[{"abstract":[{"lang":"eng","text":" In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. "}],"issue":"1794","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","intvolume":" 281","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2036","day":"17","scopus_import":1,"date_published":"2014-09-17T00:00:00Z","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","citation":{"ama":"Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.1679","ista":"Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. Royal Society, The, 2014.","apa":"Lagator, M., Colegrave, N., & Neve, P. (2014). Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2014.1679","mla":"Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20141679, Royal Society, The, 2014, doi:10.1098/rspb.2014.1679.","short":"M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2014. https://doi.org/10.1098/rspb.2014.1679."},"publist_id":"5019","article_number":"20141679","date_updated":"2023-02-23T14:06:44Z","date_created":"2018-12-11T11:55:21Z","volume":281,"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9741"}]},"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Royal Society, The","year":"2014","acknowledgement":"The project was supported by Leverhulme Trust.","month":"09","language":[{"iso":"eng"}],"doi":"10.1098/rspb.2014.1679","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/"}],"oa":1},{"article_processing_charge":"No","day":"13","month":"11","date_published":"2014-11-13T00:00:00Z","doi":"10.5061/dryad.vm0vc","citation":{"ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, 10.5061/dryad.vm0vc.","apa":"Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. https://doi.org/10.5061/dryad.vm0vc","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:10.5061/dryad.vm0vc","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. https://doi.org/10.5061/dryad.vm0vc.","mla":"Konrad, Matthias, et al. Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host. Dryad, 2014, doi:10.5061/dryad.vm0vc.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014)."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"abstract":[{"text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.","lang":"eng"}],"type":"research_data_reference","related_material":{"record":[{"id":"1993","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","date_created":"2021-07-28T08:38:40Z","date_updated":"2023-02-23T10:23:32Z","_id":"9740","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014","department":[{"_id":"SyCr"}],"publisher":"Dryad","status":"public","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments."}],"_id":"9741","year":"2014","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","department":[{"_id":"CaGu"}],"publisher":"Dryad","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}],"related_material":{"record":[{"id":"2036","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-02-23T10:25:31Z","date_created":"2021-07-28T08:48:06Z","oa_version":"Published Version","day":"21","month":"08","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.85dn7","open_access":"1"}],"oa":1,"citation":{"ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, 10.5061/dryad.85dn7.","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","apa":"Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. https://doi.org/10.5061/dryad.85dn7","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:10.5061/dryad.85dn7","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.","mla":"Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014, doi:10.5061/dryad.85dn7.","short":"M. Lagator, N. Colegrave, P. Neve, (2014)."},"doi":"10.5061/dryad.85dn7","date_published":"2014-08-21T00:00:00Z"},{"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-02-23T10:25:37Z","date_created":"2021-07-28T08:13:57Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2039"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Adlam, Ben","last_name":"Adlam","first_name":"Ben"},{"full_name":"Novak, Martin","last_name":"Novak","first_name":"Martin"}],"publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"title":"Detailed proofs for “The time scale of evolutionary innovation”","status":"public","_id":"9739","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014","article_processing_charge":"No","day":"11","month":"09","date_published":"2014-09-11T00:00:00Z","doi":"10.1371/journal.pcbi.1003818.s001","citation":{"chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","mla":"Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818.s001","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001"}},{"file":[{"file_id":"4651","relation":"main_file","checksum":"4de1ab255976a8ae77eb0e55ad62ecc9","date_created":"2018-12-12T10:07:52Z","date_updated":"2020-07-14T12:45:31Z","access_level":"open_access","file_name":"IST-2016-559-v1+1_Hearn_et_al.pdf","creator":"system","content_type":"application/pdf","file_size":807444},{"file_name":"IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1518088,"creator":"system","relation":"main_file","file_id":"4652","date_created":"2018-12-12T10:07:53Z","date_updated":"2020-07-14T12:45:31Z","checksum":"01a8073e071c088500425f910b0f1f71"}],"oa_version":"Submitted Version","pubrep_id":"559","title":"Likelihood-based inference of population history from low-coverage de novo genome assemblies","ddc":["570"],"status":"public","intvolume":" 23","_id":"2170","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":" Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources."}],"issue":"1","type":"journal_article","date_published":"2014-01-01T00:00:00Z","page":"198 - 211","publication":"Molecular Ecology","citation":{"chicago":"Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mec.12578.","short":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular Ecology 23 (2014) 198–211.","mla":"Hearn, Jack, et al. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no. 1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.","apa":"Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse, K. (2014). Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578","ieee":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse, “Likelihood-based inference of population history from low-coverage de novo genome assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211, 2014.","ista":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 23(1), 198–211.","ama":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578"},"day":"01","has_accepted_license":"1","scopus_import":1,"date_updated":"2023-02-23T14:07:09Z","date_created":"2018-12-11T11:56:07Z","volume":23,"author":[{"last_name":"Hearn","first_name":"Jack","full_name":"Hearn, Jack"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"},{"full_name":"Bunnefeld, Lynsey","first_name":"Lynsey","last_name":"Bunnefeld"},{"full_name":"Nicholls, James","first_name":"James","last_name":"Nicholls"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9754"}]},"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"acknowledgement":"This work was funded by NERC grants to G Stone, J Nicholls, K Lohse and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).","year":"2014","file_date_updated":"2020-07-14T12:45:31Z","publist_id":"4814","language":[{"iso":"eng"}],"doi":"10.1111/mec.12578","quality_controlled":"1","oa":1,"month":"01"},{"abstract":[{"lang":"eng","text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies."}],"type":"research_data_reference","related_material":{"record":[{"id":"2284","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Tragust, Simon","first_name":"Simon","last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V"},{"full_name":"Chapuisat, Michel","first_name":"Michel","last_name":"Chapuisat"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"oa_version":"Published Version","date_updated":"2023-02-23T10:36:17Z","date_created":"2021-07-30T08:24:11Z","year":"2014","_id":"9753","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"SyCr"}],"publisher":"Dryad","title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","status":"public","article_processing_charge":"No","month":"10","day":"08","doi":"10.5061/dryad.nc0gc","date_published":"2014-10-08T00:00:00Z","oa":1,"citation":{"mla":"Tragust, Simon, et al. Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies. Dryad, 2014, doi:10.5061/dryad.nc0gc.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. https://doi.org/10.5061/dryad.nc0gc.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:10.5061/dryad.nc0gc","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, 10.5061/dryad.nc0gc.","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. https://doi.org/10.5061/dryad.nc0gc"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.nc0gc","open_access":"1"}]},{"abstract":[{"text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.","lang":"eng"}],"type":"research_data_reference","date_updated":"2023-02-23T10:35:57Z","date_created":"2021-07-30T08:13:52Z","oa_version":"Published Version","author":[{"full_name":"Simmons, Kristina","last_name":"Simmons","first_name":"Kristina"},{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"first_name":"Jan","last_name":"Homann","full_name":"Homann, Jan"},{"full_name":"Yee, Heather","last_name":"Yee","first_name":"Heather"},{"full_name":"Palmer, Stephanie","last_name":"Palmer","first_name":"Stephanie"},{"full_name":"Nelson, Philip","first_name":"Philip","last_name":"Nelson"},{"full_name":"Balasubramanian, Vijay","first_name":"Vijay","last_name":"Balasubramanian"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2277"}]},"title":"Data from: Transformation of stimulus correlations by the retina","status":"public","publisher":"Dryad","department":[{"_id":"GaTk"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9752","year":"2014","day":"07","month":"11","article_processing_charge":"No","date_published":"2014-11-07T00:00:00Z","doi":"10.5061/dryad.246qg","oa":1,"citation":{"ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, 10.5061/dryad.246qg.","ieee":"K. Simmons et al., “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. https://doi.org/10.5061/dryad.246qg","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:10.5061/dryad.246qg","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/10.5061/dryad.246qg.","mla":"Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014)."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.246qg","open_access":"1"}]},{"day":"01","month":"08","doi":"10.1038/nphys3012","date_published":"2014-08-01T00:00:00Z","publication":"Nature Physics","oa":1,"citation":{"ama":"Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. 2014;10(8):572-577. doi:10.1038/nphys3012","ista":"Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. 10(8), 572–577.","apa":"Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2014). Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3012","ieee":"I. Zeljkovic et al., “Mapping the unconventional orbital texture in topological crystalline insulators,” Nature Physics, vol. 10, no. 8. Nature Publishing Group, pp. 572–577, 2014.","mla":"Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” Nature Physics, vol. 10, no. 8, Nature Publishing Group, 2014, pp. 572–77, doi:10.1038/nphys3012.","short":"I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn, F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics 10 (2014) 572–577.","chicago":"Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” Nature Physics. Nature Publishing Group, 2014. https://doi.org/10.1038/nphys3012."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.0164"}],"quality_controlled":0,"page":"572 - 577","abstract":[{"lang":"eng","text":"The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications."}],"publist_id":"6423","issue":"8","extern":1,"type":"journal_article","author":[{"last_name":"Zeljkovic","first_name":"Ilija","full_name":"Zeljkovic, Ilija"},{"last_name":"Okada","first_name":"Yoshinori","full_name":"Okada, Yoshinori"},{"last_name":"Huang","first_name":"Chengyi","full_name":"Huang, Chengyi"},{"first_name":"Raman","last_name":"Sankar","full_name":"Sankar, Raman"},{"full_name":"Walkup, Daniel","last_name":"Walkup","first_name":"Daniel"},{"first_name":"Wenwen","last_name":"Zhou","full_name":"Zhou, Wenwen"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn"},{"first_name":"Fangcheng","last_name":"Chou","full_name":"Chou, Fangcheng"},{"full_name":"Tsai, Wei-Feng","last_name":"Tsai","first_name":"Wei"},{"first_name":"Hsin","last_name":"Lin","full_name":"Lin, Hsin"},{"full_name":"Bansil, Arun","last_name":"Bansil","first_name":"Arun"},{"full_name":"Fu, Liang","last_name":"Fu","first_name":"Liang"},{"full_name":"Hasan, Md Z","first_name":"Md","last_name":"Hasan"},{"first_name":"Vidya","last_name":"Madhavan","full_name":"Madhavan, Vidya"}],"date_updated":"2021-01-12T08:22:23Z","date_created":"2018-12-11T11:49:30Z","volume":10,"acknowledgement":"V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105 for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231. W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009. W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.","_id":"978","year":"2014","publication_status":"published","title":"Mapping the unconventional orbital texture in topological crystalline insulators","status":"public","publisher":"Nature Publishing Group","intvolume":" 10"},{"abstract":[{"text":"In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators.","lang":"eng"}],"issue":"3","publist_id":"6422","extern":1,"type":"journal_article","author":[{"full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Liang","last_name":"Fu","full_name":"Fu, Liang"}],"date_created":"2018-12-11T11:49:31Z","date_updated":"2021-01-12T08:22:23Z","volume":90,"_id":"979","year":"2014","acknowledgement":"We thank V. Madhavan and Y. Okada for related collaborations, and P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR 1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0010526.","title":"Symmetry breaking and Landau quantization in topological crystalline insulators","status":"public","publication_status":"published","publisher":"American Physical Society","intvolume":" 90","day":"03","month":"07","doi":"10.1103/PhysRevB.90.035402","date_published":"2014-07-03T00:00:00Z","publication":"Physical Review B - Condensed Matter and Materials Physics","citation":{"apa":"Serbyn, M., & Fu, L. (2014). Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.035402","ieee":"M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological crystalline insulators,” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 3. American Physical Society, 2014.","ista":"Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. 90(3).","ama":"Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. 2014;90(3). doi:10.1103/PhysRevB.90.035402","chicago":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.035402.","short":"M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics 90 (2014).","mla":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 3, American Physical Society, 2014, doi:10.1103/PhysRevB.90.035402."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.8153"}],"oa":1,"quality_controlled":0},{"article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2014-06-03T00:00:00Z","citation":{"mla":"Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Evolution, vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:10.1111/evo.12373.","short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12373.","ama":"Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 2014;68(6):1775-1791. doi:10.1111/evo.12373","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 68(6), 1775–1791.","apa":"Dhar, R., Bergmiller, T., & Wagner, A. (2014). Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. Wiley. https://doi.org/10.1111/evo.12373","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,” Evolution, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014."