--- _id: '1020' abstract: - lang: eng text: Cellulose is the most abundant biopolymer on Earth. Cellulose fibers, such as the one extracted form cotton or woodpulp, have been used by humankind for hundreds of years to make textiles and paper. Here we show how, by engineering light-matter interaction, we can optimize light scattering using exclusively cellulose nanocrystals. The produced material is sustainable, biocompatible, and when compared to ordinary microfiber-based paper, it shows enhanced scattering strength (×4), yielding a transport mean free path as low as 3.5 μm in the visible light range. The experimental results are in a good agreement with the theoretical predictions obtained with a diffusive model for light propagation. acknowledgement: This research was funded by the EPSRC (EP/M027961/1), the Leverhulme Trust (RPG-2014-238), Royal Society (RG140457), the BBSRC David Phillips fellowship (BB/K014617/1), and the European Research Council (ERC-2014-STG H2020 639088). All data created during this research are provided in full in the results section and Supporting Information. They are openly available from figshare and can be accessed at ref 30. article_processing_charge: No author: - first_name: Soraya full_name: Caixeiro, Soraya last_name: Caixeiro - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Olimpia full_name: Onelli, Olimpia last_name: Onelli - first_name: Silvia full_name: Vignolini, Silvia last_name: Vignolini - first_name: Riccardo full_name: Sapienza, Riccardo last_name: Sapienza citation: ama: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 2017;9(9):7885-7890. doi:10.1021/acsami.6b15986 apa: Caixeiro, S., Peruzzo, M., Onelli, O., Vignolini, S., & Sapienza, R. (2017). Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.6b15986 chicago: Caixeiro, Soraya, Matilda Peruzzo, Olimpia Onelli, Silvia Vignolini, and Riccardo Sapienza. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces. American Chemical Society, 2017. https://doi.org/10.1021/acsami.6b15986. ieee: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, and R. Sapienza, “Disordered cellulose based nanostructures for enhanced light scattering,” ACS Applied Materials and Interfaces, vol. 9, no. 9. American Chemical Society, pp. 7885–7890, 2017. ista: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. 2017. Disordered cellulose based nanostructures for enhanced light scattering. ACS Applied Materials and Interfaces. 9(9), 7885–7890. mla: Caixeiro, Soraya, et al. “Disordered Cellulose Based Nanostructures for Enhanced Light Scattering.” ACS Applied Materials and Interfaces, vol. 9, no. 9, American Chemical Society, 2017, pp. 7885–90, doi:10.1021/acsami.6b15986. short: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied Materials and Interfaces 9 (2017) 7885–7890. date_created: 2018-12-11T11:49:44Z date_published: 2017-03-08T00:00:00Z date_updated: 2023-09-22T09:40:14Z day: '08' department: - _id: JoFi doi: 10.1021/acsami.6b15986 external_id: isi: - '000396186000002' intvolume: ' 9' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.01415 month: '03' oa: 1 oa_version: Submitted Version page: 7885 - 7890 publication: ACS Applied Materials and Interfaces publication_identifier: issn: - '19448244' publication_status: published publisher: American Chemical Society publist_id: '6372' quality_controlled: '1' scopus_import: '1' status: public title: Disordered cellulose based nanostructures for enhanced light scattering type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2017' ... --- _id: '1021' abstract: - lang: eng text: Most flows in nature and engineering are turbulent because of their large velocities and spatial scales. Laboratory experiments on rotating quasi-Keplerian flows, for which the angular velocity decreases radially but the angular momentum increases, are however laminar at Reynolds numbers exceeding one million. This is in apparent contradiction to direct numerical simulations showing that in these experiments turbulence transition is triggered by the axial boundaries. We here show numerically that as the Reynolds number increases, turbulence becomes progressively confined to the boundary layers and the flow in the bulk fully relaminarizes. Our findings support that turbulence is unlikely to occur in isothermal constant-density quasi-Keplerian flows. article_processing_charge: No author: - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Lopez Alonso JM, Avila M. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 2017;817:21-34. doi:10.1017/jfm.2017.109 apa: Lopez Alonso, J. M., & Avila, M. (2017). Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.109 chicago: Lopez Alonso, Jose M, and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.109. ieee: J. M. Lopez Alonso and M. Avila, “Boundary layer turbulence in experiments on quasi Keplerian flows,” Journal of Fluid Mechanics, vol. 817. Cambridge University Press, pp. 21–34, 2017. ista: Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34. mla: Lopez Alonso, Jose M., and Marc Avila. “Boundary Layer Turbulence in Experiments on Quasi Keplerian Flows.” Journal of Fluid Mechanics, vol. 817, Cambridge University Press, 2017, pp. 21–34, doi:10.1017/jfm.2017.109. short: J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34. date_created: 2018-12-11T11:49:44Z date_published: 2017-04-25T00:00:00Z date_updated: 2023-09-22T09:39:46Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.109 external_id: isi: - '000398179100006' intvolume: ' 817' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.05527 month: '04' oa: 1 oa_version: Submitted Version page: 21 - 34 project: - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: Journal of Fluid Mechanics publication_identifier: issn: - '00221120' publication_status: published publisher: Cambridge University Press publist_id: '6371' quality_controlled: '1' scopus_import: '1' status: public title: Boundary layer turbulence in experiments on quasi Keplerian flows type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 817 year: '2017' ... --- _id: '1017' abstract: - lang: eng text: The development of the vertebrate central nervous system is reliant on a complex cascade of biological processes that include mitotic division, relocation of migrating neurons, and the extension of dendritic and axonal processes. Each of these cellular events requires the diverse functional repertoire of the microtubule cytoskeleton for the generation of forces, assembly of macromolecular complexes and transport of molecules and organelles. The tubulins are a multi-gene family that encode for the constituents of microtubules, and have been implicated in a spectrum of neurological disorders. Evidence is building that different tubulins tune the functional properties of the microtubule cytoskeleton dependent on the cell type, developmental profile and subcellular localisation. Here we review of the origins of the functional specification of the tubulin gene family in the developing brain at a transcriptional, translational, and post-transcriptional level. We remind the reader that tubulins are not just loading controls for your average Western blot. article_processing_charge: No author: - first_name: Martin full_name: Breuss, Martin last_name: Breuss - first_name: Ines full_name: Leca, Ines last_name: Leca - first_name: Thomas full_name: Gstrein, Thomas last_name: Gstrein - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: David full_name: Keays, David last_name: Keays citation: ama: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 2017;84:58-67. doi:10.1016/j.mcn.2017.03.002' apa: 'Breuss, M., Leca, I., Gstrein, T., Hansen, A. H., & Keays, D. (2017). Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. Academic Press. https://doi.org/10.1016/j.mcn.2017.03.002' chicago: 'Breuss, Martin, Ines Leca, Thomas Gstrein, Andi H Hansen, and David Keays. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience. Academic Press, 2017. https://doi.org/10.1016/j.mcn.2017.03.002.' ieee: 'M. Breuss, I. Leca, T. Gstrein, A. H. Hansen, and D. Keays, “Tubulins and brain development: The origins of functional specification,” Molecular and Cellular Neuroscience, vol. 84. Academic Press, pp. 58–67, 2017.' ista: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. 2017. Tubulins and brain development: The origins of functional specification. Molecular and Cellular Neuroscience. 84, 58–67.' mla: 'Breuss, Martin, et al. “Tubulins and Brain Development: The Origins of Functional Specification.” Molecular and Cellular Neuroscience, vol. 84, Academic Press, 2017, pp. 58–67, doi:10.1016/j.mcn.2017.03.002.' short: M. Breuss, I. Leca, T. Gstrein, A.H. Hansen, D. Keays, Molecular and Cellular Neuroscience 84 (2017) 58–67. date_created: 2018-12-11T11:49:42Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-22T09:42:15Z day: '01' ddc: - '571' department: - _id: SiHi doi: 10.1016/j.mcn.2017.03.002 external_id: isi: - '000415140700007' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:09:19Z date_updated: 2018-12-12T10:09:19Z file_id: '4742' file_name: IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf file_size: 1436377 relation: main_file file_date_updated: 2018-12-12T10:09:19Z has_accepted_license: '1' intvolume: ' 84' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 58 - 67 publication: Molecular and Cellular Neuroscience publication_identifier: issn: - '10447431' publication_status: published publisher: Academic Press publist_id: '6377' pubrep_id: '806' quality_controlled: '1' scopus_import: '1' status: public title: 'Tubulins and brain development: The origins of functional specification' 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: 84 year: '2017' ... --- _id: '1015' abstract: - lang: eng text: 'Vortices are commonly observed in the context of classical hydrodynamics: from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon such as a tornado, all classical vortices are characterized by an arbitrary circulation value of the local velocity field. On the other hand the appearance of vortices with quantized circulation represents one of the fundamental signatures of macroscopic quantum phenomena. In two-dimensional superfluids quantized vortices play a key role in determining finite-temperature properties, as the superfluid phase and the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless transition. Very recent experiments with two-dimensional superfluid fermions motivate the present work: we present theoretical results based on the renormalization group showing that the universal jump of the superfluid density and the critical temperature crucially depend on the interaction strength, providing a strong benchmark for forthcoming investigations.' article_number: '45702' 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: Luca full_name: Salasnich, Luca last_name: Salasnich citation: ama: Bighin G, Salasnich L. Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. 2017;7. doi:10.1038/srep45702 apa: Bighin, G., & Salasnich, L. (2017). Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep45702 chicago: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep45702. ieee: G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional ultracold Fermi gases,” Scientific Reports, vol. 7. Nature Publishing Group, 2017. ista: Bighin G, Salasnich L. 2017. Vortices and antivortices in two-dimensional ultracold Fermi gases. Scientific Reports. 7, 45702. mla: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional Ultracold Fermi Gases.” Scientific Reports, vol. 7, 45702, Nature Publishing Group, 2017, doi:10.1038/srep45702. short: G. Bighin, L. Salasnich, Scientific Reports 7 (2017). date_created: 2018-12-11T11:49:42Z date_published: 2017-04-04T00:00:00Z date_updated: 2023-09-22T09:43:10Z day: '04' ddc: - '539' department: - _id: MiLe doi: 10.1038/srep45702 external_id: isi: - '000398148100001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:12:32Z date_updated: 2018-12-12T10:12:32Z file_id: '4950' file_name: IST-2017-809-v1+1_srep45702.pdf file_size: 478289 relation: main_file file_date_updated: 2018-12-12T10:12:32Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: issn: - '20452322' publication_status: published publisher: Nature Publishing Group publist_id: '6380' pubrep_id: '809' quality_controlled: '1' scopus_import: '1' status: public title: Vortices and antivortices in two-dimensional ultracold Fermi gases 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: 7 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 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 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: '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: '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: '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: '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 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: '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' ... --- _id: '916' abstract: - lang: eng text: We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each. article_processing_charge: No author: - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Carsten full_name: Abu Alhaija, Carsten last_name: Abu Alhaija - first_name: Dagmar full_name: Kainmueller, Dagmar last_name: Kainmueller - first_name: Bogdan full_name: Savchynskyy, Bogdan last_name: Savchynskyy citation: ama: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747' apa: 'Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747' chicago: Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747. ieee: 'P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071.' ista: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.' mla: Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747. short: P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071. 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: 2018-12-11T11:49:11Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-26T15:41:40Z day: '01' ddc: - '000' department: - _id: VlKo doi: 10.1109/CVPR.2017.747 ec_funded: 1 external_id: isi: - '000418371407018' file: - access_level: open_access checksum: e38a2740daad1ea178465843b5072906 content_type: application/pdf creator: dernst date_created: 2019-01-18T12:49:38Z date_updated: 2020-07-14T12:48:15Z file_id: '5848' file_name: 2017_CVPR_Swoboda2.pdf file_size: 944332 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 2017' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 7062-7071 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: isbn: - 978-153860457-1 publication_status: published publisher: IEEE publist_id: '6525' quality_controlled: '1' scopus_import: '1' status: public title: A study of lagrangean decompositions and dual ascent solvers for graph matching type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2017 year: '2017' ... --- _id: '915' abstract: - lang: eng text: We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining. article_processing_charge: No author: - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Bjoern full_name: Andres, Bjoern last_name: Andres citation: ama: 'Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530' apa: 'Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530' chicago: Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530. ieee: 'P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.' ista: 'Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.' mla: Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530. short: P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999. 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: 2018-12-11T11:49:11Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-09-26T15:43:27Z day: '01' ddc: - '000' department: - _id: VlKo doi: 10.1109/CVPR.2017.530 ec_funded: 1 external_id: isi: - '000418371405009' file: - access_level: open_access checksum: 7e51dacefa693574581a32da3eff63dc content_type: application/pdf creator: dernst date_created: 2019-01-18T12:52:46Z date_updated: 2020-07-14T12:48:15Z file_id: '5849' file_name: Swoboda_A_Message_Passing_CVPR_2017_paper.pdf file_size: 883264 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 2017' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 4990-4999 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: isbn: - 978-153860457-1 publication_status: published publisher: IEEE publist_id: '6526' quality_controlled: '1' scopus_import: '1' status: public title: A message passing algorithm for the minimum cost multicut problem type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2017 year: '2017' ... --- _id: '917' abstract: - lang: eng text: We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers. article_processing_charge: No author: - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Jan full_name: Kuske, Jan last_name: Kuske - first_name: Bogdan full_name: Savchynskyy, Bogdan last_name: Savchynskyy citation: ama: 'Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526' apa: 'Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.526' chicago: Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.526. ieee: 'P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.' ista: 'Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960.' mla: Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526. short: P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960. 