: 28 - 31 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Computational Geometry: Theory and Applications' publication_identifier: issn: - '09257721' publication_status: published publisher: Elsevier publist_id: '6861' quality_controlled: '1' status: public title: On the existence of ordinary triangles type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2017' ... --- _id: '794' abstract: - lang: eng text: We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle. acknowledgement: I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous referees for many comments and suggestions that helped to improve the presentation of the result. article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 citation: ama: 'Fulek R. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 2017;66:1-13. doi:10.1016/j.comgeo.2017.06.016' apa: 'Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.016' chicago: 'Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.06.016.' ieee: 'R. Fulek, “C-planarity of embedded cyclic c-graphs,” Computational Geometry: Theory and Applications, vol. 66. Elsevier, pp. 1–13, 2017.' ista: 'Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 66, 1–13.' mla: 'Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 1–13, doi:10.1016/j.comgeo.2017.06.016.' short: 'R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13.' date_created: 2018-12-11T11:48:32Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-27T12:14:49Z day: '01' department: - _id: UlWa doi: 10.1016/j.comgeo.2017.06.016 external_id: isi: - '000412039700001' intvolume: ' 66' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.01346 month: '12' oa: 1 oa_version: Preprint page: 1 - 13 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '6860' quality_controlled: '1' related_material: record: - id: '1165' relation: earlier_version status: public scopus_import: '1' status: public title: C-planarity of embedded cyclic c-graphs type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2017' ... --- _id: '736' abstract: - lang: eng text: The neurotransmitter receptor subtype, number, density, and distribution relative to the location of transmitter release sites are key determinants of signal transmission. AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits are prominently expressed in subsets of neurons capable of firing action potentials at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics; thus, we investigated whether the number, density, and localization of GluA3 and GluA4 subunits in these synapses are differentially organized using quantitative freeze-fracture replica immunogold labeling. We identify a positive correlation between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller. A higher number and density of GluA3 subunits are observed at AN-BC synapses, whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses. The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits, particularly GluA3, are concentrated at the center of the AN-BC synapses. The central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles are evenly distributed along the postsynaptic density. GluA4 gold labeling was homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits are distributed at AN synapses in a target-cell-dependent manner. article_processing_charge: No author: - first_name: María full_name: Rubio, María last_name: Rubio - first_name: Ko full_name: Matsui, Ko last_name: Matsui - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Naomi full_name: Kamasawa, Naomi last_name: Kamasawa - first_name: Harumi full_name: Harada, Harumi id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87 last_name: Harada orcid: 0000-0001-7429-7896 - first_name: Makoto full_name: Itakura, Makoto last_name: Itakura - first_name: Elek full_name: Molnár, Elek last_name: Molnár - first_name: Manabu full_name: Abe, Manabu last_name: Abe - first_name: Kenji full_name: Sakimura, Kenji last_name: Sakimura - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Rubio M, Matsui K, Fukazawa Y, et al. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. 2017;222(8):3375-3393. doi:10.1007/s00429-017-1408-0 apa: Rubio, M., Matsui, K., Fukazawa, Y., Kamasawa, N., Harada, H., Itakura, M., … Shigemoto, R. (2017). The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1408-0 chicago: Rubio, María, Ko Matsui, Yugo Fukazawa, Naomi Kamasawa, Harumi Harada, Makoto Itakura, Elek Molnár, Manabu Abe, Kenji Sakimura, and Ryuichi Shigemoto. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” Brain Structure and Function. Springer, 2017. https://doi.org/10.1007/s00429-017-1408-0. ieee: M. Rubio et al., “The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells,” Brain Structure and Function, vol. 222, no. 8. Springer, pp. 3375–3393, 2017. ista: Rubio M, Matsui K, Fukazawa Y, Kamasawa N, Harada H, Itakura M, Molnár E, Abe M, Sakimura K, Shigemoto R. 2017. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. 222(8), 3375–3393. mla: Rubio, María, et al. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” Brain Structure and Function, vol. 222, no. 8, Springer, 2017, pp. 3375–93, doi:10.1007/s00429-017-1408-0. short: M. Rubio, K. Matsui, Y. Fukazawa, N. Kamasawa, H. Harada, M. Itakura, E. Molnár, M. Abe, K. Sakimura, R. Shigemoto, Brain Structure and Function 222 (2017) 3375–3393. date_created: 2018-12-11T11:48:14Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-09-27T14:14:51Z day: '01' ddc: - '571' department: - _id: RySh doi: 10.1007/s00429-017-1408-0 external_id: isi: - '000414761700002' file: - access_level: open_access checksum: 73787a22507de8fb585bb598e1418ca7 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:20Z date_updated: 2020-07-14T12:47:56Z file_id: '4806' file_name: IST-2017-881-v1+1_s00429-017-1408-0.pdf file_size: 4011126 relation: main_file file_date_updated: 2020-07-14T12:47:56Z has_accepted_license: '1' intvolume: ' 222' isi: 1 issue: '8' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 3375 - 3393 publication: Brain Structure and Function publication_identifier: issn: - '18632653' publication_status: published publisher: Springer publist_id: '6932' pubrep_id: '881' quality_controlled: '1' scopus_import: '1' status: public title: The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells 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: 222 year: '2017' ... --- _id: '740' abstract: - lang: eng text: 'Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits. Together, the gains from these advances can decrease the time required for the analysis of targeted circuit motifs by over two orders of magnitude. These genetic encoded tags for electron microscopy promise to simplify the analysis of circuit motifs and become a central tool for structure‐function studies of synaptic connections in the brain. We review the current state‐of‐the‐art with an emphasis on connectomics, the quantitative analysis of neuronal structures and motifs.' article_number: e288 article_processing_charge: No article_type: original author: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 citation: ama: Shigemoto R, Jösch MA. The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. 2017;6(6). doi:10.1002/wdev.288 apa: Shigemoto, R., & Jösch, M. A. (2017). The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. Wiley-Blackwell. https://doi.org/10.1002/wdev.288 chicago: Shigemoto, Ryuichi, and Maximilian A Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” WIREs Developmental Biology. Wiley-Blackwell, 2017. https://doi.org/10.1002/wdev.288. ieee: R. Shigemoto and M. A. Jösch, “The genetic encoded toolbox for electron microscopy and connectomics,” WIREs Developmental Biology, vol. 6, no. 6. Wiley-Blackwell, 2017. ista: Shigemoto R, Jösch MA. 2017. The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. 6(6), e288. mla: Shigemoto, Ryuichi, and Maximilian A. Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” WIREs Developmental Biology, vol. 6, no. 6, e288, Wiley-Blackwell, 2017, doi:10.1002/wdev.288. short: R. Shigemoto, M.A. Jösch, WIREs Developmental Biology 6 (2017). date_created: 2018-12-11T11:48:15Z date_published: 2017-08-11T00:00:00Z date_updated: 2023-09-27T12:51:41Z day: '11' ddc: - '570' department: - _id: RySh - _id: MaJö doi: 10.1002/wdev.288 external_id: isi: - '000412827400005' pmid: - '28800674' file: - access_level: open_access checksum: a9370f27b1591773b7a0de299bc81c8c content_type: application/pdf creator: dernst date_created: 2019-11-19T07:36:18Z date_updated: 2020-07-14T12:47:57Z file_id: '7045' file_name: 2017_WIREs_Shigemoto.pdf file_size: 1647787 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '08' oa: 1 oa_version: Submitted Version pmid: 1 publication: WIREs Developmental Biology publication_identifier: issn: - '17597684' publication_status: published publisher: Wiley-Blackwell publist_id: '6927' quality_controlled: '1' scopus_import: '1' status: public title: The genetic encoded toolbox for electron microscopy and connectomics tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6 year: '2017' ... --- _id: '741' abstract: - lang: eng text: We prove that a system of N fermions interacting with an additional particle via point interactions is stable if the ratio of the mass of the additional particle to the one of the fermions is larger than some critical m*. The value of m* is independent of N and turns out to be less than 1. This fact has important implications for the stability of the unitary Fermi gas. We also characterize the domain of the Hamiltonian of this model, and establish the validity of the Tan relations for all wave functions in the domain. article_processing_charge: No author: - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Moser T, Seiringer R. Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. 2017;356(1):329-355. doi:10.1007/s00220-017-2980-0 apa: Moser, T., & Seiringer, R. (2017). Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-2980-0 chicago: Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle System with Point Interactions.” Communications in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s00220-017-2980-0. ieee: T. Moser and R. Seiringer, “Stability of a fermionic N+1 particle system with point interactions,” Communications in Mathematical Physics, vol. 356, no. 1. Springer, pp. 329–355, 2017. ista: Moser T, Seiringer R. 2017. Stability of a fermionic N+1 particle system with point interactions. Communications in Mathematical Physics. 356(1), 329–355. mla: Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle System with Point Interactions.” Communications in Mathematical Physics, vol. 356, no. 1, Springer, 2017, pp. 329–55, doi:10.1007/s00220-017-2980-0. short: T. Moser, R. Seiringer, Communications in Mathematical Physics 356 (2017) 329–355. date_created: 2018-12-11T11:48:15Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-09-27T12:34:15Z day: '01' ddc: - '539' department: - _id: RoSe doi: 10.1007/s00220-017-2980-0 ec_funded: 1 external_id: isi: - '000409821300010' file: - access_level: open_access checksum: 0fd9435400f91e9b3c5346319a2d24e3 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:50Z date_updated: 2020-07-14T12:47:57Z file_id: '4841' file_name: IST-2017-880-v1+1_s00220-017-2980-0.pdf file_size: 952639 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 356' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 329 - 355 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Communications in Mathematical Physics publication_identifier: issn: - '00103616' publication_status: published publisher: Springer publist_id: '6926' pubrep_id: '880' quality_controlled: '1' related_material: record: - id: '52' relation: dissertation_contains status: public scopus_import: '1' status: public title: Stability of a fermionic N+1 particle system with point interactions 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: 356 year: '2017' ... --- _id: '739' abstract: - lang: eng text: We study the norm approximation to the Schrödinger dynamics of N bosons in with an interaction potential of the form . Assuming that in the initial state the particles outside of the condensate form a quasi-free state with finite kinetic energy, we show that in the large N limit, the fluctuations around the condensate can be effectively described using Bogoliubov approximation for all . The range of β is expected to be optimal for this large class of initial states. article_processing_charge: No author: - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski citation: ama: Nam P, Napiórkowski MM. A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 2017;108(5):662-688. doi:10.1016/j.matpur.2017.05.013 apa: Nam, P., & Napiórkowski, M. M. (2017). A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2017.05.013 chicago: Nam, Phan, and Marcin M Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2017. https://doi.org/10.1016/j.matpur.2017.05.013. ieee: P. Nam and M. M. Napiórkowski, “A note on the validity of Bogoliubov correction to mean field dynamics,” Journal de Mathématiques Pures et Appliquées, vol. 108, no. 5. Elsevier, pp. 662–688, 2017. ista: Nam P, Napiórkowski MM. 2017. A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 108(5), 662–688. mla: Nam, Phan, and Marcin M. Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées, vol. 108, no. 5, Elsevier, 2017, pp. 662–88, doi:10.1016/j.matpur.2017.05.013. short: P. Nam, M.M. Napiórkowski, Journal de Mathématiques Pures et Appliquées 108 (2017) 662–688. date_created: 2018-12-11T11:48:15Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-09-27T12:52:07Z day: '01' department: - _id: RoSe doi: 10.1016/j.matpur.2017.05.013 external_id: isi: - '000414113600003' intvolume: ' 108' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.05240 month: '11' oa: 1 oa_version: Submitted Version page: 662 - 688 project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Journal de Mathématiques Pures et Appliquées publication_identifier: issn: - '00217824' publication_status: published publisher: Elsevier publist_id: '6928' quality_controlled: '1' scopus_import: '1' status: public title: A note on the validity of Bogoliubov correction to mean field dynamics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 108 year: '2017' ... --- _id: '737' abstract: - lang: eng text: We generalize Brazas’ topology on the fundamental group to the whole universal path space X˜ i.e., to the set of homotopy classes of all based paths. We develop basic properties of the new notion and provide a complete comparison of the obtained topology with the established topologies, in particular with the Lasso topology and the CO topology, i.e., the topology that is induced by the compact-open topology. It turns out that the new topology is the finest topology contained in the CO topology, for which the action of the fundamental group on the universal path space is a continuous group action. article_processing_charge: No author: - first_name: Ziga full_name: Virk, Ziga id: 2E36B656-F248-11E8-B48F-1D18A9856A87 last_name: Virk - first_name: Andreas full_name: Zastrow, Andreas last_name: Zastrow citation: ama: Virk Z, Zastrow A. A new topology on the universal path space. Topology and its Applications. 2017;231:186-196. doi:10.1016/j.topol.2017.09.015 apa: Virk, Z., & Zastrow, A. (2017). A new topology on the universal path space. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2017.09.015 chicago: Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path Space.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2017.09.015. ieee: Z. Virk and A. Zastrow, “A new topology on the universal path space,” Topology and its Applications, vol. 231. Elsevier, pp. 186–196, 2017. ista: Virk Z, Zastrow A. 2017. A new topology on the universal path space. Topology and its Applications. 231, 186–196. mla: Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path Space.” Topology and Its Applications, vol. 231, Elsevier, 2017, pp. 186–96, doi:10.1016/j.topol.2017.09.015. short: Z. Virk, A. Zastrow, Topology and Its Applications 231 (2017) 186–196. date_created: 2018-12-11T11:48:14Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-09-27T12:53:01Z day: '01' department: - _id: HeEd doi: 10.1016/j.topol.2017.09.015 external_id: isi: - '000413889100012' intvolume: ' 231' isi: 1 language: - iso: eng month: '11' oa_version: None page: 186 - 196 publication: Topology and its Applications publication_identifier: issn: - '01668641' publication_status: published publisher: Elsevier publist_id: '6930' quality_controlled: '1' scopus_import: '1' status: public title: A new topology on the universal path space type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 231 year: '2017' ... --- _id: '733' abstract: - lang: eng text: Let A and B be two N by N deterministic Hermitian matrices and let U be an N by N Haar distributed unitary matrix. It is well known that the spectral distribution of the sum H = A + UBU∗ converges weakly to the free additive convolution of the spectral distributions of A and B, as N tends to infinity. We establish the optimal convergence rate in the bulk of the spectrum. acknowledgement: Partially supported by ERC Advanced Grant RANMAT No. 338804, Hong Kong RGC grant ECS 26301517, and the Göran Gustafsson Foundation article_processing_charge: No author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Bao Z, Erdös L, Schnelli K. Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. 2017;319:251-291. doi:10.1016/j.aim.2017.08.028 apa: Bao, Z., Erdös, L., & Schnelli, K. (2017). Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2017.08.028 chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2017.08.028. ieee: Z. Bao, L. Erdös, and K. Schnelli, “Convergence rate for spectral distribution of addition of random matrices,” Advances in Mathematics, vol. 319. Academic Press, pp. 251–291, 2017. ista: Bao Z, Erdös L, Schnelli K. 2017. Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. 319, 251–291. mla: Bao, Zhigang, et al. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” Advances in Mathematics, vol. 319, Academic Press, 2017, pp. 251–91, doi:10.1016/j.aim.2017.08.028. short: Z. Bao, L. Erdös, K. Schnelli, Advances in Mathematics 319 (2017) 251–291. date_created: 2018-12-11T11:48:13Z date_published: 2017-10-15T00:00:00Z date_updated: 2023-09-28T11:30:42Z day: '15' department: - _id: LaEr doi: 10.1016/j.aim.2017.08.028 ec_funded: 1 external_id: isi: - '000412150400010' intvolume: ' 319' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.03076 month: '10' oa: 1 oa_version: Submitted Version page: 251 - 291 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Advances in Mathematics publication_status: published publisher: Academic Press publist_id: '6935' quality_controlled: '1' scopus_import: '1' status: public title: Convergence rate for spectral distribution of addition of random matrices type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 319 year: '2017' ... --- _id: '840' abstract: - lang: eng text: Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements. acknowledged_ssus: - _id: M-Shop article_processing_charge: No author: - first_name: Lada full_name: Vukusic, Lada id: 31E9F056-F248-11E8-B48F-1D18A9856A87 last_name: Vukusic orcid: 0000-0003-2424-8636 - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka - first_name: Hannes full_name: Watzinger, Hannes id: 35DF8E50-F248-11E8-B48F-1D18A9856A87 last_name: Watzinger - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627 apa: Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627 chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627. ieee: L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” Nano Letters, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017. ista: Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710. mla: Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627. short: L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710. date_created: 2018-12-11T11:48:47Z date_published: 2017-08-10T00:00:00Z date_updated: 2023-09-26T15:50:22Z day: '10' ddc: - '539' department: - _id: GeKa doi: 10.1021/acs.nanolett.7b02627 ec_funded: 1 external_id: isi: - '000411043500078' file: - access_level: open_access checksum: 761371a0129b2aa442424b9561450ece content_type: application/pdf creator: system date_created: 2018-12-12T10:12:33Z date_updated: 2020-07-14T12:48:13Z file_id: '4951' file_name: IST-2017-865-v1+1_acs.nanolett.7b02627.pdf file_size: 2449546 relation: main_file file_date_updated: 2020-07-14T12:48:13Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '9' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 5706 - 5710 project: - _id: 25517E86-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335497' name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires publication: Nano Letters publication_identifier: issn: - '15306984' publication_status: published publisher: American Chemical Society publist_id: '6808' pubrep_id: '865' quality_controlled: '1' related_material: record: - id: '7977' relation: popular_science - id: '69' relation: dissertation_contains status: public - id: '7996' relation: dissertation_contains status: public scopus_import: '1' status: public title: Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry 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: 17 year: '2017' ... --- _id: '914' abstract: - lang: eng text: Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect. acknowledgement: We thank two anonymous reviewers for helpful suggestions on the manuscript. article_number: '170547' article_processing_charge: No author: - first_name: Julia full_name: Giehr, Julia last_name: Giehr - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf citation: ama: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 2017;4(7). doi:10.1098/rsos.170547 apa: Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.170547 chicago: Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science. Royal Society, The, 2017. https://doi.org/10.1098/rsos.170547. ieee: J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” Royal Society Open Science, vol. 4, no. 7. Royal Society, The, 2017. ista: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547. mla: Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:10.1098/rsos.170547. short: J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017). date_created: 2018-12-11T11:49:10Z date_published: 2017-07-05T00:00:00Z date_updated: 2023-09-26T15:45:47Z day: '05' ddc: - '576' - '592' department: - _id: SyCr doi: 10.1098/rsos.170547 external_id: isi: - '000406670000025' file: - access_level: open_access checksum: 351ae5e7a37e6e7d9295cd41146c4190 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:24Z date_updated: 2020-07-14T12:48:15Z file_id: '4684' file_name: IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf file_size: 530412 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Royal Society Open Science publication_identifier: issn: - '20545703' publication_status: published publisher: Royal Society, The publist_id: '6527' pubrep_id: '849' quality_controlled: '1' related_material: record: - id: '9853' relation: research_data status: public scopus_import: '1' status: public title: Ant queens increase their reproductive efforts after pathogen infection 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: 4 year: '2017' ... --- _id: '910' abstract: - lang: eng text: "Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n" article_processing_charge: No author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak orcid: 0000-0002-2519-824X - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129 apa: Novak, S., & Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129 chicago: Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.117.300129. ieee: S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017. ista: Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668. mla: Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129. short: S. Novak, N.H. Barton, Genetics 207 (2017) 653–668. date_created: 2018-12-11T11:49:09Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-26T15:49:15Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1534/genetics.117.300129 ec_funded: 1 external_id: isi: - '000412232600019' file: - access_level: open_access checksum: f7c32dabf52e6d9e709d9203761e39fd content_type: application/pdf creator: system date_created: 2018-12-12T10:17:12Z date_updated: 2020-07-14T12:48:15Z file_id: '5264' file_name: IST-2018-974-v1+1_manuscript.pdf file_size: 494268 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 207' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 653 - 668 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '6533' pubrep_id: '974' quality_controlled: '1' scopus_import: '1' status: public title: When does frequency-independent selection maintain genetic variation? type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 207 year: '2017' ...