},"publication":"Evolution","page":"1775-1791","article_type":"original","issue":"6","abstract":[{"text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"9931","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","intvolume":" 68","title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","status":"public","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"06","doi":"10.1111/evo.12373","language":[{"iso":"eng"}],"external_id":{"pmid":["24495000"]},"quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"9932"}]},"author":[{"first_name":"Riddhiman","last_name":"Dhar","full_name":"Dhar, Riddhiman"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"full_name":"Wagner, Andreas","last_name":"Wagner","first_name":"Andreas"}],"volume":68,"date_created":"2021-08-17T09:03:09Z","date_updated":"2023-02-23T14:13:27Z","pmid":1,"year":"2014","acknowledgement":"We thank the Functional Genomics Center Zurich for its service in generating sequencing data, M. Ackermann and E. Hayden for helpful discussions, A. de Visser for comments on earlier versions of this manuscript, and M. Moser for help with quantitative PCR. This work was supported by Swiss National Science Foundation (grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in Systems Biology at the University of Zurich. RD acknowledges support from the Forschungskredit program of the University of Zurich. The authors declare no conflict of interest.","publisher":"Wiley","department":[{"_id":"CaGu"}],"publication_status":"published"},{"day":"27","month":"01","article_processing_charge":"No","date_published":"2014-01-27T00:00:00Z","doi":"10.5061/dryad.jc402","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.jc402"}],"citation":{"ista":"Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes, Dryad, 10.5061/dryad.jc402.","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.” Dryad, 2014.","apa":"Dhar, R., Bergmiller, T., & Wagner, A. (2014). Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Dryad. https://doi.org/10.5061/dryad.jc402","ama":"Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. 2014. doi:10.5061/dryad.jc402","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Dryad, 2014. https://doi.org/10.5061/dryad.jc402.","mla":"Dhar, Riddhiman, et al. Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes. Dryad, 2014, doi:10.5061/dryad.jc402.","short":"R. Dhar, T. Bergmiller, A. Wagner, (2014)."},"abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"type":"research_data_reference","date_created":"2021-08-17T09:11:40Z","date_updated":"2023-02-23T14:13:24Z","oa_version":"Published Version","author":[{"full_name":"Dhar, Riddhiman","last_name":"Dhar","first_name":"Riddhiman"},{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Wagner","first_name":"Andreas","full_name":"Wagner, Andreas"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9931"}]},"status":"public","title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","publisher":"Dryad","department":[{"_id":"CaGu"}],"_id":"9932","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014"},{"month":"03","publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"doi":"10.1002/2013wr014506","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2013WR014506"}],"oa":1,"quality_controlled":"1","extern":"1","author":[{"full_name":"Immerzeel, W. W.","first_name":"W. W.","last_name":"Immerzeel"},{"last_name":"Petersen","first_name":"L.","full_name":"Petersen, L."},{"last_name":"Ragettli","first_name":"S.","full_name":"Ragettli, S."},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"}],"date_updated":"2023-02-24T08:28:23Z","date_created":"2023-02-20T08:17:01Z","volume":50,"year":"2014","publication_status":"published","publisher":"American Geophysical Union","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Water Science and Technology"],"date_published":"2014-03-01T00:00:00Z","publication":"Water Resources Research","citation":{"chicago":"Immerzeel, W. W., L. Petersen, S. Ragettli, and Francesca Pellicciotti. “The Importance of Observed Gradients of Air Temperature and Precipitation for Modeling Runoff from a Glacierized Watershed in the Nepalese Himalayas.” Water Resources Research. American Geophysical Union, 2014. https://doi.org/10.1002/2013wr014506.","short":"W.W. Immerzeel, L. Petersen, S. Ragettli, F. Pellicciotti, Water Resources Research 50 (2014) 2212–2226.","mla":"Immerzeel, W. W., et al. “The Importance of Observed Gradients of Air Temperature and Precipitation for Modeling Runoff from a Glacierized Watershed in the Nepalese Himalayas.” Water Resources Research, vol. 50, no. 3, American Geophysical Union, 2014, pp. 2212–26, doi:10.1002/2013wr014506.","apa":"Immerzeel, W. W., Petersen, L., Ragettli, S., & Pellicciotti, F. (2014). The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas. Water Resources Research. American Geophysical Union. https://doi.org/10.1002/2013wr014506","ieee":"W. W. Immerzeel, L. Petersen, S. Ragettli, and F. Pellicciotti, “The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas,” Water Resources Research, vol. 50, no. 3. American Geophysical Union, pp. 2212–2226, 2014.","ista":"Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. 2014. The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas. Water Resources Research. 50(3), 2212–2226.","ama":"Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas. Water Resources Research. 2014;50(3):2212-2226. doi:10.1002/2013wr014506"},"article_type":"original","page":"2212-2226","abstract":[{"text":"The performance of glaciohydrological models which simulate catchment response to climate variability depends to a large degree on the data used to force the models. The forcing data become increasingly important in high-elevation, glacierized catchments where the interplay between extreme topography, climate, and the cryosphere is complex. It is challenging to generate a reliable forcing data set that captures this spatial heterogeneity. In this paper, we analyze the results of a 1 year field campaign focusing on air temperature and precipitation observations in the Langtang valley in the Nepalese Himalayas. We use the observed time series to characterize both temperature lapse rates (LRs) and precipitation gradients (PGs). We study their spatial and temporal variability, and we attempt to identify possible controlling factors. We show that very clear LRs exist in the valley and that there are strong seasonal differences related to the water vapor content in the atmosphere. Results also show that the LRs are generally shallower than the commonly used environmental lapse rates. The analysis of the precipitation observations reveals that there is great variability in precipitation over short horizontal distances. A uniform valley wide PG cannot be established, and several scale-dependent mechanisms may explain our observations. We complete our analysis by showing the impact of the observed LRs and PGs on the outputs of the TOPKAPI-ETH glaciohydrological model. We conclude that LRs and PGs have a very large impact on the water balance composition and that short-term monitoring campaigns have the potential to improve model quality considerably.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Published Version","_id":"12637","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas","intvolume":" 50"},{"extern":"1","volume":150,"date_created":"2023-02-20T08:16:56Z","date_updated":"2023-02-24T08:32:39Z","author":[{"last_name":"Immerzeel","first_name":"W.W.","full_name":"Immerzeel, W.W."},{"full_name":"Kraaijenbrink, P.D.A.","first_name":"P.D.A.","last_name":"Kraaijenbrink"},{"last_name":"Shea","first_name":"J.M.","full_name":"Shea, J.M."},{"full_name":"Shrestha, A.B.","first_name":"A.B.","last_name":"Shrestha"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca"},{"last_name":"Bierkens","first_name":"M.F.P.","full_name":"Bierkens, M.F.P."},{"last_name":"de Jong","first_name":"S.M.","full_name":"de Jong, S.M."}],"publisher":"Elsevier","publication_status":"published","year":"2014","publication_identifier":{"issn":["0034-4257"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1016/j.rse.2014.04.025","quality_controlled":"1","issue":"7","abstract":[{"text":"Himalayan glacier tongues are commonly debris covered and they are an important source of melt water. However, they remain relatively unstudied because of the inaccessibility of the terrain and the difficulties in field work caused by the thick debris mantles. Observations of debris-covered glaciers are therefore scarce and airborne remote sensing may bridge the gap between scarce field observations and coarse resolution space-borne remote sensing. In this study we deploy an Unmanned Aerial Vehicle (UAV) before and after the melt and monsoon season (May and October 2013) over the debris-covered tongue of the Lirung Glacier in Nepal. Based on stereo-imaging and the structure for motion algorithm we derive highly detailed ortho-mosaics and digital elevation models (DEMs), which we geometrically correct using differential GPS observations collected in the field. Based on DEM differencing and manual feature tracking we derive the mass loss and the surface velocity of the glacier at a high spatial accuracy. On average, mass loss is limited and the surface velocity is very small. However, the spatial variability of melt rates is very high, and ice cliffs and supra-glacial ponds show mass losses that can be an order of magnitude higher than the average. We suggest that future research should focus on the interaction between supra-glacial ponds, ice cliffs and englacial hydrology to further understand the dynamics of debris-covered glaciers. Finally, we conclude that UAV deployment has large potential in glaciology and it may revolutionize methods currently applied in studying glacier surface features.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 150","title":"High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles","status":"public","_id":"12636","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","keyword":["Computers in Earth Sciences","Geology","Soil Science"],"scopus_import":"1","date_published":"2014-07-01T00:00:00Z","page":"93-103","article_type":"original","citation":{"ama":"Immerzeel WW, Kraaijenbrink PDA, Shea JM, et al. High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing of Environment. 2014;150(7):93-103. doi:10.1016/j.rse.2014.04.025","apa":"Immerzeel, W. W., Kraaijenbrink, P. D. A., Shea, J. M., Shrestha, A. B., Pellicciotti, F., Bierkens, M. F. P., & de Jong, S. M. (2014). High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing of Environment. Elsevier. https://doi.org/10.1016/j.rse.2014.04.025","ieee":"W. W. Immerzeel et al., “High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles,” Remote Sensing of Environment, vol. 150, no. 7. Elsevier, pp. 93–103, 2014.","ista":"Immerzeel WW, Kraaijenbrink PDA, Shea JM, Shrestha AB, Pellicciotti F, Bierkens MFP, de Jong SM. 2014. High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing of Environment. 150(7), 93–103.","short":"W.W. Immerzeel, P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, F. Pellicciotti, M.F.P. Bierkens, S.M. de Jong, Remote Sensing of Environment 150 (2014) 93–103.","mla":"Immerzeel, W. W., et al. “High-Resolution Monitoring of Himalayan Glacier Dynamics Using Unmanned Aerial Vehicles.” Remote Sensing of Environment, vol. 150, no. 7, Elsevier, 2014, pp. 93–103, doi:10.1016/j.rse.2014.04.025.","chicago":"Immerzeel, W.W., P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, Francesca Pellicciotti, M.F.P. Bierkens, and S.M. de Jong. “High-Resolution Monitoring of Himalayan Glacier Dynamics Using Unmanned Aerial Vehicles.” Remote Sensing of Environment. Elsevier, 2014. https://doi.org/10.1016/j.rse.2014.04.025."},"publication":"Remote Sensing of Environment"},{"citation":{"mla":"Pellicciotti, Francesca, et al. “Changes in Glaciers in the Swiss Alps and Impact on Basin Hydrology: Current State of the Art and Future Research.” Science of The Total Environment, vol. 493, Elsevier, 2014, pp. 1152–70, doi:10.1016/j.scitotenv.2014.04.022.","short":"F. Pellicciotti, M. Carenzo, R. Bordoy, M. Stoffel, Science of The Total Environment 493 (2014) 1152–1170.","chicago":"Pellicciotti, Francesca, M. Carenzo, R. Bordoy, and M. Stoffel. “Changes in Glaciers in the Swiss Alps and Impact on Basin Hydrology: Current State of the Art and Future Research.” Science of The Total Environment. Elsevier, 2014. https://doi.org/10.1016/j.scitotenv.2014.04.022.","ama":"Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research. Science of The Total Environment. 2014;493:1152-1170. doi:10.1016/j.scitotenv.2014.04.022","ista":"Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. 2014. Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research. Science of The Total Environment. 493, 1152–1170.","apa":"Pellicciotti, F., Carenzo, M., Bordoy, R., & Stoffel, M. (2014). Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research. Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2014.04.022","ieee":"F. Pellicciotti, M. Carenzo, R. Bordoy, and M. Stoffel, “Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research,” Science of The Total Environment, vol. 493. Elsevier, pp. 1152–1170, 2014."},"publication":"Science of The Total Environment","page":"1152-1170","quality_controlled":"1","article_type":"review","doi":"10.1016/j.scitotenv.2014.04.022","date_published":"2014-09-15T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"publication_identifier":{"issn":["0048-9697"]},"article_processing_charge":"No","day":"15","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12635","year":"2014","publisher":"Elsevier","intvolume":" 493","publication_status":"published","title":"Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research","status":"public","author":[{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"full_name":"Carenzo, M.","first_name":"M.","last_name":"Carenzo"},{"full_name":"Bordoy, R.","last_name":"Bordoy","first_name":"R."},{"first_name":"M.","last_name":"Stoffel","full_name":"Stoffel, M."}],"volume":493,"oa_version":"None","date_updated":"2023-02-24T08:36:04Z","date_created":"2023-02-20T08:16:51Z","type":"journal_article","abstract":[{"lang":"eng","text":"Switzerland is one of the countries with some of the longest and best glaciological data sets. Its glaciers and their changes in response to climate have been extensively investigated, and the number and quality of related studies are notable. However, a comprehensive review of glacier changes and their impact on the hydrology of glacierised catchments for Switzerland is missing and we use the opportunity provided by the EU-FP7 ACQWA project to review the current state of knowledge about past changes and future projections. We examine the type of models that have been applied to infer glacier evolution and identify knowledge gaps that should be addressed in future research in addition to those indicated in previous publications. Common characteristics in long-term series of projected future glacier runoff are an initial peak followed by a decline, associated with shifts in seasonality, earlier melt onset and reduced summer runoff. However, the quantitative predictions are difficult to compare, as studies differ in terms of model structure, calibration strategies, input data, temporal and spatial resolution as well as future scenarios used for impact studies. We identify two sources of uncertainties among those emerging from recent research, and use simulations over four glaciers to: i) quantify the importance of the correct extrapolation of air temperature, and ii) point at the key role played by debris cover in modulating glacier response."}],"extern":"1"},{"extern":"1","year":"2014","publisher":"International Glaciological Society","publication_status":"published","author":[{"last_name":"Gabbi","first_name":"Jeannette","full_name":"Gabbi, Jeannette"},{"full_name":"Carenzo, Marco","first_name":"Marco","last_name":"Carenzo"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"first_name":"Andreas","last_name":"Bauder","full_name":"Bauder, Andreas"},{"full_name":"Funk, Martin","last_name":"Funk","first_name":"Martin"}],"volume":60,"date_created":"2023-02-20T08:16:34Z","date_updated":"2023-02-24T08:56:35Z","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"month":"08","main_file_link":[{"url":"https://doi.org/10.3189/2014JoG14J011","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.3189/2014jog14j011","language":[{"iso":"eng"}],"type":"journal_article","issue":"224","abstract":[{"lang":"eng","text":"We investigate the performance of five glacier melt models over a multi-decadal period in order to assess their ability to model future glacier response. The models range from a simple degree-day model, based solely on air temperature, to more-sophisticated models, including the full shortwave radiation balance. In addition to the empirical models, the performance of a physically based energy-balance (EB) model is examined. The melt models are coupled to an accumulation and a surface evolution model and applied in a distributed manner to Rhonegletscher, Switzerland, over the period 1929–2012 at hourly resolution. For calibration, seasonal mass-balance measurements (2006–12) are used. Decadal ice volume changes for six periods in the years 1929–2012 serve for model validation. Over the period 2006–12, there are almost no differences in performance between the models, except for EB, which is less consistent with observations, likely due to lack of meteorological in situ data. However, simulations over the long term (1929–2012) reveal that models which include a separate term for shortwave radiation agree best with the observed ice volume changes, indicating that their melt relationships are robust in time and thus suitable for long-term modelling, in contrast to more empirical approaches that are oversensitive to temperature fluctuations."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12632","intvolume":" 60","title":"A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response","status":"public","oa_version":"Published Version","scopus_import":"1","keyword":["Earth-Surface Processes"],"article_processing_charge":"No","day":"01","citation":{"ama":"Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response. Journal of Glaciology. 2014;60(224):1140-1154. doi:10.3189/2014jog14j011","ista":"Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. 2014. A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response. Journal of Glaciology. 60(224), 1140–1154.","ieee":"J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, and M. Funk, “A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response,” Journal of Glaciology, vol. 60, no. 224. International Glaciological Society, pp. 1140–1154, 2014.","apa":"Gabbi, J., Carenzo, M., Pellicciotti, F., Bauder, A., & Funk, M. (2014). A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2014jog14j011","mla":"Gabbi, Jeannette, et al. “A Comparison of Empirical and Physically Based Glacier Surface Melt Models for Long-Term Simulations of Glacier Response.” Journal of Glaciology, vol. 60, no. 224, International Glaciological Society, 2014, pp. 1140–54, doi:10.3189/2014jog14j011.","short":"J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, M. Funk, Journal of Glaciology 60 (2014) 1140–1154.","chicago":"Gabbi, Jeannette, Marco Carenzo, Francesca Pellicciotti, Andreas Bauder, and Martin Funk. “A Comparison of Empirical and Physically Based Glacier Surface Melt Models for Long-Term Simulations of Glacier Response.” Journal of Glaciology. International Glaciological Society, 2014. https://doi.org/10.3189/2014jog14j011."},"publication":"Journal of Glaciology","page":"1140-1154","article_type":"original","date_published":"2014-08-01T00:00:00Z"},{"page":"1197-1210","quality_controlled":"1","article_type":"review","citation":{"ista":"Pellicciotti F, Ragettli S, Carenzo M, McPhee J. 2014. Changes of glaciers in the Andes of Chile and priorities for future work. Science of The Total Environment. 493, 1197–1210.","ieee":"F. Pellicciotti, S. Ragettli, M. Carenzo, and J. McPhee, “Changes of glaciers in the Andes of Chile and priorities for future work,” Science of The Total Environment, vol. 493. Elsevier, pp. 1197–1210, 2014.","apa":"Pellicciotti, F., Ragettli, S., Carenzo, M., & McPhee, J. (2014). Changes of glaciers in the Andes of Chile and priorities for future work. Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2013.10.055","ama":"Pellicciotti F, Ragettli S, Carenzo M, McPhee J. Changes of glaciers in the Andes of Chile and priorities for future work. Science of The Total Environment. 2014;493:1197-1210. doi:10.1016/j.scitotenv.2013.10.055","chicago":"Pellicciotti, Francesca, S. Ragettli, M. Carenzo, and J. McPhee. “Changes of Glaciers in the Andes of Chile and Priorities for Future Work.” Science of The Total Environment. Elsevier, 2014. https://doi.org/10.1016/j.scitotenv.2013.10.055.","mla":"Pellicciotti, Francesca, et al. “Changes of Glaciers in the Andes of Chile and Priorities for Future Work.” Science of The Total Environment, vol. 493, Elsevier, 2014, pp. 1197–210, doi:10.1016/j.scitotenv.2013.10.055.","short":"F. Pellicciotti, S. Ragettli, M. Carenzo, J. McPhee, Science of The Total Environment 493 (2014) 1197–1210."},"publication":"Science of The Total Environment","language":[{"iso":"eng"}],"doi":"10.1016/j.scitotenv.2013.10.055","date_published":"2014-09-15T00:00:00Z","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"issn":["0048-9697"]},"month":"09","day":"15","publisher":"Elsevier","intvolume":" 493","status":"public","title":"Changes of glaciers in the Andes of Chile and priorities for future work","publication_status":"published","_id":"12634","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","oa_version":"None","volume":493,"date_updated":"2023-02-24T08:37:57Z","date_created":"2023-02-20T08:16:46Z","author":[{"first_name":"Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"last_name":"Ragettli","first_name":"S.","full_name":"Ragettli, S."},{"full_name":"Carenzo, M.","last_name":"Carenzo","first_name":"M."},{"first_name":"J.","last_name":"McPhee","full_name":"McPhee, J."}],"type":"journal_article","extern":"1","abstract":[{"text":"Glaciers in the Andes of Chile seem to be shrinking and possibly loosing mass, but the number and types of studies conducted, constrained mainly by data availability, are not sufficient to provide a synopsis of glacier changes for the past or future or explain in an explicit way causes of the observed changes. In this paper, we provide a systematic review of changes in glaciers for the entire country, followed by a discussion of the studies that have provided evidence of such changes. We identify a missing type of work in distributed, physically-oriented modelling studies that are needed to bridge the gap between the numerous remote sensing studies and the specific, point scale works focused on process understanding. We use an advanced mass balance model applied to one of the best monitored glaciers in the region to investigate four main research issues that should be addressed in modelling studies for a sound assessment of glacier changes: 1) the use of physically-based models of glacier ablation (energy balance models) versus more empirical models (enhanced temperature index approaches); 2) the importance of the correct extrapolation of air temperature forcing on glaciers and in high elevation areas and the large uncertainty in model outputs associated with it; 3) the role played by snow gravitational redistribution; and 4) the uncertainty associated with future climate scenarios. We quantify differences in model outputs associated with each of these choices, and conclude with suggestions for future work directions.","lang":"eng"}]},{"issue":"12","abstract":[{"lang":"eng","text":"Nature has long inspired scientists with its seemingly unlimited ability to harness solar energy and to utilize it to drive various physiological processes. With the help of man-made molecular photoswitches, we now have the potential to outperform natural systems in many ways, with the ultimate goal of fabricating multifunctional materials that operate at different light wavelengths. An important challenge in developing light-controlled artificial molecular machines lies in attaining a detailed understanding of the photoisomerization-coupled conformational changes that occur in macromolecules and molecular assemblies. In this issue of ACS Nano, Bléger, Rabe, and co-workers use force microscopy to provide interesting insights into the behavior of individual photoresponsive molecules and to identify contraction, extension, and crawling events accompanying light-induced isomerization."}],"type":"journal_article","oa_version":"None","intvolume":" 8","status":"public","title":"Watching single molecules move in response to light","_id":"13399","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"23","keyword":["General Physics and Astronomy","General Engineering","General Materials Science"],"scopus_import":"1","date_published":"2014-12-23T00:00:00Z","page":"11913-11916","article_type":"original","citation":{"ama":"Kundu PK, Klajn R. Watching single molecules move in response to light. ACS Nano. 2014;8(12):11913-11916. doi:10.1021/nn506656r","ista":"Kundu PK, Klajn R. 2014. Watching single molecules move in response to light. ACS Nano. 8(12), 11913–11916.","ieee":"P. K. Kundu and R. Klajn, “Watching single molecules move in response to light,” ACS Nano, vol. 8, no. 12. American Chemical Society, pp. 11913–11916, 2014.","apa":"Kundu, P. K., & Klajn, R. (2014). Watching single molecules move in response to light. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn506656r","mla":"Kundu, Pintu K., and Rafal Klajn. “Watching Single Molecules Move in Response to Light.” ACS Nano, vol. 8, no. 12, American Chemical Society, 2014, pp. 11913–16, doi:10.1021/nn506656r.","short":"P.K. Kundu, R. Klajn, ACS Nano 8 (2014) 11913–11916.","chicago":"Kundu, Pintu K., and Rafal Klajn. “Watching Single Molecules Move in Response to Light.” ACS Nano. American Chemical Society, 2014. https://doi.org/10.1021/nn506656r."},"publication":"ACS Nano","extern":"1","volume":8,"date_updated":"2023-08-08T07:18:58Z","date_created":"2023-08-01T09:45:42Z","author":[{"full_name":"Kundu, Pintu K.","last_name":"Kundu","first_name":"Pintu K."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2014","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1021/nn506656r","quality_controlled":"1","external_id":{"pmid":["25474733"]}},{"citation":{"ista":"Kundu PK, Olsen GL, Kiss V, Klajn R. 2014. Nanoporous frameworks exhibiting multiple stimuli responsiveness. Nature Communications. 5, 3588.","ieee":"P. K. Kundu, G. L. Olsen, V. Kiss, and R. Klajn, “Nanoporous frameworks exhibiting multiple stimuli responsiveness,” Nature Communications, vol. 5. Springer Nature, 2014.","apa":"Kundu, P. K., Olsen, G. L., Kiss, V., & Klajn, R. (2014). Nanoporous frameworks exhibiting multiple stimuli responsiveness. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms4588","ama":"Kundu PK, Olsen GL, Kiss V, Klajn R. Nanoporous frameworks exhibiting multiple stimuli responsiveness. Nature Communications. 2014;5. doi:10.1038/ncomms4588","chicago":"Kundu, Pintu K., Gregory L. Olsen, Vladimir Kiss, and Rafal Klajn. “Nanoporous Frameworks Exhibiting Multiple Stimuli Responsiveness.” Nature Communications. Springer Nature, 2014. https://doi.org/10.1038/ncomms4588.","mla":"Kundu, Pintu K., et al. “Nanoporous Frameworks Exhibiting Multiple Stimuli Responsiveness.” Nature Communications, vol. 5, 3588, Springer Nature, 2014, doi:10.1038/ncomms4588.","short":"P.K. Kundu, G.L. Olsen, V. Kiss, R. Klajn, Nature Communications 5 (2014)."},"publication":"Nature Communications","article_type":"original","date_published":"2014-04-07T00:00:00Z","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"article_processing_charge":"No","day":"07","_id":"13402","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","title":"Nanoporous frameworks exhibiting multiple stimuli responsiveness","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Nanoporous frameworks are polymeric materials built from rigid molecules, which give rise to their nanoporous structures with applications in gas sorption and storage, catalysis and others. Conceptually new applications could emerge, should these beneficial properties be manipulated by external stimuli in a reversible manner. One approach to render nanoporous frameworks responsive to external signals would be to immobilize molecular switches within their nanopores. Although the majority of molecular switches require conformational freedom to isomerize, and switching in the solid state is prohibited, the nanopores may provide enough room for the switches to efficiently isomerize. Here we describe two families of nanoporous materials incorporating the spiropyran molecular switch. These materials exhibit a variety of interesting properties, including reversible photochromism and acidochromism under solvent-free conditions, light-controlled capture and release of metal ions, as well reversible chromism induced by solvation/desolvation."}],"oa":1,"external_id":{"pmid":["24709950"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms4588"}],"quality_controlled":"1","doi":"10.1038/ncomms4588","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"04","pmid":1,"year":"2014","publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Pintu K.","last_name":"Kundu","full_name":"Kundu, Pintu K."},{"last_name":"Olsen","first_name":"Gregory L.","full_name":"Olsen, Gregory L."},{"full_name":"Kiss, Vladimir","first_name":"Vladimir","last_name":"Kiss"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"volume":5,"date_updated":"2023-08-08T07:28:10Z","date_created":"2023-08-01T09:46:27Z","article_number":"3588","extern":"1"},{"date_created":"2023-08-01T09:45:56Z","date_updated":"2023-08-08T07:23:05Z","volume":345,"author":[{"full_name":"Singh, Gurvinder","first_name":"Gurvinder","last_name":"Singh"},{"full_name":"Chan, Henry","last_name":"Chan","first_name":"Henry"},{"full_name":"Baskin, Artem","last_name":"Baskin","first_name":"Artem"},{"full_name":"Gelman, Elijah","first_name":"Elijah","last_name":"Gelman"},{"full_name":"Repnin, Nikita","first_name":"Nikita","last_name":"Repnin"},{"full_name":"Král, Petr","first_name":"Petr","last_name":"Král"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"publication_status":"published","publisher":"American Association for the Advancement of Science","year":"2014","pmid":1,"extern":"1","language":[{"iso":"eng"}],"doi":"10.1126/science.1254132","quality_controlled":"1","external_id":{"pmid":["25061133"]},"month":"07","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa_version":"None","title":"Self-assembly of magnetite nanocubes into helical superstructures","status":"public","intvolume":" 345","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13400","abstract":[{"lang":"eng","text":"Organizing inorganic nanocrystals into complex architectures is challenging and typically relies on preexisting templates, such as properly folded DNA or polypeptide chains. We found that under carefully controlled conditions, cubic nanocrystals of magnetite self-assemble into arrays of helical superstructures in a template-free manner with >99% yield. Computer simulations revealed that the formation of helices is determined by the interplay of van der Waals and magnetic dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed to spontaneous formation of chiral nanocube clusters. Neighboring helices within their densely packed ensembles tended to adopt the same handedness in order to maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality amplification."}],"issue":"6201","type":"journal_article","date_published":"2014-07-24T00:00:00Z","article_type":"original","page":"1149-1153","publication":"Science","citation":{"mla":"Singh, Gurvinder, et al. “Self-Assembly of Magnetite Nanocubes into Helical Superstructures.” Science, vol. 345, no. 6201, American Association for the Advancement of Science, 2014, pp. 1149–53, doi:10.1126/science.1254132.","short":"G. Singh, H. Chan, A. Baskin, E. Gelman, N. Repnin, P. Král, R. Klajn, Science 345 (2014) 1149–1153.","chicago":"Singh, Gurvinder, Henry Chan, Artem Baskin, Elijah Gelman, Nikita Repnin, Petr Král, and Rafal Klajn. “Self-Assembly of Magnetite Nanocubes into Helical Superstructures.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1254132.","ama":"Singh G, Chan H, Baskin A, et al. Self-assembly of magnetite nanocubes into helical superstructures. Science. 2014;345(6201):1149-1153. doi:10.1126/science.1254132","ista":"Singh G, Chan H, Baskin A, Gelman E, Repnin N, Král P, Klajn R. 2014. Self-assembly of magnetite nanocubes into helical superstructures. Science. 345(6201), 1149–1153.","apa":"Singh, G., Chan, H., Baskin, A., Gelman, E., Repnin, N., Král, P., & Klajn, R. (2014). Self-assembly of magnetite nanocubes into helical superstructures. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254132","ieee":"G. Singh et al., “Self-assembly of magnetite nanocubes into helical superstructures,” Science, vol. 345, no. 6201. American Association for the Advancement of Science, pp. 1149–1153, 2014."},"day":"24","article_processing_charge":"No","keyword":["Multidisciplinary"],"scopus_import":"1"},{"pmid":1,"year":"2014","publisher":"Royal Society of Chemistry","publication_status":"published","author":[{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"volume":43,"date_updated":"2023-08-08T07:41:38Z","date_created":"2023-08-01T09:47:03Z","extern":"1","oa":1,"external_id":{"pmid":["23979515"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C3CS60181A"}],"quality_controlled":"1","doi":"10.1039/c3cs60181a","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"month":"01","_id":"13404","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 43","title":"Spiropyran-based dynamic materials","status":"public","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"In the past few years, spiropyran has emerged as the molecule-of-choice for the construction of novel dynamic materials. This unique molecular switch undergoes structural isomerisation in response to a variety of orthogonal stimuli, e.g. light, temperature, metal ions, redox potential, and mechanical stress. Incorporation of this switch onto macromolecular supports or inorganic scaffolds allows for the creation of robust dynamic materials. This review discusses the synthesis, switching conditions, and use of dynamic materials in which spiropyran has been attached to the surfaces of polymers, biomacromolecules, inorganic nanoparticles, as well as solid surfaces. The resulting materials show fascinating properties whereby the state of the switch intimately affects a multitude of useful properties of the support. The utility of the spiropyran switch will undoubtedly endow these materials with far-reaching applications in the near future."}],"citation":{"short":"R. Klajn, Chemical Society Reviews 43 (2014) 148–184.","mla":"Klajn, Rafal. “Spiropyran-Based Dynamic Materials.” Chemical Society Reviews, vol. 43, no. 1, Royal Society of Chemistry, 2014, pp. 148–84, doi:10.1039/c3cs60181a.","chicago":"Klajn, Rafal. “Spiropyran-Based Dynamic Materials.” Chemical Society Reviews. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c3cs60181a.","ama":"Klajn R. Spiropyran-based dynamic materials. Chemical Society Reviews. 2014;43(1):148-184. doi:10.1039/c3cs60181a","apa":"Klajn, R. (2014). Spiropyran-based dynamic materials. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c3cs60181a","ieee":"R. Klajn, “Spiropyran-based dynamic materials,” Chemical Society Reviews, vol. 43, no. 1. Royal Society of Chemistry, pp. 148–184, 2014.","ista":"Klajn R. 2014. Spiropyran-based dynamic materials. Chemical Society Reviews. 43(1), 148–184."},"publication":"Chemical Society Reviews","page":"148-184","article_type":"original","date_published":"2014-01-27T00:00:00Z","scopus_import":"1","keyword":["General Chemistry"],"article_processing_charge":"No","day":"27"},{"type":"journal_article","issue":"32","abstract":[{"lang":"eng","text":"A compound combining the features of a molecular rotor and a photoswitch was synthesized and was shown to exist as three diastereomers, which interconvert via a reversible cyclic reaction scheme. Each of the three diastereomers was isolated, and by following the equilibration kinetics, activation barriers for all reactions were calculated. The results indicate that the properties of molecular switches depend heavily on their immediate chemical environment. The conclusions are important in the context of designing new switchable molecules and materials."}],"intvolume":" 136","status":"public","title":"Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran","_id":"13401","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"scopus_import":"1","article_processing_charge":"No","day":"13","page":"11276-11279","article_type":"original","citation":{"chicago":"Kundu, Pintu K., Avishai Lerner, Kristina Kučanda, Gregory Leitus, and Rafal Klajn. “Cyclic Kinetics during Thermal Equilibration of an Axially Chiral Bis-Spiropyran.” Journal of the American Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja505948q.","short":"P.K. Kundu, A. Lerner, K. Kučanda, G. Leitus, R. Klajn, Journal of the American Chemical Society 136 (2014) 11276–11279.","mla":"Kundu, Pintu K., et al. “Cyclic Kinetics during Thermal Equilibration of an Axially Chiral Bis-Spiropyran.” Journal of the American Chemical Society, vol. 136, no. 32, American Chemical Society, 2014, pp. 11276–79, doi:10.1021/ja505948q.","apa":"Kundu, P. K., Lerner, A., Kučanda, K., Leitus, G., & Klajn, R. (2014). Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja505948q","ieee":"P. K. Kundu, A. Lerner, K. Kučanda, G. Leitus, and R. Klajn, “Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran,” Journal of the American Chemical Society, vol. 136, no. 32. American Chemical Society, pp. 11276–11279, 2014.","ista":"Kundu PK, Lerner A, Kučanda K, Leitus G, Klajn R. 2014. Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran. Journal of the American Chemical Society. 136(32), 11276–11279.","ama":"Kundu PK, Lerner A, Kučanda K, Leitus G, Klajn R. Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran. Journal of the American Chemical Society. 2014;136(32):11276-11279. doi:10.1021/ja505948q"},"publication":"Journal of the American Chemical Society","date_published":"2014-08-13T00:00:00Z","extern":"1","publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2014","volume":136,"date_created":"2023-08-01T09:46:12Z","date_updated":"2023-08-08T07:25:37Z","author":[{"full_name":"Kundu, Pintu K.","first_name":"Pintu K.","last_name":"Kundu"},{"full_name":"Lerner, Avishai","last_name":"Lerner","first_name":"Avishai"},{"first_name":"Kristina","last_name":"Kučanda","full_name":"Kučanda, Kristina"},{"first_name":"Gregory","last_name":"Leitus","full_name":"Leitus, Gregory"},{"first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"month":"08","quality_controlled":"1","external_id":{"pmid":["25072292"]},"language":[{"iso":"eng"}],"doi":"10.1021/ja505948q"},{"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"We show that bimolecular reactions between species confined to the surfaces of nanoparticles can be manipulated by the nature of the linker, as well as by the curvature of the underlying particles."}],"intvolume":" 136","status":"public","title":"Support curvature and conformational freedom control chemical reactivity of immobilized species","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13403","oa_version":"None","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"scopus_import":"1","article_processing_charge":"No","day":"19","page":"2711-2714","article_type":"original","citation":{"chicago":"Zdobinsky, Tino, Pradipta Sankar Maiti, and Rafal Klajn. “Support Curvature and Conformational Freedom Control Chemical Reactivity of Immobilized Species.” Journal of the American Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja411573a.","short":"T. Zdobinsky, P. Sankar Maiti, R. Klajn, Journal of the American Chemical Society 136 (2014) 2711–2714.","mla":"Zdobinsky, Tino, et al. “Support Curvature and Conformational Freedom Control Chemical Reactivity of Immobilized Species.” Journal of the American Chemical Society, vol. 136, no. 7, American Chemical Society, 2014, pp. 2711–14, doi:10.1021/ja411573a.","ieee":"T. Zdobinsky, P. Sankar Maiti, and R. Klajn, “Support curvature and conformational freedom control chemical reactivity of immobilized species,” Journal of the American Chemical Society, vol. 136, no. 7. American Chemical Society, pp. 2711–2714, 2014.","apa":"Zdobinsky, T., Sankar Maiti, P., & Klajn, R. (2014). Support curvature and conformational freedom control chemical reactivity of immobilized species. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja411573a","ista":"Zdobinsky T, Sankar Maiti P, Klajn R. 2014. Support curvature and conformational freedom control chemical reactivity of immobilized species. Journal of the American Chemical Society. 136(7), 2711–2714.","ama":"Zdobinsky T, Sankar Maiti P, Klajn R. Support curvature and conformational freedom control chemical reactivity of immobilized species. Journal of the American Chemical Society. 2014;136(7):2711-2714. doi:10.1021/ja411573a"},"publication":"Journal of the American Chemical Society","date_published":"2014-02-19T00:00:00Z","extern":"1","publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2014","volume":136,"date_created":"2023-08-01T09:46:44Z","date_updated":"2023-08-08T07:32:11Z","author":[{"last_name":"Zdobinsky","first_name":"Tino","full_name":"Zdobinsky, Tino"},{"full_name":"Sankar Maiti, Pradipta","first_name":"Pradipta","last_name":"Sankar Maiti"},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"month":"02","quality_controlled":"1","external_id":{"pmid":["24320557"]},"language":[{"iso":"eng"}],"doi":"10.1021/ja411573a"},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14018","status":"public","title":"The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics","intvolume":" 171","abstract":[{"text":"The sensitivities of high-harmonic generation (HHG) and strong-field ionization (SFI) to coupled electronic and nuclear dynamics are studied, using the nitric oxide (NO) molecule as an example. A coherent superposition of electronic and rotational states of NO is prepared by impulsive stimulated Raman scattering and probed by simultaneous detection of HHG and SFI yields. We observe a fourfold higher sensitivity of high-harmonic generation to electronic dynamics and attribute it to the presence of inelastic quantum paths connecting coherently related electronic states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic orders display very different sensitivities to rotational or electronic dynamics, strong-field ionization is found to be most sensitive to electronic motion. We introduce a general theoretical formalism for high-harmonic generation from coupled nuclear-electronic wave packets. We show that the unequal sensitivities of different harmonic orders to electronic or rotational dynamics result from the angle dependence of the photorecombination matrix elements which encode several autoionizing and shape resonances in the photoionization continuum of NO. We further study the dependence of rotational and electronic coherences on the intensity of the excitation pulse and support the observations with calculations.","lang":"eng"}],"type":"journal_article","date_published":"2014-04-14T00:00:00Z","publication":"Faraday Discussions","citation":{"ista":"Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. 2014. The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. 171, 113–132.","apa":"Baykusheva, D. R., Kraus, P. M., Zhang, S. B., Rohringer, N., & Wörner, H. J. (2014). The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00018h","ieee":"D. R. Baykusheva, P. M. Kraus, S. B. Zhang, N. Rohringer, and H. J. Wörner, “The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics,” Faraday Discussions, vol. 171. Royal Society of Chemistry, pp. 113–132, 2014.","ama":"Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. 2014;171:113-132. doi:10.1039/c4fd00018h","chicago":"Baykusheva, Denitsa Rangelova, Peter M. Kraus, Song Bin Zhang, Nina Rohringer, and Hans Jakob Wörner. “The Sensitivities of High-Harmonic Generation and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4fd00018h.","mla":"Baykusheva, Denitsa Rangelova, et al. “The Sensitivities of High-Harmonic Generation and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions, vol. 171, Royal Society of Chemistry, 2014, pp. 113–32, doi:10.1039/c4fd00018h.","short":"D.R. Baykusheva, P.M. Kraus, S.B. Zhang, N. Rohringer, H.J. Wörner, Faraday Discussions 171 (2014) 113–132."},"article_type":"original","page":"113-132","day":"14","article_processing_charge":"No","scopus_import":"1","keyword":["Physical and Theoretical Chemistry"],"author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"full_name":"Kraus, Peter M.","last_name":"Kraus","first_name":"Peter M."},{"last_name":"Zhang","first_name":"Song Bin","full_name":"Zhang, Song Bin"},{"full_name":"Rohringer, Nina","first_name":"Nina","last_name":"Rohringer"},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"}],"date_updated":"2023-08-22T08:58:12Z","date_created":"2023-08-10T06:38:19Z","volume":171,"year":"2014","pmid":1,"publication_status":"published","publisher":"Royal Society of Chemistry","extern":"1","doi":"10.1039/c4fd00018h","language":[{"iso":"eng"}],"external_id":{"pmid":["25415558"]},"quality_controlled":"1","month":"04","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]}},{"article_type":"original","citation":{"chicago":"Vasilatou, K., J. M. Michaud, Denitsa Rangelova Baykusheva, G. Grassi, and F. Merkt. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4890744.","short":"K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal of Chemical Physics 141 (2014).","mla":"Vasilatou, K., et al. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of Chemical Physics, vol. 141, no. 6, 064317, AIP Publishing, 2014, doi:10.1063/1.4890744.","ieee":"K. Vasilatou, J. M. Michaud, D. R. Baykusheva, G. Grassi, and F. Merkt, “The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra,” The Journal of Chemical Physics, vol. 141, no. 6. AIP Publishing, 2014.","apa":"Vasilatou, K., Michaud, J. M., Baykusheva, D. R., Grassi, G., & Merkt, F. (2014). The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4890744","ista":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. 2014. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. 141(6), 064317.","ama":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. 2014;141(6). doi:10.1063/1.4890744"},"publication":"The Journal of Chemical Physics","date_published":"2014-08-14T00:00:00Z","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"scopus_import":"1","article_processing_charge":"No","day":"14","intvolume":" 141","status":"public","title":"The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14019","oa_version":"None","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity."}],"quality_controlled":"1","external_id":{"pmid":["25134581"]},"language":[{"iso":"eng"}],"doi":"10.1063/1.4890744","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"08","publisher":"AIP Publishing","publication_status":"published","pmid":1,"year":"2014","volume":141,"date_updated":"2023-08-22T09:01:31Z","date_created":"2023-08-10T06:38:30Z","author":[{"first_name":"K.","last_name":"Vasilatou","full_name":"Vasilatou, K."},{"last_name":"Michaud","first_name":"J. M.","full_name":"Michaud, J. M."},{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Grassi, G.","last_name":"Grassi","first_name":"G."},{"last_name":"Merkt","first_name":"F.","full_name":"Merkt, F."}],"article_number":"064317","extern":"1"},{"author":[{"full_name":"Kraus, P M","first_name":"P M","last_name":"Kraus"},{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Wörner, H J","last_name":"Wörner","first_name":"H J"}],"date_updated":"2023-08-22T09:04:30Z","date_created":"2023-08-10T06:38:48Z","volume":47,"year":"2014","publication_status":"published","publisher":"IOP Publishing","extern":"1","article_number":"124030","doi":"10.1088/0953-4075/47/12/124030","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1311.3923"]},"main_file_link":[{"url":"https://arxiv.org/abs/1311.3923","open_access":"1"}],"quality_controlled":"1","month":"06","publication_identifier":{"eissn":["1361-6455"],"issn":["0953-4075"]},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14021","title":"Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules","status":"public","intvolume":" 47","abstract":[{"text":"We present the detailed analysis of a new two-pulse orientation scheme that achieves macroscopic field-free orientation at the high particle densities required for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923). Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour non-resonant femtosecond laser pulses. High-harmonic generation is used to probe the oriented wave-packet dynamics and reveals that a very high degree of orientation (Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting carbonyl sulphide molecules. We show that the present two-pulse scheme selectively enhances orientation created by the hyperpolarizability interaction whereas the ionization-depletion mechanism plays no role. We further control and optimize orientation through the delay between the one- and two-colour pump pulses. Finally, we demonstrate a complementary encoding of electronic-structure features, such as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress makes two-pulse field-free orientation an attractive tool for a broad class of time-resolved measurements.","lang":"eng"}],"issue":"12","type":"journal_article","date_published":"2014-06-10T00:00:00Z","publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","citation":{"apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/0953-4075/47/12/124030","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12. IOP Publishing, 2014.","ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 47(12), 124030.","ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 2014;47(12). doi:10.1088/0953-4075/47/12/124030","chicago":"Kraus, P M, Denitsa Rangelova Baykusheva, and H J Wörner. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2014. https://doi.org/10.1088/0953-4075/47/12/124030.","short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 47 (2014).","mla":"Kraus, P. M., et al. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12, 124030, IOP Publishing, 2014, doi:10.1088/0953-4075/47/12/124030."},"article_type":"original","day":"10","article_processing_charge":"No","scopus_import":"1","keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"]},{"type":"journal_article","abstract":[{"text":"We report the observation of macroscopic field-free orientation, i.e., more than 73% of CO molecules pointing in the same direction. This is achieved through an all-optical scheme operating at high particle densities (>10(17) cm(-3)) that combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses. We show that the achieved orientation solely relies on the hyperpolarizability interaction as opposed to an ionization-depletion mechanism, thus, opening a wide range of applications. The achieved strong orientation enables us to reveal the molecular-frame anisotropies of the photorecombination amplitudes and phases caused by a shape resonance. The resonance appears as a local maximum in the even-harmonic emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in this spectral region through the combined effects of an asymmetric photorecombination phase and a subcycle Stark effect, generic for polar molecules, that we experimentally identify.","lang":"eng"}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14020","title":"Two-pulse field-free orientation reveals anisotropy of molecular shape resonance","status":"public","intvolume":" 113","oa_version":"Preprint","scopus_import":"1","keyword":["General Physics and Astronomy"],"day":"11","article_processing_charge":"No","publication":"Physical Review Letters","citation":{"short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Physical Review Letters 113 (2014).","mla":"Kraus, P. M., et al. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters, vol. 113, no. 2, 023001, American Physical Society, 2014, doi:10.1103/physrevlett.113.023001.","chicago":"Kraus, P. M., Denitsa Rangelova Baykusheva, and H. J. Wörner. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.113.023001.","ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 2014;113(2). doi:10.1103/physrevlett.113.023001","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse field-free orientation reveals anisotropy of molecular shape resonance,” Physical Review Letters, vol. 113, no. 2. American Physical Society, 2014.","apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.113.023001","ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 113(2), 023001."},"article_type":"original","date_published":"2014-07-11T00:00:00Z","article_number":"023001","extern":"1","year":"2014","pmid":1,"publication_status":"published","publisher":"American Physical Society","author":[{"full_name":"Kraus, P. M.","last_name":"Kraus","first_name":"P. M."},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"full_name":"Wörner, H. J.","first_name":"H. J.","last_name":"Wörner"}],"date_updated":"2023-08-22T09:02:56Z","date_created":"2023-08-10T06:38:38Z","volume":113,"month":"07","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3923"}],"external_id":{"pmid":["25062172"],"arxiv":["1311.3923"]},"quality_controlled":"1","doi":"10.1103/physrevlett.113.023001","language":[{"iso":"eng"}]},{"month":"11","doi":"10.1007/s00453-013-9843-7","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1604.08234","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1604.08234"]},"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"ec_funded":1,"publist_id":"7282","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10905"}]},"date_updated":"2023-09-05T14:09:29Z","date_created":"2018-12-11T11:47:01Z","volume":70,"year":"2014","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2014-11-01T00:00:00Z","publication":"Algorithmica","citation":{"mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:10.1007/s00453-013-9843-7.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 2014;70(3):457-492. doi:10.1007/s00453-013-9843-7","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. Algorithmica. Springer. https://doi.org/10.1007/s00453-013-9843-7","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” Algorithmica, vol. 70, no. 3. Springer, pp. 457–492, 2014."},"article_type":"original","page":"457 - 492","abstract":[{"text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","_id":"535","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","title":"Polynomial-time algorithms for energy games with special weight structures","intvolume":" 70"},{"day":"19","month":"03","publication_identifier":{"eissn":["2197-666X"],"isbn":["9783319040981"],"issn":["1612-3786"],"eisbn":["9783319040998"]},"article_processing_charge":"No","scopus_import":"1","doi":"10.1007/978-3-319-04099-8_16","date_published":"2014-03-19T00:00:00Z","language":[{"iso":"eng"}],"publication":"Topological Methods in Data Analysis and Visualization III ","citation":{"short":"V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–262.","mla":"Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In Topological Methods in Data Analysis and Visualization III , 249–62. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_16.","ama":"Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In: Topological Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature,” in Topological Methods in Data Analysis and Visualization III , 2014, pp. 249–262.","apa":"Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In Topological Methods in Data Analysis and Visualization III (pp. 249–262). Springer. https://doi.org/10.1007/978-3-319-04099-8_16","ista":"Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. Topological Methods in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262."},"quality_controlled":"1","page":"249-262","abstract":[{"lang":"eng","text":"We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set."}],"type":"conference","alternative_title":["Mathematics and Visualization"],"author":[{"full_name":"Zobel, Valentin","last_name":"Zobel","first_name":"Valentin"},{"first_name":"Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan"},{"full_name":"Hotz, Ingrid","first_name":"Ingrid","last_name":"Hotz"}],"date_updated":"2023-09-05T14:13:16Z","date_created":"2022-03-18T13:05:39Z","oa_version":"None","year":"2014","_id":"10886","acknowledgement":"This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","status":"public","title":"Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature","publisher":"Springer","department":[{"_id":"HeEd"}]},{"volume":1189,"date_updated":"2023-09-05T14:12:00Z","date_created":"2019-03-26T08:55:59Z","author":[{"full_name":"Smutny, Michael","first_name":"Michael","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090"},{"full_name":"Behrndt, Martin","last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Campinho, Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","first_name":"Pedro","last_name":"Campinho"},{"last_name":"Ruprecht","first_name":"Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"CaHe"}],"publisher":"Springer","editor":[{"first_name":"Celeste","last_name":"Nelson","full_name":"Nelson, Celeste"}],"publication_status":"published","pmid":1,"year":"2014","place":"New York, NY","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-1164-6_15","quality_controlled":"1","external_id":{"pmid":["25245697"]},"publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781493911639","9781493911646"]},"month":"08","oa_version":"None","intvolume":" 1189","title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","status":"public","_id":"6178","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo.","lang":"eng"}],"type":"book_chapter","date_published":"2014-08-22T00:00:00Z","page":"219-235","citation":{"ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. Methods in Molecular Biology. New York, NY: Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.","ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson, Ed. New York, NY: Springer, 2014, pp. 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis (Vol. 1189, pp. 219–235). New York, NY: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis, edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York, NY: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15."},"publication":"Tissue Morphogenesis","article_processing_charge":"No","day":"22","series_title":"Methods in Molecular Biology"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field."}],"_id":"10814","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2014","publisher":"Springer Nature","intvolume":" 116","department":[{"_id":"RoSe"}],"status":"public","publication_status":"published","title":"The excitation spectrum for Bose fluids with weak interactions","author":[{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","volume":116,"date_created":"2022-03-04T07:54:39Z","date_updated":"2023-09-05T14:19:47Z","scopus_import":"1","keyword":["General Medicine"],"article_processing_charge":"No","publication_identifier":{"issn":["0012-0456"],"eissn":["1869-7135"]},"day":"01","month":"03","citation":{"mla":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” Jahresbericht Der Deutschen Mathematiker-Vereinigung, vol. 116, Springer Nature, 2014, pp. 21–41, doi:10.1365/s13291-014-0083-9.","short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41.","chicago":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature, 2014. https://doi.org/10.1365/s13291-014-0083-9.","ama":"Seiringer R. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 2014;116:21-41. doi:10.1365/s13291-014-0083-9","ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","apa":"Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions. Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature. https://doi.org/10.1365/s13291-014-0083-9","ieee":"R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,” Jahresbericht der Deutschen Mathematiker-Vereinigung, vol. 116. Springer Nature, pp. 21–41, 2014."},"publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","page":"21-41","quality_controlled":"1","article_type":"original","date_published":"2014-03-01T00:00:00Z","doi":"10.1365/s13291-014-0083-9","language":[{"iso":"eng"}]},{"date_updated":"2023-09-05T15:33:45Z","date_created":"2022-03-04T08:33:57Z","author":[{"last_name":"Günther","first_name":"David","full_name":"Günther, David"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seidel","first_name":"Hans-Peter","full_name":"Seidel, Hans-Peter"},{"first_name":"Tino","last_name":"Weinkauf","full_name":"Weinkauf, Tino"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","editor":[{"full_name":"Bremer, Peer-Timo","first_name":"Peer-Timo","last_name":"Bremer"},{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"},{"full_name":"Pascucci, Valerio","last_name":"Pascucci","first_name":"Valerio"},{"first_name":"Ronald","last_name":"Peikert","full_name":"Peikert, Ronald"}],"year":"2014","acknowledgement":"This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.","ec_funded":1,"place":"Cham","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-04099-8_9","quality_controlled":"1","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems"}],"month":"03","publication_identifier":{"isbn":["9783319040981"],"eissn":["2197-666X"],"issn":["1612-3786"],"eisbn":["9783319040998"]},"oa_version":"None","title":"Notes on the simplification of the Morse-Smale complex","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10817","abstract":[{"text":"The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption.","lang":"eng"}],"type":"book_chapter","date_published":"2014-03-19T00:00:00Z","page":"135-150","publication":"Topological Methods in Data Analysis and Visualization III.","citation":{"mla":"Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.” Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.","short":"D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.","chicago":"Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf. “Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9.","ama":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9","ista":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization III. , 135–150.","ieee":"D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the simplification of the Morse-Smale complex,” in Topological Methods in Data Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.","apa":"Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9"},"day":"19","article_processing_charge":"No","series_title":"Mathematics and Visualization","scopus_import":"1"},{"supervisor":[{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia M","full_name":"Cremer, Sylvia M"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"date_published":"2014-02-01T00:00:00Z","page":"131","citation":{"ama":"Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 2014.","ieee":"M. Konrad, “Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology Austria, 2014.","apa":"Konrad, M. (2014). Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","ista":"Konrad M. 2014. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","short":"M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology Austria, 2014.","mla":"Konrad, Matthias. Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus. Institute of Science and Technology Austria, 2014.","chicago":"Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and Technology Austria, 2014."},"day":"01","month":"02","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","date_created":"2018-12-11T11:51:46Z","date_updated":"2023-09-07T11:38:56Z","oa_version":"None","author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias"}],"publication_status":"published","title":"Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus","status":"public","department":[{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","_id":"1395","year":"2014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants."}],"publist_id":"5814","alternative_title":["ISTA Thesis"],"type":"dissertation"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"publist_id":"5805","abstract":[{"lang":"eng","text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants."}],"year":"2014","_id":"1402","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","status":"public","publication_status":"published","title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","first_name":"Petra","full_name":"Marhavá, Petra"}],"oa_version":"None","date_updated":"2023-09-07T11:39:38Z","date_created":"2018-12-11T11:51:49Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","month":"12","day":"01","citation":{"chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.","mla":"Marhavá, Petra. Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2014.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.","ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","apa":"Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014."},"page":"90","date_published":"2014-12-01T00:00:00Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}]},{"_id":"2255","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 50","title":"Stable length estimates of tube-like shapes","status":"public","ddc":["000"],"pubrep_id":"549","file":[{"relation":"main_file","file_id":"5204","checksum":"2f93f3e63a38a85cd4404d7953913b14","date_updated":"2020-07-14T12:45:35Z","date_created":"2018-12-12T10:16:18Z","access_level":"open_access","file_name":"IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf","content_type":"application/pdf","file_size":3941391,"creator":"system"}],"oa_version":"Submitted Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm."}],"citation":{"chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” Journal of Mathematical Imaging and Vision. Springer, 2014. https://doi.org/10.1007/s10851-013-0468-x.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” Journal of Mathematical Imaging and Vision, vol. 50, no. 1, Springer, 2014, pp. 164–77, doi:10.1007/s10851-013-0468-x.","short":"H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision 50 (2014) 164–177.","ista":"Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 50(1), 164–177.","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” Journal of Mathematical Imaging and Vision, vol. 50, no. 1. Springer, pp. 164–177, 2014.","apa":"Edelsbrunner, H., & Pausinger, F. (2014). Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. Springer. https://doi.org/10.1007/s10851-013-0468-x","ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 2014;50(1):164-177. doi:10.1007/s10851-013-0468-x"},"publication":"Journal of Mathematical Imaging and Vision","page":"164 - 177","date_published":"2014-09-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","year":"2014","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","related_material":{"record":[{"id":"2843","relation":"earlier_version","status":"public"},{"id":"1399","status":"public","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768","first_name":"Florian","last_name":"Pausinger","full_name":"Pausinger, Florian"}],"volume":50,"date_updated":"2023-09-07T11:41:25Z","date_created":"2018-12-11T11:56:36Z","publist_id":"4691","ec_funded":1,"file_date_updated":"2020-07-14T12:45:35Z","oa":1,"project":[{"name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"quality_controlled":"1","doi":"10.1007/s10851-013-0468-x","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09249907"]},"month":"09"},{"date_published":"2014-06-08T00:00:00Z","page":"171 - 180","citation":{"chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue of the Whitney Trick.” In Proceedings of the Annual Symposium on Computational Geometry, 171–80. ACM, 2014. https://doi.org/10.1145/2582112.2582134.","short":"I. Mabillard, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 171–180.","mla":"Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue of the Whitney Trick.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 171–80, doi:10.1145/2582112.2582134.","apa":"Mabillard, I., & Wagner, U. (2014). Eliminating Tverberg points, I. An analogue of the Whitney trick. In Proceedings of the Annual Symposium on Computational Geometry (pp. 171–180). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582134","ieee":"I. Mabillard and U. Wagner, “Eliminating Tverberg points, I. An analogue of the Whitney trick,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 171–180.","ista":"Mabillard I, Wagner U. 2014. Eliminating Tverberg points, I. An analogue of the Whitney trick. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 171–180.","ama":"Mabillard I, Wagner U. Eliminating Tverberg points, I. An analogue of the Whitney trick. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:171-180. doi:10.1145/2582112.2582134"},"publication":"Proceedings of the Annual Symposium on Computational Geometry","has_accepted_license":"1","day":"08","scopus_import":1,"oa_version":"Submitted Version","file":[{"file_name":"IST-2016-534-v1+1_Eliminating_Tverberg_points_I._An_analogue_of_the_Whitney_trick.pdf","access_level":"open_access","file_size":914396,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4735","date_updated":"2020-07-14T12:45:30Z","date_created":"2018-12-12T10:09:12Z","checksum":"2aae223fee8ffeaf57bbabd8d92b6a2c"}],"pubrep_id":"534","ddc":["510"],"status":"public","title":"Eliminating Tverberg points, I. An analogue of the Whitney trick","_id":"2159","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Motivated by topological Tverberg-type problems, we consider multiple (double, triple, and higher multiplicity) selfintersection points of maps from finite simplicial complexes (compact polyhedra) into ℝd and study conditions under which such multiple points can be eliminated. The most classical case is that of embeddings (i.e., maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem, the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary condition for embeddability (namely, vanishing of the van Kampen ob-struction). For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes then one can successively remove these double points by local modifications of the map f. One of the main tools is the famous Whitney trick that permits eliminating pairs of double points of opposite intersection sign. We are interested in generalizing this approach to intersection points of higher multiplicity. We call a point y 2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e., does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time algorithm for deciding this (based on the vanishing of a cohomological obstruction, as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney trick: Given r pairwise disjoint simplices of K such that the intersection of their images contains two r-fold Tverberg points y+ and y- of opposite intersection sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper, we plan to develop this further and present a generalization of the classical Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability of κ-complexes into ℝd for a wider range of dimensions) to intersection points of higher multiplicity.","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1145/2582112.2582134","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2014-06-11","start_date":"2014-06-08","location":"Kyoto, Japan"},"quality_controlled":"1","oa":1,"month":"06","date_created":"2018-12-11T11:56:03Z","date_updated":"2023-09-07T11:56:27Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1123"}]},"author":[{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard","first_name":"Isaac","full_name":"Mabillard, Isaac"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"department":[{"_id":"UlWa"}],"publisher":"ACM","publication_status":"published","year":"2014","acknowledgement":"Swiss National Science Foundation (Project SNSF-PP00P2-138948)","publist_id":"4847","file_date_updated":"2020-07-14T12:45:30Z"},{"ec_funded":1,"publist_id":"5049","file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","year":"2014","volume":4,"date_created":"2018-12-11T11:55:16Z","date_updated":"2023-09-07T11:55:53Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1125"}]},"author":[{"full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"}],"month":"11","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/ece3.1289","type":"journal_article","issue":"24","abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"intvolume":" 4","status":"public","title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","ddc":["570"],"_id":"2023","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"9ab43db1b0fede7bfe560ed77e177b76","date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-12T10:12:28Z","file_id":"4946","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":118813,"access_level":"open_access","file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf"}],"oa_version":"Published Version","pubrep_id":"462","scopus_import":1,"has_accepted_license":"1","day":"27","page":"4589 - 4597","citation":{"ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597. doi:10.1002/ece3.1289","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” Ecology and Evolution, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1289","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289."},"publication":"Ecology and Evolution","date_published":"2014-11-27T00:00:00Z"},{"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-08867-9_38","conference":{"end_date":"2014-07-22","start_date":"2014-07-18","location":"Vienna, Austria","name":"CAV: Computer Aided Verification"},"publication_identifier":{"isbn":["978-331908866-2"]},"month":"07","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2014","volume":8559,"date_updated":"2023-09-07T11:57:01Z","date_created":"2018-12-11T11:56:23Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1130"}]},"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun","full_name":"Radhakrishna, Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"first_name":"Thorsten","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten"}],"publist_id":"4749","ec_funded":1,"file_date_updated":"2020-07-14T12:45:33Z","page":"568 - 584","citation":{"ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:10.1007/978-3-319-08867-9_38","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free synthesis for concurrency,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 568–584.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach, T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_38","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559, 568–584.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2014, pp. 568–584.","mla":"Cerny, Pavol, et al. Regression-Free Synthesis for Concurrency. Vol. 8559, Springer, 2014, pp. 568–84, doi:10.1007/978-3-319-08867-9_38.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_38."},"date_published":"2014-07-22T00:00:00Z","has_accepted_license":"1","day":"22","intvolume":" 8559","ddc":["000"],"status":"public","title":"Regression-free synthesis for concurrency","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2218","oa_version":"Submitted Version","file":[{"file_size":416732,"content_type":"application/pdf","creator":"system","file_name":"IST-2014-297-v1+1_cav14-final.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:33Z","date_created":"2018-12-12T10:13:14Z","checksum":"a631d3105509f239724644e77a1212e2","relation":"main_file","file_id":"4995"},{"file_name":"IST-2014-297-v2+1_cav14-final2.pdf","access_level":"open_access","creator":"system","file_size":616293,"content_type":"application/pdf","file_id":"4996","relation":"main_file","date_created":"2018-12-12T10:13:15Z","date_updated":"2020-07-14T12:45:33Z","checksum":"f8b0f748cc9fa697ca992cc56c87bc4e"}],"pubrep_id":"297","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs.","lang":"eng"}]},{"publication_identifier":{"isbn":["978-1-4799-2255-0"],"issn":["2159-4848"]},"month":"03","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.07083"}],"external_id":{"arxiv":["1904.07083"]},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"quality_controlled":"1","doi":"10.1109/ICST.2014.50","conference":{"name":"ICST: International Conference on Software Testing, Verification and Validation","end_date":"2014-04-04","start_date":"2014-03-31","location":"Cleveland, USA"},"language":[{"iso":"eng"}],"article_number":"6823899","ec_funded":1,"publist_id":"4817","year":"2014","department":[{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5411"},{"status":"public","relation":"dissertation_contains","id":"1155"}]},"author":[{"first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Krenn, Willibald","first_name":"Willibald","last_name":"Krenn"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"}],"date_updated":"2023-09-07T11:58:33Z","date_created":"2018-12-11T11:56:06Z","scopus_import":1,"article_processing_charge":"No","day":"01","citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. “Compositional Specifications for IOCO Testing.” In IEEE 7th International Conference on Software Testing, Verification and Validation. IEEE, 2014. https://doi.org/10.1109/ICST.2014.50.","mla":"Daca, Przemyslaw, et al. “Compositional Specifications for IOCO Testing.” IEEE 7th International Conference on Software Testing, Verification and Validation, 6823899, IEEE, 2014, doi:10.1109/ICST.2014.50.","short":"P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, in:, IEEE 7th International Conference on Software Testing, Verification and Validation, IEEE, 2014.","ista":"Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing. IEEE 7th International Conference on Software Testing, Verification and Validation. ICST: International Conference on Software Testing, Verification and Validation, 6823899.","ieee":"P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, “Compositional specifications for IOCO testing,” in IEEE 7th International Conference on Software Testing, Verification and Validation, Cleveland, USA, 2014.","apa":"Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional specifications for IOCO testing. In IEEE 7th International Conference on Software Testing, Verification and Validation. Cleveland, USA: IEEE. https://doi.org/10.1109/ICST.2014.50","ama":"Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional specifications for IOCO testing. In: IEEE 7th International Conference on Software Testing, Verification and Validation. IEEE; 2014. doi:10.1109/ICST.2014.50"},"publication":"IEEE 7th International Conference on Software Testing, Verification and Validation","date_published":"2014-03-01T00:00:00Z","type":"conference","abstract":[{"text":"Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing. In this paper, we study compositional properties of the ioco-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the ioco conformance relation, the resulting methodology can be applied to a broader class of systems.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2167","status":"public","title":"Compositional specifications for IOCO testing","oa_version":"Preprint"},{"month":"07","day":"01","citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_31.","short":"K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.","mla":"Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. Vol. 8559, Springer, 2014, pp. 473–90, doi:10.1007/978-3-319-08867-9_31.","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2014). CEGAR for qualitative analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_31","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 473–490.","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic systems. In: Vol 8559. Springer; 2014:473-490. doi:10.1007/978-3-319-08867-9_31"},"quality_controlled":"1","page":"473 - 490","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"conference":{"start_date":"2014-07-18","location":"Vienna, Austria","end_date":"2014-07-22","name":"CAV: Computer Aided Verification"},"date_published":"2014-07-01T00:00:00Z","doi":"10.1007/978-3-319-08867-9_31","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements."}],"ec_funded":1,"publist_id":"4978","_id":"2063","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","publication_status":"published","status":"public","title":"CEGAR for qualitative analysis of probabilistic systems","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"intvolume":" 8559","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5412"},{"id":"5413","status":"public","relation":"earlier_version"},{"id":"5414","status":"public","relation":"earlier_version"},{"status":"public","relation":"dissertation_contains","id":"1155"}]},"date_created":"2018-12-11T11:55:30Z","date_updated":"2023-09-07T11:58:33Z","oa_version":"None","volume":8559},{"day":"22","scopus_import":1,"date_published":"2014-06-22T00:00:00Z","page":"545 - 557","citation":{"ieee":"K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their combinations,” Environmental Microbiology Reports, vol. 6, no. 6. Wiley, pp. 545–557, 2014.","apa":"Mitosch, K., & Bollenbach, M. T. (2014). Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.12190","ista":"Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 6(6), 545–557.","ama":"Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 2014;6(6):545-557. doi:10.1111/1758-2229.12190","chicago":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” Environmental Microbiology Reports. Wiley, 2014. https://doi.org/10.1111/1758-2229.12190.","short":"K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014) 545–557.","mla":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” Environmental Microbiology Reports, vol. 6, no. 6, Wiley, 2014, pp. 545–57, doi:10.1111/1758-2229.12190."},"publication":"Environmental Microbiology Reports","issue":"6","abstract":[{"lang":"eng","text":"Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria."}],"type":"journal_article","oa_version":"None","intvolume":" 6","status":"public","title":"Bacterial responses to antibiotics and their combinations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2001","month":"06","language":[{"iso":"eng"}],"doi":"10.1111/1758-2229.12190","project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"},{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5076","volume":6,"date_created":"2018-12-11T11:55:08Z","date_updated":"2023-09-07T12:00:25Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"818"}]},"author":[{"full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"publisher":"Wiley","department":[{"_id":"ToBo"}],"publication_status":"published","year":"2014"},{"has_accepted_license":"1","day":"01","citation":{"mla":"Gazi, Peter, et al. The Exact PRF-Security of NMAC and HMAC. Edited by Juan Garay and Rosario Gennaro, vol. 8616, no. 1, Springer, 2014, pp. 113–30, doi:10.1007/978-3-662-44371-2_7.","short":"P. Gazi, K.Z. Pietrzak, M. Rybar, in:, J. Garay, R. Gennaro (Eds.), Springer, 2014, pp. 113–130.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact PRF-Security of NMAC and HMAC.” edited by Juan Garay and Rosario Gennaro, 8616:113–30. Springer, 2014. https://doi.org/10.1007/978-3-662-44371-2_7.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact PRF-security of NMAC and HMAC. In: Garay J, Gennaro R, eds. Vol 8616. Springer; 2014:113-130. doi:10.1007/978-3-662-44371-2_7","ista":"Gazi P, Pietrzak KZ, Rybar M. 2014. The exact PRF-security of NMAC and HMAC. CRYPTO: International Cryptology Conference, LNCS, vol. 8616, 113–130.","apa":"Gazi, P., Pietrzak, K. Z., & Rybar, M. (2014). The exact PRF-security of NMAC and HMAC. In J. Garay & R. Gennaro (Eds.) (Vol. 8616, pp. 113–130). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA: Springer. https://doi.org/10.1007/978-3-662-44371-2_7","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact PRF-security of NMAC and HMAC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA, 2014, vol. 8616, no. 1, pp. 113–130."},"page":"113 - 130","date_published":"2014-01-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"issue":"1","abstract":[{"text":"NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC was introduced by Bellare, Canetti and Krawczyk [Crypto'96], who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1) f is a PRF and (2) the function we get when cascading f is weakly collision-resistant. Unfortunately, HMAC is typically instantiated with cryptographic hash functions like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable guarantees for NMAC, Bellare [Crypto'06] showed its security based solely on the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first contribution is a simpler and uniform proof for this fact: If f is an ε-secure PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries), then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security of a modification of NMAC called NI [An and Bellare, Crypto'99] that differs mainly by using a compression function with an additional keying input. This avoids the constant rekeying on multi-block messages in NMAC and allows for a security proof starting by the standard switch from a PRF to a random function, followed by an information-theoretic analysis. We carry out such an analysis, obtaining a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c. The proof borrows combinatorial techniques originally developed for proving the security of CBC-MAC [Bellare et al., Crypto'05].","lang":"eng"}],"_id":"2082","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 8616","ddc":["000","004"],"status":"public","title":"The exact PRF-security of NMAC and HMAC","pubrep_id":"682","file":[{"relation":"main_file","file_id":"4999","checksum":"dab6ab36a5f6af94f2b597e6404ed11d","date_created":"2018-12-12T10:13:17Z","date_updated":"2020-07-14T12:45:28Z","access_level":"open_access","file_name":"IST-2016-682-v1+1_578.pdf","file_size":492310,"content_type":"application/pdf","creator":"system"}],"oa_version":"Submitted Version","month":"01","oa":1,"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1","doi":"10.1007/978-3-662-44371-2_7","conference":{"name":"CRYPTO: International Cryptology Conference","location":"Santa Barbara, USA","start_date":"2014-08-17","end_date":"2014-08-21"},"language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"4955","file_date_updated":"2020-07-14T12:45:28Z","year":"2014","publisher":"Springer","editor":[{"full_name":"Garay, Juan","last_name":"Garay","first_name":"Juan"},{"first_name":"Rosario","last_name":"Gennaro","full_name":"Gennaro, Rosario"}],"department":[{"_id":"KrPi"}],"publication_status":"published","related_material":{"record":[{"id":"838","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","last_name":"Gazi","first_name":"Peter","full_name":"Gazi, Peter"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal"}],"volume":8616,"date_updated":"2023-09-07T12:02:27Z","date_created":"2018-12-11T11:55:36Z"},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/25535919"}],"external_id":{"pmid":["25535919"]},"oa":1,"quality_controlled":"1","doi":"10.1016/j.devcel.2014.11.003","language":[{"iso":"eng"}],"month":"12","pmid":1,"year":"2014","acknowledgement":"We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus, and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing reagents. This work was supported by the Institute of Science and Technology Austria and an Alexander von Humboldt Foundation fellowship to J.C.","publisher":"Cell Press","department":[{"_id":"CaHe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"}]},"author":[{"full_name":"Compagnon, Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","first_name":"Julien","last_name":"Compagnon"},{"orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"first_name":"Srivarsha","last_name":"Rajshekar","full_name":"Rajshekar, Srivarsha"},{"last_name":"Kottmeier","first_name":"Rita","full_name":"Kottmeier, Rita"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija"},{"full_name":"Behrndt, Martin","first_name":"Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"volume":31,"date_created":"2018-12-11T11:54:41Z","date_updated":"2023-09-07T12:05:08Z","publist_id":"5182","citation":{"chicago":"Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier, Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell. Cell Press, 2014. https://doi.org/10.1016/j.devcel.2014.11.003.","mla":"Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell, vol. 31, no. 6, Cell Press, 2014, pp. 774–83, doi:10.1016/j.devcel.2014.11.003.","short":"J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha, M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.","ista":"Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783.","apa":"Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K., Behrndt, M., & Heisenberg, C.-P. J. (2014). The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2014.11.003","ieee":"J. Compagnon et al., “The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ,” Developmental Cell, vol. 31, no. 6. Cell Press, pp. 774–783, 2014.","ama":"Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 2014;31(6):774-783. doi:10.1016/j.devcel.2014.11.003"},"publication":"Developmental Cell","page":"774 - 783","date_published":"2014-12-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1912","intvolume":" 31","title":"The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ","status":"public","oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"text":"Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function.","lang":"eng"}]},{"doi":"10.15252/embj.201387695","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194103/"}],"oa":1,"quality_controlled":"1","month":"07","related_material":{"record":[{"id":"418","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Grusch","first_name":"Michael","full_name":"Grusch, Michael"},{"last_name":"Schelch","first_name":"Karin","full_name":"Schelch, Karin"},{"full_name":"Riedler, Robert","last_name":"Riedler","first_name":"Robert"},{"last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva"},{"full_name":"Differ, Christopher","last_name":"Differ","first_name":"Christopher"},{"first_name":"Walter","last_name":"Berger","full_name":"Berger, Walter"},{"full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","first_name":"Álvaro","last_name":"Inglés Prieto"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"}],"volume":33,"date_created":"2018-12-11T11:55:37Z","date_updated":"2023-09-07T12:49:09Z","year":"2014","acknowledgement":"European Union Seventh Framework Programme; Human Frontier Science Program; Oesterreichische Nationalbank Anniversary Fund 14211; Austrian Research Promotion Agency; FemTech","publisher":"Wiley-Blackwell","department":[{"_id":"HaJa"}],"publication_status":"published","publist_id":"4953","date_published":"2014-07-01T00:00:00Z","citation":{"apa":"Grusch, M., Schelch, K., Riedler, R., Gschaider-Reichhart, E., Differ, C., Berger, W., … Janovjak, H. L. (2014). Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. Wiley-Blackwell. https://doi.org/10.15252/embj.201387695","ieee":"M. Grusch et al., “Spatio-temporally precise activation of engineered receptor tyrosine kinases by light,” EMBO Journal, vol. 33, no. 15. Wiley-Blackwell, pp. 1713–1726, 2014.","ista":"Grusch M, Schelch K, Riedler R, Gschaider-Reichhart E, Differ C, Berger W, Inglés Prieto Á, Janovjak HL. 2014. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 33(15), 1713–1726.","ama":"Grusch M, Schelch K, Riedler R, et al. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 2014;33(15):1713-1726. doi:10.15252/embj.201387695","chicago":"Grusch, Michael, Karin Schelch, Robert Riedler, Eva Gschaider-Reichhart, Christopher Differ, Walter Berger, Álvaro Inglés Prieto, and Harald L Janovjak. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal. Wiley-Blackwell, 2014. https://doi.org/10.15252/embj.201387695.","short":"M. Grusch, K. Schelch, R. Riedler, E. Gschaider-Reichhart, C. Differ, W. Berger, Á. Inglés Prieto, H.L. Janovjak, EMBO Journal 33 (2014) 1713–1726.","mla":"Grusch, Michael, et al. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal, vol. 33, no. 15, Wiley-Blackwell, 2014, pp. 1713–26, doi:10.15252/embj.201387695."},"publication":"EMBO Journal","page":"1713 - 1726","day":"01","scopus_import":1,"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2084","intvolume":" 33","title":"Spatio-temporally precise activation of engineered receptor tyrosine kinases by light","status":"public","issue":"15","abstract":[{"lang":"eng","text":"Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour."}],"type":"journal_article"},{"abstract":[{"text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, i.e., an essential curve in the boundary of X bounding a disk in S3 nX with length bounded by a computable function of the number of tetrahedra of X.","lang":"eng"}],"publist_id":"4849","type":"conference","author":[{"last_name":"Matoušek","first_name":"Jiří","full_name":"Matoušek, Jiří"},{"full_name":"Sedgwick, Eric","first_name":"Eric","last_name":"Sedgwick"},{"first_name":"Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"425","status":"public","relation":"later_version"}]},"date_updated":"2023-09-11T13:38:49Z","date_created":"2018-12-11T11:56:02Z","oa_version":"Submitted Version","year":"2014","_id":"2157","acknowledgement":"ERC Advanced Grant No. 267165; Grant GRADR Eurogiga GIG/11/E023 (SNSF-PP00P2-138948); Swiss National Science Foundation (SNSF-200020-138230).","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Embeddability in the 3 sphere is decidable","status":"public","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"ACM","month":"06","day":"01","scopus_import":1,"conference":{"location":"Kyoto, Japan","start_date":"2014-06-08","end_date":"2014-06-11","name":"SoCG: Symposium on Computational Geometry"},"date_published":"2014-06-01T00:00:00Z","doi":"10.1145/2582112.2582137","language":[{"iso":"eng"}],"publication":"Proceedings of the Annual Symposium on Computational Geometry","citation":{"short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3 Sphere Is Decidable.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84, doi:10.1145/2582112.2582137.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3 Sphere Is Decidable.” In Proceedings of the Annual Symposium on Computational Geometry, 78–84. ACM, 2014. https://doi.org/10.1145/2582112.2582137.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3 sphere is decidable. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:78-84. doi:10.1145/2582112.2582137","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2014). Embeddability in the 3 sphere is decidable. In Proceedings of the Annual Symposium on Computational Geometry (pp. 78–84). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582137","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3 sphere is decidable,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 78–84.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2014. Embeddability in the 3 sphere is decidable. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 78–84."