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: 2018-12-11T11:49:11Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-09-26T15:41:11Z day: '01' ddc: - '000' department: - _id: VlKo doi: 10.1109/CVPR.2017.526 ec_funded: 1 external_id: isi: - '000418371405005' file: - access_level: open_access checksum: 72fd291046bd8e5717961bd68f6b6f03 content_type: application/pdf creator: dernst date_created: 2019-01-18T12:45:55Z date_updated: 2020-07-14T12:48:15Z file_id: '5847' file_name: 2017_CVPR_Swoboda.pdf file_size: 898652 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 2017' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 4950-4960 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: isbn: - 978-153860457-1 publication_status: published publisher: IEEE publist_id: '6524' quality_controlled: '1' scopus_import: '1' status: public title: A dual ascent framework for Lagrangean decomposition of combinatorial problems type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2017 year: '2017' ... --- _id: '943' abstract: - lang: eng text: Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation. article_processing_charge: No author: - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Yoji full_name: Tabata, Yoji last_name: Tabata - first_name: Nathalie full_name: Brandenberg, Nathalie last_name: Brandenberg - first_name: Matthias full_name: Lutolf, Matthias last_name: Lutolf - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Tobias full_name: Bollenbach, Tobias last_name: Bollenbach - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887 apa: Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887 chicago: Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887. ieee: M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017. ista: Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383. mla: Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887. short: M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383. date_created: 2018-12-11T11:49:20Z date_published: 2017-06-30T00:00:00Z date_updated: 2023-09-26T15:38:05Z day: '30' department: - _id: AnKi - _id: GaTk doi: 10.1126/science.aam5887 ec_funded: 1 external_id: isi: - '000404351500036' pmid: - '28663499' intvolume: ' 356' isi: 1 issue: '6345' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/ month: '06' oa: 1 oa_version: Submitted Version page: 1379 - 1383 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2524F500-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '201439' name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish publication: Science publication_identifier: issn: - '00368075' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6474' quality_controlled: '1' scopus_import: '1' status: public title: Decoding of position in the developing neural tube from antiparallel morphogen gradients type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 356 year: '2017' ... --- _id: '939' abstract: - lang: eng text: We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding. article_number: '033905' article_processing_charge: No author: - first_name: Bikashkali full_name: Midya, Bikashkali id: 456187FC-F248-11E8-B48F-1D18A9856A87 last_name: Midya - first_name: Vladimir full_name: Konotop, Vladimir last_name: Konotop citation: ama: 'Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 2017;119(3). doi:10.1103/PhysRevLett.119.033905' apa: 'Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905' chicago: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.' ieee: 'B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.' ista: 'Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.' mla: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.' short: B. Midya, V. Konotop, Physical Review Letters 119 (2017). date_created: 2018-12-11T11:49:18Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-09-26T15:39:46Z day: '18' department: - _id: MiLe doi: 10.1103/PhysRevLett.119.033905 ec_funded: 1 external_id: isi: - '000405718200012' intvolume: ' 119' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: 'https://arxiv.org/abs/1706.04085 ' 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 Letters publication_identifier: issn: - '00319007' publication_status: published publisher: American Physical Society publist_id: '6481' quality_controlled: '1' scopus_import: '1' status: public title: 'Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 119 year: '2017' ... --- _id: '9853' abstract: - lang: eng text: Egg laying rates and infection loads of C. obscurior queens 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. Raw data from ant queens increase their reproductive efforts after pathogen infection. 2017. doi:10.6084/m9.figshare.5117788.v1 apa: Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Raw data from ant queens increase their reproductive efforts after pathogen infection. The Royal Society. https://doi.org/10.6084/m9.figshare.5117788.v1 chicago: Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5117788.v1. ieee: J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Raw data from ant queens increase their reproductive efforts after pathogen infection.” The Royal Society, 2017. ista: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Raw data from ant queens increase their reproductive efforts after pathogen infection, The Royal Society, 10.6084/m9.figshare.5117788.v1. mla: Giehr, Julia, et al. Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection. The Royal Society, 2017, doi:10.6084/m9.figshare.5117788.v1. short: J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, (2017). date_created: 2021-08-10T06:57:57Z date_published: 2017-06-19T00:00:00Z date_updated: 2023-09-26T15:45:47Z day: '19' department: - _id: SyCr doi: 10.6084/m9.figshare.5117788.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.5117788.v1 month: '06' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '914' relation: used_in_publication status: public status: public title: Raw data from ant queens increase their reproductive efforts after pathogen infection type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '822' abstract: - lang: eng text: 'Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. ' article_processing_charge: No author: - first_name: Marjon full_name: De Vos, Marjon id: 3111FFAC-F248-11E8-B48F-1D18A9856A87 last_name: De Vos - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Alan full_name: Mcnally, Alan last_name: Mcnally - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114 apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114 chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114. ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017. ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671. mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114. short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671. date_created: 2018-12-11T11:48:41Z date_published: 2017-10-03T00:00:00Z date_updated: 2023-09-26T16:18:48Z day: '03' department: - _id: ToBo doi: 10.1073/pnas.1713372114 ec_funded: 1 external_id: isi: - '000412130500061' pmid: - '28923953' intvolume: ' 114' isi: 1 issue: '40' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/ month: '10' oa: 1 oa_version: Submitted Version page: 10666 - 10671 pmid: 1 project: - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '6827' quality_controlled: '1' scopus_import: '1' status: public title: Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 114 year: '2017' ... --- _id: '833' abstract: - lang: eng text: We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams. alternative_title: - LNCS article_processing_charge: No author: - first_name: Teresa full_name: Heiss, Teresa id: 4879BB4E-F248-11E8-B48F-1D18A9856A87 last_name: Heiss orcid: 0000-0002-1780-2689 - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: 'Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:10.1007/978-3-319-64689-3_32' apa: 'Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32' chicago: Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32. ieee: 'T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.' ista: 'Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.' mla: Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32. short: T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409. conference: end_date: 2017-08-24 location: Ystad, Sweden name: 'CAIP: Computer Analysis of Images and Patterns' start_date: 2017-08-22 date_created: 2018-12-11T11:48:45Z date_published: 2017-07-28T00:00:00Z date_updated: 2023-09-26T16:10:03Z day: '28' department: - _id: HeEd doi: 10.1007/978-3-319-64689-3_32 editor: - first_name: Michael full_name: Felsberg, Michael last_name: Felsberg - first_name: Anders full_name: Heyden, Anders last_name: Heyden - first_name: Norbert full_name: Krüger, Norbert last_name: Krüger external_id: isi: - '000432085900032' intvolume: ' 10424' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.02045 month: '07' oa: 1 oa_version: Submitted Version page: 397 - 409 publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6815' quality_controlled: '1' scopus_import: '1' status: public title: Streaming algorithm for Euler characteristic curves of multidimensional images type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10424 year: '2017' ... --- _id: '834' abstract: - lang: eng text: 'Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition.' acknowledgement: We acknowledge useful discussions with V. Kravtsov, T. Grover, and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915) article_number: '104201' article_processing_charge: No author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Papic full_name: Zlatko, Papic last_name: Zlatko - first_name: Dmitry full_name: Abanin, Dmitry last_name: Abanin citation: ama: Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201 apa: Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201 chicago: Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201. ieee: M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10. American Physical Society, 2017. ista: Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201. mla: Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201. short: M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017). date_created: 2018-12-11T11:48:45Z date_published: 2017-09-06T00:00:00Z date_updated: 2023-09-26T15:51:54Z day: '06' department: - _id: MaSe doi: 10.1103/PhysRevB.96.104201 external_id: isi: - '000409429300004' intvolume: ' 96' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.02389 month: '09' oa: 1 oa_version: Submitted Version publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - '24699950' publication_status: published publisher: American Physical Society publist_id: '6814' quality_controlled: '1' scopus_import: '1' status: public title: Thouless energy and multifractality across the many-body localization transition type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 96 year: '2017' ... --- _id: '823' abstract: - lang: eng text: The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region. article_number: '093404' article_processing_charge: No author: - first_name: Simona full_name: Colabrese, Simona last_name: Colabrese - 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: Luca full_name: Leuzzi, Luca last_name: Leuzzi - first_name: Enzo full_name: Marinari, Enzo last_name: Marinari citation: ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3' apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3' chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.' ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9. IOPscience, 2017.' ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.' mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.' short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).' date_created: 2018-12-11T11:48:41Z date_published: 2017-09-26T00:00:00Z date_updated: 2023-09-26T16:18:12Z day: '26' department: - _id: GaTk doi: 10.1088/1742-5468/aa85c3 ec_funded: 1 external_id: isi: - '000411842900001' intvolume: ' 2017' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.06303 month: '09' 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: ' Journal of Statistical Mechanics: Theory and Experiment' publication_identifier: issn: - '17425468' publication_status: published publisher: IOPscience publist_id: '6826' quality_controlled: '1' scopus_import: '1' status: public title: Phase transitions in integer linear problems type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2017 year: '2017' ... --- _id: '824' abstract: - lang: eng text: 'In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff.' article_number: R1 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: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516 apa: Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.516 chicago: Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.516. ieee: N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University Press, 2017. ista: Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1. mla: Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge University Press, 2017, doi:10.1017/jfm.2017.516. short: N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017). date_created: 2018-12-11T11:48:42Z date_published: 2017-08-18T00:00:00Z date_updated: 2023-09-26T16:17:43Z day: '18' department: - _id: BjHo doi: 10.1017/jfm.2017.516 external_id: isi: - '000408326300001' intvolume: ' 827' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.10484 month: '08' oa: 1 oa_version: Submitted Version publication: Journal of Fluid Mechanics publication_identifier: issn: - '00221120' publication_status: published publisher: Cambridge University Press publist_id: '6824' quality_controlled: '1' scopus_import: '1' status: public title: Heteroclinic path to spatially localized chaos in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 827 year: '2017' ... --- _id: '799' abstract: - lang: eng text: Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis. article_number: 1801-1811 article_processing_charge: No author: - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Yuki full_name: Matsuura, Yuki last_name: Matsuura - first_name: Luca full_name: Santuari, Luca last_name: Santuari - first_name: Hirotaka full_name: Kouno, Hirotaka last_name: Kouno - first_name: Kohei full_name: Arima, Kohei last_name: Arima - first_name: Christian full_name: Hardtke, Christian last_name: Hardtke - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Tatsuo full_name: Kakimoto, Tatsuo last_name: Kakimoto - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka citation: ama: Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118 apa: Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118 chicago: Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118. ieee: S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017. ista: Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811. mla: Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:10.1093/pcp/pcx118. short: S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017). date_created: 2018-12-11T11:48:34Z date_published: 2017-08-21T00:00:00Z date_updated: 2023-09-27T11:00:19Z day: '21' ddc: - '581' department: - _id: JiFr doi: 10.1093/pcp/pcx118 external_id: isi: - '000413220400019' pmid: - '29016942' file: - access_level: open_access checksum: bd3e3a94d55416739cbb19624bb977f8 content_type: application/pdf creator: dernst date_created: 2019-04-17T07:52:34Z date_updated: 2020-07-14T12:48:06Z file_id: '6333' file_name: 2017_PlantCellPhysio_Kitakura.pdf file_size: 1352913 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 58' isi: 1 issue: '10' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version pmid: 1 publication: Plant and Cell Physiology publication_identifier: issn: - '00320781' publication_status: published publisher: Oxford University Press publist_id: '6854' pubrep_id: '1009' quality_controlled: '1' scopus_import: '1' status: public title: BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 58 year: '2017' ... --- _id: '800' abstract: - lang: eng text: Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers. article_number: '758' article_processing_charge: No author: - first_name: Michael full_name: Strüber, Michael last_name: Strüber - first_name: Jonas full_name: Sauer, Jonas last_name: Sauer - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos citation: ama: Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00936-3 apa: Strüber, M., Sauer, J., Jonas, P. M., & Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00936-3 chicago: Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00936-3. ieee: M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758. mla: Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature Communications, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00936-3. short: M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017). date_created: 2018-12-11T11:48:34Z date_published: 2017-10-02T00:00:00Z date_updated: 2023-09-27T10:59:41Z day: '02' ddc: - '571' department: - _id: PeJo doi: 10.1038/s41467-017-00936-3 ec_funded: 1 external_id: isi: - '000412053100004' file: - access_level: open_access checksum: 7e2c7621afd5f802338e92e8619f024d content_type: application/pdf creator: system date_created: 2018-12-12T10:15:17Z date_updated: 2020-07-14T12:48:07Z file_id: '5135' file_name: IST-2017-914-v1+1_s41467-017-00936-3.pdf file_size: 4261832 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6853' pubrep_id: '914' quality_controlled: '1' scopus_import: '1' status: public title: Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus 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: '803' abstract: - lang: eng text: Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function. acknowledged_ssus: - _id: Bio article_processing_charge: No author: - first_name: Matthias full_name: Samwer, Matthias last_name: Samwer - first_name: Maximilian full_name: Schneider, Maximilian last_name: Schneider - first_name: Rudolf full_name: Hoefler, Rudolf last_name: Hoefler - first_name: Philipp S full_name: Schmalhorst, Philipp S id: 309D50DA-F248-11E8-B48F-1D18A9856A87 last_name: Schmalhorst orcid: 0000-0002-5795-0133 - first_name: Julian full_name: Jude, Julian last_name: Jude - first_name: Johannes full_name: Zuber, Johannes last_name: Zuber - first_name: Daniel full_name: Gerlic, Daniel last_name: Gerlic citation: ama: Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 2017;170(5):956-972. doi:10.1016/j.cell.2017.07.038 apa: Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., & Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.07.038 chicago: Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.038. ieee: M. Samwer et al., “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” Cell, vol. 170, no. 5. Cell Press, pp. 956–972, 2017. ista: Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972. mla: Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” Cell, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:10.1016/j.cell.2017.07.038. short: M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972. date_created: 2018-12-11T11:48:35Z date_published: 2017-08-24T00:00:00Z date_updated: 2023-09-27T10:59:14Z day: '24' ddc: - '570' department: - _id: CaHe doi: 10.1016/j.cell.2017.07.038 external_id: isi: - '000408372400014' file: - access_level: open_access checksum: 64897b0c5373f22273f598e4672c60ff content_type: application/pdf creator: dernst date_created: 2019-01-18T13:45:40Z date_updated: 2020-07-14T12:48:08Z file_id: '5852' file_name: 2017_Cell_Samwer.pdf file_size: 17666637 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 170' isi: 1 issue: '5' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 956 - 972 publication: Cell publication_identifier: issn: - '00928674' publication_status: published publisher: Cell Press publist_id: '6848' quality_controlled: '1' scopus_import: '1' status: public title: DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes 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: 170 year: '2017' ... --- _id: '804' abstract: - lang: eng text: Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides. acknowledged_ssus: - _id: ScienComp acknowledgement: P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support. article_processing_charge: No author: - first_name: Philipp S full_name: Schmalhorst, Philipp S id: 309D50DA-F248-11E8-B48F-1D18A9856A87 last_name: Schmalhorst orcid: 0000-0002-5795-0133 - first_name: Felix full_name: Deluweit, Felix last_name: Deluweit - first_name: Roger full_name: Scherrers, Roger last_name: Scherrers - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora citation: ama: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374 apa: Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., & Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374 chicago: Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation. American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374. ieee: P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017. ista: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053. mla: Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:10.1021/acs.jctc.7b00374. short: P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053. date_created: 2018-12-11T11:48:35Z date_published: 2017-10-10T00:00:00Z date_updated: 2023-09-27T10:58:45Z day: '10' department: - _id: CaHe doi: 10.1021/acs.jctc.7b00374 external_id: isi: - '000412965700036' intvolume: ' 13' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.03773 month: '10' oa: 1 oa_version: Submitted Version page: 5039 - 5053 publication: Journal of Chemical Theory and Computation publication_identifier: issn: - '15499618' publication_status: published publisher: American Chemical Society publist_id: '6847' quality_controlled: '1' scopus_import: '1' status: public title: Overcoming the limitations of the MARTINI force field in simulations of polysaccharides type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13 year: '2017' ... --- _id: '746' abstract: - lang: eng text: Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics. article_number: '1103' article_processing_charge: No author: - first_name: Elisabetta full_name: Aloisi, Elisabetta last_name: Aloisi - first_name: Katy full_name: Le Corf, Katy last_name: Le Corf - first_name: Julien full_name: Dupuis, Julien last_name: Dupuis - first_name: Pei full_name: Zhang, Pei last_name: Zhang - first_name: Melanie full_name: Ginger, Melanie last_name: Ginger - first_name: Virginie full_name: Labrousse, Virginie last_name: Labrousse - first_name: Michela full_name: Spatuzza, Michela last_name: Spatuzza - first_name: Matthias full_name: Georg Haberl, Matthias last_name: Georg Haberl - first_name: Lara full_name: Costa, Lara last_name: Costa - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Anke full_name: Tappe Theodor, Anke last_name: Tappe Theodor - first_name: Fillippo full_name: Drago, Fillippo last_name: Drago - first_name: Pier full_name: Vincenzo Piazza, Pier last_name: Vincenzo Piazza - first_name: Christophe full_name: Mulle, Christophe last_name: Mulle - first_name: Laurent full_name: Groc, Laurent last_name: Groc - first_name: Lucia full_name: Ciranna, Lucia last_name: Ciranna - first_name: Maria full_name: Catania, Maria last_name: Catania - first_name: Andreas full_name: Frick, Andreas last_name: Frick citation: ama: Aloisi E, Le Corf K, Dupuis J, et al. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01191-2 apa: Aloisi, E., Le Corf, K., Dupuis, J., Zhang, P., Ginger, M., Labrousse, V., … Frick, A. (2017). Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01191-2 chicago: Aloisi, Elisabetta, Katy Le Corf, Julien Dupuis, Pei Zhang, Melanie Ginger, Virginie Labrousse, Michela Spatuzza, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01191-2. ieee: E. Aloisi et al., “Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Aloisi E, Le Corf K, Dupuis J, Zhang P, Ginger M, Labrousse V, Spatuzza M, Georg Haberl M, Costa L, Shigemoto R, Tappe Theodor A, Drago F, Vincenzo Piazza P, Mulle C, Groc L, Ciranna L, Catania M, Frick A. 2017. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 8(1), 1103. mla: Aloisi, Elisabetta, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications, vol. 8, no. 1, 1103, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01191-2. short: E. Aloisi, K. Le Corf, J. Dupuis, P. Zhang, M. Ginger, V. Labrousse, M. Spatuzza, M. Georg Haberl, L. Costa, R. Shigemoto, A. Tappe Theodor, F. Drago, P. Vincenzo Piazza, C. Mulle, L. Groc, L. Ciranna, M. Catania, A. Frick, Nature Communications 8 (2017). date_created: 2018-12-11T11:48:17Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-27T12:27:30Z day: '01' ddc: - '571' department: - _id: RySh doi: 10.1038/s41467-017-01191-2 external_id: isi: - '000413571300004' file: - access_level: open_access checksum: 99ceee57549dc0461e3adfc037ec70a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:32Z date_updated: 2020-07-14T12:47:58Z file_id: '5287' file_name: IST-2017-915-v1+1_s41467-017-01191-2.pdf file_size: 1841650 relation: main_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6921' pubrep_id: '915' quality_controlled: '1' scopus_import: '1' status: public title: Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice 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: '749' abstract: - lang: eng text: 'Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, Syt7 is strongly expressed in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. To resolve this apparent contradiction, we examined the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment, and facilitation. In combination, these three effects ensure efficient transmitter release during high-frequency activity and guarantee frequency independence of inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency of high-frequency inhibitory synaptic transmission' acknowledged_ssus: - _id: PreCl article_processing_charge: No author: - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Rachel full_name: Satterfield, Rachel last_name: Satterfield - first_name: Samuel full_name: Young, Samuel last_name: Young - 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, Satterfield R, Young S, Jonas PM. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. 2017;21(8):2082-2089. doi:10.1016/j.celrep.2017.10.122 apa: Chen, C., Satterfield, R., Young, S., & Jonas, P. M. (2017). Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.10.122 chicago: Chen, Chong, Rachel Satterfield, Samuel Young, and Peter M Jonas. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.10.122. ieee: C. Chen, R. Satterfield, S. Young, and P. M. Jonas, “Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses,” Cell Reports, vol. 21, no. 8. Cell Press, pp. 2082–2089, 2017. ista: Chen C, Satterfield R, Young S, Jonas PM. 2017. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. 21(8), 2082–2089. mla: Chen, Chong, et al. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports, vol. 21, no. 8, Cell Press, 2017, pp. 2082–89, doi:10.1016/j.celrep.2017.10.122. short: C. Chen, R. Satterfield, S. Young, P.M. Jonas, Cell Reports 21 (2017) 2082–2089. date_created: 2018-12-11T11:48:18Z date_published: 2017-11-21T00:00:00Z date_updated: 2023-09-27T12:26:04Z day: '21' ddc: - '570' - '571' department: - _id: PeJo doi: 10.1016/j.celrep.2017.10.122 ec_funded: 1 external_id: isi: - '000416216700007' file: - access_level: open_access checksum: a6afa3764909bf6edafa07982d8e1cee content_type: application/pdf creator: system date_created: 2018-12-12T10:09:14Z date_updated: 2020-07-14T12:47:59Z file_id: '4737' file_name: IST-2017-874-v1+1_PIIS2211124717316029.pdf file_size: 2759195 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '8' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 2082 - 2089 project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse publication: Cell Reports publication_identifier: issn: - '22111247' publication_status: published publisher: Cell Press publist_id: '6907' pubrep_id: '874' quality_controlled: '1' related_material: record: - id: '324' relation: dissertation_contains status: public scopus_import: '1' status: public title: Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses 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: 21 year: '2017' ... --- _id: '744' abstract: - lang: eng text: In evolutionary game theory interactions between individuals are often assumed obligatory. However, in many real-life situations, individuals can decide to opt out of an interaction depending on the information they have about the opponent. We consider a simple evolutionary game theoretic model to study such a scenario, where at each encounter between two individuals the type of the opponent (cooperator/defector) is known with some probability, and where each individual either accepts or opts out of the interaction. If the type of the opponent is unknown, a trustful individual accepts the interaction, whereas a suspicious individual opts out of the interaction. If either of the two individuals opt out both individuals remain without an interaction. We show that in the prisoners dilemma optional interactions along with suspicious behaviour facilitates the emergence of trustful cooperation. article_processing_charge: No article_type: original author: - first_name: Tadeas full_name: Priklopil, Tadeas id: 3C869AA0-F248-11E8-B48F-1D18A9856A87 last_name: Priklopil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Priklopil T, Chatterjee K, Nowak M. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. 2017;433:64-72. doi:10.1016/j.jtbi.2017.08.025 apa: Priklopil, T., Chatterjee, K., & Nowak, M. (2017). Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2017.08.025 chicago: Priklopil, Tadeas, Krishnendu Chatterjee, and Martin Nowak. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” Journal of Theoretical Biology. Elsevier, 2017. https://doi.org/10.1016/j.jtbi.2017.08.025. ieee: T. Priklopil, K. Chatterjee, and M. Nowak, “Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma,” Journal of Theoretical Biology, vol. 433. Elsevier, pp. 64–72, 2017. ista: Priklopil T, Chatterjee K, Nowak M. 2017. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical Biology. 433, 64–72. mla: Priklopil, Tadeas, et al. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” Journal of Theoretical Biology, vol. 433, Elsevier, 2017, pp. 64–72, doi:10.1016/j.jtbi.2017.08.025. short: T. Priklopil, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 433 (2017) 64–72. date_created: 2018-12-11T11:48:16Z date_published: 2017-11-21T00:00:00Z date_updated: 2023-09-27T12:29:02Z day: '21' ddc: - '000' - '570' department: - _id: KrCh doi: 10.1016/j.jtbi.2017.08.025 ec_funded: 1 external_id: isi: - '000412039800007' pmid: - '28867224' file: - access_level: open_access checksum: 4b43af1615ebf1a861840cb03d8a320c content_type: application/pdf creator: dernst date_created: 2019-11-19T07:57:39Z date_updated: 2020-07-14T12:47:58Z file_id: '7047' file_name: 2017_JournTheoretBio_Priklopil.pdf file_size: 537323 relation: main_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' intvolume: ' 433' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 64 - 72 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: ' Journal of Theoretical Biology' publication_identifier: issn: - '00225193' publication_status: published publisher: Elsevier publist_id: '6923' quality_controlled: '1' scopus_import: '1' status: public title: Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma 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: 433 year: '2017' ... --- _id: '745' abstract: - lang: eng text: 'Fluid flows in nature and applications are frequently subject to periodic velocity modulations. Surprisingly, even for the generic case of flow through a straight pipe, there is little consensus regarding the influence of pulsation on the transition threshold to turbulence: while most studies predict a monotonically increasing threshold with pulsation frequency (i.e. Womersley number, ), others observe a decreasing threshold for identical parameters and only observe an increasing threshold at low . In the present study we apply recent advances in the understanding of transition in steady shear flows to pulsating pipe flow. For moderate pulsation amplitudes we find that the first instability encountered is subcritical (i.e. requiring finite amplitude disturbances) and gives rise to localized patches of turbulence (''puffs'') analogous to steady pipe flow. By monitoring the impact of pulsation on the lifetime of turbulence we map the onset of turbulence in parameter space. Transition in pulsatile flow can be separated into three regimes. At small Womersley numbers the dynamics is dominated by the decay turbulence suffers during the slower part of the cycle and hence transition is delayed significantly. As shown in this regime thresholds closely agree with estimates based on a quasi-steady flow assumption only taking puff decay rates into account. The transition point predicted in the zero limit equals to the critical point for steady pipe flow offset by the oscillation Reynolds number (i.e. the dimensionless oscillation amplitude). In the high frequency limit on the other hand, puff lifetimes are identical to those in steady pipe flow and hence the transition threshold appears to be unaffected by flow pulsation. In the intermediate frequency regime the transition threshold sharply drops (with increasing ) from the decay dominated (quasi-steady) threshold to the steady pipe flow level.' article_processing_charge: No author: - first_name: Duo full_name: Xu, Duo id: 3454D55E-F248-11E8-B48F-1D18A9856A87 last_name: Xu - first_name: Sascha full_name: Warnecke, Sascha last_name: Warnecke - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Xingyu full_name: Ma, Xingyu id: 34BADBA6-F248-11E8-B48F-1D18A9856A87 last_name: Ma orcid: 0000-0002-0179-9737 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Xu D, Warnecke S, Song B, Ma X, Hof B. Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. 2017;831:418-432. doi:10.1017/jfm.2017.620 apa: Xu, D., Warnecke, S., Song, B., Ma, X., & Hof, B. (2017). Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.620 chicago: Xu, Duo, Sascha Warnecke, Baofang Song, Xingyu Ma, and Björn Hof. “Transition to Turbulence in Pulsating Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.620. ieee: D. Xu, S. Warnecke, B. Song, X. Ma, and B. Hof, “Transition to turbulence in pulsating pipe flow,” Journal of Fluid Mechanics, vol. 831. Cambridge University Press, pp. 418–432, 2017. ista: Xu D, Warnecke S, Song B, Ma X, Hof B. 2017. Transition to turbulence in pulsating pipe flow. Journal of Fluid Mechanics. 831, 418–432. mla: Xu, Duo, et al. “Transition to Turbulence in Pulsating Pipe Flow.” Journal of Fluid Mechanics, vol. 831, Cambridge University Press, 2017, pp. 418–32, doi:10.1017/jfm.2017.620. short: D. Xu, S. Warnecke, B. Song, X. Ma, B. Hof, Journal of Fluid Mechanics 831 (2017) 418–432. date_created: 2018-12-11T11:48:17Z date_published: 2017-11-25T00:00:00Z date_updated: 2023-09-27T12:28:12Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.620 ec_funded: 1 external_id: isi: - '000412934800005' intvolume: ' 831' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.03738 month: '11' oa: 1 oa_version: Submitted Version page: 418 - 432 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_identifier: issn: - '00221120' publication_status: published publisher: Cambridge University Press publist_id: '6922' quality_controlled: '1' scopus_import: '1' status: public title: Transition to turbulence in pulsating pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 831 year: '2017' ... --- _id: '747' abstract: - lang: eng text: Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia. article_processing_charge: No article_type: original author: - first_name: Eugen full_name: Brǎiloiu, Eugen last_name: Brǎiloiu - first_name: Matthew full_name: Mcguire, Matthew last_name: Mcguire - first_name: Shadaria full_name: Shuler, Shadaria last_name: Shuler - first_name: Elena full_name: Deliu, Elena id: 37A40D7E-F248-11E8-B48F-1D18A9856A87 last_name: Deliu orcid: 0000-0002-7370-5293 - first_name: Jeffrey full_name: Barr, Jeffrey last_name: Barr - first_name: Mary full_name: Abood, Mary last_name: Abood - first_name: Gabriela full_name: Brailoiu, Gabriela last_name: Brailoiu citation: ama: Brǎiloiu E, Mcguire M, Shuler S, et al. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 2017;365:23-32. doi:10.1016/j.neuroscience.2017.09.034 apa: Brǎiloiu, E., Mcguire, M., Shuler, S., Deliu, E., Barr, J., Abood, M., & Brailoiu, G. (2017). Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2017.09.034 chicago: Brǎiloiu, Eugen, Matthew Mcguire, Shadaria Shuler, Elena Deliu, Jeffrey Barr, Mary Abood, and Gabriela Brailoiu. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” Neuroscience. Elsevier, 2017. https://doi.org/10.1016/j.neuroscience.2017.09.034. ieee: E. Brǎiloiu et al., “Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus,” Neuroscience, vol. 365. Elsevier, pp. 23–32, 2017. ista: Brǎiloiu E, Mcguire M, Shuler S, Deliu E, Barr J, Abood M, Brailoiu G. 2017. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 365, 23–32. mla: Brǎiloiu, Eugen, et al. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” Neuroscience, vol. 365, Elsevier, 2017, pp. 23–32, doi:10.1016/j.neuroscience.2017.09.034. short: E. Brǎiloiu, M. Mcguire, S. Shuler, E. Deliu, J. Barr, M. Abood, G. Brailoiu, Neuroscience 365 (2017) 23–32. date_created: 2018-12-11T11:48:17Z date_published: 2017-12-04T00:00:00Z date_updated: 2023-09-27T12:26:59Z day: '04' department: - _id: GaNo doi: 10.1016/j.neuroscience.2017.09.034 external_id: isi: - '000415966200003' pmid: - '28951324' intvolume: ' 365' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798458 month: '12' oa: 1 oa_version: Submitted Version page: 23 - 32 pmid: 1 publication: Neuroscience publication_identifier: issn: - '03064522' publication_status: published publisher: Elsevier publist_id: '6911' quality_controlled: '1' scopus_import: '1' status: public title: Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 365 year: '2017' ... --- _id: '961' abstract: - lang: eng text: Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation. acknowledgement: "Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall the good science I witnessed \ and participated in. It has been a \r\nblast, an incredibly \r\nexciting \ one! Thanks to JLo, for teaching me how to master my pipettes and \ showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout zebrafish and being always there to advice, \ sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether for all the good laughs we\r\nhad. My start in Vienna would \ have been a lot more \r\ndifficult without you guys. Also it would not \ have been possible without Elena and Inês: \r\nthanks for helping setting \ up this lab and for the dinners in Gugging. Thanks to Martin, for \r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp, \ for the interest and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat. \ To Shayan, for being such a motivated student. To Matt, for helping \ out\r\nwith coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful \ atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor setting up an amazing imaging facility and for building the best \ team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand \ to Patrick Lemaire f\r\nor the helpful insight and extremely interesting \ discussion we had \r\nabout the project. Also, this journey would not \ have been the same without all the friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William, \ e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 citation: ama: 'Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:10.15479/AT:ISTA:th_825' apa: 'Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_825' chicago: 'Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_825.' ieee: 'V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.' ista: 'Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.' mla: 'Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_825.' short: 'V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.' date_created: 2018-12-11T11:49:25Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-27T14:16:45Z day: '01' ddc: - '570' - '590' degree_awarded: PhD department: - _id: CaHe doi: 10.15479/AT:ISTA:th_825 file: - access_level: closed checksum: 242f88c87f2cf267bf05049fa26a687b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:36:52Z date_updated: 2020-07-14T12:48:16Z file_id: '6205' file_name: 2017_Barone_thesis_final.docx file_size: 14497822 relation: source_file - access_level: open_access checksum: ba5b0613ed8bade73a409acdd880fb8a content_type: application/pdf creator: dernst date_created: 2019-04-05T08:36:52Z date_updated: 2020-07-14T12:48:16Z file_id: '6206' file_name: 2017_Barone_thesis_.pdf file_size: 14995941 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '109' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6444' pubrep_id: '825' related_material: record: - id: '1100' relation: part_of_dissertation status: public - id: '1537' relation: part_of_dissertation status: public - id: '1912' relation: part_of_dissertation status: public - id: '2926' relation: part_of_dissertation status: public - id: '3246' relation: part_of_dissertation status: public - id: '676' relation: part_of_dissertation status: public - id: '735' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: 'Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation' 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '734' abstract: - lang: eng text: 'Social insect societies are long-standing models for understanding social behaviour and evolution. Unlike other advanced biological societies (such as the multicellular body), the component parts of social insect societies can be easily deconstructed and manipulated. Recent methodological and theoretical innovations have exploited this trait to address an expanded range of biological questions. We illustrate the broadening range of biological insight coming from social insect biology with four examples. These new frontiers promote open-minded, interdisciplinary exploration of one of the richest and most complex of biological phenomena: sociality.' article_processing_charge: No article_type: original author: - first_name: Patrick full_name: Kennedy, Patrick last_name: Kennedy - first_name: Gemma full_name: Baron, Gemma last_name: Baron - first_name: Bitao full_name: Qiu, Bitao last_name: Qiu - first_name: Dalial full_name: Freitak, Dalial last_name: Freitak - first_name: Heikki full_name: Helantera, Heikki last_name: Helantera - first_name: Edmund full_name: Hunt, Edmund last_name: Hunt - first_name: Fabio full_name: Manfredini, Fabio last_name: Manfredini - first_name: Thomas full_name: O'Shea Wheller, Thomas last_name: O'Shea Wheller - first_name: Solenn full_name: Patalano, Solenn last_name: Patalano - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Takao full_name: Sasaki, Takao last_name: Sasaki - first_name: Daisy full_name: Taylor, Daisy last_name: Taylor - first_name: Christopher full_name: Wyatt, Christopher last_name: Wyatt - first_name: Seirian full_name: Sumner, Seirian last_name: Sumner citation: ama: Kennedy P, Baron G, Qiu B, et al. Deconstructing superorganisms and societies to address big questions in biology. Trends in Ecology and Evolution. 2017;32(11):861-872. doi:10.1016/j.tree.2017.08.004 apa: Kennedy, P., Baron, G., Qiu, B., Freitak, D., Helantera, H., Hunt, E., … Sumner, S. (2017). Deconstructing superorganisms and societies to address big questions in biology. Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2017.08.004 chicago: Kennedy, Patrick, Gemma Baron, Bitao Qiu, Dalial Freitak, Heikki Helantera, Edmund Hunt, Fabio Manfredini, et al. “Deconstructing Superorganisms and Societies to Address Big Questions in Biology.” Trends in Ecology and Evolution. Cell Press, 2017. https://doi.org/10.1016/j.tree.2017.08.004. ieee: P. Kennedy et al., “Deconstructing superorganisms and societies to address big questions in biology,” Trends in Ecology and Evolution, vol. 32, no. 11. Cell Press, pp. 861–872, 2017. ista: Kennedy P, Baron G, Qiu B, Freitak D, Helantera H, Hunt E, Manfredini F, O’Shea Wheller T, Patalano S, Pull C, Sasaki T, Taylor D, Wyatt C, Sumner S. 2017. Deconstructing superorganisms and societies to address big questions in biology. Trends in Ecology and Evolution. 32(11), 861–872. mla: Kennedy, Patrick, et al. “Deconstructing Superorganisms and Societies to Address Big Questions in Biology.” Trends in Ecology and Evolution, vol. 32, no. 11, Cell Press, 2017, pp. 861–72, doi:10.1016/j.tree.2017.08.004. short: P. Kennedy, G. Baron, B. Qiu, D. Freitak, H. Helantera, E. Hunt, F. Manfredini, T. O’Shea Wheller, S. Patalano, C. Pull, T. Sasaki, D. Taylor, C. Wyatt, S. Sumner, Trends in Ecology and Evolution 32 (2017) 861–872. date_created: 2018-12-11T11:48:13Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-09-27T14:15:15Z day: '01' ddc: - '570' department: - _id: SyCr doi: 10.1016/j.tree.2017.08.004 external_id: isi: - '000413231900011' file: - access_level: open_access checksum: c8f49309ed9436201814fa7153d66a99 content_type: application/pdf creator: dernst date_created: 2020-05-14T16:22:27Z date_updated: 2020-07-14T12:47:56Z file_id: '7842' file_name: 2017_TrendsEcology_Kennedy.pdf file_size: 15018382 relation: main_file file_date_updated: 2020-07-14T12:47:56Z has_accepted_license: '1' intvolume: ' 32' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 861 - 872 publication: Trends in Ecology and Evolution publication_identifier: issn: - '01695347' publication_status: published publisher: Cell Press publist_id: '6933' quality_controlled: '1' related_material: record: - id: '819' relation: dissertation_contains status: public scopus_import: '1' status: public title: Deconstructing superorganisms and societies to address big questions in biology type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2017' ... --- _id: '819' abstract: - lang: eng text: 'Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. ' acknowledgement: "ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 citation: ama: Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861 apa: Pull, C. (2017). Disease defence in garden ants. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861 chicago: Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861. ieee: C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017. ista: Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria. mla: Pull, Christopher. Disease Defence in Garden Ants. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861. short: C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:40Z date_published: 2017-09-26T00:00:00Z date_updated: 2023-09-28T11:31:32Z day: '26' ddc: - '576' - '577' - '578' - '579' - '590' - '592' degree_awarded: PhD department: - _id: SyCr doi: 10.15479/AT:ISTA:th_861 file: - access_level: closed checksum: 4993cdd5382295758ecc3ecbd2a9aaff content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T07:53:04Z date_updated: 2020-07-14T12:48:09Z file_id: '6199' file_name: 2017_Thesis_Pull.docx file_size: 18580400 relation: source_file - access_level: open_access checksum: ee2e3ebb5b53c154c866f5b052b25153 content_type: application/pdf creator: dernst date_created: 2019-04-05T07:53:04Z date_updated: 2020-07-14T12:48:09Z file_id: '6200' file_name: 2017_Thesis_Pull.pdf file_size: 14400681 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '122' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6830' pubrep_id: '861' related_material: record: - id: '616' relation: part_of_dissertation status: public - id: '806' relation: part_of_dissertation status: public - id: '734' relation: part_of_dissertation status: public - id: '732' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sylvia M full_name: Cremer, Sylvia M id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: Disease defence in garden ants 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '732' abstract: - lang: eng text: 'Background: Social insects form densely crowded societies in environments with high pathogen loads, but have evolved collective defences that mitigate the impact of disease. However, colony-founding queens lack this protection and suffer high rates of mortality. The impact of pathogens may be exacerbated in species where queens found colonies together, as healthy individuals may contract pathogens from infectious co-founders. Therefore, we tested whether ant queens avoid founding colonies with pathogen-exposed conspecifics and how they might limit disease transmission from infectious individuals. Results: Using Lasius Niger queens and a naturally infecting fungal pathogen Metarhizium brunneum, we observed that queens were equally likely to found colonies with another pathogen-exposed or sham-treated queen. However, when one queen died, the surviving individual performed biting, burial and removal of the corpse. These undertaking behaviours were performed prophylactically, i.e. targeted equally towards non-infected and infected corpses, as well as carried out before infected corpses became infectious. Biting and burial reduced the risk of the queens contracting and dying from disease from an infectious corpse of a dead co-foundress. Conclusions: We show that co-founding ant queens express undertaking behaviours that, in mature colonies, are performed exclusively by workers. Such infection avoidance behaviours act before the queens can contract the disease and will therefore improve the overall chance of colony founding success in ant queens.' article_number: '219' article_processing_charge: Yes article_type: original author: - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Pull C, Cremer S. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. 2017;17(1). doi:10.1186/s12862-017-1062-4 apa: Pull, C., & Cremer, S. (2017). Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/s12862-017-1062-4 chicago: Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” BMC Evolutionary Biology. BioMed Central, 2017. https://doi.org/10.1186/s12862-017-1062-4. ieee: C. Pull and S. Cremer, “Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour,” BMC Evolutionary Biology, vol. 17, no. 1. BioMed Central, 2017. ista: Pull C, Cremer S. 2017. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. 17(1), 219. mla: Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” BMC Evolutionary Biology, vol. 17, no. 1, 219, BioMed Central, 2017, doi:10.1186/s12862-017-1062-4. short: C. Pull, S. Cremer, BMC Evolutionary Biology 17 (2017). date_created: 2018-12-11T11:48:12Z date_published: 2017-10-13T00:00:00Z date_updated: 2023-09-28T11:31:32Z day: '13' ddc: - '576' - '592' department: - _id: SyCr doi: 10.1186/s12862-017-1062-4 ec_funded: 1 external_id: isi: - '000412816800001' file: - access_level: open_access checksum: 3e24a2cfd48f49f7b3643d08d30fb480 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:18Z date_updated: 2020-07-14T12:47:55Z file_id: '5271' file_name: IST-2017-882-v1+1_12862_2017_Article_1062.pdf file_size: 949857 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' publication: BMC Evolutionary Biology publication_identifier: issn: - '14712148' publication_status: published publisher: BioMed Central publist_id: '6937' pubrep_id: '882' quality_controlled: '1' related_material: record: - id: '819' relation: dissertation_contains status: public scopus_import: '1' status: public title: Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour 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: '726' abstract: - lang: eng text: The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Colinda full_name: Scheele, Colinda last_name: Scheele - first_name: Mohammad full_name: Moad, Mohammad last_name: Moad - first_name: Nicholas full_name: Drogo, Nicholas last_name: Drogo - first_name: Rakesh full_name: Heer, Rakesh last_name: Heer - first_name: Rosemary full_name: Sampogna, Rosemary last_name: Sampogna - first_name: Jacco full_name: Van Rheenen, Jacco last_name: Van Rheenen - first_name: Benjamin full_name: Simons, Benjamin last_name: Simons citation: ama: Hannezo EB, Scheele C, Moad M, et al. A unifying theory of branching morphogenesis. Cell. 2017;171(1):242-255. doi:10.1016/j.cell.2017.08.026 apa: Hannezo, E. B., Scheele, C., Moad, M., Drogo, N., Heer, R., Sampogna, R., … Simons, B. (2017). A unifying theory of branching morphogenesis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.08.026 chicago: Hannezo, Edouard B, Colinda Scheele, Mohammad Moad, Nicholas Drogo, Rakesh Heer, Rosemary Sampogna, Jacco Van Rheenen, and Benjamin Simons. “A Unifying Theory of Branching Morphogenesis.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.08.026. ieee: E. B. Hannezo et al., “A unifying theory of branching morphogenesis,” Cell, vol. 171, no. 1. Cell Press, pp. 242–255, 2017. ista: Hannezo EB, Scheele C, Moad M, Drogo N, Heer R, Sampogna R, Van Rheenen J, Simons B. 2017. A unifying theory of branching morphogenesis. Cell. 171(1), 242–255. mla: Hannezo, Edouard B., et al. “A Unifying Theory of Branching Morphogenesis.” Cell, vol. 171, no. 1, Cell Press, 2017, pp. 242–55, doi:10.1016/j.cell.2017.08.026. short: E.B. Hannezo, C. Scheele, M. Moad, N. Drogo, R. Heer, R. Sampogna, J. Van Rheenen, B. Simons, Cell 171 (2017) 242–255. date_created: 2018-12-11T11:48:10Z date_published: 2017-09-21T00:00:00Z date_updated: 2023-09-28T11:34:17Z day: '21' ddc: - '539' department: - _id: EdHa doi: 10.1016/j.cell.2017.08.026 external_id: isi: - '000411331800024' file: - access_level: open_access checksum: 7a036d93a9e2e597af9bb504d6133aca content_type: application/pdf creator: system date_created: 2018-12-12T10:11:17Z date_updated: 2020-07-14T12:47:55Z file_id: '4870' file_name: IST-2017-883-v1+1_PIIS0092867417309510.pdf file_size: 12670204 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 171' isi: 1 issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 242 - 255 publication: Cell publication_identifier: issn: - '00928674' publication_status: published publisher: Cell Press publist_id: '6952' pubrep_id: '883' quality_controlled: '1' scopus_import: '1' status: public title: A unifying theory of branching morphogenesis 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: 171 year: '2017' ... --- _id: '548' abstract: - lang: eng text: In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region. alternative_title: - Rapid Communications article_number: '060401' 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. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 2017;96(6). doi:10.1103/PhysRevE.96.060401 apa: De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.96.060401 chicago: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401. ieee: D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6. American Physical Society, 2017. ista: De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401. mla: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.060401. short: D. De Martino, Physical Review E 96 (2017). date_created: 2018-12-11T11:47:06Z date_published: 2017-12-21T00:00:00Z date_updated: 2023-10-10T13:29:38Z day: '21' department: - _id: GaTk doi: 10.1103/PhysRevE.96.060401 ec_funded: 1 intvolume: ' 96' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1707.00320 month: '12' 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 publication_identifier: issn: - 2470-0045 publication_status: published publisher: American Physical Society publist_id: '7266' quality_controlled: '1' scopus_import: '1' status: public title: Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ... --- _id: '673' abstract: - lang: eng text: We present a numerical study of wavy supercritical cylindrical Couette flow between counter-rotating cylinders in which the wavy pattern propagates either prograde with the inner cylinder or retrograde opposite the rotation of the inner cylinder. The wave propagation reversals from prograde to retrograde and vice versa occur at distinct values of the inner cylinder Reynolds number when the associated frequency of the wavy instability vanishes. The reversal occurs for both twofold and threefold symmetric wavy vortices. Moreover, the wave propagation reversal only occurs for sufficiently strong counter-rotation. The flow pattern reversal appears to be intrinsic in the system as either periodic boundary conditions or fixed end wall boundary conditions for different system sizes always result in the wave propagation reversal. We present a detailed bifurcation sequence and parameter space diagram with respect to retrograde behavior of wavy flows. The retrograde propagation of the instability occurs when the inner Reynolds number is about two times the outer Reynolds number. The mechanism for the retrograde propagation is associated with the inviscidly unstable region near the inner cylinder and the direction of the global average azimuthal velocity. Flow dynamics, spatio-temporal behavior, global mean angular velocity, and torque of the flow with the wavy pattern are explored. article_number: '053103' article_processing_charge: No author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Richard full_name: Lueptow, Richard last_name: Lueptow citation: ama: Altmeyer S, Lueptow R. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 2017;95(5). doi:10.1103/PhysRevE.95.053103 apa: Altmeyer, S., & Lueptow, R. (2017). Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.95.053103 chicago: Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.95.053103. ieee: S. Altmeyer and R. Lueptow, “Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow,” Physical Review E, vol. 95, no. 5. American Physical Society, 2017. ista: Altmeyer S, Lueptow R. 2017. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 95(5), 053103. mla: Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical Review E, vol. 95, no. 5, 053103, American Physical Society, 2017, doi:10.1103/PhysRevE.95.053103. short: S. Altmeyer, R. Lueptow, Physical Review E 95 (2017). date_created: 2018-12-11T11:47:50Z date_published: 2017-05-10T00:00:00Z date_updated: 2023-10-10T13:30:03Z day: '10' department: - _id: BjHo doi: 10.1103/PhysRevE.95.053103 intvolume: ' 95' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/pdf/physics/0505164.pdf month: '05' oa: 1 oa_version: Submitted Version publication: Physical Review E publication_identifier: issn: - 2470-0045 publication_status: published publisher: American Physical Society publist_id: '7049' scopus_import: '1' status: public title: Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 95 year: '2017' ... --- _id: '447' abstract: - lang: eng text: We consider last passage percolation (LPP) models with exponentially distributed random variables, which are linked to the totally asymmetric simple exclusion process (TASEP). The competition interface for LPP was introduced and studied in Ferrari and Pimentel (2005a) for cases where the corresponding exclusion process had a rarefaction fan. Here we consider situations with a shock and determine the law of the fluctuations of the competition interface around its deter- ministic law of large number position. We also study the multipoint distribution of the LPP around the shock, extending our one-point result of Ferrari and Nejjar (2015). article_processing_charge: No article_type: original author: - first_name: Patrik full_name: Ferrari, Patrik last_name: Ferrari - first_name: Peter full_name: Nejjar, Peter id: 4BF426E2-F248-11E8-B48F-1D18A9856A87 last_name: Nejjar citation: ama: Ferrari P, Nejjar P. Fluctuations of the competition interface in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística. 2017;9:299-325. doi:10.30757/ALEA.v14-17 apa: Ferrari, P., & Nejjar, P. (2017). Fluctuations of the competition interface in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística. Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v14-17 chicago: Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface in Presence of Shocks.” Revista Latino-Americana de Probabilidade e Estatística. Instituto Nacional de Matematica Pura e Aplicada, 2017. https://doi.org/10.30757/ALEA.v14-17. ieee: P. Ferrari and P. Nejjar, “Fluctuations of the competition interface in presence of shocks,” Revista Latino-Americana de Probabilidade e Estatística, vol. 9. Instituto Nacional de Matematica Pura e Aplicada, pp. 299–325, 2017. ista: Ferrari P, Nejjar P. 2017. Fluctuations of the competition interface in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística. 9, 299–325. mla: Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface in Presence of Shocks.” Revista Latino-Americana de Probabilidade e Estatística, vol. 9, Instituto Nacional de Matematica Pura e Aplicada, 2017, pp. 299–325, doi:10.30757/ALEA.v14-17. short: P. Ferrari, P. Nejjar, Revista Latino-Americana de Probabilidade e Estatística 9 (2017) 299–325. date_created: 2018-12-11T11:46:31Z date_published: 2017-03-23T00:00:00Z date_updated: 2023-10-10T13:10:32Z day: '23' department: - _id: LaEr - _id: JaMa doi: 10.30757/ALEA.v14-17 ec_funded: 1 intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: http://alea.impa.br/articles/v14/14-17.pdf month: '03' oa: 1 oa_version: Submitted Version page: 299 - 325 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Revista Latino-Americana de Probabilidade e Estatística publication_status: published publisher: Instituto Nacional de Matematica Pura e Aplicada publist_id: '7376' quality_controlled: '1' scopus_import: '1' status: public title: Fluctuations of the competition interface in presence of shocks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '557' abstract: - lang: eng text: PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer. article_processing_charge: No author: - first_name: Robert full_name: Nickells, Robert last_name: Nickells - first_name: Heather full_name: Schmitt, Heather last_name: Schmitt - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Cassandra full_name: Schlamp, Cassandra last_name: Schlamp citation: ama: Nickells R, Schmitt H, Maes ME, Schlamp C. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 2017;58(14):6091-6104. doi:10.1167/iovs.17-22634 apa: Nickells, R., Schmitt, H., Maes, M. E., & Schlamp, C. (2017). AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/iovs.17-22634 chicago: Nickells, Robert, Heather Schmitt, Margaret E Maes, and Cassandra Schlamp. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology, 2017. https://doi.org/10.1167/iovs.17-22634. ieee: R. Nickells, H. Schmitt, M. E. Maes, and C. Schlamp, “AAV2 mediated transduction of the mouse retina after optic nerve injury,” Investigative Ophthalmology and Visual Science, vol. 58, no. 14. Association for Research in Vision and Ophthalmology, pp. 6091–6104, 2017. ista: Nickells R, Schmitt H, Maes ME, Schlamp C. 2017. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 58(14), 6091–6104. mla: Nickells, Robert, et al. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” Investigative Ophthalmology and Visual Science, vol. 58, no. 14, Association for Research in Vision and Ophthalmology, 2017, pp. 6091–104, doi:10.1167/iovs.17-22634. short: R. Nickells, H. Schmitt, M.E. Maes, C. Schlamp, Investigative Ophthalmology and Visual Science 58 (2017) 6091–6104. date_created: 2018-12-11T11:47:10Z date_published: 2017-12-14T00:00:00Z date_updated: 2023-10-10T14:06:18Z day: '14' ddc: - '576' department: - _id: SaSi doi: 10.1167/iovs.17-22634 file: - access_level: open_access checksum: d7a7b6f1fa9211a04e5e65634a0265d9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:53Z date_updated: 2020-07-14T12:47:04Z file_id: '5311' file_name: IST-2018-920-v1+1_i1552-5783-58-14-6091.pdf file_size: 2955559 relation: main_file file_date_updated: 2020-07-14T12:47:04Z has_accepted_license: '1' intvolume: ' 58' issue: '14' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 6091 - 6104 publication: Investigative Ophthalmology and Visual Science publication_identifier: issn: - '01460404' publication_status: published publisher: Association for Research in Vision and Ophthalmology publist_id: '7254' pubrep_id: '920' quality_controlled: '1' scopus_import: '1' status: public title: AAV2 mediated transduction of the mouse retina after optic nerve injury 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2017' ... --- _id: '997' abstract: - lang: eng text: Recently it was shown that molecules rotating in superfluid helium can be described in terms of the angulon quasiparticles (Phys. Rev. Lett. 118, 095301 (2017)). Here we demonstrate that in the experimentally realized regime the angulon can be seen as a point charge on a 2-sphere interacting with a gauge field of a non-abelian magnetic monopole. Unlike in several other settings, the gauge fields of the angulon problem emerge in the real coordinate space, as opposed to the momentum space or some effective parameter space. Furthermore, we find a topological transition associated with making the monopole abelian, which takes place in the vicinity of the previously reported angulon instabilities. These results pave the way for studying topological phenomena in experiments on molecules trapped in superfluid helium nanodroplets, as well as on other realizations of orbital impurity problems. article_number: '235301' article_processing_charge: No article_type: original author: - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Yakaboylu E, Deuchert A, Lemeshko M. Emergence of non-abelian magnetic monopoles in a quantum impurity problem. Physical Review Letters. 2017;119(23). doi:10.1103/PhysRevLett.119.235301 apa: Yakaboylu, E., Deuchert, A., & Lemeshko, M. (2017). Emergence of non-abelian magnetic monopoles in a quantum impurity problem. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.235301 chicago: Yakaboylu, Enderalp, Andreas Deuchert, and Mikhail Lemeshko. “Emergence of Non-Abelian Magnetic Monopoles in a Quantum Impurity Problem.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.235301. ieee: E. Yakaboylu, A. Deuchert, and M. Lemeshko, “Emergence of non-abelian magnetic monopoles in a quantum impurity problem,” Physical Review Letters, vol. 119, no. 23. American Physical Society, 2017. ista: Yakaboylu E, Deuchert A, Lemeshko M. 2017. Emergence of non-abelian magnetic monopoles in a quantum impurity problem. Physical Review Letters. 119(23), 235301. mla: Yakaboylu, Enderalp, et al. “Emergence of Non-Abelian Magnetic Monopoles in a Quantum Impurity Problem.” Physical Review Letters, vol. 119, no. 23, 235301, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.235301. short: E. Yakaboylu, A. Deuchert, M. Lemeshko, Physical Review Letters 119 (2017). date_created: 2018-12-11T11:49:36Z date_published: 2017-12-06T00:00:00Z date_updated: 2023-10-10T13:31:54Z day: '06' department: - _id: MiLe - _id: RoSe doi: 10.1103/PhysRevLett.119.235301 ec_funded: 1 external_id: arxiv: - '1705.05162' isi: - '000417132100007' intvolume: ' 119' isi: 1 issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.05162 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _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 Letters publication_identifier: issn: - 0031-9007 publication_status: published publisher: American Physical Society publist_id: '6401' quality_controlled: '1' scopus_import: '1' status: public title: Emergence of non-abelian magnetic monopoles in a quantum impurity problem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2017' ... --- _id: '911' abstract: - lang: eng text: We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset. article_processing_charge: No author: - first_name: Amélie full_name: Royer, Amélie id: 3811D890-F248-11E8-B48F-1D18A9856A87 last_name: Royer orcid: 0000-0002-8407-0705 - 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: 'Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:10.5244/c.31.85' apa: 'Royer, A., Kolesnikov, A., & Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. https://doi.org/10.5244/c.31.85' chicago: Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. https://doi.org/10.5244/c.31.85. ieee: 'A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.' ista: 'Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.' mla: Royer, Amélie, et al. Probabilistic Image Colorization. BMVA Press, 2017, p. 85.1-85.12, doi:10.5244/c.31.85. short: A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12. conference: end_date: 2017-09-07 location: London, United Kingdom name: 'BMVC: British Machine Vision Conference' start_date: 2017-09-04 date_created: 2018-12-11T11:49:09Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-10-16T10:04:02Z day: '01' ddc: - '000' department: - _id: ChLa doi: 10.5244/c.31.85 ec_funded: 1 external_id: arxiv: - '1705.04258' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-10T07:14:33Z date_updated: 2020-08-10T07:14:33Z file_id: '8224' file_name: 2017_BMVC_Royer.pdf file_size: 1625363 relation: main_file success: 1 file_date_updated: 2020-08-10T07:14:33Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 85.1-85.12 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: eisbn: - 190172560X publication_status: published publisher: BMVA Press publist_id: '6532' quality_controlled: '1' related_material: record: - id: '8390' relation: dissertation_contains status: public scopus_import: '1' status: public title: Probabilistic image colorization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '627' abstract: - lang: eng text: Beige adipocytes are a new type of recruitable brownish adipocytes, with highly mitochondrial membrane uncoupling protein 1 expression and thermogenesis. Beige adipocytes were found among white adipocytes, especially in subcutaneous white adipose tissue (sWAT). Therefore, beige adipocytes may be involved in the regulation of energy metabolism and fat deposition. Transient receptor potential melastatin 8 (TRPM8), a Ca2+-permeable non-selective cation channel, plays vital roles in the regulation of various cellular functions. It has been reported that TRPM8 activation enhanced the thermogenic function of brown adiposytes. However, the involvement of TRPM8 in the thermogenic function of WAT remains unexplored. Our data revealed that TRPM8 was expressed in mouse white adipocytes at mRNA, protein and functional levels. The mRNA expression of Trpm8 was significantly increased in the differentiated white adipocytes than pre-adipocytes. Moreover, activation of TRPM8 by menthol enhanced the expression of thermogenic genes in cultured white aidpocytes. And menthol-induced increases of the thermogenic genes in white adipocytes was inhibited by either KT5720 (a protein kinase A inhibitor) or BAPTA-AM. In addition, high fat diet (HFD)-induced obesity in mice was significantly recovered by co-treatment with menthol. Dietary menthol enhanced WAT "browning" and improved glucose metabolism in HFD-induced obesity mice as well. Therefore, we concluded that TRPM8 might be involved in WAT "browning" by increasing the expression levels of genes related to thermogenesis and energy metabolism. And dietary menthol could be a novel approach for combating human obesity and related metabolic diseases. article_processing_charge: No author: - first_name: Changyu full_name: Jiang, Changyu last_name: Jiang - first_name: Ming-Zhu full_name: Zhai, Ming-Zhu id: 34009CFA-F248-11E8-B48F-1D18A9856A87 last_name: Zhai - first_name: Dong full_name: Yan, Dong last_name: Yan - first_name: Da full_name: Li, Da last_name: Li - first_name: Chen full_name: Li, Chen last_name: Li - first_name: Yonghong full_name: Zhang, Yonghong last_name: Zhang - first_name: Lizu full_name: Xiao, Lizu last_name: Xiao - first_name: Donglin full_name: Xiong, Donglin last_name: Xiong - first_name: Qiwen full_name: Deng, Qiwen last_name: Deng - first_name: Wuping full_name: Sun, Wuping last_name: Sun citation: ama: Jiang C, Zhai M-Z, Yan D, et al. Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity. Oncotarget. 2017;8(43):75114-75126. doi:10.18632/oncotarget.20540 apa: Jiang, C., Zhai, M.-Z., Yan, D., Li, D., Li, C., Zhang, Y., … Sun, W. (2017). Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.20540 chicago: Jiang, Changyu, Ming-Zhu Zhai, Dong Yan, Da Li, Chen Li, Yonghong Zhang, Lizu Xiao, Donglin Xiong, Qiwen Deng, and Wuping Sun. “Dietary Menthol-Induced TRPM8 Activation Enhances WAT ‘Browning’ and Ameliorates Diet-Induced Obesity.” Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20540. ieee: C. Jiang et al., “Dietary menthol-induced TRPM8 activation enhances WAT ‘browning’ and ameliorates diet-induced obesity,” Oncotarget, vol. 8, no. 43. Impact Journals, pp. 75114–75126, 2017. ista: Jiang C, Zhai M-Z, Yan D, Li D, Li C, Zhang Y, Xiao L, Xiong D, Deng Q, Sun W. 2017. Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity. Oncotarget. 8(43), 75114–75126. mla: Jiang, Changyu, et al. “Dietary Menthol-Induced TRPM8 Activation Enhances WAT ‘Browning’ and Ameliorates Diet-Induced Obesity.” Oncotarget, vol. 8, no. 43, Impact Journals, 2017, pp. 75114–26, doi:10.18632/oncotarget.20540. short: C. Jiang, M.-Z. Zhai, D. Yan, D. Li, C. Li, Y. Zhang, L. Xiao, D. Xiong, Q. Deng, W. Sun, Oncotarget 8 (2017) 75114–75126. date_created: 2018-12-11T11:47:34Z date_published: 2017-08-24T00:00:00Z date_updated: 2023-10-17T08:56:37Z day: '24' ddc: - '571' department: - _id: RySh doi: 10.18632/oncotarget.20540 file: - access_level: open_access checksum: 2219e5348bbfe1aac2725aa620c33280 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:15Z date_updated: 2020-07-14T12:47:26Z file_id: '5201' file_name: IST-2017-907-v1+1_20540-294640-4-PB.pdf file_size: 6101606 relation: main_file file_date_updated: 2020-07-14T12:47:26Z has_accepted_license: '1' intvolume: ' 8' issue: '43' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 75114 - 75126 publication: Oncotarget publication_identifier: issn: - 1949-2553 publication_status: published publisher: Impact Journals publist_id: '7167' pubrep_id: '907' quality_controlled: '1' scopus_import: '1' status: public title: Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '1007' abstract: - lang: eng text: 'A nonlinear system possesses an invariance with respect to a set of transformations if its output dynamics remain invariant when transforming the input, and adjusting the initial condition accordingly. Most research has focused on invariances with respect to time-independent pointwise transformations like translational-invariance (u(t) -> u(t) + p, p in R) or scale-invariance (u(t) -> pu(t), p in R>0). In this article, we introduce the concept of s0-invariances with respect to continuous input transformations exponentially growing/decaying over time. We show that s0-invariant systems not only encompass linear time-invariant (LTI) systems with transfer functions having an irreducible zero at s0 in R, but also that the input/output relationship of nonlinear s0-invariant systems possesses properties well known from their linear counterparts. Furthermore, we extend the concept of s0-invariances to second- and higher-order s0-invariances, corresponding to invariances with respect to transformations of the time-derivatives of the input, and encompassing LTI systems with zeros of multiplicity two or higher. Finally, we show that nth-order 0-invariant systems realize – under mild conditions – nth-order nonlinear differential operators: when excited by an input of a characteristic functional form, the system’s output converges to a constant value only depending on the nth (nonlinear) derivative of the input.' article_processing_charge: Yes (in subscription journal) author: - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Eduardo full_name: Sontag, Eduardo last_name: Sontag citation: ama: Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica. 2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030 apa: Lang, M., & Sontag, E. (2017). Zeros of nonlinear systems with input invariances. Automatica. International Federation of Automatic Control. https://doi.org/10.1016/j.automatica.2017.03.030 chicago: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica. International Federation of Automatic Control, 2017. https://doi.org/10.1016/j.automatica.2017.03.030. ieee: M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,” Automatica, vol. 81C. International Federation of Automatic Control, pp. 46–55, 2017. ista: Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances. Automatica. 