[{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Rasic, Gordana","last_name":"Rasic","first_name":"Gordana"},{"full_name":"Turley, Andrew","first_name":"Andrew","last_name":"Turley"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"first_name":"Inaki","last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"last_name":"Ritchie","first_name":"Scott","full_name":"Ritchie, Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"last_name":"O’Neill","first_name":"Scott","full_name":"O’Neill, Scott"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"article_processing_charge":"No","citation":{"apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015","mla":"Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015.","ieee":"T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017.","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015."},"year":"2017","day":"30","oa_version":"Published Version","date_updated":"2023-09-22T10:02:51Z","type":"research_data_reference","_id":"9857","department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"doi":"10.1371/journal.pbio.2001894.s015","title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","date_published":"2017-05-30T00:00:00Z","publisher":"Public Library of Science ","status":"public","month":"05","date_created":"2021-08-10T07:41:52Z"},{"date_published":"2017-05-30T00:00:00Z","publisher":"Public Library of Science","date_created":"2021-08-10T07:47:07Z","month":"05","status":"public","citation":{"apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016","mla":"Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016.","ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016."},"article_processing_charge":"No","author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Rasic, Gordana","first_name":"Gordana","last_name":"Rasic"},{"full_name":"Turley, Andrew","last_name":"Turley","first_name":"Andrew"},{"last_name":"Montgomery","first_name":"Brian","full_name":"Montgomery, Brian"},{"first_name":"Inaki","last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"last_name":"Ryan","first_name":"Peter","full_name":"Ryan, Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"last_name":"Hoffmann","first_name":"Ary","full_name":"Hoffmann, Ary"},{"last_name":"O’Neill","first_name":"Scott","full_name":"O’Neill, Scott"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","date_updated":"2023-09-22T10:02:51Z","oa_version":"Published Version","day":"30","year":"2017","title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","related_material":{"record":[{"id":"951","relation":"used_in_publication","status":"public"}]},"doi":"10.1371/journal.pbio.2001894.s016","department":[{"_id":"NiBa"}],"_id":"9858"},{"day":"26","year":"2017","type":"research_data_reference","date_updated":"2023-09-22T09:47:44Z","oa_version":"Published Version","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Jenny","last_name":"Greenwood","full_name":"Greenwood, Jenny"},{"first_name":"Barbara","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Peuß","full_name":"Peuß, Robert"},{"first_name":"Sarah","last_name":"Behrens","full_name":"Behrens, Sarah"},{"first_name":"Daniela","last_name":"Essar","full_name":"Essar, Daniela"},{"full_name":"Rosenstiel, Philip","first_name":"Philip","last_name":"Rosenstiel"},{"last_name":"Schulenburg","first_name":"Hinrich","full_name":"Schulenburg, Hinrich"},{"full_name":"Kurtz, Joachim","first_name":"Joachim","last_name":"Kurtz"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1","open_access":"1"}],"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","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.","short":"J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (2017).","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.","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.","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"},"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)"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1006"}]},"oa":1,"doi":"10.6084/m9.figshare.c.3756974_d1.v1","department":[{"_id":"SyCr"}],"_id":"9859","title":"Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae","publisher":"Springer Nature","date_published":"2017-04-26T00:00:00Z","status":"public","date_created":"2021-08-10T07:59:02Z","month":"04"},{"month":"04","date_created":"2021-08-10T08:07:12Z","status":"public","publisher":"Springer Nature","date_published":"2017-04-26T00:00:00Z","title":"Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae","department":[{"_id":"SyCr"}],"_id":"9860","related_material":{"record":[{"id":"1006","relation":"used_in_publication","status":"public"}]},"oa":1,"doi":"10.6084/m9.figshare.c.3756974_d5.v1","oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-09-22T09:47:44Z","year":"2017","day":"26","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1"}],"citation":{"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.","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","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.","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","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.","short":"J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel, H. Schulenburg, J. Kurtz, (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."},"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Greenwood, Jenny","last_name":"Greenwood","first_name":"Jenny"},{"last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758"},{"last_name":"Peuß","first_name":"Robert","full_name":"Peuß, Robert"},{"full_name":"Behrens, Sarah","first_name":"Sarah","last_name":"Behrens"},{"last_name":"Essar","first_name":"Daniela","full_name":"Essar, Daniela"},{"full_name":"Rosenstiel, Philip","first_name":"Philip","last_name":"Rosenstiel"},{"full_name":"Schulenburg, Hinrich","first_name":"Hinrich","last_name":"Schulenburg"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}]},{"abstract":[{"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.","lang":"eng"}],"oa":1,"doi":"10.5061/dryad.02f6r","related_material":{"record":[{"id":"1019","relation":"used_in_publication","status":"public"}]},"_id":"9861","department":[{"_id":"BeVi"}],"title":"Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","day":"14","year":"2017","type":"research_data_reference","date_updated":"2023-09-22T09:41:20Z","oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Argyridou","first_name":"Eliza","full_name":"Argyridou, Eliza"},{"last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Annabella","last_name":"Königer","full_name":"Königer, Annabella"},{"last_name":"Parsch","first_name":"John","full_name":"Parsch, John"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.02f6r"}],"citation":{"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.","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","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.","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","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.","short":"E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (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."},"status":"public","date_created":"2021-08-10T08:12:52Z","month":"02","publisher":"Dryad","date_published":"2017-02-14T00:00:00Z"},{"publication_identifier":{"issn":["15306984"]},"scopus_import":"1","date_published":"2017-05-05T00:00:00Z","external_id":{"isi":["000403631600011"]},"file":[{"relation":"main_file","date_created":"2018-12-12T10:13:50Z","file_size":508638,"content_type":"application/pdf","creator":"system","file_id":"5037","date_updated":"2020-07-14T12:48:18Z","file_name":"IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf","checksum":"22021daa90cf13b01becd776838acb7b","access_level":"open_access"}],"page":"3396 - 3401","doi":"10.1021/acs.nanolett.7b00097","language":[{"iso":"eng"}],"department":[{"_id":"NanoFab"}],"has_accepted_license":"1","type":"journal_article","date_updated":"2023-09-22T09:56:21Z","oa_version":"Published Version","day":"05","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_created":"2018-12-11T11:49:33Z","month":"05","status":"public","intvolume":" 17","publist_id":"6412","isi":1,"file_date_updated":"2020-07-14T12:48:18Z","publisher":"American Chemical Society","volume":17,"issue":"6","pubrep_id":"826","publication_status":"published","abstract":[{"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.","lang":"eng"}],"publication":"Nano Letters","title":"Current-phase relation of ballistic graphene Josephson junctions","oa":1,"ddc":["621"],"_id":"988","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2017","citation":{"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.","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","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.","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.","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.","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","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."},"author":[{"first_name":"Gaurav","last_name":"Nanda","full_name":"Nanda, Gaurav"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L"},{"full_name":"Rakyta, Péter","last_name":"Rakyta","first_name":"Péter"},{"first_name":"Andor","last_name":"Kormányos","full_name":"Kormányos, Andor"},{"full_name":"Kleiner, Reinhold","first_name":"Reinhold","last_name":"Kleiner"},{"last_name":"Koelle","first_name":"Dieter","full_name":"Koelle, Dieter"},{"full_name":"Watanabe, Kazuo","first_name":"Kazuo","last_name":"Watanabe"},{"full_name":"Taniguchi, Takashi","last_name":"Taniguchi","first_name":"Takashi"},{"full_name":"Vandersypen, Lieven","first_name":"Lieven","last_name":"Vandersypen"},{"last_name":"Goswami","first_name":"Srijit","full_name":"Goswami, Srijit"}],"quality_controlled":"1"},{"status":"public","date_created":"2018-12-11T11:49:34Z","month":"05","conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","end_date":"2017-06-08","start_date":"2017-06-04","location":"Kolding, Denmark"},"publist_id":"6410","isi":1,"intvolume":" 10302","publisher":"Springer","editor":[{"full_name":"Lauze, François","last_name":"Lauze","first_name":"François"},{"last_name":"Dong","first_name":"Yiqiu","full_name":"Dong, Yiqiu"},{"full_name":"Bjorholm Dahl, Anders","last_name":"Bjorholm Dahl","first_name":"Anders"}],"volume":10302,"publication_status":"published","abstract":[{"text":"We present a generalized optimal transport model in which the mass-preserving constraint for the L2-Wasserstein distance is relaxed by introducing a source term in the continuity equation. The source term is also incorporated in the path energy by means of its squared L2-norm in time of a functional with linear growth in space. This extension of the original transport model enables local density modulations, which is a desirable feature in applications such as image warping and blending. A key advantage of the use of a functional with linear growth in space is that it allows for singular sources and sinks, which can be supported on points or lines. On a technical level, the L2-norm in time ensures a disintegration of the source in time, which we use to obtain the well-posedness of the model and the existence of geodesic paths. The numerical discretization is based on the proximal splitting approach [18] and selected numerical test cases show the potential of the proposed approach. Furthermore, the approach is applied to the warping and blending of textures.","lang":"eng"}],"_id":"989","title":"Transport based image morphing with intensity modulation","year":"2017","quality_controlled":"1","author":[{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"},{"last_name":"Rumpf","first_name":"Martin","full_name":"Rumpf, Martin"},{"first_name":"Stefan","last_name":"Simon","full_name":"Simon, Stefan"}],"citation":{"apa":"Maas, J., Rumpf, M., & Simon, S. (2017). Transport based image morphing with intensity modulation. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 563–577). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_45","mla":"Maas, Jan, et al. Transport Based Image Morphing with Intensity Modulation. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 563–77, doi:10.1007/978-3-319-58771-4_45.","ista":"Maas J, Rumpf M, Simon S. 2017. Transport based image morphing with intensity modulation. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 563–577.","chicago":"Maas, Jan, Martin Rumpf, and Stefan Simon. “Transport Based Image Morphing with Intensity Modulation.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:563–77. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_45.","short":"J. Maas, M. Rumpf, S. Simon, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 563–577.","ieee":"J. Maas, M. Rumpf, and S. Simon, “Transport based image morphing with intensity modulation,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 563–577.","ama":"Maas J, Rumpf M, Simon S. Transport based image morphing with intensity modulation. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:563-577. doi:10.1007/978-3-319-58771-4_45"},"publication_identifier":{"issn":["03029743"]},"scopus_import":"1","alternative_title":["LNCS"],"page":"563 - 577","date_published":"2017-05-18T00:00:00Z","external_id":{"isi":["000432210900045"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-58771-4_45","department":[{"_id":"JaMa"}],"day":"18","date_updated":"2023-09-22T09:55:50Z","type":"conference","oa_version":"None","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"scopus_import":"1","publication_identifier":{"issn":["00143820"]},"external_id":{"pmid":["28419447"],"isi":["000403014800005"]},"file":[{"access_level":"open_access","checksum":"6d4c38cb1347fd43620d1736c6df5c79","file_name":"2017_Evolution_Sachdeva_supplement.pdf","date_updated":"2020-07-14T12:48:18Z","file_id":"6329","content_type":"application/pdf","creator":"dernst","file_size":625260,"date_created":"2019-04-17T07:37:04Z","relation":"main_file"},{"checksum":"f1d90dd8831b44baf49b4dd176f263af","file_name":"2017_Evolution_Sachdeva_article.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:18Z","file_id":"6330","creator":"dernst","content_type":"application/pdf","file_size":520110,"relation":"main_file","date_created":"2019-04-17T07:37:04Z"}],"date_published":"2017-06-01T00:00:00Z","page":"1478 - 1493 ","ec_funded":1,"has_accepted_license":"1","department":[{"_id":"NiBa"}],"doi":"10.1111/evo.13252","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","oa_version":"Submitted Version","date_updated":"2025-05-28T11:42:51Z","type":"journal_article","day":"01","intvolume":" 71","isi":1,"publist_id":"6409","month":"06","date_created":"2018-12-11T11:49:34Z","status":"public","pubrep_id":"977","issue":"6","volume":71,"file_date_updated":"2020-07-14T12:48:18Z","publisher":"Wiley-Blackwell","pmid":1,"publication":"Evolution; International Journal of Organic Evolution","title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","_id":"990","oa":1,"ddc":["576"],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","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","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.","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.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493.","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","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."},"quality_controlled":"1","author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"year":"2017"},{"quality_controlled":"1","author":[{"full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chong"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas"}],"citation":{"mla":"Chen, Chong, and Peter M. Jonas. “Synaptotagmins: That’s Why so Many.” Neuron, vol. 94, no. 4, Elsevier, 2017, pp. 694–96, doi:10.1016/j.neuron.2017.05.011.","apa":"Chen, C., & Jonas, P. M. (2017). Synaptotagmins: That’s why so many. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.05.011","short":"C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696.","chicago":"Chen, Chong, and Peter M Jonas. “Synaptotagmins: That’s Why so Many.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.05.011.","ista":"Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4), 694–696.","ama":"Chen C, Jonas PM. Synaptotagmins: That’s why so many. Neuron. 2017;94(4):694-696. doi:10.1016/j.neuron.2017.05.011","ieee":"C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron, vol. 94, no. 4. Elsevier, pp. 694–696, 2017."},"year":"2017","_id":"991","publication":"Neuron","title":"Synaptotagmins: That’s why so many","abstract":[{"text":"Synaptotagmin 7 (Syt7) was originally identified as a slow Ca2+ sensor for lysosome fusion, but its function at fast synapses is controversial. The paper by Luo and Südhof (2017) in this issue of Neuron shows that at the calyx of Held in the auditory brainstem Syt7 triggers asynchronous release during stimulus trains, resulting in reliable and temporally precise high-frequency transmission. Thus, a slow Ca2+ sensor contributes to the fast signaling properties of the calyx synapse.","lang":"eng"}],"publication_status":"published","volume":94,"issue":"4","publisher":"Elsevier","isi":1,"publist_id":"6408","intvolume":" 94","status":"public","month":"05","date_created":"2018-12-11T11:49:34Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"17","oa_version":"None","type":"journal_article","date_updated":"2023-09-22T09:54:37Z","department":[{"_id":"PeJo"}],"doi":"10.1016/j.neuron.2017.05.011","language":[{"iso":"eng"}],"page":"694 - 696","external_id":{"isi":["000401415100002"]},"date_published":"2017-05-17T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["08966273"]}},{"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"date_published":"2017-05-01T00:00:00Z","file":[{"date_updated":"2020-07-14T12:48:18Z","file_id":"4654","file_name":"IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf","checksum":"81761fb939acb7585c36629f765b4373","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:07:55Z","content_type":"application/pdf","creator":"system","file_size":786145},{"checksum":"2b2d7e1d6c1c79a9795a7aa0f860baf3","file_name":"2017_Thesis_Rolinek_source.zip","access_level":"closed","file_id":"6208","date_updated":"2020-07-14T12:48:18Z","creator":"dernst","content_type":"application/zip","file_size":5936337,"relation":"source_file","date_created":"2019-04-05T08:43:24Z"}],"page":"97","acknowledgement":"FP7/2007-2013/ERC grant agreement no 616160","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_815","has_accepted_license":"1","department":[{"_id":"VlKo"}],"type":"dissertation","date_updated":"2023-09-07T12:05:41Z","oa_version":"Published Version","day":"01","supervisor":[{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_created":"2018-12-11T11:49:35Z","month":"05","status":"public","publist_id":"6407","degree_awarded":"PhD","file_date_updated":"2020-07-14T12:48:18Z","publisher":"Institute of Science and Technology Austria","pubrep_id":"815","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"publication_status":"published","abstract":[{"text":"An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language).","lang":"eng"}],"title":"Complexity of constraint satisfaction","ddc":["004"],"oa":1,"_id":"992","year":"2017","citation":{"mla":"Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815.","apa":"Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815","ista":"Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria.","chicago":"Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815.","short":"M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017.","ama":"Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815","ieee":"M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017."},"author":[{"last_name":"Rolinek","first_name":"Michal","full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}]},{"ddc":["005","571"],"oa":1,"_id":"993","title":"Subsampling scaling","publication":"Nature Communications","publication_status":"published","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."}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Anna","last_name":"Levina (Martius)","id":"35AF8020-F248-11E8-B48F-1D18A9856A87","full_name":"Levina (Martius), Anna"},{"full_name":"Priesemann, Viola","first_name":"Viola","last_name":"Priesemann"}],"quality_controlled":"1","citation":{"ista":"Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140.","chicago":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140.","short":"A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).","ieee":"A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","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","mla":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140."},"year":"2017","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"6406","isi":1,"intvolume":" 8","status":"public","article_number":"15140","date_created":"2018-12-11T11:49:35Z","month":"05","volume":8,"pubrep_id":"819","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:48:19Z","doi":"10.1038/ncomms15140","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"JoCs"}],"has_accepted_license":"1","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (in subscription journal)","day":"04","type":"journal_article","date_updated":"2023-09-22T09:54:07Z","oa_version":"Published Version","publication_identifier":{"issn":["20411723"]},"scopus_import":"1","date_published":"2017-05-04T00:00:00Z","external_id":{"isi":["000400560700001"]},"file":[{"relation":"main_file","date_created":"2018-12-12T10:15:05Z","content_type":"application/pdf","creator":"system","file_size":746224,"date_updated":"2020-07-14T12:48:19Z","file_id":"5122","checksum":"9880212f8c4c53404c7c6fbf9023c53a","file_name":"IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf","access_level":"open_access"}]},{"volume":1,"issue":"3","publisher":"American Physical Society","intvolume":" 1","isi":1,"publist_id":"6405","month":"08","date_created":"2018-12-11T11:49:35Z","status":"public","citation":{"ista":"Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 1(3).","short":"I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017).","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.","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","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."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.09220"}],"author":[{"first_name":"Igor","last_name":"Cherepanov","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","full_name":"Cherepanov, Igor"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"}],"quality_controlled":"1","year":"2017","title":"Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules","publication":"Physical Review Materials","_id":"994","oa":1,"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000416564000004"]},"date_published":"2017-08-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","date_updated":"2023-09-22T09:53:42Z","type":"journal_article","day":"08","ec_funded":1,"department":[{"_id":"MiLe"}],"doi":"10.1103/PhysRevMaterials.1.035602","language":[{"iso":"eng"}]},{"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"07","oa_version":"Submitted Version","type":"journal_article","date_updated":"2023-09-22T09:53:17Z","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.96.085410","external_id":{"isi":["000407017100009"]},"date_published":"2017-08-07T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["24699950"]},"author":[{"last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"quality_controlled":"1","citation":{"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","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.","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.","short":"G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 96 (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.","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","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."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.02616"}],"year":"2017","_id":"995","oa":1,"title":"Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment","publication":"Physical Review B - Condensed Matter and Materials Physics","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."}],"publication_status":"published","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"}],"volume":96,"issue":"8","publisher":"American Physical Society","isi":1,"publist_id":"6404","intvolume":" 96","article_number":"085410","status":"public","month":"08","date_created":"2018-12-11T11:49:36Z"},{"intvolume":" 147","isi":1,"publist_id":"6403","month":"06","date_created":"2018-12-11T11:49:36Z","article_number":"013946","status":"public","volume":147,"issue":"1","publisher":"AIP Publishing","publication":"The Journal of Chemical Physics","title":"Strongly aligned molecules inside helium droplets in the near-adiabatic regime","_id":"996","oa":1,"abstract":[{"lang":"eng","text":"Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas of isolated molecules each with an effective rotational constant of 0.6 times the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using the angulon quasiparticle to describe rotating molecules in superfluid helium rationalizes why the alignment mechanism is similar to that of isolated molecules with an effective rotational constant. A major advantage of molecules in He droplets is that their 0.4 K temperature leads to stronger alignment than what can generally be achieved for gas phase molecules -- here demonstrated by a direct comparison of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated molecules. This point is further illustrated for more complex system by measurements on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. "}],"publication_status":"published","citation":{"apa":"Shepperson, B., Chatterley, A., Søndergaard, A., Christiansen, L., Lemeshko, M., & Stapelfeldt, H. (2017). Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4983703","mla":"Shepperson, Benjamin, et al. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics, vol. 147, no. 1, 013946, AIP Publishing, 2017, doi:10.1063/1.4983703.","ista":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. 2017. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 147(1), 013946.","chicago":"Shepperson, Benjamin, Adam Chatterley, Anders Søndergaard, Lars Christiansen, Mikhail Lemeshko, and Henrik Stapelfeldt. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4983703.","short":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, H. Stapelfeldt, The Journal of Chemical Physics 147 (2017).","ama":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 2017;147(1). doi:10.1063/1.4983703","ieee":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, and H. Stapelfeldt, “Strongly aligned molecules inside helium droplets in the near-adiabatic regime,” The Journal of Chemical Physics, vol. 147, no. 1. AIP Publishing, 2017."},"main_file_link":[{"url":"https://arxiv.org/abs/1704.03684","open_access":"1"}],"author":[{"first_name":"Benjamin","last_name":"Shepperson","full_name":"Shepperson, Benjamin"},{"last_name":"Chatterley","first_name":"Adam","full_name":"Chatterley, Adam"},{"full_name":"Søndergaard, Anders","first_name":"Anders","last_name":"Søndergaard"},{"full_name":"Christiansen, Lars","first_name":"Lars","last_name":"Christiansen"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"}],"quality_controlled":"1","year":"2017","scopus_import":"1","publication_identifier":{"issn":["00219606"]},"external_id":{"isi":["000405089400047"]},"date_published":"2017-06-01T00:00:00Z","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"doi":"10.1063/1.4983703","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","date_updated":"2024-02-28T13:02:26Z","type":"journal_article","day":"01"},{"abstract":[{"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.","lang":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"997","oa":1,"title":"Emergence of non-abelian magnetic monopoles in a quantum impurity problem","publication":"Physical Review Letters","year":"2017","author":[{"first_name":"Enderalp","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05162"}],"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","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.","short":"E. Yakaboylu, A. Deuchert, M. Lemeshko, Physical Review Letters 119 (2017).","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.","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.","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"},"status":"public","article_number":"235301","month":"12","date_created":"2018-12-11T11:49:36Z","isi":1,"publist_id":"6401","intvolume":" 119","publisher":"American Physical