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0815"}],"quality_controlled":"1","page":"78 - 84"},{"article_processing_charge":"No","day":"01","series_title":"LNCS","scopus_import":"1","date_published":"2014-09-01T00:00:00Z","page":"137-143","citation":{"ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms Toolbox. In: ICMS 2014: International Congress on Mathematical Software. Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143. doi:10.1007/978-3-662-44199-2_24","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology Algorithms Toolbox,” in ICMS 2014: International Congress on Mathematical Software, Seoul, South Korea, 2014, vol. 8592, pp. 137–143.","apa":"Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2014). PHAT – Persistent Homology Algorithms Toolbox. In ICMS 2014: International Congress on Mathematical Software (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-662-44199-2_24","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software. ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, pp. 137–143.","mla":"Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” ICMS 2014: International Congress on Mathematical Software, vol. 8592, Springer Berlin Heidelberg, 2014, pp. 137–43, doi:10.1007/978-3-662-44199-2_24.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT – Persistent Homology Algorithms Toolbox.” In ICMS 2014: International Congress on Mathematical Software, 8592:137–43. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. https://doi.org/10.1007/978-3-662-44199-2_24."},"publication":"ICMS 2014: International Congress on Mathematical Software","abstract":[{"lang":"eng","text":"PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations."}],"type":"conference","oa_version":"None","intvolume":" 8592","title":"PHAT – Persistent Homology Algorithms Toolbox","status":"public","_id":"10894","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783662441985"],"issn":["0302-9743"],"eisbn":["9783662441992"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-44199-2_24","conference":{"name":"ICMS: International Congress on Mathematical Software","location":"Seoul, South Korea","start_date":"2014-08-05","end_date":"2014-08-09"},"quality_controlled":"1","place":"Berlin, Heidelberg","volume":8592,"date_updated":"2023-09-20T09:42:40Z","date_created":"2022-03-21T07:12:16Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"1433"}]},"author":[{"last_name":"Bauer","first_name":"Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"},{"last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan"},{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert"}],"department":[{"_id":"HeEd"}],"publisher":"Springer Berlin Heidelberg","publication_status":"published","year":"2014"},{"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata."}],"file_date_updated":"2020-07-14T12:46:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5428","year":"2014","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"IST Austria","publication_status":"published","title":"Quantitative fair simulation games","status":"public","ddc":["004"],"pubrep_id":"315","related_material":{"record":[{"id":"1066","relation":"later_version","status":"public"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"file":[{"date_updated":"2020-07-14T12:46:52Z","date_created":"2018-12-12T11:53:59Z","checksum":"b1d573bc04365625ff9974880c0aa807","relation":"main_file","file_id":"5521","content_type":"application/pdf","file_size":531046,"creator":"system","file_name":"IST-2014-315-v1+1_report.pdf","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2023-09-20T12:07:48Z","date_created":"2018-12-12T11:39:16Z","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"05","month":"12","oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. Quantitative Fair Simulation Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-315-v1-1.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation Games, IST Austria, 2014.","mla":"Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST Austria, 2014, doi:10.15479/AT:IST-2014-315-v1-1.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair simulation games. IST Austria, 2014.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2014). Quantitative fair simulation games. IST Austria. https://doi.org/10.15479/AT:IST-2014-315-v1-1","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative Fair Simulation Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-315-v1-1"},"page":"26","doi":"10.15479/AT:IST-2014-315-v1-1","date_published":"2014-12-05T00:00:00Z","language":[{"iso":"eng"}]},{"publist_id":"5208","type":"journal_article","date_updated":"2023-10-17T07:54:57Z","date_created":"2018-12-11T11:54:33Z","oa_version":"Published Version","author":[{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"status":"public","publication_status":"published","title":"Gemeinsame Krankheitsabwehr in Ameisengesellschaften","publisher":"Deutsche Zoologische Gesellschaft","department":[{"_id":"SyCr"}],"_id":"1887","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","month":"01","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2014-01-01T00:00:00Z","article_type":"original","quality_controlled":"1","page":"23 - 30","publication":"Zoologie","main_file_link":[{"url":"https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf","open_access":"1"}],"oa":1,"citation":{"apa":"Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie. Deutsche Zoologische Gesellschaft.","ieee":"S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” Zoologie. Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.","ista":"Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie., 23–30.","ama":"Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie. 2014:23-30.","chicago":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie. Deutsche Zoologische Gesellschaft, 2014.","short":"S. Cremer, Zoologie (2014) 23–30.","mla":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie, Deutsche Zoologische Gesellschaft, 2014, pp. 23–30."}},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2014-05-01T00:00:00Z","page":"323 - 340","publication":"Future Neurology","citation":{"mla":"Postiglione, Maria P., and Simon Hippenmeyer. “Monitoring Neurogenesis in the Cerebral Cortex: An Update.” Future Neurology, vol. 9, no. 3, Future Science Group, 2014, pp. 323–40, doi:10.2217/fnl.14.18.","short":"M.P. Postiglione, S. Hippenmeyer, Future Neurology 9 (2014) 323–340.","chicago":"Postiglione, Maria P, and Simon Hippenmeyer. “Monitoring Neurogenesis in the Cerebral Cortex: An Update.” Future Neurology. Future Science Group, 2014. https://doi.org/10.2217/fnl.14.18.","ama":"Postiglione MP, Hippenmeyer S. Monitoring neurogenesis in the cerebral cortex: an update. Future Neurology. 2014;9(3):323-340. doi:10.2217/fnl.14.18","ista":"Postiglione MP, Hippenmeyer S. 2014. Monitoring neurogenesis in the cerebral cortex: an update. Future Neurology. 9(3), 323–340.","apa":"Postiglione, M. P., & Hippenmeyer, S. (2014). Monitoring neurogenesis in the cerebral cortex: an update. Future Neurology. Future Science Group. https://doi.org/10.2217/fnl.14.18","ieee":"M. P. Postiglione and S. Hippenmeyer, “Monitoring neurogenesis in the cerebral cortex: an update,” Future Neurology, vol. 9, no. 3. Future Science Group, pp. 323–340, 2014."},"abstract":[{"text":"The cerebral cortex, the seat of our cognitive abilities, is composed of an intricate network of billions of excitatory projection and inhibitory interneurons. Postmitotic cortical neurons are generated by a diverse set of neural stem cell progenitors within dedicated zones and defined periods of neurogenesis during embryonic development. Disruptions in neurogenesis can lead to alterations in the neuronal cytoarchitecture, which is thought to represent a major underlying cause for several neurological disorders, including microcephaly, autism and epilepsy. Although a number of signaling pathways regulating neurogenesis have been described, the precise cellular and molecular mechanisms regulating the functional neural stem cell properties in cortical neurogenesis remain unclear. Here, we discuss the most up-to-date strategies to monitor the fundamental mechanistic parameters of neuronal progenitor proliferation, and recent advances deciphering the logic and dynamics of neurogenesis.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"4812","relation":"main_file","checksum":"ba06659ecadabceec9a37dd8c4586dce","date_updated":"2020-07-14T12:45:31Z","date_created":"2018-12-12T10:10:25Z","access_level":"open_access","file_name":"IST-2016-528-v1+1_fnl.14.18.pdf","creator":"system","content_type":"application/pdf","file_size":3848424}],"pubrep_id":"528","title":"Monitoring neurogenesis in the cerebral cortex: an update","ddc":["570"],"status":"public","intvolume":" 9","_id":"2175","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publication_identifier":{"issn":["1479-6708"],"eissn":["1748-6971"]},"language":[{"iso":"eng"}],"doi":"10.2217/fnl.14.18","quality_controlled":"1","project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:45:31Z","ec_funded":1,"publist_id":"4806","date_updated":"2023-10-17T08:34:27Z","date_created":"2018-12-11T11:56:09Z","volume":9,"author":[{"full_name":"Postiglione, Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","last_name":"Postiglione","first_name":"Maria P"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Future Science Group","year":"2014"},{"oa":1,"main_file_link":[{"url":"https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf","open_access":"1"}],"external_id":{"pmid":["25195847"]},"quality_controlled":"1","doi":"10.1159/000365548","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1420-8008"]},"month":"11","pmid":1,"acknowledgement":"This study was supported by the European Commission’s 7th Framework Programme under GA No. 278486, ‘DEVELAGE’.","year":"2014","publisher":"Karger Publishers","department":[{"_id":"CaGu"}],"publication_status":"published","author":[{"full_name":"Milenković, Ivan","first_name":"Ivan","last_name":"Milenković"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana"},{"first_name":"Gábor","last_name":"Kovács","full_name":"Kovács, Gábor"}],"volume":38,"date_created":"2018-12-11T11:54:41Z","date_updated":"2023-10-17T10:21:17Z","publist_id":"5181","citation":{"mla":"Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders, vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:10.1159/000365548.","short":"I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders 38 (2014) 375–388.","chicago":"Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders. Karger Publishers, 2014. https://doi.org/10.1159/000365548.","ama":"Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 2014;38(5-6):375-388. doi:10.1159/000365548","ista":"Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 38(5–6), 375–388.","apa":"Milenković, I., Petrov, T., & Kovács, G. (2014). Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. Karger Publishers. https://doi.org/10.1159/000365548","ieee":"I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology differentiate neurodegenerative dementias,” Dementia and Geriatric Cognitive Disorders, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014."},"publication":"Dementia and Geriatric Cognitive Disorders","page":"375 - 388","article_type":"original","date_published":"2014-11-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1913","intvolume":" 38","status":"public","title":"Patterns of hippocampal tau pathology differentiate neurodegenerative dementias","oa_version":"Published Version","type":"journal_article","issue":"5-6","abstract":[{"lang":"eng","text":"Deposits of phosphorylated tau protein and convergence of pathology in the hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed to evaluate whether regional and cellular vulnerability patterns in the hippocampus distinguish tauopathies or are influenced by their concomitant presence. Methods: We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal subregions/layers in individuals with Alzheimer's disease (AD)-related neurofibrillary degeneration (n = 40), Pick's disease (n = 8), progressive supranuclear palsy (n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n = 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly (n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis. Results: Our study reveals disease-specific hot spots and regional selective vulnerability for these disorders. The pattern of hippocampal AD-related tau pathology is strongly influenced by concomitant AGD. Mathematical analysis reveals that hippocampal involvement in primary tauopathies is distinguishable from early-stage AD-related neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies, which primarily do not affect the hippocampus. These hot spots can be shifted to other regions by the co-occurrence of tauopathies like AGD. Our observations support the notion that globular glial tauopathies and tau-astrogliopathy of the elderly are distinct entities."}]},{"month":"08","language":[{"iso":"eng"}],"conference":{"end_date":"2014-08-21","location":"Seoul, Korea","start_date":"2014-08-13","name":"ICM: International Congress of Mathematicians"},"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.5752"}],"ec_funded":1,"publist_id":"5670","volume":3,"date_created":"2018-12-11T11:52:25Z","date_updated":"2023-10-17T11:12:55Z","author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"}],"department":[{"_id":"LaEr"}],"publisher":"International Congress of Mathematicians","publication_status":"published","year":"2014","acknowledgement":"The author is partially supported by SFB-TR 12 Grant of the German Research Council.","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2014-08-01T00:00:00Z","page":"214 - 236","citation":{"ista":"Erdös L. 2014. Random matrices, log-gases and Hölder regularity. Proceedings of the International Congress of Mathematicians. ICM: International Congress of Mathematicians vol. 3, 214–236.","apa":"Erdös, L. (2014). Random matrices, log-gases and Hölder regularity. In Proceedings of the International Congress of Mathematicians (Vol. 3, pp. 214–236). Seoul, Korea: International Congress of Mathematicians.","ieee":"L. Erdös, “Random matrices, log-gases and Hölder regularity,” in Proceedings of the International Congress of Mathematicians, Seoul, Korea, 2014, vol. 3, pp. 214–236.","ama":"Erdös L. Random matrices, log-gases and Hölder regularity. In: Proceedings of the International Congress of Mathematicians. Vol 3. International Congress of Mathematicians; 2014:214-236.","chicago":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” In Proceedings of the International Congress of Mathematicians, 3:214–36. International Congress of Mathematicians, 2014.","mla":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” Proceedings of the International Congress of Mathematicians, vol. 3, International Congress of Mathematicians, 2014, pp. 214–36.","short":"L. Erdös, in:, Proceedings of the International Congress of Mathematicians, International Congress of Mathematicians, 2014, pp. 214–236."},"publication":"Proceedings of the International Congress of Mathematicians","abstract":[{"lang":"eng","text":"The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large real and complex Hermitian matrices with independent, identically distributed entries are universal in a sense that they depend only on the symmetry class of the matrix and otherwise are independent of the details of the distribution. We present the recent solution to this half-century old conjecture. We explain how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also show related results for log-gases that represent a universal model for strongly correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss the extensions of these universality results to more realistic physical systems such as random band matrices."}],"type":"conference","oa_version":"Submitted Version","intvolume":" 3","status":"public","title":"Random matrices, log-gases and Hölder regularity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1507"}]