81C, 46–55. mla: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica, vol. 81C, International Federation of Automatic Control, 2017, pp. 46–55, doi:10.1016/j.automatica.2017.03.030. short: M. Lang, E. Sontag, Automatica 81C (2017) 46–55. date_created: 2018-12-11T11:49:39Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-10-17T08:51:18Z day: '01' ddc: - '000' department: - _id: CaGu - _id: GaTk doi: 10.1016/j.automatica.2017.03.030 ec_funded: 1 external_id: isi: - '000403513900006' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:11:29Z date_updated: 2018-12-12T10:11:29Z file_id: '4884' file_name: IST-2017-813-v1+1_ZerosOfNonlinearSystems.pdf file_size: 1401954 relation: main_file file_date_updated: 2018-12-12T10:11:29Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 46 - 55 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Automatica publication_identifier: issn: - 0005-1098 publication_status: published publisher: International Federation of Automatic Control publist_id: '6391' pubrep_id: '813' quality_controlled: '1' scopus_import: '1' status: public title: Zeros of nonlinear systems with input invariances 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81C year: '2017' ... --- _id: '1108' abstract: - lang: eng text: In this work we study the learnability of stochastic processes with respect to the conditional risk, i.e. the existence of a learning algorithm that improves its next-step performance with the amount of observed data. We introduce a notion of pairwise discrepancy between conditional distributions at different times steps and show how certain properties of these discrepancies can be used to construct a successful learning algorithm. Our main results are two theorems that establish criteria for learnability for many classes of stochastic processes, including all special cases studied previously in the literature. alternative_title: - PMLR article_processing_charge: No author: - first_name: Alexander full_name: Zimin, Alexander id: 37099E9C-F248-11E8-B48F-1D18A9856A87 last_name: Zimin - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Zimin A, Lampert C. Learning theory for conditional risk minimization. In: Vol 54. ML Research Press; 2017:213-222.' apa: 'Zimin, A., & Lampert, C. (2017). Learning theory for conditional risk minimization (Vol. 54, pp. 213–222). Presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States: ML Research Press.' chicago: Zimin, Alexander, and Christoph Lampert. “Learning Theory for Conditional Risk Minimization,” 54:213–22. ML Research Press, 2017. ieee: 'A. Zimin and C. Lampert, “Learning theory for conditional risk minimization,” presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 213–222.' ista: 'Zimin A, Lampert C. 2017. Learning theory for conditional risk minimization. AISTATS: Artificial Intelligence and Statistics, PMLR, vol. 54, 213–222.' mla: Zimin, Alexander, and Christoph Lampert. Learning Theory for Conditional Risk Minimization. Vol. 54, ML Research Press, 2017, pp. 213–22. short: A. Zimin, C. Lampert, in:, ML Research Press, 2017, pp. 213–222. conference: end_date: 2017-04-22 location: Fort Lauderdale, FL, United States name: 'AISTATS: Artificial Intelligence and Statistics' start_date: 2017-04-20 date_created: 2018-12-11T11:50:11Z date_published: 2017-04-01T00:00:00Z date_updated: 2023-10-17T10:01:12Z day: '01' department: - _id: ChLa ec_funded: 1 external_id: isi: - '000509368500024' intvolume: ' 54' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://proceedings.mlr.press/v54/zimin17a/zimin17a.pdf month: '04' oa: 1 oa_version: Submitted Version page: 213 - 222 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: ML Research Press publist_id: '6261' quality_controlled: '1' status: public title: Learning theory for conditional risk minimization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2017' ... --- _id: '909' abstract: - lang: eng text: We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor ½ cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape. article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Vladislav full_name: Vysotsky, Vladislav last_name: Vysotsky citation: ama: Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 2017;124(7):588-596. doi:10.4169/amer.math.monthly.124.7.588 apa: Akopyan, A., & Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.124.7.588 chicago: Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly. Mathematical Association of America, 2017. https://doi.org/10.4169/amer.math.monthly.124.7.588. ieee: A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” The American Mathematical Monthly, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017. ista: Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596. mla: Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:10.4169/amer.math.monthly.124.7.588. short: A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596. date_created: 2018-12-11T11:49:09Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-10-17T11:24:57Z day: '01' department: - _id: HeEd doi: 10.4169/amer.math.monthly.124.7.588 ec_funded: 1 external_id: arxiv: - '1605.07997' isi: - '000413947300002' intvolume: ' 124' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1605.07997 month: '01' oa: 1 oa_version: Submitted Version page: 588 - 596 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: The American Mathematical Monthly publication_identifier: issn: - '00029890' publication_status: published publisher: Mathematical Association of America publist_id: '6534' quality_controlled: '1' scopus_import: '1' status: public title: On the lengths of curves passing through boundary points of a planar convex shape type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2017' ... --- _id: '431' abstract: - lang: eng text: 'Parallel implementations of stochastic gradient descent (SGD) have received significant research attention, thanks to its excellent scalability properties. A fundamental barrier when parallelizing SGD is the high bandwidth cost of communicating gradient updates between nodes; consequently, several lossy compresion heuristics have been proposed, by which nodes only communicate quantized gradients. Although effective in practice, these heuristics do not always converge. In this paper, we propose Quantized SGD (QSGD), a family of compression schemes with convergence guarantees and good practical performance. QSGD allows the user to smoothly trade off communication bandwidth and convergence time: nodes can adjust the number of bits sent per iteration, at the cost of possibly higher variance. We show that this trade-off is inherent, in the sense that improving it past some threshold would violate information-theoretic lower bounds. QSGD guarantees convergence for convex and non-convex objectives, under asynchrony, and can be extended to stochastic variance-reduced techniques. When applied to training deep neural networks for image classification and automated speech recognition, QSGD leads to significant reductions in end-to-end training time. For instance, on 16GPUs, we can train the ResNet-152 network to full accuracy on ImageNet 1.8 × faster than the full-precision variant. ' alternative_title: - Advances in Neural Information Processing Systems 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: Demjan full_name: Grubic, Demjan last_name: Grubic - first_name: Jerry full_name: Li, Jerry last_name: Li - first_name: Ryota full_name: Tomioka, Ryota last_name: Tomioka - first_name: Milan full_name: Vojnović, Milan last_name: Vojnović citation: ama: 'Alistarh D-A, Grubic D, Li J, Tomioka R, Vojnović M. QSGD: Communication-efficient SGD via gradient quantization and encoding. In: Vol 2017. Neural Information Processing Systems Foundation; 2017:1710-1721.' apa: 'Alistarh, D.-A., Grubic, D., Li, J., Tomioka, R., & Vojnović, M. (2017). QSGD: Communication-efficient SGD via gradient quantization and encoding (Vol. 2017, pp. 1710–1721). Presented at the NIPS: Neural Information Processing System, Long Beach, CA, United States: Neural Information Processing Systems Foundation.' chicago: 'Alistarh, Dan-Adrian, Demjan Grubic, Jerry Li, Ryota Tomioka, and Milan Vojnović. “QSGD: Communication-Efficient SGD via Gradient Quantization and Encoding,” 2017:1710–21. Neural Information Processing Systems Foundation, 2017.' ieee: 'D.-A. Alistarh, D. Grubic, J. Li, R. Tomioka, and M. Vojnović, “QSGD: Communication-efficient SGD via gradient quantization and encoding,” presented at the NIPS: Neural Information Processing System, Long Beach, CA, United States, 2017, vol. 2017, pp. 1710–1721.' ista: 'Alistarh D-A, Grubic D, Li J, Tomioka R, Vojnović M. 2017. QSGD: Communication-efficient SGD via gradient quantization and encoding. NIPS: Neural Information Processing System, Advances in Neural Information Processing Systems, vol. 2017, 1710–1721.' mla: 'Alistarh, Dan-Adrian, et al. QSGD: Communication-Efficient SGD via Gradient Quantization and Encoding. Vol. 2017, Neural Information Processing Systems Foundation, 2017, pp. 1710–21.' short: D.-A. Alistarh, D. Grubic, J. Li, R. Tomioka, M. Vojnović, in:, Neural Information Processing Systems Foundation, 2017, pp. 1710–1721. conference: end_date: 2017-12-09 location: Long Beach, CA, United States name: 'NIPS: Neural Information Processing System' start_date: 2017-12-04 date_created: 2018-12-11T11:46:26Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-10-17T11:48:03Z day: '01' department: - _id: DaAl external_id: arxiv: - '1610.02132' intvolume: ' 2017' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.02132 month: '01' oa: 1 oa_version: Submitted Version page: 1710-1721 publication_identifier: issn: - '10495258' publication_status: published publisher: Neural Information Processing Systems Foundation publist_id: '7392' quality_controlled: '1' status: public title: 'QSGD: Communication-efficient SGD via gradient quantization and encoding' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2017 year: '2017' ... --- _id: '549' abstract: - lang: eng text: Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a new class of model checking algorithms that capture the causal relationships in a special data structure called concurrent traces. Concurrent traces identify key events in an execution history and link them through their cause-effect relationships. The model checker builds a tableau of concurrent traces, where the case splits represent different causal explanations of a hypothetical error. Causality-based model checking has been implemented in the ARCTOR tool, and applied to previously intractable multi-threaded benchmarks. alternative_title: - EPTCS article_processing_charge: No author: - first_name: Bernd full_name: Finkbeiner, Bernd last_name: Finkbeiner - first_name: Andrey full_name: Kupriyanov, Andrey id: 2C311BF8-F248-11E8-B48F-1D18A9856A87 last_name: Kupriyanov citation: ama: 'Finkbeiner B, Kupriyanov A. Causality-based model checking. In: Electronic Proceedings in Theoretical Computer Science. Vol 259. Open Publishing Association; 2017:31-38. doi:10.4204/EPTCS.259.3' apa: 'Finkbeiner, B., & Kupriyanov, A. (2017). Causality-based model checking. In Electronic Proceedings in Theoretical Computer Science (Vol. 259, pp. 31–38). Uppsala, Sweden: Open Publishing Association. https://doi.org/10.4204/EPTCS.259.3' chicago: Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” In Electronic Proceedings in Theoretical Computer Science, 259:31–38. Open Publishing Association, 2017. https://doi.org/10.4204/EPTCS.259.3. ieee: B. Finkbeiner and A. Kupriyanov, “Causality-based model checking,” in Electronic Proceedings in Theoretical Computer Science, Uppsala, Sweden, 2017, vol. 259, pp. 31–38. ista: 'Finkbeiner B, Kupriyanov A. 2017. Causality-based model checking. Electronic Proceedings in Theoretical Computer Science. CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies, EPTCS, vol. 259, 31–38.' mla: Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” Electronic Proceedings in Theoretical Computer Science, vol. 259, Open Publishing Association, 2017, pp. 31–38, doi:10.4204/EPTCS.259.3. short: B. Finkbeiner, A. Kupriyanov, in:, Electronic Proceedings in Theoretical Computer Science, Open Publishing Association, 2017, pp. 31–38. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies' start_date: 2017-04-29 date_created: 2018-12-11T11:47:07Z date_published: 2017-10-10T00:00:00Z date_updated: 2023-10-17T12:02:46Z day: '10' ddc: - '004' department: - _id: ToHe doi: 10.4204/EPTCS.259.3 file: - access_level: open_access checksum: 6274f6c0da3376a7b079180d81568518 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:21Z date_updated: 2020-07-14T12:47:00Z file_id: '4939' file_name: IST-2018-925-v1+1_1710.03391v1.pdf file_size: 209294 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 259' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1710.03391v1 month: '10' oa: 1 oa_version: Submitted Version page: 31 - 38 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: Electronic Proceedings in Theoretical Computer Science publication_identifier: issn: - 2075-2180 publication_status: published publisher: Open Publishing Association publist_id: '7264' pubrep_id: '925' quality_controlled: '1' scopus_import: '1' status: public title: Causality-based model checking type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 259 year: '2017' ... --- _id: '999' abstract: - lang: eng text: 'In multi-task learning, a learner is given a collection of prediction tasks and needs to solve all of them. In contrast to previous work, which required that annotated training data must be available for all tasks, we consider a new setting, in which for some tasks, potentially most of them, only unlabeled training data is provided. Consequently, to solve all tasks, information must be transferred between tasks with labels and tasks without labels. Focusing on an instance-based transfer method we analyze two variants of this setting: when the set of labeled tasks is fixed, and when it can be actively selected by the learner. We state and prove a generalization bound that covers both scenarios and derive from it an algorithm for making the choice of labeled tasks (in the active case) and for transferring information between the tasks in a principled way. We also illustrate the effectiveness of the algorithm on synthetic and real data. ' alternative_title: - PMLR article_processing_charge: No author: - first_name: Anastasia full_name: Pentina, Anastasia id: 42E87FC6-F248-11E8-B48F-1D18A9856A87 last_name: Pentina - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Pentina A, Lampert C. Multi-task learning with labeled and unlabeled tasks. In: Vol 70. ML Research Press; 2017:2807-2816.' apa: 'Pentina, A., & Lampert, C. (2017). Multi-task learning with labeled and unlabeled tasks (Vol. 70, pp. 2807–2816). Presented at the ICML: International Conference on Machine Learning, Sydney, Australia: ML Research Press.' chicago: Pentina, Anastasia, and Christoph Lampert. “Multi-Task Learning with Labeled and Unlabeled Tasks,” 70:2807–16. ML Research Press, 2017. ieee: 'A. Pentina and C. Lampert, “Multi-task learning with labeled and unlabeled tasks,” presented at the ICML: International Conference on Machine Learning, Sydney, Australia, 2017, vol. 70, pp. 2807–2816.' ista: 'Pentina A, Lampert C. 2017. Multi-task learning with labeled and unlabeled tasks. ICML: International Conference on Machine Learning, PMLR, vol. 70, 2807–2816.' mla: Pentina, Anastasia, and Christoph Lampert. Multi-Task Learning with Labeled and Unlabeled Tasks. Vol. 70, ML Research Press, 2017, pp. 2807–16. short: A. Pentina, C. Lampert, in:, ML Research Press, 2017, pp. 2807–2816. 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: 2017-06-08T00:00:00Z date_updated: 2023-10-17T11:53:32Z day: '08' department: - _id: ChLa ec_funded: 1 external_id: isi: - '000683309502093' intvolume: ' 70' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.06518 month: '06' oa: 1 oa_version: Submitted Version page: 2807 - 2816 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: isbn: - '9781510855144' publication_status: published publisher: ML Research Press publist_id: '6399' quality_controlled: '1' scopus_import: '1' status: public title: Multi-task learning with labeled and unlabeled tasks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '459' abstract: - lang: eng text: The social insects bees, wasps, ants, and termites are species-rich, occur in many habitats, and often constitute a large part of the biomass. Many are also invasive, including species of termites, the red imported fire ant, and the Argentine ant. While invasive social insects have been a problem in Southern Europe for some time, Central Europa was free of invasive ant species until recently because most ants are adapted to warmer climates. Only in the 1990s, did Lasius neglectus, a close relative of the common black garden ant, arrive in Germany. First described in 1990 based on individuals collected in Budapest, the species has since been detected for example in France, Germany, Spain, England, and Kyrgyzstan. The species is spread with soil during construction work or plantings, and L. neglectus therefore is often found in parks and botanical gardens. Another invasive ant now spreading in southern Germany is Formica fuscocinerea, which occurs along rivers, including in the sandy floodplains of the river Isar. As is typical of pioneer species, F. fuscocinerea quickly becomes extremely abundant and therefore causes problems for example on playgrounds in Munich. All invasive ant species are characterized by cooperation across nests, leading to strongly interconnected, very large super-colonies. The resulting dominance results in the extinction of native ant species as well as other arthropod species and thus in the reduction of biodiversity. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Cremer S. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. 2017;46:105-116.' apa: 'Cremer, S. (2017). Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. Verlag Dr. Friedrich Pfeil.' chicago: 'Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” Rundgespräche Forum Ökologie. Verlag Dr. Friedrich Pfeil, 2017.' ieee: 'S. Cremer, “Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern,” Rundgespräche Forum Ökologie, vol. 46. Verlag Dr. Friedrich Pfeil, pp. 105–116, 2017.' ista: 'Cremer S. 2017. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. 46, 105–116.' mla: 'Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” Rundgespräche Forum Ökologie, vol. 46, Verlag Dr. Friedrich Pfeil, 2017, pp. 105–16.' short: S. Cremer, Rundgespräche Forum Ökologie 46 (2017) 105–116. date_created: 2018-12-11T11:46:35Z date_published: 2017-04-04T00:00:00Z date_updated: 2023-10-17T12:28:13Z day: '04' ddc: - '592' department: - _id: SyCr file: - access_level: open_access checksum: 4919baf9050415ca151fe22497379f78 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:52Z date_updated: 2020-07-14T12:46:32Z file_id: '5175' file_name: IST-2018-962-v1+1_044676698_07_Cremer__Invasive_Ameisen_in_Europa_...