Society","article_type":"original","issue":"23","volume":119,"department":[{"_id":"MiLe"},{"_id":"RoSe"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.119.235301","ec_funded":1,"day":"06","oa_version":"Preprint","date_updated":"2023-10-10T13:31:54Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","arxiv":1,"scopus_import":"1","publication_identifier":{"issn":["0031-9007"]},"external_id":{"arxiv":["1705.05162"],"isi":["000417132100007"]},"date_published":"2017-12-06T00:00:00Z"},{"date_published":"2017-04-14T00:00:00Z","external_id":{"isi":["000418371405066"]},"page":"5533 - 5542","publication_identifier":{"isbn":["978-153860457-1"]},"scopus_import":"1","type":"conference","date_updated":"2023-09-22T09:51:58Z","oa_version":"Submitted Version","day":"14","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1109/CVPR.2017.587","department":[{"_id":"ChLa"},{"_id":"ChWo"}],"publisher":"IEEE","volume":2017,"date_created":"2018-12-11T11:49:37Z","month":"04","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26","location":"Honolulu, HA, United States","start_date":"2017-07-21"},"status":"public","intvolume":" 2017","publist_id":"6400","isi":1,"year":"2017","main_file_link":[{"url":"https://arxiv.org/abs/1611.07725","open_access":"1"}],"citation":{"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.","short":"S.A. Rebuffi, A. Kolesnikov, G. Sperl, C. Lampert, in:, IEEE, 2017, pp. 5533–5542.","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.","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","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.","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.","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"},"quality_controlled":"1","author":[{"full_name":"Rebuffi, Sylvestre Alvise","last_name":"Rebuffi","first_name":"Sylvestre Alvise"},{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","first_name":"Alexander","last_name":"Kolesnikov"},{"first_name":"Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert"}],"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"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. ","lang":"eng"}],"title":"iCaRL: Incremental classifier and representation learning","oa":1,"_id":"998"},{"page":"2807 - 2816","date_published":"2017-06-08T00:00:00Z","external_id":{"isi":["000683309502093"]},"publication_identifier":{"isbn":["9781510855144"]},"scopus_import":"1","alternative_title":["PMLR"],"day":"08","type":"conference","date_updated":"2023-10-17T11:53:32Z","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"ec_funded":1,"publisher":"ML Research Press","volume":70,"status":"public","date_created":"2018-12-11T11:49:37Z","month":"06","conference":{"end_date":"2017-08-11","name":"ICML: International Conference on Machine Learning","location":"Sydney, Australia","start_date":"2017-08-06"},"publist_id":"6399","isi":1,"intvolume":" 70","year":"2017","author":[{"full_name":"Pentina, Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","last_name":"Pentina"},{"last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1602.06518","open_access":"1"}],"citation":{"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.","mla":"Pentina, Anastasia, and Christoph Lampert. Multi-Task Learning with Labeled and Unlabeled Tasks. Vol. 70, ML Research Press, 2017, pp. 2807–16.","chicago":"Pentina, Anastasia, and Christoph Lampert. “Multi-Task Learning with Labeled and Unlabeled Tasks,” 70:2807–16. ML Research Press, 2017.","short":"A. Pentina, C. Lampert, in:, ML Research Press, 2017, 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.","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.","ama":"Pentina A, Lampert C. Multi-task learning with labeled and unlabeled tasks. In: Vol 70. ML Research Press; 2017:2807-2816."},"publication_status":"published","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. "}],"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"oa":1,"_id":"999","title":"Multi-task learning with labeled and unlabeled tasks"},{"status":"public","date_created":"2018-12-11T11:50:03Z","month":"04","publist_id":"6294","isi":1,"intvolume":" 104","publisher":"Wiley-Blackwell","issue":"1","volume":104,"publication_status":"published","abstract":[{"text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.","lang":"eng"}],"_id":"1084","publication":"Molecular Microbiology","title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","year":"2017","quality_controlled":"1","author":[{"first_name":"Chong","last_name":"Fang","full_name":"Fang, Chong"},{"full_name":"Nagy-Staron, Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron"},{"last_name":"Grafe","first_name":"Martin","full_name":"Grafe, Martin"},{"first_name":"Ralf","last_name":"Heermann","full_name":"Heermann, Ralf"},{"first_name":"Kirsten","last_name":"Jung","full_name":"Jung, Kirsten"},{"first_name":"Susanne","last_name":"Gebhard","full_name":"Gebhard, Susanne"},{"last_name":"Mascher","first_name":"Thorsten","full_name":"Mascher, Thorsten"}],"citation":{"ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597","ieee":"C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., & Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.13597","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597."},"publication_identifier":{"issn":[" 0950382X"]},"scopus_import":"1","page":"16 - 31","date_published":"2017-04-01T00:00:00Z","external_id":{"isi":["000398059200002"]},"language":[{"iso":"eng"}],"doi":"10.1111/mmi.13597","department":[{"_id":"CaGu"}],"day":"01","type":"journal_article","date_updated":"2023-09-20T11:48:43Z","oa_version":"None","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"intvolume":" 8","publist_id":"6292","isi":1,"date_created":"2018-12-11T11:50:04Z","month":"01","article_number":"14251","status":"public","volume":8,"pubrep_id":"791","file_date_updated":"2018-12-12T10:15:22Z","publisher":"Nature Publishing Group","title":"Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation","publication":"Nature Communications","ddc":["570","576"],"oa":1,"_id":"1085","publication_status":"published","abstract":[{"lang":"eng","text":"Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution."}],"citation":{"ista":"Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251.","chicago":"Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14251.","short":"A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).","ama":"Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 2017;8. doi:10.1038/ncomms14251","ieee":"A. Wright et al., “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14251","mla":"Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications, vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251."},"quality_controlled":"1","author":[{"full_name":"Wright, Alison","last_name":"Wright","first_name":"Alison"},{"last_name":"Darolti","first_name":"Iulia","full_name":"Darolti, Iulia"},{"full_name":"Bloch, Natasha","last_name":"Bloch","first_name":"Natasha"},{"first_name":"Vicencio","last_name":"Oostra","full_name":"Oostra, Vicencio"},{"full_name":"Sandkam, Benjamin","first_name":"Benjamin","last_name":"Sandkam"},{"full_name":"Buechel, Séverine","first_name":"Séverine","last_name":"Buechel"},{"full_name":"Kolm, Niclas","last_name":"Kolm","first_name":"Niclas"},{"full_name":"Breden, Felix","first_name":"Felix","last_name":"Breden"},{"last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mank, Judith","last_name":"Mank","first_name":"Judith"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","publication_identifier":{"issn":["20411723"]},"scopus_import":"1","date_published":"2017-01-31T00:00:00Z","external_id":{"isi":["000392953700001"]},"file":[{"date_created":"2018-12-12T10:15:22Z","relation":"main_file","file_size":955256,"creator":"system","content_type":"application/pdf","file_id":"5141","date_updated":"2018-12-12T10:15:22Z","access_level":"open_access","file_name":"IST-2017-791-v1+1_ncomms14251.pdf"}],"language":[{"iso":"eng"}],"doi":"10.1038/ncomms14251","department":[{"_id":"BeVi"}],"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-20T11:48:16Z","type":"journal_article","oa_version":"Published Version","day":"31"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","type":"journal_article","date_updated":"2023-09-20T11:47:22Z","oa_version":"Submitted Version","day":"25","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1017/jfm.2017.14","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"date_published":"2017-02-25T00:00:00Z","external_id":{"isi":["000394376400044"]},"page":"1045 - 1059","publication_identifier":{"issn":["00221120"]},"scopus_import":"1","citation":{"mla":"Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:10.1017/jfm.2017.14.","apa":"Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.14","ama":"Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14","ieee":"B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University Press, pp. 1045–1059, 2017.","chicago":"Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.14.","short":"B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059.","ista":"Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059."},"main_file_link":[{"url":"https://arxiv.org/abs/1603.04077","open_access":"1"}],"quality_controlled":"1","author":[{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"full_name":"Barkley, Dwight","last_name":"Barkley","first_name":"Dwight"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"year":"2017","publication":"Journal of Fluid Mechanics","title":"Speed and structure of turbulent fronts in pipe flow","oa":1,"_id":"1087","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to."}],"volume":813,"publisher":"Cambridge University Press","intvolume":" 813","publist_id":"6290","isi":1,"date_created":"2018-12-11T11:50:04Z","month":"02","status":"public"}]