__BY-ND_.pdf file_size: 1711131 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 46' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '04' oa: 1 oa_version: Published Version page: 105 - 116 publication: Rundgespräche Forum Ökologie publication_identifier: issn: - 2366-2875 publication_status: published publisher: Verlag Dr. Friedrich Pfeil publist_id: '7362' pubrep_id: '962' quality_controlled: '1' status: public title: 'Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern' tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2017' ... --- _id: '432' abstract: - lang: eng text: 'Recently there has been significant interest in training machine-learning models at low precision: by reducing precision, one can reduce computation and communication by one order of magnitude. We examine training at reduced precision, both from a theoretical and practical perspective, and ask: is it possible to train models at end-to-end low precision with provable guarantees? Can this lead to consistent order-of-magnitude speedups? We mainly focus on linear models, and the answer is yes for linear models. We develop a simple framework called ZipML based on one simple but novel strategy called double sampling. Our ZipML framework is able to execute training at low precision with no bias, guaranteeing convergence, whereas naive quanti- zation would introduce significant bias. We val- idate our framework across a range of applica- tions, and show that it enables an FPGA proto- type that is up to 6.5 × faster than an implemen- tation using full 32-bit precision. We further de- velop a variance-optimal stochastic quantization strategy and show that it can make a significant difference in a variety of settings. When applied to linear models together with double sampling, we save up to another 1.7 × in data movement compared with uniform quantization. When training deep networks with quantized models, we achieve higher accuracy than the state-of-the- art XNOR-Net. ' alternative_title: - PMLR Press article_processing_charge: No author: - first_name: Hantian full_name: Zhang, Hantian last_name: Zhang - first_name: Jerry full_name: Li, Jerry last_name: Li - first_name: Kaan full_name: Kara, Kaan last_name: Kara - 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: Ji full_name: Liu, Ji last_name: Liu - first_name: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Zhang H, Li J, Kara K, Alistarh D-A, Liu J, Zhang C. ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning. In: Proceedings of Machine Learning Research. Vol 70. ML Research Press; 2017:4035-4043.' apa: 'Zhang, H., Li, J., Kara, K., Alistarh, D.-A., Liu, J., & Zhang, C. (2017). ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning. In Proceedings of Machine Learning Research (Vol. 70, pp. 4035–4043). Sydney, Australia: ML Research Press.' chicago: 'Zhang, Hantian, Jerry Li, Kaan Kara, Dan-Adrian Alistarh, Ji Liu, and Ce Zhang. “ZipML: Training Linear Models with End-to-End Low Precision, and a Little Bit of Deep Learning.” In Proceedings of Machine Learning Research, 70:4035–43. ML Research Press, 2017.' ieee: 'H. Zhang, J. Li, K. Kara, D.-A. Alistarh, J. Liu, and C. Zhang, “ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning,” in Proceedings of Machine Learning Research, Sydney, Australia, 2017, vol. 70, pp. 4035–4043.' ista: 'Zhang H, Li J, Kara K, Alistarh D-A, Liu J, Zhang C. 2017. ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning. Proceedings of Machine Learning Research. ICML: International  Conference  on  Machine Learning, PMLR Press, vol. 70, 4035–4043.' mla: 'Zhang, Hantian, et al. “ZipML: Training Linear Models with End-to-End Low Precision, and a Little Bit of Deep Learning.” Proceedings of Machine Learning Research, vol. 70, ML Research Press, 2017, pp. 4035–43.' short: H. Zhang, J. Li, K. Kara, D.-A. Alistarh, J. Liu, C. Zhang, in:, Proceedings of Machine Learning Research, ML Research Press, 2017, pp. 4035–4043. conference: end_date: 2017-08-11 location: Sydney, Australia name: 'ICML: International Conference on Machine Learning' start_date: 2017-08-06 date_created: 2018-12-11T11:46:26Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-10-17T12:31:15Z day: '01' ddc: - '000' department: - _id: DaAl file: - access_level: open_access checksum: 86156ba7f4318e47cef3eb9092593c10 content_type: application/pdf creator: dernst date_created: 2019-01-22T08:23:58Z date_updated: 2020-07-14T12:46:26Z file_id: '5869' file_name: 2017_ICML_Zhang.pdf file_size: 849345 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 4035 - 4043 publication: Proceedings of Machine Learning Research publication_identifier: isbn: - 978-151085514-4 publication_status: published publisher: ML Research Press publist_id: '7391' quality_controlled: '1' scopus_import: '1' status: public title: 'ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: ' 70' year: '2017' ... --- _id: '274' abstract: - lang: eng text: We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation. article_processing_charge: No author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: Proceedings of the 31st Conference On Learning Theory. Vol 75. ML Research Press; 2017:228-249.' apa: Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In Proceedings of the 31st Conference On Learning Theory (Vol. 75, pp. 228–249). ML Research Press. chicago: Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In Proceedings of the 31st Conference On Learning Theory, 75:228–49. ML Research Press, 2017. ieee: V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in Proceedings of the 31st Conference On Learning Theory, 2017, vol. 75, pp. 228–249. ista: 'Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory vol. 75, 228–249.' mla: Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” Proceedings of the 31st Conference On Learning Theory, vol. 75, ML Research Press, 2017, pp. 228–49. short: V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249. conference: end_date: 2018-07-09 name: 'COLT: Annual Conference on Learning Theory ' start_date: 2018-07-06 date_created: 2018-12-11T11:45:33Z date_published: 2017-12-27T00:00:00Z date_updated: 2023-10-17T12:32:13Z day: '27' ddc: - '510' department: - _id: VlKo ec_funded: 1 external_id: arxiv: - '1608.04223' file: - access_level: open_access checksum: 89db06a0e8083524449cb59b56bf4e5b content_type: application/pdf creator: dernst date_created: 2020-05-12T09:23:27Z date_updated: 2020-07-14T12:45:45Z file_id: '7820' file_name: 2018_PMLR_Kolmogorov.pdf file_size: 408974 relation: main_file file_date_updated: 2020-07-14T12:45:45Z has_accepted_license: '1' intvolume: ' 75' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 228-249 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Proceedings of the 31st Conference On Learning Theory publication_status: published publisher: ML Research Press publist_id: '7628' quality_controlled: '1' status: public title: A faster approximation algorithm for the Gibbs partition function 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 75 year: '2017' ... --- _id: '1030' abstract: - lang: ger text: Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die Bibliothek auf eine erfolgreiche Implementierung zurückblicken. - lang: eng text: "IST Austria was looking for a new library system until 2014 when the research institute decided\r\nto implement Koha. The library first activated basic functions of the open-source product and\r\nthen brought additional tools into operation. The high flexibility of the system allows customized\r\nsolutions for different institutions. Although the library faced some challenges, it can now look\r\nback on a successful implementation." article_processing_charge: No article_type: original author: - first_name: Márton full_name: Villányi, Márton id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87 last_name: Villányi orcid: 0000-0001-8126-0426 citation: ama: Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 2017;3(1). doi:10.11588/ip.2017.1.35227 apa: Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. Verein Informationspraxis . https://doi.org/10.11588/ip.2017.1.35227 chicago: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis. Verein Informationspraxis , 2017. https://doi.org/10.11588/ip.2017.1.35227. ieee: M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library,” Informationspraxis, vol. 3, no. 1. Verein Informationspraxis , 2017. ista: Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 3(1). mla: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis, vol. 3, no. 1, Verein Informationspraxis , 2017, doi:10.11588/ip.2017.1.35227. short: M. Villányi, Informationspraxis 3 (2017). date_created: 2018-12-11T11:49:46Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-10-18T07:49:29Z day: '01' ddc: - '020' department: - _id: E-Lib doi: 10.11588/ip.2017.1.35227 file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:08:20Z date_updated: 2018-12-12T10:08:20Z file_id: '4680' file_name: IST-2017-799-v1+1_35227-112025-1-PB.pdf file_size: 201163 relation: main_file file_date_updated: 2018-12-12T10:08:20Z has_accepted_license: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version popular_science: '1' publication: Informationspraxis publication_identifier: issn: - 2297-3249 publication_status: published publisher: 'Verein Informationspraxis ' publist_id: '6360' pubrep_id: '799' status: public title: Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2017' ... --- _id: '12193' abstract: - lang: eng text: DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants. acknowledgement: We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W. article_processing_charge: No article_type: original author: - first_name: James full_name: Walker, James last_name: Walker - first_name: Hongbo full_name: Gao, Hongbo last_name: Gao - first_name: Jingyi full_name: Zhang, Jingyi last_name: Zhang - first_name: Billy full_name: Aldridge, Billy last_name: Aldridge - first_name: Martin full_name: Vickers, Martin last_name: Vickers - first_name: James D. full_name: Higgins, James D. last_name: Higgins - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5 apa: Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., & Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5 chicago: Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5. ieee: J. Walker et al., “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research, pp. 130–137, 2017. ista: Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137. mla: Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:10.1038/s41588-017-0008-5. short: J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137. date_created: 2023-01-16T09:18:05Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-10-18T07:21:53Z day: '18' department: - _id: XiFe doi: 10.1038/s41588-017-0008-5 external_id: pmid: - '29255257' intvolume: ' 50' issue: '1' keyword: - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/ month: '12' oa: 1 oa_version: None page: 130-137 pmid: 1 publication: Nature Genetics publication_identifier: eissn: - 1546-1718 issn: - 1061-4036 publication_status: published publisher: Nature Research quality_controlled: '1' scopus_import: '1' status: public title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2017' ... --- _id: '1194' abstract: - lang: eng text: 'Termination is one of the basic liveness properties, and we study the termination problem for probabilistic programs with real-valued variables. Previous works focused on the qualitative problem that asks whether an input program terminates with probability~1 (almost-sure termination). A powerful approach for this qualitative problem is the notion of ranking supermartingales with respect to a given set of invariants. The quantitative problem (probabilistic termination) asks for bounds on the termination probability. A fundamental and conceptual drawback of the existing approaches to address probabilistic termination is that even though the supermartingales consider the probabilistic behavior of the programs, the invariants are obtained completely ignoring the probabilistic aspect. In this work we address the probabilistic termination problem for linear-arithmetic probabilistic programs with nondeterminism. We define the notion of {\em stochastic invariants}, which are constraints along with a probability bound that the constraints hold. We introduce a concept of {\em repulsing supermartingales}. First, we show that repulsing supermartingales can be used to obtain bounds on the probability of the stochastic invariants. Second, we show the effectiveness of repulsing supermartingales in the following three ways: (1)~With a combination of ranking and repulsing supermartingales we can compute lower bounds on the probability of termination; (2)~repulsing supermartingales provide witnesses for refutation of almost-sure termination; and (3)~with a combination of ranking and repulsing supermartingales we can establish persistence properties of probabilistic programs. We also present results on related computational problems and an experimental evaluation of our approach on academic examples. ' alternative_title: - ACM SIGPLAN Notices 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: Djordje full_name: Zikelic, Djordje last_name: Zikelic citation: ama: 'Chatterjee K, Novotný P, Zikelic D. Stochastic invariants for probabilistic termination. In: Vol 52. ACM; 2017:145-160. doi:10.1145/3009837.3009873' apa: 'Chatterjee, K., Novotný, P., & Zikelic, D. (2017). Stochastic invariants for probabilistic termination (Vol. 52, pp. 145–160). Presented at the POPL: Principles of Programming Languages, Paris, France: ACM. https://doi.org/10.1145/3009837.3009873' chicago: Chatterjee, Krishnendu, Petr Novotný, and Djordje Zikelic. “Stochastic Invariants for Probabilistic Termination,” 52:145–60. ACM, 2017. https://doi.org/10.1145/3009837.3009873. ieee: 'K. Chatterjee, P. Novotný, and D. Zikelic, “Stochastic invariants for probabilistic termination,” presented at the POPL: Principles of Programming Languages, Paris, France, 2017, vol. 52, no. 1, pp. 145–160.' ista: 'Chatterjee K, Novotný P, Zikelic D. 2017. Stochastic invariants for probabilistic termination. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 52, 145–160.' mla: Chatterjee, Krishnendu, et al. Stochastic Invariants for Probabilistic Termination. Vol. 52, no. 1, ACM, 2017, pp. 145–60, doi:10.1145/3009837.3009873. short: K. Chatterjee, P. Novotný, D. Zikelic, in:, ACM, 2017, pp. 145–160. conference: end_date: 2017-01-21 location: Paris, France name: 'POPL: Principles of Programming Languages' start_date: 2017-01-15 date_created: 2018-12-11T11:50:39Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-11-30T10:55:36Z day: '01' department: - _id: KrCh doi: 10.1145/3009837.3009873 ec_funded: 1 external_id: isi: - '000408311200013' intvolume: ' 52' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.01063 month: '01' oa: 1 oa_version: Submitted Version page: 145 - 160 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _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 publication_identifier: issn: - '07308566' publication_status: published publisher: ACM publist_id: '6157' quality_controlled: '1' related_material: record: - id: '14539' relation: dissertation_contains status: public scopus_import: '1' status: public title: Stochastic invariants for probabilistic termination type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 52 year: '2017' ... --- _id: '545' abstract: - lang: eng text: Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis. alternative_title: - Agricultural and Biological Sciences author: - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Mazur E, Friml J. Vascular tissue development and regeneration in the model plant arabidopsis. In: Jurić S, ed. Plant Engineering. Plant Engineering. InTech; 2017:113-140. doi:10.5772/intechopen.69712' apa: Mazur, E., & Friml, J. (2017). Vascular tissue development and regeneration in the model plant arabidopsis. In S. Jurić (Ed.), Plant Engineering (pp. 113–140). InTech. https://doi.org/10.5772/intechopen.69712 chicago: Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” In Plant Engineering, edited by Snježana Jurić, 113–40. Plant Engineering. InTech, 2017. https://doi.org/10.5772/intechopen.69712. ieee: E. Mazur and J. Friml, “Vascular tissue development and regeneration in the model plant arabidopsis,” in Plant Engineering, S. Jurić, Ed. InTech, 2017, pp. 113–140. ista: 'Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences, , 113–140.' mla: Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” Plant Engineering, edited by Snježana Jurić, InTech, 2017, pp. 113–40, doi:10.5772/intechopen.69712. short: E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, InTech, 2017, pp. 113–140. date_created: 2018-12-11T11:47:05Z date_published: 2017-11-17T00:00:00Z date_updated: 2024-02-12T12:03:42Z day: '17' ddc: - '581' department: - _id: JiFr doi: 10.5772/intechopen.69712 ec_funded: 1 editor: - first_name: Snježana full_name: Jurić, Snježana last_name: Jurić file: - access_level: open_access checksum: e1f05e5850dfd9f9434d2d373ca61941 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:49Z date_updated: 2020-07-14T12:46:58Z file_id: '4969' file_name: IST-2018-929-v1+1_56106.pdf file_size: 7443683 relation: main_file file_date_updated: 2020-07-14T12:46:58Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 113 - 140 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant Engineering publication_status: published publisher: InTech publist_id: '7269' pubrep_id: '929' quality_controlled: '1' related_material: record: - id: '1274' relation: earlier_version status: public series_title: Plant Engineering status: public title: Vascular tissue development and regeneration in the model plant arabidopsis 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: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '621' abstract: - lang: eng text: The mammalian cerebral cortex is responsible for higher cognitive functions such as perception, consciousness, and acquiring and processing information. The neocortex is organized into six distinct laminae, each composed of a rich diversity of cell types which assemble into highly complex cortical circuits. Radial glia progenitors (RGPs) are responsible for producing all neocortical neurons and certain glia lineages. Here, we discuss recent discoveries emerging from clonal lineage analysis at the single RGP cell level that provide us with an inaugural quantitative framework of RGP lineage progression. We further discuss the importance of the relative contribution of intrinsic gene functions and non-cell-autonomous or community effects in regulating RGP proliferation behavior and lineage progression. article_processing_charge: Yes (in subscription journal) author: - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Beattie RJ, Hippenmeyer S. Mechanisms of radial glia progenitor cell lineage progression. FEBS letters. 2017;591(24):3993-4008. doi:10.1002/1873-3468.12906 apa: Beattie, R. J., & Hippenmeyer, S. (2017). Mechanisms of radial glia progenitor cell lineage progression. FEBS Letters. Wiley-Blackwell. https://doi.org/10.1002/1873-3468.12906 chicago: Beattie, Robert J, and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor Cell Lineage Progression.” FEBS Letters. Wiley-Blackwell, 2017. https://doi.org/10.1002/1873-3468.12906. ieee: R. J. Beattie and S. Hippenmeyer, “Mechanisms of radial glia progenitor cell lineage progression,” FEBS letters, vol. 591, no. 24. Wiley-Blackwell, pp. 3993–4008, 2017. ista: Beattie RJ, Hippenmeyer S. 2017. Mechanisms of radial glia progenitor cell lineage progression. FEBS letters. 591(24), 3993–4008. mla: Beattie, Robert J., and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor Cell Lineage Progression.” FEBS Letters, vol. 591, no. 24, Wiley-Blackwell, 2017, pp. 3993–4008, doi:10.1002/1873-3468.12906. short: R.J. Beattie, S. Hippenmeyer, FEBS Letters 591 (2017) 3993–4008. date_created: 2018-12-11T11:47:32Z date_published: 2017-12-01T00:00:00Z date_updated: 2024-02-14T12:02:08Z day: '01' ddc: - '571' - '610' department: - _id: SiHi doi: 10.1002/1873-3468.12906 ec_funded: 1 external_id: pmid: - '29121403' file: - access_level: open_access checksum: a46dadc84e0c28d389dd3e9e954464db content_type: application/pdf creator: system date_created: 2018-12-12T10:16:24Z date_updated: 2020-07-14T12:47:24Z file_id: '5211' file_name: IST-2018-928-v1+1_Beattie_et_al-2017-FEBS_Letters.pdf file_size: 644149 relation: main_file file_date_updated: 2020-07-14T12:47:24Z has_accepted_license: '1' intvolume: ' 591' issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 3993 - 4008 pmid: 1 project: - _id: 25D7962E-B435-11E9-9278-68D0E5697425 grant_number: RGP0053/2014 name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development publication: FEBS letters publication_identifier: issn: - '00145793' publication_status: published publisher: Wiley-Blackwell publist_id: '7183' pubrep_id: '928' quality_controlled: '1' scopus_import: '1' status: public title: Mechanisms of radial glia progenitor cell lineage progression 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 591 year: '2017' ... --- _id: '5562' abstract: - lang: eng text: "This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408." article_processing_charge: No author: - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Dario full_name: Amodei, Dario last_name: Amodei - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61 apa: Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:61 chicago: Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61. ieee: O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017. ista: Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:61. mla: Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61. short: O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017). datarep_id: '61' date_created: 2018-12-12T12:31:33Z date_published: 2017-02-27T00:00:00Z date_updated: 2024-02-21T13:46:14Z day: '27' ddc: - '570' department: - _id: GaTk doi: 10.15479/AT:ISTA:61 file: - access_level: open_access checksum: e620eff260646f57b479a69492c8b765 content_type: application/octet-stream creator: system date_created: 2018-12-12T13:03:04Z date_updated: 2020-07-14T12:47:03Z file_id: '5622' file_name: IST-2017-61-v1+1_bint_fishmovie32_100.mat file_size: 1336936 relation: main_file - access_level: open_access checksum: de83f9b81ea0aae3cddfc3ed982e0759 content_type: application/zip creator: system date_created: 2018-12-12T13:03:05Z date_updated: 2020-07-14T12:47:03Z file_id: '5623' file_name: IST-2017-61-v1+2_bint_fishmovie32_100.zip file_size: 1897543 relation: main_file file_date_updated: 2020-07-14T12:47:03Z has_accepted_license: '1' keyword: - multi-electrode recording - retinal ganglion cells month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '2257' relation: research_paper status: public status: public title: Multi-electrode array recording from salamander retinal ganglion cells tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '5561' abstract: - lang: eng text: 'Graph matching problems as described in "Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans." by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in "Feature Correspondence via Graph Matching: Models and Global Optimization." by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. ' acknowledgement: We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions. article_processing_charge: No author: - first_name: Dagmar full_name: Kainmueller, Dagmar last_name: Kainmueller - first_name: Florian full_name: Jug, Florian last_name: Jug - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Gene full_name: Meyers, Gene last_name: Meyers citation: ama: Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating C. Elegans. 2017. doi:10.15479/AT:ISTA:57 apa: Kainmueller, D., Jug, F., Rother, C., & Meyers, G. (2017). Graph matching problems for annotating C. Elegans. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:57 chicago: Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph Matching Problems for Annotating C. Elegans.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:57. ieee: D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems for annotating C. Elegans.” Institute of Science and Technology Austria, 2017. ista: Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for annotating C. Elegans, Institute of Science and Technology Austria, 10.15479/AT:ISTA:57. mla: Kainmueller, Dagmar, et al. Graph Matching Problems for Annotating C. Elegans. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:57. short: D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017). datarep_id: '57' date_created: 2018-12-12T12:31:32Z date_published: 2017-02-13T00:00:00Z date_updated: 2024-02-21T13:46:31Z day: '13' ddc: - '000' department: - _id: VlKo doi: 10.15479/AT:ISTA:57 file: - access_level: open_access checksum: 3dc3e1306a66028a34181ebef2923139 content_type: application/zip creator: system date_created: 2018-12-12T13:02:54Z date_updated: 2020-07-14T12:47:03Z file_id: '5614' file_name: IST-2017-57-v1+1_wormMatchingProblems.zip file_size: 327042819 relation: main_file file_date_updated: 2020-07-14T12:47:03Z has_accepted_license: '1' keyword: - graph matching - feature matching - QAP - MAP-inference month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: Graph matching problems for annotating C. Elegans tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '5563' abstract: - lang: eng text: "MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions" article_processing_charge: No author: - first_name: Martin full_name: Lukacisin, Martin id: 298FFE8C-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisin orcid: 0000-0001-6549-4177 citation: ama: Lukacisin M. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2017. doi:10.15479/AT:ISTA:64 apa: Lukacisin, M. (2017). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:64 chicago: Lukacisin, Martin. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:64. ieee: M. Lukacisin, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017. ista: Lukacisin M. 2017. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:64. mla: Lukacisin, Martin. MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:64. short: M. Lukacisin, (2017). datarep_id: '64' date_created: 2018-12-12T12:31:33Z date_published: 2017-03-20T00:00:00Z date_updated: 2024-02-21T13:46:47Z day: '20' ddc: - '571' department: - _id: ToBo doi: 10.15479/AT:ISTA:64 file: - access_level: open_access checksum: ee697f2b1ade4dc14d6ac0334dd832ab content_type: application/zip creator: system date_created: 2018-12-12T13:02:37Z date_updated: 2020-07-14T12:47:03Z file_id: '5602' file_name: IST-2016-45-v1+1_PaperCode.zip file_size: 296722548 relation: main_file file_date_updated: 2020-07-14T12:47:03Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '839' abstract: - lang: eng text: 'This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material''s toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. ' acknowledgement: "ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all, let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for supporting me throughout my PhD. Obviously, none of this work would\r\nhave been possible without you.\r\nFurthermore, Thank You to all the people who have contributed to this work in various\r\nways, in particular Martin Schanz and his group for providing and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel, and all the members – past and present – of his\r\nand Chris’ research groups at IST Austria for always providing honest and insightful\r\nfeedback throughout many joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs only virtual objects have been harmed in the process of creating this work, I would\r\nlike to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo” models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different ways.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Hahn, David id: 357A6A66-F248-11E8-B48F-1D18A9856A87 last_name: Hahn citation: ama: Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:10.15479/AT:ISTA:th_855 apa: Hahn, D. (2017). Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_855 chicago: Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_855. ieee: D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017. ista: Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. mla: Hahn, David. Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_855. short: D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:47Z date_published: 2017-08-14T00:00:00Z date_updated: 2024-02-21T13:48:02Z day: '14' ddc: - '004' - '005' - '006' - '531' - '621' degree_awarded: PhD department: - _id: ChWo doi: 10.15479/AT:ISTA:th_855 ec_funded: 1 file: - access_level: open_access checksum: 6c1ae8c90bfaba5e089417fefbc4a272 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:46Z date_updated: 2020-07-14T12:48:13Z file_id: '5100' file_name: IST-2017-855-v1+1_thesis_online_pdfA.pdf file_size: 14596191 relation: main_file - access_level: closed checksum: 421672f68d563b029869c5cf1713f919 content_type: application/zip creator: dernst date_created: 2019-04-05T08:40:30Z date_updated: 2020-07-14T12:48:13Z file_id: '6207' file_name: 2017_thesis_Hahn_source.zip file_size: 15060566 relation: source_file file_date_updated: 2020-07-14T12:48:13Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '124' project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6809' pubrep_id: '855' related_material: record: - id: '1362' relation: part_of_dissertation status: public - id: '1633' relation: part_of_dissertation status: public - id: '5568' relation: popular_science status: public status: public supervisor: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 title: Brittle fracture simulation with boundary elements for computer graphics tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '614' abstract: - lang: eng text: 'Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.' article_number: '1486' article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Marion A full_name: Picard, Marion A id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01663-5 apa: Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5 chicago: Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5. ieee: C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486. mla: Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5. short: C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:30Z date_published: 2017-12-01T00:00:00Z date_updated: 2024-02-21T13:47:47Z day: '01' ddc: - '570' - '576' department: - _id: BeVi - _id: NiBa doi: 10.1038/s41467-017-01663-5 external_id: pmid: - '29133797' file: - access_level: open_access checksum: 4da2651303c8afc2f7fc419be42a2433 content_type: application/pdf creator: dernst date_created: 2020-03-03T15:55:50Z date_updated: 2020-07-14T12:47:20Z file_id: '7562' file_name: 2017_NatureComm_Fraisse.pdf file_size: 1201520 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7190' pubrep_id: '910' quality_controlled: '1' related_material: record: - id: '7163' relation: popular_science status: public scopus_import: 1 status: public title: The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '5564' abstract: - lang: eng text: Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication. article_processing_charge: No author: - first_name: Magdalena full_name: Steinrück, Magdalena id: 2C023F40-F248-11E8-B48F-1D18A9856A87 last_name: Steinrück orcid: 0000-0003-1229-9719 - 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: Steinrück M, Guet CC. Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” 2017. doi:10.15479/AT:ISTA:65 apa: Steinrück, M., & Guet, C. C. (2017). Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:65 chicago: Steinrück, Magdalena, and Calin C Guet. “Fastq Files for ‘Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:65. ieee: M. Steinrück and C. C. Guet, “Fastq files for ‘Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.’” Institute of Science and Technology Austria, 2017. ista: Steinrück M, Guet CC. 2017. Fastq files for ‘Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:65. mla: Steinrück, Magdalena, and Calin C. Guet. Fastq Files for “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:65. short: M. Steinrück, C.C. Guet, (2017). datarep_id: '65' date_created: 2018-12-12T12:31:33Z date_published: 2017-04-11T00:00:00Z date_updated: 2024-02-21T13:47:28Z day: '11' ddc: - '576' department: - _id: CaGu doi: 10.15479/AT:ISTA:65 file: - access_level: open_access checksum: 31a0c01d022721073241a23d192cc37e content_type: application/zip creator: system date_created: 2018-12-12T13:03:18Z date_updated: 2020-07-14T12:47:03Z file_id: '5627' file_name: IST-2017-65-v1+1_D_anc_1.fastq.zip file_size: 1225959109 relation: main_file - access_level: open_access checksum: d8f26f83ce7e7e45436121f9c6cd9b83 content_type: application/zip creator: system date_created: 2018-12-12T13:03:30Z date_updated: 2020-07-14T12:47:03Z file_id: '5628' file_name: IST-2017-65-v1+1_D_anc_2.fastq.zip file_size: 1422656107 relation: main_file - access_level: open_access checksum: e07b99bcfe55b5f132ca03b8b48c8cbc content_type: application/zip creator: system date_created: 2018-12-12T13:03:33Z date_updated: 2020-07-14T12:47:03Z file_id: '5629' file_name: IST-2017-65-v1+2_D_A11_1.fastq.zip file_size: 565014975 relation: main_file - access_level: open_access checksum: eda86143d5f32d844b54f8530041e32b content_type: application/zip creator: system date_created: 2018-12-12T13:03:42Z date_updated: 2020-07-14T12:47:03Z file_id: '5630' file_name: IST-2017-65-v1+3_D_A11_2.fastq.zip file_size: 564490030 relation: main_file - access_level: open_access checksum: 906d44f950c1626d9b99f34fbf89cb12 content_type: application/zip creator: system date_created: 2018-12-12T13:03:46Z date_updated: 2020-07-14T12:47:03Z file_id: '5631' file_name: IST-2017-65-v1+4_D_C10_1.fastq.zip file_size: 875430169 relation: main_file - access_level: open_access checksum: 6ca14a032a79e0c787106bdf635725c9 content_type: application/zip creator: system date_created: 2018-12-12T13:03:54Z date_updated: 2020-07-14T12:47:03Z file_id: '5632' file_name: IST-2017-65-v1+6_D_C08_2.fastq.zip file_size: 638298201 relation: main_file - access_level: open_access checksum: 66ab16ddb5ba64b2e263ef746ebf2893 content_type: application/zip creator: system date_created: 2018-12-12T13:04:01Z date_updated: 2020-07-14T12:47:03Z file_id: '5633' file_name: IST-2017-65-v1+5_D_C10_2.fastq.zip file_size: 894702866 relation: main_file - access_level: open_access checksum: 82607970174f8d37773b7d3acc712195 content_type: application/zip creator: system date_created: 2018-12-12T13:04:07Z date_updated: 2020-07-14T12:47:03Z file_id: '5634' file_name: IST-2017-65-v1+7_D_C08_1.fastq.zip file_size: 623648989 relation: main_file - access_level: open_access checksum: 225c30b243268c7dda9d6f8327933252 content_type: application/zip creator: system date_created: 2018-12-12T13:04:11Z date_updated: 2020-07-14T12:47:03Z file_id: '5635' file_name: IST-2017-65-v1+8_D_D08_1.fastq.zip file_size: 259359583 relation: main_file file_date_updated: 2020-07-14T12:47:03Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '704' relation: research_paper status: public status: public title: Fastq files for "Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection" tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '5568' abstract: - lang: eng text: Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena) article_processing_charge: No author: - first_name: David full_name: Hahn, David id: 357A6A66-F248-11E8-B48F-1D18A9856A87 last_name: Hahn citation: ama: 'Hahn D. Source codes: Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:10.15479/AT:ISTA:73' apa: 'Hahn, D. (2017). Source codes: Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:73' chicago: 'Hahn, David. “Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:73.' ieee: 'D. Hahn, “Source codes: Brittle fracture simulation with boundary elements for computer graphics.” Institute of Science and Technology Austria, 2017.' ista: 'Hahn D. 2017. Source codes: Brittle fracture simulation with boundary elements for computer graphics, Institute of Science and Technology Austria, 10.15479/AT:ISTA:73.' mla: 'Hahn, David. Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:73.' short: D. Hahn, (2017). datarep_id: '73' date_created: 2018-12-12T12:31:35Z date_published: 2017-08-16T00:00:00Z date_updated: 2024-02-21T13:48:02Z day: '16' ddc: - '004' department: - _id: ChWo doi: 10.15479/AT:ISTA:73 ec_funded: 1 file: - access_level: open_access checksum: 2323a755842a3399cbc47d76545fc9a0 content_type: application/zip creator: system date_created: 2018-12-12T13:02:57Z date_updated: 2020-07-14T12:47:04Z file_id: '5615' file_name: IST-2017-73-v1+1_FractureRB_v1.1_2017_07_20_final_public.zip file_size: 199353471 relation: main_file file_date_updated: 2020-07-14T12:47:04Z has_accepted_license: '1' keyword: - Boundary elements - brittle fracture - computer graphics - fracture simulation month: '08' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publisher: Institute of Science and Technology Austria related_material: record: - id: '839' relation: research_paper status: public status: public title: 'Source codes: Brittle fracture simulation with boundary elements for computer graphics' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '7163' abstract: - lang: eng text: The de novo genome assemblies generated for this study, and the associated metadata. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 citation: ama: Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163 apa: Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7163 chicago: Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:7163. ieee: C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017. ista: Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7163. mla: Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163. short: C. Fraisse, (2017). contributor: - first_name: Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Marion A L id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 date_created: 2019-12-09T23:03:03Z date_published: 2017-12-01T00:00:00Z date_updated: 2024-02-21T13:47:47Z day: '01' ddc: - '576' department: - _id: BeVi - _id: NiBa doi: 10.15479/AT:ISTA:7163 file: - access_level: open_access checksum: 3cae8a2e3cbf8703399b9c483aaba7f3 content_type: application/zip creator: cfraisse date_created: 2019-12-10T08:46:46Z date_updated: 2020-07-14T12:47:50Z file_id: '7164' file_name: Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip file_size: 841375478 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' month: '12' oa: 1 oa_version: Published Version project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publisher: Institute of Science and Technology Austria related_material: record: - id: '614' relation: research_paper status: public status: public title: Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W" 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ...