--- _id: '8022' abstract: - lang: eng text: Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Wulfram full_name: Gerstner, Wulfram last_name: Gerstner citation: ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406. doi:10.1016/j.neuron.2014.04.045 apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045 chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045. ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient dynamics in balanced networks supports generation of complex movements,” Neuron, vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014. ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 82(6), 1394–1406. mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045. short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406. date_created: 2020-06-25T13:07:37Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T08:16:35Z day: '18' doi: 10.1016/j.neuron.2014.04.045 extern: '1' external_id: pmid: - '24945778' intvolume: ' 82' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/ month: '06' oa: 1 oa_version: Submitted Version page: 1394-1406 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Optimal control of transient dynamics in balanced networks supports generation of complex movements type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 82 year: '2014' ... --- _id: '809' abstract: - lang: eng text: The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position. acknowledgement: 'The authors thank Leonardo Trabuco for help with running MDFF, Maria Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber (robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal screening, and the European Molecular Biology Laboratory (EMBL) Information Technology Services Unit and Frank Thommen for technical support. This study was supported by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship (to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL and the Chica und Heinz Schaller Stiftung. ' author: - first_name: Tanmay full_name: Bharata, Tanmay A last_name: Bharata - first_name: Luis full_name: Menendez, Luis R last_name: Menendez - first_name: Wim full_name: Hagena, Wim J last_name: Hagena - first_name: Vanda full_name: Luxd, Vanda last_name: Luxd - first_name: Sebastien full_name: Igonete, Sebastien last_name: Igonete - first_name: Martin full_name: Schorba, Martin last_name: Schorba - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Hans full_name: Kraüsslich, Hans Georg last_name: Kraüsslich - first_name: John full_name: Briggsa, John A last_name: Briggsa citation: ama: Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 2014;111(22):8233-8238. doi:10.1073/pnas.1401455111 apa: Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M., … Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1401455111 chicago: Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete, Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1401455111. ieee: T. Bharata et al., “Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly,” PNAS, vol. 111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014. ista: Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 111(22), 8233–8238. mla: Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS, vol. 111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:10.1073/pnas.1401455111. short: T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K. Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238. date_created: 2018-12-11T11:48:37Z date_published: 2014-06-03T00:00:00Z date_updated: 2021-01-12T08:16:50Z day: '03' doi: 10.1073/pnas.1401455111 extern: 1 intvolume: ' 111' issue: '22' license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '06' page: 8233 - 8238 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6838' quality_controlled: 0 status: public title: Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 111 year: '2014' ... --- _id: '8244' abstract: - lang: eng text: Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer. article_processing_charge: No article_type: original author: - first_name: J. full_name: Singer, J. last_name: Singer - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: W. full_name: Wang, W. last_name: Wang - first_name: M. full_name: Weichselbaumer, M. last_name: Weichselbaumer - first_name: M. full_name: Matz, M. last_name: Matz - first_name: A. full_name: Mader, A. last_name: Mader - first_name: W. full_name: Steinfellner, W. last_name: Steinfellner - first_name: S. full_name: Meitz, S. last_name: Meitz - first_name: D. full_name: Mechtcheriakova, D. last_name: Mechtcheriakova - first_name: Y. full_name: Sobanov, Y. last_name: Sobanov - first_name: M. full_name: Willmann, M. last_name: Willmann - first_name: T. full_name: Stockner, T. last_name: Stockner - first_name: E. full_name: Spillner, E. last_name: Spillner - first_name: R. full_name: Kunert, R. last_name: Kunert - first_name: E. full_name: Jensen-Jarolim, E. last_name: Jensen-Jarolim citation: ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288 apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A., … Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288 chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics. American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288. ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics, vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014. ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E, Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 13(7), 1777–1790. mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics, vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288. short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner, R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790. date_created: 2020-08-10T11:54:29Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T08:17:42Z day: '01' doi: 10.1158/1535-7163.mct-13-0288 extern: '1' intvolume: ' 13' issue: '7' language: - iso: eng month: '07' oa_version: None page: 1777-1790 publication: Molecular Cancer Therapeutics publication_identifier: issn: - 1535-7163 - 1538-8514 publication_status: published publisher: American Association for Cancer Research quality_controlled: '1' status: public title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2014' ... --- _id: '8459' abstract: - lang: eng text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis. article_processing_charge: No article_type: original author: - first_name: Sébastien full_name: Morin, Sébastien last_name: Morin - first_name: Troels E full_name: Linnet, Troels E last_name: Linnet - first_name: Mathilde full_name: Lescanne, Mathilde last_name: Lescanne - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Gary S full_name: Thompson, Gary S last_name: Thompson - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger - first_name: Kaare full_name: Teilum, Kaare last_name: Teilum - first_name: Stéphane full_name: Gagné, Stéphane last_name: Gagné - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Christian full_name: Griesinger, Christian last_name: Griesinger - first_name: Martin full_name: Blackledge, Martin last_name: Blackledge - first_name: Edward J full_name: d’Auvergne, Edward J last_name: d’Auvergne citation: ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166' apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btu166' chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics. Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.' ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.' ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.' mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.' short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220. date_created: 2020-09-18T10:08:07Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/bioinformatics/btu166 extern: '1' intvolume: ' 30' issue: '15' keyword: - Statistics and Probability - Computational Theory and Mathematics - Biochemistry - Molecular Biology - Computational Mathematics - Computer Science Applications language: - iso: eng month: '08' oa_version: None page: 2219-2220 publication: Bioinformatics publication_identifier: issn: - 1367-4803 - 1460-2059 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/bioinformatics/btz397 status: public title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2014' ... --- _id: '8458' abstract: - lang: eng text: The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Sébastien full_name: Triboulet, Sébastien last_name: Triboulet - first_name: Cédric full_name: Laguri, Cédric last_name: Laguri - first_name: Catherine M. full_name: Bougault, Catherine M. last_name: Bougault - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Morgane full_name: Callon, Morgane last_name: Callon - first_name: Michel full_name: Arthur, Michel last_name: Arthur - first_name: Jean-Pierre full_name: Simorre, Jean-Pierre last_name: Simorre citation: ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987 apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon, M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987 chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja5105987. ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan,” Journal of the American Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860, 2014. ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 136(51), 17852–17860. mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60, doi:10.1021/ja5105987. short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon, M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014) 17852–17860. date_created: 2020-09-18T10:07:52Z date_published: 2014-11-27T00:00:00Z date_updated: 2021-01-12T08:19:24Z day: '27' doi: 10.1021/ja5105987 extern: '1' intvolume: ' 136' issue: '51' language: - iso: eng month: '11' oa_version: None page: 17852-17860 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2014' ... --- _id: '8460' abstract: - lang: eng text: The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states. article_processing_charge: No article_type: original author: - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Jens D. full_name: Haller, Jens D. last_name: Haller - first_name: Jérémy full_name: Zajakala, Jérémy last_name: Zajakala - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Dieter full_name: Willbold, Dieter last_name: Willbold - first_name: Jérôme full_name: Boisbouvier, Jérôme last_name: Boisbouvier - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275 apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201311275 chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275. ieee: P. Ma et al., “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014. ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317. mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275. short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317. date_created: 2020-09-18T10:08:53Z date_published: 2014-03-18T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '18' doi: 10.1002/anie.201311275 extern: '1' intvolume: ' 53' issue: '17' language: - iso: eng month: '03' oa_version: None page: 4312-4317 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2014' ... --- _id: '8501' abstract: - lang: eng text: In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation. article_processing_charge: No article_type: original author: - first_name: Abed full_name: Bounemoura, Abed last_name: Bounemoura - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203 apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203 chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203. ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014. ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203. mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203. short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203. date_created: 2020-09-18T10:47:09Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T08:19:43Z day: '01' doi: 10.17323/1609-4514-2014-14-2-181-203 extern: '1' external_id: arxiv: - '1304.3050' intvolume: ' 14' issue: '2' keyword: - General Mathematics language: - iso: eng month: '04' oa_version: Preprint page: 181-203 publication: Moscow Mathematical Journal publication_identifier: issn: - 1609-3321 - 1609-4514 publication_status: published publisher: Independent University of Moscow quality_controlled: '1' status: public title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '8500' abstract: - lang: eng text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way. article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Mark full_name: Levi, Mark last_name: Levi - first_name: Maria full_name: Saprykina, Maria last_name: Saprykina citation: ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509 apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21509 chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley, 2014. https://doi.org/10.1002/cpa.21509. ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley, pp. 748–775, 2014. ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775. mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:10.1002/cpa.21509. short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775. date_created: 2020-09-18T10:47:01Z date_published: 2014-05-01T00:00:00Z date_updated: 2022-08-25T13:58:13Z day: '01' doi: 10.1002/cpa.21509 extern: '1' intvolume: ' 67' issue: '5' keyword: - Applied Mathematics - General Mathematics language: - iso: eng month: '05' oa_version: None page: 748-775 publication: Communications on Pure and Applied Mathematics publication_identifier: issn: - 0010-3640 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Arnol′d diffusion in a pendulum lattice type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2014' ... --- _id: '852' abstract: - lang: eng text: 'Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. ' author: - first_name: Oriol full_name: Rosello, Oriol P last_name: Rosello - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955. doi:10.1093/gbe/evu159 apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evu159 chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159. ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” Genome Biology and Evolution, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014. ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955. mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159. short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955. date_created: 2018-12-11T11:48:51Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:51Z day: '01' doi: 10.1093/gbe/evu159 extern: 1 intvolume: ' 6' issue: '8' license: https://creativecommons.org/licenses/by/4.0/ month: '08' page: 1949 - 1955 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6797' quality_controlled: 0 status: public title: Long-Term asymmetrical acceleration of protein evolution after gene duplication tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2014' ... --- _id: '856' abstract: - lang: eng text: The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network. acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.' author: - first_name: Ksenia full_name: Pougach, Ksenia S last_name: Pougach - first_name: Arnout full_name: Voet, Arnout R last_name: Voet - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Karin full_name: Voordeckers, Karin last_name: Voordeckers - first_name: Joaquin full_name: Christiaens, Joaquin F last_name: Christiaens - first_name: Bianka full_name: Baying, Bianka last_name: Baying - first_name: Vladimı́R full_name: Bénès, Vladimı́r last_name: Bénès - first_name: Ryo full_name: Sakai, Ryo last_name: Sakai - first_name: Jan full_name: Aerts, Jan A last_name: Aerts - first_name: Bo full_name: Zhu, Bo last_name: Zhu - first_name: Patrick full_name: Van Dijck, Patrick last_name: Van Dijck - first_name: Kevin full_name: Verstrepen, Kevin J last_name: Verstrepen citation: ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 2014;5. doi:10.1038/ncomms5868 apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms5868 chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868. ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5. mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications, vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868. short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014). date_created: 2018-12-11T11:48:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:20:01Z day: '01' doi: 10.1038/ncomms5868 extern: 1 intvolume: ' 5' month: '01' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '6790' quality_controlled: 0 status: public title: Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 5 year: '2014' ... --- _id: '863' abstract: - lang: eng text: The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals. acknowledgement: We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22. author: - first_name: Leonid full_name: Moroz, Leonid L last_name: Moroz - first_name: Kevin full_name: Kocot, Kevin M last_name: Kocot - first_name: Mathew full_name: Citarella, Mathew R last_name: Citarella - first_name: Sohn full_name: Dosung, Sohn last_name: Dosung - first_name: Tigran full_name: Norekian, Tigran P last_name: Norekian - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Anastasia full_name: Grigorenko, Anastasia P last_name: Grigorenko - first_name: Christopher full_name: Dailey, Christopher A last_name: Dailey - first_name: Eugene full_name: Berezikov, Eugene last_name: Berezikov - first_name: Katherine full_name: Buckley, Katherine M last_name: Buckley - first_name: Andrey full_name: Ptitsyn, Andrey A last_name: Ptitsyn - first_name: Denis full_name: Reshetov, Denis A last_name: Reshetov - first_name: Krishanu full_name: Mukherjee, Krishanu last_name: Mukherjee - first_name: Tatiana full_name: Moroz, Tatiana P last_name: Moroz - first_name: Yelena full_name: Bobkova, Yelena V last_name: Bobkova - first_name: Fahong full_name: Yu, Fahong last_name: Yu - first_name: Vladimir full_name: Kapitonov, Vladimir V last_name: Kapitonov - first_name: Jerzy full_name: Jurka, Jerzy W last_name: Jurka - first_name: Yuriy full_name: Bobkov, Yuriy V last_name: Bobkov - first_name: Joshua full_name: Swore, Joshua J last_name: Swore - first_name: David full_name: Girardo, David O last_name: Girardo - first_name: Alexander full_name: Fodor, Alexander last_name: Fodor - first_name: Fedor full_name: Gusev, Fedor E last_name: Gusev - first_name: Rachel full_name: Sanford, Rachel S last_name: Sanford - first_name: Rebecca full_name: Bruders, Rebecca last_name: Bruders - first_name: Ellen full_name: Kittler, Ellen L last_name: Kittler - first_name: Claudia full_name: Mills, Claudia E last_name: Mills - first_name: Jonathan full_name: Rast, Jonathan P last_name: Rast - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Victor full_name: Solovyev, Victor last_name: Solovyev - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Billie full_name: Swalla, Billie J last_name: Swalla - first_name: Jonathan full_name: Sweedler, Jonathan V last_name: Sweedler - first_name: Evgeny full_name: Rogaev, Evgeny I last_name: Rogaev - first_name: Kenneth full_name: Halanych, Kenneth M last_name: Halanych - first_name: Andrea full_name: Kohn, Andrea B last_name: Kohn citation: ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400 apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400 chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13400. ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014. ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114. mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:10.1038/nature13400. short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114. date_created: 2018-12-11T11:48:54Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:20:21Z day: '01' doi: 10.1038/nature13400 extern: 1 intvolume: ' 510' issue: '7503' license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '01' page: 109 - 114 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6785' quality_controlled: 0 status: public title: The ctenophore genome and the evolutionary origins of neural systems tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article volume: 510 year: '2014' ... --- _id: '865' abstract: - lang: eng text: Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers. author: - first_name: Alexey full_name: Koval, Alexey V last_name: Koval - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Polina full_name: Shichkova, Polina last_name: Shichkova - first_name: S full_name: Khunderyakova, S last_name: Khunderyakova - first_name: Yury full_name: Markov, Yury last_name: Markov - first_name: J full_name: Panchenko, J last_name: Panchenko - first_name: A full_name: Volodina, A last_name: Volodina - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Katanaev, Vladimir L last_name: Katanaev citation: ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007 apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007 chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014. https://doi.org/10.1016/j.bcp.2013.12.007. ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014. ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578. mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007. short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578. date_created: 2018-12-11T11:48:55Z date_published: 2014-02-15T00:00:00Z date_updated: 2021-01-12T08:20:24Z day: '15' doi: 10.1016/j.bcp.2013.12.007 extern: 1 intvolume: ' 87' issue: '4' month: '02' page: 571 - 578 publication: Biochemical Pharmacology publication_status: published publisher: Elsevier publist_id: '6782' quality_controlled: 0 status: public title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling type: journal_article volume: 87 year: '2014' ... --- _id: '925' abstract: - lang: eng text: The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape. acknowledgement: We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D. article_processing_charge: No author: - first_name: Bo full_name: Dong, Bo last_name: Dong - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Shigeo full_name: Hayashi, Shigeo last_name: Hayashi citation: ama: Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950. doi:10.1016/j.celrep.2014.03.066 apa: Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066 chicago: Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066. ieee: B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” Cell Reports, vol. 7, no. 4. Cell Press, pp. 941–950, 2014. ista: Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950. mla: Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066. short: B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950. date_created: 2018-12-11T11:49:14Z date_published: 2014-05-22T00:00:00Z date_updated: 2021-01-12T08:21:57Z day: '22' doi: 10.1016/j.celrep.2014.03.066 extern: '1' intvolume: ' 7' issue: '4' language: - iso: eng month: '05' oa_version: None page: 941 - 950 publication: Cell Reports publication_status: published publisher: Cell Press publist_id: '6515' status: public title: Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2014' ... --- _id: '927' abstract: - lang: eng text: Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1312076111. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014. ista: Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32. mla: Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:10.1073/pnas.1312076111. short: E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32. date_created: 2018-12-11T11:49:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:21:58Z day: '01' doi: 10.1073/pnas.1312076111 extern: '1' intvolume: ' 111' issue: '1' language: - iso: eng month: '01' oa_version: None page: 27 - 32 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6517' status: public title: Theory of epithelial sheet morphology in three dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '9519' abstract: - lang: eng text: Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression. article_processing_charge: No article_type: review author: - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014 apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014 chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014. ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326, 2014. ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326. mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:10.1016/j.tplants.2014.01.014. short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326. date_created: 2021-06-07T14:38:09Z date_published: 2014-05-04T00:00:00Z date_updated: 2021-12-14T08:24:48Z day: '04' department: - _id: DaZi doi: 10.1016/j.tplants.2014.01.014 extern: '1' external_id: pmid: - '24618094 ' intvolume: ' 19' issue: '5' language: - iso: eng month: '05' oa_version: None page: 320-326 pmid: 1 publication: Trends in Plant Science publication_identifier: eissn: - 1878-4372 issn: - 1360-1385 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation as a system of plant genomic immunity type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 19 year: '2014' ... --- _id: '96' abstract: - lang: eng text: Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (>1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range. acknowledgement: The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation. article_number: '026801' author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth - first_name: Micah full_name: Hanson, Micah last_name: Hanson - first_name: Arthur full_name: Gossard, Arthur last_name: Gossard - first_name: Charles full_name: Marcus, Charles last_name: Marcus citation: ama: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 2014;112(2). doi:10.1103/PhysRevLett.112.026801 apa: Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., & Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. American Physiological Society. https://doi.org/10.1103/PhysRevLett.112.026801 chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” APS Physics, Physical Review Letters. American Physiological Society, 2014. https://doi.org/10.1103/PhysRevLett.112.026801. ieee: A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” APS Physics, Physical Review Letters, vol. 112, no. 2. American Physiological Society, 2014. ista: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801. mla: Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” APS Physics, Physical Review Letters, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:10.1103/PhysRevLett.112.026801. short: A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014). date_created: 2018-12-11T11:44:36Z date_published: 2014-01-14T00:00:00Z date_updated: 2021-01-12T08:22:14Z day: '14' doi: 10.1103/PhysRevLett.112.026801 extern: '1' external_id: arxiv: - '1306.2720' intvolume: ' 112' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1306.2720 month: '01' oa: 1 oa_version: Preprint publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physiological Society publist_id: '7958' quality_controlled: '1' status: public title: Coherent operations and screening in multielectron spin qubits type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2014' ... --- _id: '9594' abstract: - lang: eng text: Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture. article_number: P1.45 article_processing_charge: No article_type: original author: - first_name: Catherine full_name: Greenhill, Catherine last_name: Greenhill - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: David full_name: Wind, David last_name: Wind citation: ama: Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752 apa: Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752 chicago: Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752. ieee: C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” The Electronic Journal of Combinatorics, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014. ista: Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45. mla: Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752. short: C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014). date_created: 2021-06-23T06:29:35Z date_published: 2014-02-28T00:00:00Z date_updated: 2023-02-23T14:02:12Z day: '28' doi: 10.37236/3752 extern: '1' external_id: arxiv: - '1309.6710' intvolume: ' 21' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.37236/3752 month: '02' oa: 1 oa_version: Published Version publication: The Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: The Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: On the number of spanning trees in random regular graphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 21 year: '2014' ... --- _id: '9655' abstract: - lang: eng text: Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells. article_processing_charge: No article_type: original author: - first_name: Mario full_name: Perkovic, Mario last_name: Perkovic - first_name: Michael full_name: Kunz, Michael last_name: Kunz - first_name: Ulrike full_name: Endesfelder, Ulrike last_name: Endesfelder - first_name: Stefanie full_name: Bunse, Stefanie last_name: Bunse - first_name: Christoph full_name: Wigge, Christoph last_name: Wigge - first_name: Zhou full_name: Yu, Zhou last_name: Yu - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Margot P. full_name: Scheffer, Margot P. last_name: Scheffer - first_name: Anja full_name: Seybert, Anja last_name: Seybert - first_name: Sebastian full_name: Malkusch, Sebastian last_name: Malkusch - first_name: Erin M. full_name: Schuman, Erin M. last_name: Schuman - first_name: Mike full_name: Heilemann, Mike last_name: Heilemann - first_name: Achilleas S. full_name: Frangakis, Achilleas S. last_name: Frangakis citation: ama: Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 2014;186(2):205-213. doi:10.1016/j.jsb.2014.03.018 apa: Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018 chicago: Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.jsb.2014.03.018. ieee: M. Perkovic et al., “Correlative light- and electron microscopy with chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier, pp. 205–213, 2014. ista: Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213. mla: Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:10.1016/j.jsb.2014.03.018. short: M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213. date_created: 2021-07-14T09:05:42Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-07-22T08:26:32Z day: '01' ddc: - '570' doi: 10.1016/j.jsb.2014.03.018 extern: '1' external_id: pmid: - '24698954' file: - access_level: open_access checksum: a322991b43cdc5935c99db88d285aa3a content_type: application/pdf creator: asandaue date_created: 2021-07-22T08:06:34Z date_updated: 2021-07-22T08:06:34Z file_id: '9701' file_name: 2014_JournalOfStructuralBiology_Perkovic.pdf file_size: 3454628 relation: main_file success: 1 file_date_updated: 2021-07-22T08:06:34Z has_accepted_license: '1' intvolume: ' 186' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/3.0/ month: '05' oa: 1 oa_version: Published Version page: 205-213 pmid: 1 publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Correlative light- and electron microscopy with chemical tags tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 186 year: '2014' ... --- _id: '9686' abstract: - lang: eng text: It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings. article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: H.S. full_name: Leung, H.S. last_name: Leung - first_name: A.H.W. full_name: Ngan, A.H.W. last_name: Ngan citation: ama: Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 2014;95(16-18):1845-1865. doi:10.1080/14786435.2014.897008 apa: Cheng, B., Leung, H. S., & Ngan, A. H. W. (2014). Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. Taylor & Francis. https://doi.org/10.1080/14786435.2014.897008 chicago: Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical Magazine. Taylor & Francis, 2014. https://doi.org/10.1080/14786435.2014.897008. ieee: B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations – dislocation-density-function dynamics simulations,” Philosophical Magazine, vol. 95, no. 16–18. Taylor & Francis, pp. 1845–1865, 2014. ista: Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865. mla: Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical Magazine, vol. 95, no. 16–18, Taylor & Francis, 2014, pp. 1845–65, doi:10.1080/14786435.2014.897008. short: B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865. date_created: 2021-07-19T09:27:15Z date_published: 2014-06-23T00:00:00Z date_updated: 2023-02-23T14:04:59Z day: '23' doi: 10.1080/14786435.2014.897008 extern: '1' intvolume: ' 95' issue: 16-18 language: - iso: eng month: '06' oa_version: None page: 1845-1865 publication: Philosophical Magazine publication_identifier: eissn: - 1478-6443 issn: - 1478-6435 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: Strength of metals under vibrations – dislocation-density-function dynamics simulations type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 95 year: '2014' ... --- _id: '2083' abstract: - lang: eng text: Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment. acknowledgement: The authors are grateful to the Leverhulme Trust (F/00 215/AW) for funding this work. article_processing_charge: No article_type: original author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Andrew full_name: Morgan, Andrew last_name: Morgan - first_name: Paul full_name: Neve, Paul last_name: Neve - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave citation: ama: Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation to sink environments. Evolution. 2014;68(8):2296-2305. doi:10.1111/evo.12440 apa: Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Role of sex and migration in adaptation to sink environments. Evolution. Wiley. https://doi.org/10.1111/evo.12440 chicago: Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12440. ieee: M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley, pp. 2296–2305, 2014. ista: Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305. mla: Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:10.1111/evo.12440. short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305. date_created: 2018-12-11T11:55:36Z date_published: 2014-04-25T00:00:00Z date_updated: 2023-02-23T14:06:51Z day: '25' ddc: - '570' department: - _id: CaGu doi: 10.1111/evo.12440 file: - access_level: open_access checksum: 8d459b07e4a11bb5fde92d969184fe48 content_type: application/pdf creator: dernst date_created: 2020-05-14T16:40:31Z date_updated: 2020-07-14T12:45:28Z file_id: '7845' file_name: 2014_Evolution_Lagator.pdf file_size: 467254 relation: main_file file_date_updated: 2020-07-14T12:45:28Z has_accepted_license: '1' intvolume: ' 68' issue: '8' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 2296 - 2305 publication: Evolution publication_status: published publisher: Wiley publist_id: '4954' quality_controlled: '1' related_material: record: - id: '9747' relation: research_data status: public scopus_import: 1 status: public title: Role of sex and migration in adaptation to sink environments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2014' ... --- _id: '9747' abstract: - lang: eng text: Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment. article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Andrew full_name: Morgan, Andrew last_name: Morgan - first_name: Paul full_name: Neve, Paul last_name: Neve - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave citation: ama: 'Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1' apa: 'Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1' chicago: 'Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.' ieee: 'M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.' ista: 'Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.' mla: 'Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.' short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014). date_created: 2021-07-28T15:32:55Z date_published: 2014-04-17T00:00:00Z date_updated: 2023-02-23T10:27:31Z day: '17' department: - _id: CaGu doi: 10.5061/dryad.s42n1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.s42n1 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2083' relation: used_in_publication status: public status: public title: 'Data from: Role of sex and migration in adaptation to sink environments' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '977' abstract: - lang: eng text: We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems. acknowledgement: |- We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario. M. S., M. K., and S. G. contributed equally to this work. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Michael full_name: Knap, Michael J last_name: Knap - first_name: Sarang full_name: Gopalakrishnan, Sarang last_name: Gopalakrishnan - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Norman full_name: Yao, Norman Y last_name: Yao - first_name: Chris full_name: Laumann, Chris R last_name: Laumann - first_name: Dmitry full_name: Abanin, Dmitry A last_name: Abanin - first_name: Mikhail full_name: Lukin, Mikhail D last_name: Lukin - first_name: Eugene full_name: Demler, Eugene A last_name: Demler citation: ama: Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204 apa: Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C., … Demler, E. (2014). Interferometric probes of many-body localization. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204 chicago: Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric Probes of Many-Body Localization.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204. ieee: M. Serbyn et al., “Interferometric probes of many-body localization,” Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014. ista: Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin M, Demler E. 2014. Interferometric probes of many-body localization. Physical Review Letters. 113(14). mla: Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.” Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.147204. short: M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin, M. Lukin, E. Demler, Physical Review Letters 113 (2014). date_created: 2018-12-11T11:49:30Z date_published: 2014-10-03T00:00:00Z date_updated: 2021-01-12T08:22:22Z day: '03' doi: 10.1103/PhysRevLett.113.147204 extern: 1 intvolume: ' 113' issue: '14' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.0693 month: '10' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6421' quality_controlled: 0 status: public title: Interferometric probes of many-body localization type: journal_article volume: 113 year: '2014' ... --- _id: '980' abstract: - lang: eng text: Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization. acknowledgement: Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. We acknowledge support by NSERC Discovery Grant (D.A.). author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Dmitry full_name: Abanin, Dmitry A last_name: Abanin citation: ama: Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 2014;90(17). doi:10.1103/PhysRevB.90.174302 apa: Serbyn, M., Papić, Z., & Abanin, D. (2014). Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.174302 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.174302. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized phase,” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17. American Physical Society, 2014. ista: Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 90(17). mla: Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17, American Physical Society, 2014, doi:10.1103/PhysRevB.90.174302. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 90 (2014). date_created: 2018-12-11T11:49:31Z date_published: 2014-11-06T00:00:00Z date_updated: 2021-01-12T08:22:24Z day: '06' doi: 10.1103/PhysRevB.90.174302 extern: 1 intvolume: ' 90' issue: '17' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.4105 month: '11' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6420' quality_controlled: 0 status: public title: Quantum quenches in the many-body localized phase type: journal_article volume: 90 year: '2014' ... --- _id: '98' abstract: - lang: eng text: Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing. acknowledgement: Funding from the Department of Energy, Office of Science & SCGF, the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation is acknowledged. author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Thorvald full_name: Larsen, Thorvald last_name: Larsen - first_name: Jun full_name: Yao, Jun last_name: Yao - first_name: Hao full_name: Yan, Hao last_name: Yan - first_name: Charles full_name: Lieber, Charles last_name: Lieber - first_name: Charles full_name: Marcus, Charles last_name: Marcus - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth citation: ama: Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 2014;14(6):3582-3586. doi:10.1021/nl501242b apa: Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C., & Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. American Chemical Society. https://doi.org/10.1021/nl501242b chicago: Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber, Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” Nano Letters. American Chemical Society, 2014. https://doi.org/10.1021/nl501242b. ieee: A. P. Higginbotham et al., “Hole spin coherence in a Ge/Si heterostructure nanowire,” Nano Letters, vol. 14, no. 6. American Chemical Society, pp. 3582–3586, 2014. ista: Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6), 3582–3586. mla: Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” Nano Letters, vol. 14, no. 6, American Chemical Society, 2014, pp. 3582–86, doi:10.1021/nl501242b. short: A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth, Nano Letters 14 (2014) 3582–3586. date_created: 2018-12-11T11:44:37Z date_published: 2014-05-05T00:00:00Z date_updated: 2021-01-12T08:22:24Z day: '05' doi: 10.1021/nl501242b extern: '1' external_id: arxiv: - '1403.2093' intvolume: ' 14' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.2093 month: '05' oa: 1 oa_version: Preprint page: 3582 - 3586 publication: Nano Letters publication_status: published publisher: American Chemical Society publist_id: '7956' quality_controlled: '1' status: public title: Hole spin coherence in a Ge/Si heterostructure nanowire type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '2086' abstract: - lang: eng text: Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed. acknowledgement: This study was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative (grant numbers BB/I00097/1 and BB/I000100/1). Rothamsted Research is a national institute of bioscience strategically funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC). article_number: e103989 author: - first_name: Stephan full_name: Wolf, Stephan last_name: Wolf - first_name: Dino full_name: Mcmahon, Dino last_name: Mcmahon - first_name: Ka full_name: Lim, Ka last_name: Lim - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Suzanne full_name: Clark, Suzanne last_name: Clark - first_name: Robert full_name: Paxton, Robert last_name: Paxton - first_name: Juliet full_name: Osborne, Juliet last_name: Osborne citation: ama: 'Wolf S, Mcmahon D, Lim K, et al. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 2014;9(8). doi:10.1371/journal.pone.0103989' apa: 'Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989' chicago: 'Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.' ieee: 'S. Wolf et al., “So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees,” PLoS One, vol. 9, no. 8. Public Library of Science, 2014.' ista: 'Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 9(8), e103989.' mla: 'Wolf, Stephan, et al. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One, vol. 9, no. 8, e103989, Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.' short: S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, PLoS One 9 (2014). date_created: 2018-12-11T11:55:37Z date_published: 2014-08-06T00:00:00Z date_updated: 2023-02-23T14:11:56Z day: '06' ddc: - '570' department: - _id: SyCr doi: 10.1371/journal.pone.0103989 file: - access_level: open_access checksum: 2fc62c6739eada4bddf026afbae669db content_type: application/pdf creator: system date_created: 2018-12-12T10:13:55Z date_updated: 2020-07-14T12:45:28Z file_id: '5042' file_name: IST-2016-437-v1+1_journal.pone.0103989.pdf file_size: 1013386 relation: main_file file_date_updated: 2020-07-14T12:45:28Z has_accepted_license: '1' intvolume: ' 9' issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4949' pubrep_id: '437' quality_controlled: '1' related_material: record: - id: '9888' relation: research_data status: public scopus_import: 1 status: public title: 'So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '9888' abstract: - lang: eng text: Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results. article_processing_charge: No author: - first_name: Stephan full_name: Wolf, Stephan last_name: Wolf - first_name: Dino full_name: Mcmahon, Dino last_name: Mcmahon - first_name: Ka full_name: Lim, Ka last_name: Lim - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Suzanne full_name: Clark, Suzanne last_name: Clark - first_name: Robert full_name: Paxton, Robert last_name: Paxton - first_name: Juliet full_name: Osborne, Juliet last_name: Osborne citation: ama: Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:10.1371/journal.pone.0103989.s003 apa: Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989.s003 chicago: Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.s003. ieee: S. Wolf et al., “Supporting information.” Public Library of Science, 2014. ista: Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting information, Public Library of Science, 10.1371/journal.pone.0103989.s003. mla: Wolf, Stephan, et al. Supporting Information. Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.s003. short: S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014). date_created: 2021-08-11T14:17:53Z date_updated: 2023-02-23T10:27:38Z day: '06' department: - _id: SyCr doi: 10.1371/journal.pone.0103989.s003 month: '08' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '2086' relation: used_in_publication status: public status: public title: Supporting information type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '845' abstract: - lang: eng text: Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena. acknowledgement: The authors are grateful to Georgii Bazykin for valuable discussion and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology for Sanger sequencing. This study was supported by the Russian government grant No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute International Early Career Scientist Award and EMBO Young Investigator Program, and core funds provided by the University of Michigan. author: - first_name: Vladimir full_name: Seplyarskiy, Vladimir B last_name: Seplyarskiy - first_name: Maria full_name: Logacheva, Maria D last_name: Logacheva - first_name: Aleksey full_name: Penin, Aleksey A last_name: Penin - first_name: Maria full_name: Baranová, Maria A last_name: Baranová - first_name: Evgeny full_name: Leushkin, Evgeny V last_name: Leushkin - first_name: Natalia full_name: Demidenko, Natalia V last_name: Demidenko - first_name: Anna full_name: Klepikova, Anna V last_name: Klepikova - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Timothy full_name: James, Timothy Y last_name: James citation: ama: Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242 apa: Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N., … James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu242 chicago: Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242. ieee: V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” Molecular Biology and Evolution, vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014. ista: Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025. mla: Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242. short: V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025. date_created: 2018-12-11T11:48:48Z date_published: 2014-11-01T00:00:00Z date_updated: 2021-01-12T08:19:21Z day: '01' doi: 10.1093/molbev/msu242 extern: 1 intvolume: ' 31' issue: '11' month: '11' page: 3016 - 3025 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6801' quality_controlled: 0 status: public title: Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 31 year: '2014' ... --- _id: '892' abstract: - lang: eng text: The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution. acknowledgement: | The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants. author: - first_name: Dmitry full_name: Ivankov, Dmitry N last_name: Ivankov - first_name: Alexei full_name: Finkelstein, Alexei V last_name: Finkelstein - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004 apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective of compensatory evolution. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2014.05.004 chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004. ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” Current Opinion in Structural Biology, vol. 26, no. 1. Elsevier, pp. 104–112, 2014. ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112. mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014, pp. 104–12, doi:10.1016/j.sbi.2014.05.004. short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112. date_created: 2018-12-11T11:49:03Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T08:21:21Z day: '01' doi: 10.1016/j.sbi.2014.05.004 extern: 1 intvolume: ' 26' issue: '1' month: '06' page: 104 - 112 publication: Current Opinion in Structural Biology publication_status: published publisher: Elsevier publist_id: '6756' quality_controlled: 0 status: public title: A structural perspective of compensatory evolution tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 26 year: '2014' ... --- _id: '9050' abstract: - lang: eng text: Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter. article_number: '1784' article_processing_charge: No article_type: original author: - first_name: Daisuke full_name: Takagi, Daisuke last_name: Takagi - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Adam B. full_name: Braunschweig, Adam B. last_name: Braunschweig - first_name: Michael J. full_name: Shelley, Michael J. last_name: Shelley - first_name: Jun full_name: Zhang, Jun last_name: Zhang citation: ama: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d apa: Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d chicago: Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d. ieee: D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter, vol. 10, no. 11. Royal Society of Chemistry , 2014. ista: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784. mla: Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:10.1039/c3sm52815d. short: D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014). date_created: 2021-02-01T13:43:31Z date_published: 2014-03-21T00:00:00Z date_updated: 2023-02-23T13:47:35Z day: '21' doi: 10.1039/c3sm52815d extern: '1' external_id: arxiv: - '1309.5662' pmid: - '24800268' intvolume: ' 10' issue: '11' keyword: - General Chemistry - Condensed Matter Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1309.5662 month: '03' oa: 1 oa_version: Preprint pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Hydrodynamic capture of microswimmers into sphere-bound orbits type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 10 year: '2014' ... --- _id: '9166' abstract: - lang: eng text: Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles. article_number: '20130372' article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: S. full_name: Sacanna, S. last_name: Sacanna - first_name: S.-H. full_name: Kim, S.-H. last_name: Kim - first_name: G.-R. full_name: Yi, G.-R. last_name: Yi - first_name: D. J. full_name: Pine, D. J. last_name: Pine - first_name: P. M. full_name: Chaikin, P. M. last_name: Chaikin citation: ama: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372' apa: 'Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin, P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rsta.2013.0372' chicago: 'Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372.' ieee: 'J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029. The Royal Society, 2014.' ista: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.' mla: 'Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.' short: 'J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).' date_created: 2021-02-18T14:31:11Z date_published: 2014-11-28T00:00:00Z date_updated: 2021-02-22T10:44:16Z day: '28' doi: 10.1098/rsta.2013.0372 extern: '1' external_id: arxiv: - '1410.7278' pmid: - '25332383' intvolume: ' 372' issue: '2029' keyword: - General Engineering - General Physics and Astronomy - General Mathematics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rsta.2013.0372 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: 'Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences' publication_identifier: eissn: - 1471-2962 issn: - 1364-503X publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: Light-activated self-propelled colloids type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 372 year: '2014' ... --- _id: '926' abstract: - lang: eng text: 'The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.' acknowledgement: We thank Jens Elgeti and Silvia Fre for fruitful discussions. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93). doi:10.1098/rsif.2013.0895 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2013.0895 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” Journal of the Royal Society Interface, vol. 11, no. 93. Royal Society of London, 2014. ista: Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93). mla: Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal Society of London, 2014, doi:10.1098/rsif.2013.0895. short: E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014). date_created: 2018-12-11T11:49:14Z date_published: 2014-04-06T00:00:00Z date_updated: 2021-01-12T08:21:57Z day: '06' doi: 10.1098/rsif.2013.0895 extern: '1' intvolume: ' 11' issue: '93' language: - iso: eng month: '04' oa_version: None publication: Journal of the Royal Society Interface publication_status: published publisher: Royal Society of London publist_id: '6516' status: public title: Growth homeostatic regulation and stem cell dynamics in tissues type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2014' ... --- _id: '9458' abstract: - lang: eng text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints. article_processing_charge: No article_type: original author: - first_name: Jason T. full_name: Huff, Jason T. last_name: Huff - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029 apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029 chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029. ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014. ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297. mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029. short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297. date_created: 2021-06-04T12:00:16Z date_published: 2014-03-13T00:00:00Z date_updated: 2021-12-14T08:22:36Z day: '13' department: - _id: DaZi doi: 10.1016/j.cell.2014.01.029 extern: '1' external_id: pmid: - '24630728' intvolume: ' 156' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2014.01.029 month: '03' oa: 1 oa_version: Published Version page: 1286-1297 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 156 year: '2014' ... --- _id: '9479' abstract: - lang: eng text: Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction. article_processing_charge: No article_type: original author: - first_name: Zsuzsanna full_name: Mérai, Zsuzsanna last_name: Mérai - first_name: Nina full_name: Chumak, Nina last_name: Chumak - first_name: Marcelina full_name: García-Aguilar, Marcelina last_name: García-Aguilar - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Vera K. full_name: Schoft, Vera K. last_name: Schoft - first_name: János full_name: Bindics, János last_name: Bindics - first_name: Lucyna full_name: Ślusarz, Lucyna last_name: Ślusarz - first_name: Stéphanie full_name: Arnoux, Stéphanie last_name: Arnoux - first_name: Susanne full_name: Opravil, Susanne last_name: Opravil - first_name: Karl full_name: Mechtler, Karl last_name: Mechtler - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Hisashi full_name: Tamaru, Hisashi last_name: Tamaru citation: ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 2014;111(45):16166-16171. doi:10.1073/pnas.1418564111 apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1418564111 chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111. ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” Proceedings of the National Academy of Sciences, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014. ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171. mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111. short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171. date_created: 2021-06-07T07:23:43Z date_published: 2014-11-11T00:00:00Z date_updated: 2021-12-14T08:23:26Z day: '11' department: - _id: DaZi doi: 10.1073/pnas.1418564111 extern: '1' external_id: pmid: - '25344531' intvolume: ' 111' issue: '45' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1418564111 month: '11' oa: 1 oa_version: Published Version page: 16166-16171 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 111 year: '2014' ... --- _id: '9662' abstract: - lang: eng text: Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons. article_number: '244112' article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293 apa: Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4904293 chicago: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4904293. ieee: B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing, 2014. ista: Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112. mla: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293. short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014). date_created: 2021-07-15T09:22:49Z date_published: 2014-12-28T00:00:00Z date_updated: 2021-08-09T12:32:24Z day: '28' doi: 10.1063/1.4904293 extern: '1' external_id: arxiv: - '1412.1308' pmid: - '25554138' intvolume: ' 141' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.1308 month: '12' oa: 1 oa_version: Preprint pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Direct path integral estimators for isotope fractionation ratios type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 141 year: '2014' ... --- _id: '97' abstract: - lang: eng text: The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm). acknowledgement: Research supported by the Danish National Research Foundation, the Office of Science at the U.S. Department of Energy, the National Science Foundation (PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST Program. article_number: '216806' author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth - first_name: Thorvald full_name: Larsen, Thorvald last_name: Larsen - first_name: Mattias full_name: Fitzpatrick, Mattias last_name: Fitzpatrick - first_name: Jun full_name: Yao, Jun last_name: Yao - first_name: Hao full_name: Yan, Hao last_name: Yan - first_name: Charles full_name: Lieber, Charles last_name: Lieber - first_name: Charles full_name: Marcus, Charles last_name: Marcus citation: ama: Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.216806 apa: Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan, H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.216806 chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick, Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.216806. ieee: A. P. Higginbotham et al., “Antilocalization of coulomb blockade in a Ge/Si nanowire,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014. ista: Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 112(21), 216806. mla: Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters, vol. 112, no. 21, 216806, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.216806. short: A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan, C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014). date_created: 2018-12-11T11:44:36Z date_published: 2014-05-29T00:00:00Z date_updated: 2021-01-12T08:22:19Z day: '29' doi: 10.1103/PhysRevLett.112.216806 extern: '1' external_id: arxiv: - '1401.2948' intvolume: ' 112' issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1401.2948 month: '05' oa: 1 oa_version: None publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7957' quality_controlled: '1' status: public title: Antilocalization of coulomb blockade in a Ge/Si nanowire type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2014' ... --- _id: '2004' abstract: - lang: eng text: We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks. article_number: e111430 author: - first_name: Anna full_name: Lovrics, Anna last_name: Lovrics - first_name: Yu full_name: Gao, Yu last_name: Gao - first_name: Bianka full_name: Juhász, Bianka last_name: Juhász - first_name: István full_name: Bock, István last_name: Bock - first_name: Helen full_name: Byrne, Helen last_name: Byrne - first_name: András full_name: Dinnyés, András last_name: Dinnyés - first_name: Krisztián full_name: Kovács, Krisztián id: 2AB5821E-F248-11E8-B48F-1D18A9856A87 last_name: Kovács citation: ama: Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0111430 apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., & Kovács, K. (2014). Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430 chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430. ieee: A. Lovrics et al., “Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014. ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 9(11), e111430. mla: Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One, vol. 9, no. 11, e111430, Public Library of Science, 2014, doi:10.1371/journal.pone.0111430. short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács, PLoS One 9 (2014). date_created: 2018-12-11T11:55:09Z date_published: 2014-11-14T00:00:00Z date_updated: 2023-02-23T14:06:14Z day: '14' ddc: - '570' department: - _id: JoCs doi: 10.1371/journal.pone.0111430 ec_funded: 1 file: - access_level: open_access checksum: a2289b843f7463eb1233f9ce45e6a943 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:58Z date_updated: 2020-07-14T12:45:24Z file_id: '4850' file_name: IST-2016-435-v1+1_journal.pone.0111430.pdf file_size: 829363 relation: main_file file_date_updated: 2020-07-14T12:45:24Z has_accepted_license: '1' intvolume: ' 9' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5072' pubrep_id: '435' quality_controlled: '1' related_material: record: - id: '9722' relation: research_data status: public scopus_import: 1 status: public title: Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '9722' article_processing_charge: No author: - first_name: Anna full_name: Lovrics, Anna last_name: Lovrics - first_name: Yu full_name: Gao, Yu last_name: Gao - first_name: Bianka full_name: Juhász, Bianka last_name: Juhász - first_name: István full_name: Bock, István last_name: Bock - first_name: Helen M. full_name: Byrne, Helen M. last_name: Byrne - first_name: András full_name: Dinnyés, András last_name: Dinnyés - first_name: Krisztián full_name: Kovács, Krisztián id: 2AB5821E-F248-11E8-B48F-1D18A9856A87 last_name: Kovács citation: ama: Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006 apa: Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., & Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006 chicago: Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006. ieee: A. Lovrics et al., “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014. ista: Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, 10.1371/journal.pone.0111430.s006. mla: Lovrics, Anna, et al. Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006. short: A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014). date_created: 2021-07-26T14:35:00Z date_published: 2014-11-14T00:00:00Z date_updated: 2023-02-23T10:24:07Z day: '14' department: - _id: JoCs doi: 10.1371/journal.pone.0111430.s006 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '2004' relation: used_in_publication status: public status: public title: Transition probability between TF expression states when Dbx2 inhibits Nkx2.2 type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '2039' abstract: - lang: eng text: 'A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time.' article_number: 7p author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Ben full_name: Adlam, Ben last_name: Adlam - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818 apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time scale of evolutionary innovation. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818 chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818. ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public Library of Science, 2014. ista: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p. mla: Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818. short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014). date_created: 2018-12-11T11:55:22Z date_published: 2014-09-11T00:00:00Z date_updated: 2023-02-23T14:06:36Z day: '11' ddc: - '510' department: - _id: KrCh doi: 10.1371/journal.pcbi.1003818 ec_funded: 1 file: - access_level: open_access checksum: 712d4c5787ddf97809cfc962507f0738 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:35Z date_updated: 2020-07-14T12:45:26Z file_id: '4890' file_name: IST-2016-440-v1+1_journal.pcbi.1003818.pdf file_size: 1399093 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 10' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5012' pubrep_id: '440' quality_controlled: '1' related_material: record: - id: '9739' relation: research_data status: public scopus_import: 1 status: public title: The time scale of evolutionary innovation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2014' ... --- _id: '2161' abstract: - lang: eng text: 'Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.' acknowledgement: "We thank Katrin Kellner for colony establishment and characterization, Mike Bidochka for the fungal strain, Meghan Vyleta for fungal strain characterization, Martina Klatt and Simon Tragust for help in the laboratory, Dimitri Missoh for developing the software BioLogic, and Mark Brown and Raphaël Jeanson for discussion and help with data analysis. The study was funded by the European Research Council (ERC Starting Grant to SC; Marie Curie IEF to LVU) and the German Research Foundation DFG (to SC and to JH), and CW received funding by the doctoral school Diversité du Vivant (Cotutelle project to CD and SC).\r\n" article_processing_charge: No article_type: original author: - first_name: Claudia full_name: Westhus, Claudia id: ca9c6ca9-e8aa-11ec-a586-b9471ede0494 last_name: Westhus - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Edouard full_name: Tourdot, Edouard last_name: Tourdot - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Claudie full_name: Doums, Claudie last_name: Doums - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. 2014;68(10):1701-1710. doi:10.1007/s00265-014-1778-8 apa: Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2014). Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. Springer. https://doi.org/10.1007/s00265-014-1778-8 chicago: Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology. Springer, 2014. https://doi.org/10.1007/s00265-014-1778-8. ieee: C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Increased grooming after repeated brood care provides sanitary benefits in a clonal ant,” Behavioral Ecology and Sociobiology, vol. 68, no. 10. Springer, pp. 1701–1710, 2014. ista: Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2014. Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Behavioral Ecology and Sociobiology. 68(10), 1701–1710. mla: Westhus, Claudia, et al. “Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Behavioral Ecology and Sociobiology, vol. 68, no. 10, Springer, 2014, pp. 1701–10, doi:10.1007/s00265-014-1778-8. short: C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, Behavioral Ecology and Sociobiology 68 (2014) 1701–1710. date_created: 2018-12-11T11:56:03Z date_published: 2014-07-23T00:00:00Z date_updated: 2023-02-23T14:06:46Z day: '23' department: - _id: SyCr doi: 10.1007/s00265-014-1778-8 ec_funded: 1 intvolume: ' 68' issue: '10' language: - iso: eng month: '07' oa_version: None page: 1701 - 1710 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution publication: Behavioral Ecology and Sociobiology publication_identifier: issn: - 0340-5443 publication_status: published publisher: Springer publist_id: '4823' quality_controlled: '1' related_material: record: - id: '9742' relation: research_data status: public scopus_import: '1' status: public title: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2014' ... --- _id: '2036' 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. ' acknowledgement: The project was supported by Leverhulme Trust. article_number: '20141679' author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave - first_name: Paul full_name: Neve, Paul last_name: Neve 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 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 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. 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. 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. 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). date_created: 2018-12-11T11:55:21Z date_published: 2014-09-17T00:00:00Z date_updated: 2023-02-23T14:06:44Z day: '17' department: - _id: CaGu doi: 10.1098/rspb.2014.1679 intvolume: ' 281' issue: '1794' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/ month: '09' oa: 1 oa_version: Submitted Version publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '5019' quality_controlled: '1' related_material: record: - id: '9741' relation: research_data status: public scopus_import: 1 status: public title: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 281 year: '2014' ... --- _id: '9740' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: 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' 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' 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.' 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.' 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.' 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). date_created: 2021-07-28T08:38:40Z date_published: 2014-11-13T00:00:00Z date_updated: 2023-02-23T10:23:32Z day: '13' department: - _id: SyCr doi: 10.5061/dryad.vm0vc main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.vm0vc month: '11' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1993' relation: used_in_publication status: public status: public title: 'Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '9741' 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. article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave - first_name: Paul full_name: Neve, Paul last_name: Neve citation: 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' 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' 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.' 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.' 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.' 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). date_created: 2021-07-28T08:48:06Z date_published: 2014-08-21T00:00:00Z date_updated: 2023-02-23T10:25:31Z day: '21' department: - _id: CaGu doi: 10.5061/dryad.85dn7 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.85dn7 month: '08' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2036' relation: used_in_publication status: public status: public title: 'Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '9739' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Ben full_name: Adlam, Ben last_name: Adlam - first_name: Martin full_name: Novak, Martin last_name: Novak citation: 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 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 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. 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. 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. short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014). date_created: 2021-07-28T08:13:57Z date_published: 2014-09-11T00:00:00Z date_updated: 2023-02-23T10:25:37Z day: '11' department: - _id: KrCh doi: 10.1371/journal.pcbi.1003818.s001 month: '09' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '2039' relation: used_in_publication status: public status: public title: Detailed proofs for “The time scale of evolutionary innovation” type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '2170' 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.' 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). author: - first_name: Jack full_name: Hearn, Jack last_name: Hearn - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: Lynsey full_name: Bunnefeld, Lynsey last_name: Bunnefeld - first_name: James full_name: Nicholls, James last_name: Nicholls - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse citation: 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 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 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. 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. 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. short: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular Ecology 23 (2014) 198–211. date_created: 2018-12-11T11:56:07Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T14:07:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.12578 file: - access_level: open_access checksum: 4de1ab255976a8ae77eb0e55ad62ecc9 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:52Z date_updated: 2020-07-14T12:45:31Z file_id: '4651' file_name: IST-2016-559-v1+1_Hearn_et_al.pdf file_size: 807444 relation: main_file - access_level: open_access checksum: 01a8073e071c088500425f910b0f1f71 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:53Z date_updated: 2020-07-14T12:45:31Z file_id: '4652' file_name: IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf file_size: 1518088 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' intvolume: ' 23' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 198 - 211 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '4814' pubrep_id: '559' quality_controlled: '1' related_material: record: - id: '9754' relation: research_data status: public scopus_import: 1 status: public title: Likelihood-based inference of population history from low-coverage de novo genome assemblies type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2014' ... --- _id: '9753' 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.' article_processing_charge: No author: - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Michel full_name: Chapuisat, Michel last_name: Chapuisat - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: 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' 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' 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.' 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.' 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.' 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). date_created: 2021-07-30T08:24:11Z date_published: 2014-10-08T00:00:00Z date_updated: 2023-02-23T10:36:17Z day: '08' department: - _id: SyCr doi: 10.5061/dryad.nc0gc main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.nc0gc month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2284' relation: used_in_publication status: public status: public title: 'Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '9752' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Kristina full_name: Simmons, Kristina last_name: Simmons - first_name: Jason full_name: Prentice, Jason last_name: Prentice - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Jan full_name: Homann, Jan last_name: Homann - first_name: Heather full_name: Yee, Heather last_name: Yee - first_name: Stephanie full_name: Palmer, Stephanie last_name: Palmer - first_name: Philip full_name: Nelson, Philip last_name: Nelson - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian citation: ama: 'Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:10.5061/dryad.246qg' 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' 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.' ieee: 'K. Simmons et al., “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.' 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.' 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). date_created: 2021-07-30T08:13:52Z date_published: 2014-11-07T00:00:00Z date_updated: 2023-02-23T10:35:57Z day: '07' department: - _id: GaTk doi: 10.5061/dryad.246qg main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.246qg month: '11' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2277' relation: used_in_publication status: public status: public title: 'Data from: Transformation of stimulus correlations by the retina' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '978' 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. 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. author: - first_name: Ilija full_name: Zeljkovic, Ilija last_name: Zeljkovic - first_name: Yoshinori full_name: Okada, Yoshinori last_name: Okada - first_name: Chengyi full_name: Huang, Chengyi last_name: Huang - first_name: Raman full_name: Sankar, Raman last_name: Sankar - first_name: Daniel full_name: Walkup, Daniel last_name: Walkup - first_name: Wenwen full_name: Zhou, Wenwen last_name: Zhou - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Fangcheng full_name: Chou, Fangcheng last_name: Chou - first_name: Wei full_name: Tsai, Wei-Feng last_name: Tsai - first_name: Hsin full_name: Lin, Hsin last_name: Lin - first_name: Arun full_name: Bansil, Arun last_name: Bansil - first_name: Liang full_name: Fu, Liang last_name: Fu - first_name: Md full_name: Hasan, Md Z last_name: Hasan - first_name: Vidya full_name: Madhavan, Vidya last_name: Madhavan 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:49:30Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:22:23Z day: '01' doi: 10.1038/nphys3012 extern: 1 intvolume: ' 10' issue: '8' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1312.0164 month: '08' oa: 1 page: 572 - 577 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '6423' quality_controlled: 0 status: public title: Mapping the unconventional orbital texture in topological crystalline insulators type: journal_article volume: 10 year: '2014' ... --- _id: '979' abstract: - lang: eng 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. 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. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Liang full_name: Fu, Liang last_name: Fu citation: 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 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 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. 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). 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. short: M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics 90 (2014). date_created: 2018-12-11T11:49:31Z date_published: 2014-07-03T00:00:00Z date_updated: 2021-01-12T08:22:23Z day: '03' doi: 10.1103/PhysRevB.90.035402 extern: 1 intvolume: ' 90' issue: '3' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.8153 month: '07' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6422' quality_controlled: 0 status: public title: Symmetry breaking and Landau quantization in topological crystalline insulators type: journal_article volume: 90 year: '2014' ... --- _id: '9931' 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, 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. 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. article_processing_charge: No article_type: original author: - first_name: Riddhiman full_name: Dhar, Riddhiman last_name: Dhar - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Andreas full_name: Wagner, Andreas last_name: Wagner citation: 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 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 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. 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. 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. 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. date_created: 2021-08-17T09:03:09Z date_published: 2014-06-03T00:00:00Z date_updated: 2023-02-23T14:13:27Z day: '03' department: - _id: CaGu doi: 10.1111/evo.12373 external_id: pmid: - '24495000' intvolume: ' 68' issue: '6' language: - iso: eng month: '06' oa_version: None page: 1775-1791 pmid: 1 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9932' relation: research_data status: public scopus_import: '1' status: public title: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 68 year: '2014' ... --- _id: '9932' 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. article_processing_charge: No author: - first_name: Riddhiman full_name: Dhar, Riddhiman last_name: Dhar - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Andreas full_name: Wagner, Andreas last_name: Wagner citation: 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' 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' 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.' 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.' 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.' 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). date_created: 2021-08-17T09:11:40Z date_published: 2014-01-27T00:00:00Z date_updated: 2023-02-23T14:13:24Z day: '27' department: - _id: CaGu doi: 10.5061/dryad.jc402 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.jc402 month: '01' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9931' relation: used_in_publication status: public 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' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '12637' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: W. W. full_name: Immerzeel, W. W. last_name: Immerzeel - first_name: L. full_name: Petersen, L. last_name: Petersen - first_name: S. full_name: Ragettli, S. last_name: Ragettli - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: 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 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 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. 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. 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. short: W.W. Immerzeel, L. Petersen, S. Ragettli, F. Pellicciotti, Water Resources Research 50 (2014) 2212–2226. date_created: 2023-02-20T08:17:01Z date_published: 2014-03-01T00:00:00Z date_updated: 2023-02-24T08:28:23Z day: '01' doi: 10.1002/2013wr014506 extern: '1' intvolume: ' 50' issue: '3' keyword: - Water Science and Technology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/2013WR014506 month: '03' oa: 1 oa_version: Published Version page: 2212-2226 publication: Water Resources Research publication_identifier: eissn: - 1944-7973 issn: - 0043-1397 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2014' ... --- _id: '12636' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: W.W. full_name: Immerzeel, W.W. last_name: Immerzeel - first_name: P.D.A. full_name: Kraaijenbrink, P.D.A. last_name: Kraaijenbrink - first_name: J.M. full_name: Shea, J.M. last_name: Shea - first_name: A.B. full_name: Shrestha, A.B. last_name: Shrestha - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: M.F.P. full_name: Bierkens, M.F.P. last_name: Bierkens - first_name: S.M. full_name: de Jong, S.M. last_name: de Jong 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 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. 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. 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. 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. date_created: 2023-02-20T08:16:56Z date_published: 2014-07-01T00:00:00Z date_updated: 2023-02-24T08:32:39Z day: '01' doi: 10.1016/j.rse.2014.04.025 extern: '1' intvolume: ' 150' issue: '7' keyword: - Computers in Earth Sciences - Geology - Soil Science language: - iso: eng month: '07' oa_version: None page: 93-103 publication: Remote Sensing of Environment publication_identifier: issn: - 0034-4257 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 150 year: '2014' ... --- _id: '12635' 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.' article_processing_charge: No article_type: review author: - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: M. full_name: Carenzo, M. last_name: Carenzo - first_name: R. full_name: Bordoy, R. last_name: Bordoy - first_name: M. full_name: Stoffel, M. last_name: Stoffel citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2023-02-20T08:16:51Z date_published: 2014-09-15T00:00:00Z date_updated: 2023-02-24T08:36:04Z day: '15' doi: 10.1016/j.scitotenv.2014.04.022 extern: '1' intvolume: ' 493' keyword: - Pollution - Waste Management and Disposal - Environmental Chemistry - Environmental Engineering language: - iso: eng month: '09' oa_version: None page: 1152-1170 publication: Science of The Total Environment publication_identifier: issn: - 0048-9697 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 493 year: '2014' ... --- _id: '12632' 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. article_processing_charge: No article_type: original author: - first_name: Jeannette full_name: Gabbi, Jeannette last_name: Gabbi - first_name: Marco full_name: Carenzo, Marco last_name: Carenzo - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Andreas full_name: Bauder, Andreas last_name: Bauder - first_name: Martin full_name: Funk, Martin last_name: Funk 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 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 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. 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. 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. 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. date_created: 2023-02-20T08:16:34Z date_published: 2014-08-01T00:00:00Z date_updated: 2023-02-24T08:56:35Z day: '01' doi: 10.3189/2014jog14j011 extern: '1' intvolume: ' 60' issue: '224' keyword: - Earth-Surface Processes language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/2014JoG14J011 month: '08' oa: 1 oa_version: Published Version page: 1140-1154 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2014' ... --- _id: '12634' abstract: - lang: eng 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.' article_processing_charge: No article_type: review author: - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: S. full_name: Ragettli, S. last_name: Ragettli - first_name: M. full_name: Carenzo, M. last_name: Carenzo - first_name: J. full_name: McPhee, J. last_name: McPhee citation: 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 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 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. 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. 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. 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. date_created: 2023-02-20T08:16:46Z date_published: 2014-09-15T00:00:00Z date_updated: 2023-02-24T08:37:57Z day: '15' doi: 10.1016/j.scitotenv.2013.10.055 extern: '1' intvolume: ' 493' keyword: - Pollution - Waste Management and Disposal - Environmental Chemistry - Environmental Engineering language: - iso: eng month: '09' oa_version: None page: 1197-1210 publication: Science of The Total Environment publication_identifier: issn: - 0048-9697 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Changes of glaciers in the Andes of Chile and priorities for future work type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 493 year: '2014' ... --- _id: '13399' 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. article_processing_charge: No article_type: original author: - first_name: Pintu K. full_name: Kundu, Pintu K. last_name: Kundu - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn 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 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 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. 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. ista: Kundu PK, Klajn R. 2014. Watching single molecules move in response to light. ACS Nano. 8(12), 11913–11916. 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. date_created: 2023-08-01T09:45:42Z date_published: 2014-12-23T00:00:00Z date_updated: 2023-08-08T07:18:58Z day: '23' doi: 10.1021/nn506656r extern: '1' external_id: pmid: - '25474733' intvolume: ' 8' issue: '12' keyword: - General Physics and Astronomy - General Engineering - General Materials Science language: - iso: eng month: '12' oa_version: None page: 11913-11916 pmid: 1 publication: ACS Nano publication_identifier: eissn: - 1936-086X issn: - 1936-0851 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Watching single molecules move in response to light type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2014' ... --- _id: '13402' 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. article_number: '3588' article_processing_charge: No article_type: original author: - first_name: Pintu K. full_name: Kundu, Pintu K. last_name: Kundu - first_name: Gregory L. full_name: Olsen, Gregory L. last_name: Olsen - first_name: Vladimir full_name: Kiss, Vladimir last_name: Kiss - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Kundu PK, Olsen GL, Kiss V, Klajn R. Nanoporous frameworks exhibiting multiple stimuli responsiveness. Nature Communications. 2014;5. doi:10.1038/ncomms4588 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 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. 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. ista: Kundu PK, Olsen GL, Kiss V, Klajn R. 2014. Nanoporous frameworks exhibiting multiple stimuli responsiveness. Nature Communications. 5, 3588. 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). date_created: 2023-08-01T09:46:27Z date_published: 2014-04-07T00:00:00Z date_updated: 2023-08-08T07:28:10Z day: '07' doi: 10.1038/ncomms4588 extern: '1' external_id: pmid: - '24709950' intvolume: ' 5' keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/ncomms4588 month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Nanoporous frameworks exhibiting multiple stimuli responsiveness type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2014' ... --- _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. article_processing_charge: No article_type: original author: - first_name: Gurvinder full_name: Singh, Gurvinder last_name: Singh - first_name: Henry full_name: Chan, Henry last_name: Chan - first_name: Artem full_name: Baskin, Artem last_name: Baskin - first_name: Elijah full_name: Gelman, Elijah last_name: Gelman - first_name: Nikita full_name: Repnin, Nikita last_name: Repnin - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: 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 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 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. 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. 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. 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. date_created: 2023-08-01T09:45:56Z date_published: 2014-07-24T00:00:00Z date_updated: 2023-08-08T07:23:05Z day: '24' doi: 10.1126/science.1254132 extern: '1' external_id: pmid: - '25061133' intvolume: ' 345' issue: '6201' keyword: - Multidisciplinary language: - iso: eng month: '07' oa_version: None page: 1149-1153 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Self-assembly of magnetite nanocubes into helical superstructures type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 345 year: '2014' ... --- _id: '13404' 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. article_processing_charge: No article_type: original author: - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: 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 chicago: Klajn, Rafal. “Spiropyran-Based Dynamic Materials.” Chemical Society Reviews. Royal Society of Chemistry, 2014. 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. 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. short: R. Klajn, Chemical Society Reviews 43 (2014) 148–184. date_created: 2023-08-01T09:47:03Z date_published: 2014-01-27T00:00:00Z date_updated: 2023-08-08T07:41:38Z day: '27' doi: 10.1039/c3cs60181a extern: '1' external_id: pmid: - '23979515' intvolume: ' 43' issue: '1' keyword: - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1039/C3CS60181A month: '01' oa: 1 oa_version: Published Version page: 148-184 pmid: 1 publication: Chemical Society Reviews publication_identifier: eissn: - 1460-4744 issn: - 0306-0012 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Spiropyran-based dynamic materials type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2014' ... --- _id: '13401' 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. article_processing_charge: No article_type: original author: - first_name: Pintu K. full_name: Kundu, Pintu K. last_name: Kundu - first_name: Avishai full_name: Lerner, Avishai last_name: Lerner - first_name: Kristina full_name: Kučanda, Kristina last_name: Kučanda - first_name: Gregory full_name: Leitus, Gregory last_name: Leitus - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: 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 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 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. 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. 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. short: P.K. Kundu, A. Lerner, K. Kučanda, G. Leitus, R. Klajn, Journal of the American Chemical Society 136 (2014) 11276–11279. date_created: 2023-08-01T09:46:12Z date_published: 2014-08-13T00:00:00Z date_updated: 2023-08-08T07:25:37Z day: '13' doi: 10.1021/ja505948q extern: '1' external_id: pmid: - '25072292' intvolume: ' 136' issue: '32' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '08' oa_version: None page: 11276-11279 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2014' ... --- _id: '13403' 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. article_processing_charge: No article_type: original author: - first_name: Tino full_name: Zdobinsky, Tino last_name: Zdobinsky - first_name: Pradipta full_name: Sankar Maiti, Pradipta last_name: Sankar Maiti - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: 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 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 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. 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. 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. 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. short: T. Zdobinsky, P. Sankar Maiti, R. Klajn, Journal of the American Chemical Society 136 (2014) 2711–2714. date_created: 2023-08-01T09:46:44Z date_published: 2014-02-19T00:00:00Z date_updated: 2023-08-08T07:32:11Z day: '19' doi: 10.1021/ja411573a extern: '1' external_id: pmid: - '24320557' intvolume: ' 136' issue: '7' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '02' oa_version: None page: 2711-2714 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Support curvature and conformational freedom control chemical reactivity of immobilized species type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2014' ... --- _id: '14018' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Peter M. full_name: Kraus, Peter M. last_name: Kraus - first_name: Song Bin full_name: Zhang, Song Bin last_name: Zhang - first_name: Nina full_name: Rohringer, Nina last_name: Rohringer - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: 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 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 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. 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. 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. 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. date_created: 2023-08-10T06:38:19Z date_published: 2014-04-14T00:00:00Z date_updated: 2023-08-22T08:58:12Z day: '14' doi: 10.1039/c4fd00018h extern: '1' external_id: pmid: - '25415558' intvolume: ' 171' keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '04' oa_version: None page: 113-132 pmid: 1 publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 171 year: '2014' ... --- _id: '14019' 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. article_number: '064317' article_processing_charge: No article_type: original author: - first_name: K. full_name: Vasilatou, K. last_name: Vasilatou - first_name: J. M. full_name: Michaud, J. M. last_name: Michaud - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: G. full_name: Grassi, G. last_name: Grassi - first_name: F. full_name: Merkt, F. last_name: Merkt citation: 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' 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' 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.' 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.' 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.' 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.' short: K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal of Chemical Physics 141 (2014). date_created: 2023-08-10T06:38:30Z date_published: 2014-08-14T00:00:00Z date_updated: 2023-08-22T09:01:31Z day: '14' doi: 10.1063/1.4890744 extern: '1' external_id: pmid: - '25134581' intvolume: ' 141' issue: '6' keyword: - Physical and Theoretical Chemistry - General Physics and Astronomy language: - iso: eng month: '08' oa_version: None pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2014' ... --- _id: '14021' abstract: - lang: eng 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. article_number: '124030' article_processing_charge: No article_type: original author: - first_name: P M full_name: Kraus, P M last_name: Kraus - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: H J full_name: Wörner, H J last_name: Wörner citation: 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' 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' 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.' 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.' 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.' short: 'P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 47 (2014).' date_created: 2023-08-10T06:38:48Z date_published: 2014-06-10T00:00:00Z date_updated: 2023-08-22T09:04:30Z day: '10' doi: 10.1088/0953-4075/47/12/124030 extern: '1' external_id: arxiv: - '1311.3923' intvolume: ' 47' issue: '12' keyword: - Condensed Matter Physics - Atomic and Molecular Physics - and Optics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.3923 month: '06' oa: 1 oa_version: Preprint publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics' publication_identifier: eissn: - 1361-6455 issn: - 0953-4075 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2014' ... --- _id: '14020' abstract: - lang: eng 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. article_number: '023001' article_processing_charge: No article_type: original author: - first_name: P. M. full_name: Kraus, P. M. last_name: Kraus - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: H. J. full_name: Wörner, H. J. last_name: Wörner citation: 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 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 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. 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. 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. 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. short: P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Physical Review Letters 113 (2014). date_created: 2023-08-10T06:38:38Z date_published: 2014-07-11T00:00:00Z date_updated: 2023-08-22T09:02:56Z day: '11' doi: 10.1103/physrevlett.113.023001 extern: '1' external_id: arxiv: - '1311.3923' pmid: - '25062172' intvolume: ' 113' issue: '2' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.3923 month: '07' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Two-pulse field-free orientation reveals anisotropy of molecular shape resonance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2014' ... --- _id: '535' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:47:01Z date_published: 2014-11-01T00:00:00Z date_updated: 2023-09-05T14:09:29Z day: '01' department: - _id: KrCh doi: 10.1007/s00453-013-9843-7 ec_funded: 1 external_id: arxiv: - '1604.08234' intvolume: ' 70' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.08234 month: '11' oa: 1 oa_version: Preprint page: 457 - 492 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Algorithmica publication_status: published publisher: Springer publist_id: '7282' quality_controlled: '1' related_material: record: - id: '10905' relation: earlier_version status: public scopus_import: '1' status: public title: Polynomial-time algorithms for energy games with special weight structures type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 70 year: '2014' ... --- _id: '10886' 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. acknowledgement: This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP. alternative_title: - Mathematics and Visualization article_processing_charge: No author: - first_name: Valentin full_name: Zobel, Valentin last_name: Zobel - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Ingrid full_name: Hotz, Ingrid last_name: Hotz citation: 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' 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 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. 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. 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. 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. short: V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–262. date_created: 2022-03-18T13:05:39Z date_published: 2014-03-19T00:00:00Z date_updated: 2023-09-05T14:13:16Z day: '19' department: - _id: HeEd doi: 10.1007/978-3-319-04099-8_16 language: - iso: eng month: '03' oa_version: None page: 249-262 publication: 'Topological Methods in Data Analysis and Visualization III ' publication_identifier: eisbn: - '9783319040998' eissn: - 2197-666X isbn: - '9783319040981' issn: - 1612-3786 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2014' ... --- _id: '6178' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Pedro full_name: Campinho, Pedro id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87 last_name: Campinho orcid: 0000-0002-8526-5416 - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 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' 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' 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.' 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.' 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.' 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. date_created: 2019-03-26T08:55:59Z date_published: 2014-08-22T00:00:00Z date_updated: 2023-09-05T14:12:00Z day: '22' department: - _id: CaHe doi: 10.1007/978-1-4939-1164-6_15 editor: - first_name: Celeste full_name: Nelson, Celeste last_name: Nelson external_id: pmid: - '25245697' intvolume: ' 1189' language: - iso: eng month: '08' oa_version: None page: 219-235 place: New York, NY pmid: 1 publication: Tissue Morphogenesis publication_identifier: eissn: - 1940-6029 isbn: - '9781493911639' - '9781493911646' issn: - 1064-3745 publication_status: published publisher: Springer quality_controlled: '1' series_title: Methods in Molecular Biology status: public title: UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 1189 year: '2014' ... --- _id: '10814' 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. article_processing_charge: No article_type: original author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: 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 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 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. 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. ista: Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41. 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. date_created: 2022-03-04T07:54:39Z date_published: 2014-03-01T00:00:00Z date_updated: 2023-09-05T14:19:47Z day: '01' department: - _id: RoSe doi: 10.1365/s13291-014-0083-9 intvolume: ' 116' keyword: - General Medicine language: - iso: eng month: '03' oa_version: None page: 21-41 publication: Jahresbericht der Deutschen Mathematiker-Vereinigung publication_identifier: eissn: - 1869-7135 issn: - 0012-0456 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The excitation spectrum for Bose fluids with weak interactions type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 116 year: '2014' ... --- _id: '10817' abstract: - lang: eng 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. acknowledgement: This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC. article_processing_charge: No author: - first_name: David full_name: Günther, David last_name: Günther - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Hans-Peter full_name: Seidel, Hans-Peter last_name: Seidel - first_name: Tino full_name: Weinkauf, Tino last_name: Weinkauf citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2022-03-04T08:33:57Z date_published: 2014-03-19T00:00:00Z date_updated: 2023-09-05T15:33:45Z day: '19' department: - _id: HeEd doi: 10.1007/978-3-319-04099-8_9 ec_funded: 1 editor: - first_name: Peer-Timo full_name: Bremer, Peer-Timo last_name: Bremer - first_name: Ingrid full_name: Hotz, Ingrid last_name: Hotz - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci - first_name: Ronald full_name: Peikert, Ronald last_name: Peikert language: - iso: eng month: '03' oa_version: None page: 135-150 place: Cham project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Topological Methods in Data Analysis and Visualization III. publication_identifier: eisbn: - '9783319040998' eissn: - 2197-666X isbn: - '9783319040981' issn: - 1612-3786 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: Mathematics and Visualization status: public title: Notes on the simplification of the Morse-Smale complex type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2014' ... --- _id: '1395' 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad citation: ama: 'Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 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.' 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.' 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.' 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.' 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.' 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.' date_created: 2018-12-11T11:51:46Z date_published: 2014-02-01T00:00:00Z date_updated: 2023-09-07T11:38:56Z day: '01' degree_awarded: PhD department: - _id: SyCr language: - iso: eng month: '02' oa_version: None page: '131' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5814' status: public supervisor: - first_name: Sylvia M full_name: Cremer, Sylvia M id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: 'Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2014' ... --- _id: '1402' 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Petra full_name: Marhavá, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Marhavá citation: ama: Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014. apa: Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria. chicago: Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014. ieee: 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. 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. date_created: 2018-12-11T11:51:49Z date_published: 2014-12-01T00:00:00Z date_updated: 2023-09-07T11:39:38Z day: '01' degree_awarded: PhD department: - _id: JiFr language: - iso: eng month: '12' oa_version: None page: '90' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5805' status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2014' ... --- _id: '2255' 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. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: 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 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 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. 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. ista: Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 50(1), 164–177. 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. date_created: 2018-12-11T11:56:36Z date_published: 2014-09-01T00:00:00Z date_updated: 2023-09-07T11:41:25Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s10851-013-0468-x ec_funded: 1 file: - access_level: open_access checksum: 2f93f3e63a38a85cd4404d7953913b14 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:18Z date_updated: 2020-07-14T12:45:35Z file_id: '5204' file_name: IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf file_size: 3941391 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' intvolume: ' 50' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 164 - 177 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Journal of Mathematical Imaging and Vision publication_identifier: issn: - '09249907' publication_status: published publisher: Springer publist_id: '4691' pubrep_id: '549' quality_controlled: '1' related_material: record: - id: '2843' relation: earlier_version status: public - id: '1399' relation: dissertation_contains status: public scopus_import: 1 status: public title: Stable length estimates of tube-like shapes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2014' ... --- _id: '2159' abstract: - lang: eng 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.' acknowledgement: Swiss National Science Foundation (Project SNSF-PP00P2-138948) author: - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: 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' 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' 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. 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.' 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. short: I. Mabillard, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 171–180. conference: end_date: 2014-06-11 location: Kyoto, Japan name: 'SoCG: Symposium on Computational Geometry' start_date: 2014-06-08 date_created: 2018-12-11T11:56:03Z date_published: 2014-06-08T00:00:00Z date_updated: 2023-09-07T11:56:27Z day: '08' ddc: - '510' department: - _id: UlWa doi: 10.1145/2582112.2582134 file: - access_level: open_access checksum: 2aae223fee8ffeaf57bbabd8d92b6a2c content_type: application/pdf creator: system date_created: 2018-12-12T10:09:12Z date_updated: 2020-07-14T12:45:30Z file_id: '4735' file_name: IST-2016-534-v1+1_Eliminating_Tverberg_points_I._An_analogue_of_the_Whitney_trick.pdf file_size: 914396 relation: main_file file_date_updated: 2020-07-14T12:45:30Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 171 - 180 publication: Proceedings of the Annual Symposium on Computational Geometry publication_status: published publisher: ACM publist_id: '4847' pubrep_id: '534' quality_controlled: '1' related_material: record: - id: '1123' relation: dissertation_contains status: public scopus_import: 1 status: public title: Eliminating Tverberg points, I. An analogue of the Whitney trick type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2023' 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.' author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak orcid: 0000-0002-2519-824X 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 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 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. 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. ista: Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597. 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. date_created: 2018-12-11T11:55:16Z date_published: 2014-11-27T00:00:00Z date_updated: 2023-09-07T11:55:53Z day: '27' ddc: - '570' department: - _id: NiBa doi: 10.1002/ece3.1289 ec_funded: 1 file: - access_level: open_access checksum: 9ab43db1b0fede7bfe560ed77e177b76 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:28Z date_updated: 2020-07-14T12:45:25Z file_id: '4946' file_name: IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf file_size: 118813 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 4' issue: '24' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 4589 - 4597 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Ecology and Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '5049' pubrep_id: '462' quality_controlled: '1' related_material: record: - id: '1125' relation: dissertation_contains status: public scopus_import: 1 status: public title: Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2014' ... --- _id: '2218' abstract: - lang: eng 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. alternative_title: - LNCS author: - first_name: Pavol full_name: Cerny, Pavol last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Leonid full_name: Ryzhyk, Leonid last_name: Ryzhyk - first_name: Thorsten full_name: Tarrach, Thorsten id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87 last_name: Tarrach orcid: 0000-0003-4409-8487 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' 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' 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. 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.' 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.' 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. short: P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2014, pp. 568–584. conference: end_date: 2014-07-22 location: Vienna, Austria name: 'CAV: Computer Aided Verification' start_date: 2014-07-18 date_created: 2018-12-11T11:56:23Z date_published: 2014-07-22T00:00:00Z date_updated: 2023-09-07T11:57:01Z day: '22' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-08867-9_38 ec_funded: 1 file: - access_level: open_access checksum: a631d3105509f239724644e77a1212e2 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:14Z date_updated: 2020-07-14T12:45:33Z file_id: '4995' file_name: IST-2014-297-v1+1_cav14-final.pdf file_size: 416732 relation: main_file - access_level: open_access checksum: f8b0f748cc9fa697ca992cc56c87bc4e content_type: application/pdf creator: system date_created: 2018-12-12T10:13:15Z date_updated: 2020-07-14T12:45:33Z file_id: '4996' file_name: IST-2014-297-v2+1_cav14-final2.pdf file_size: 616293 relation: main_file file_date_updated: 2020-07-14T12:45:33Z has_accepted_license: '1' intvolume: ' 8559' language: - iso: eng main_file_link: - open_access: '1' url: https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38 month: '07' oa: 1 oa_version: Submitted Version page: 568 - 584 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication_identifier: isbn: - 978-331908866-2 publication_status: published publisher: Springer publist_id: '4749' pubrep_id: '297' quality_controlled: '1' related_material: record: - id: '1130' relation: dissertation_contains status: public status: public title: Regression-free synthesis for concurrency type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8559 year: '2014' ... --- _id: '2167' abstract: - lang: eng 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. article_number: '6823899' article_processing_charge: No author: - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Willibald full_name: Krenn, Willibald last_name: Krenn - first_name: Dejan full_name: Nickovic, Dejan last_name: Nickovic citation: 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' 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' 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. 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. 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.' 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. conference: end_date: 2014-04-04 location: Cleveland, USA name: 'ICST: International Conference on Software Testing, Verification and Validation' start_date: 2014-03-31 date_created: 2018-12-11T11:56:06Z date_published: 2014-03-01T00:00:00Z date_updated: 2023-09-07T11:58:33Z day: '01' department: - _id: ToHe doi: 10.1109/ICST.2014.50 ec_funded: 1 external_id: arxiv: - '1904.07083' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1904.07083 month: '03' oa: 1 oa_version: Preprint project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: IEEE 7th International Conference on Software Testing, Verification and Validation publication_identifier: isbn: - 978-1-4799-2255-0 issn: - 2159-4848 publication_status: published publisher: IEEE publist_id: '4817' quality_controlled: '1' related_material: record: - id: '5411' relation: earlier_version status: public - id: '1155' relation: dissertation_contains status: public scopus_import: 1 status: public title: Compositional specifications for IOCO testing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2063' 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. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca citation: 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' 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' 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. 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.' 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. short: K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490. conference: end_date: 2014-07-22 location: Vienna, Austria name: 'CAV: Computer Aided Verification' start_date: 2014-07-18 date_created: 2018-12-11T11:55:30Z date_published: 2014-07-01T00:00:00Z date_updated: 2023-09-07T11:58:33Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-08867-9_31 ec_funded: 1 intvolume: ' 8559' language: - iso: eng month: '07' oa_version: None page: 473 - 490 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '4978' quality_controlled: '1' related_material: record: - id: '5412' relation: earlier_version status: public - id: '5413' relation: earlier_version status: public - id: '5414' relation: earlier_version status: public - id: '1155' relation: dissertation_contains status: public status: public title: CEGAR for qualitative analysis of probabilistic systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8559 year: '2014' ... --- _id: '2001' 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. author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: 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 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 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. 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. ista: Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 6(6), 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. short: K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014) 545–557. date_created: 2018-12-11T11:55:08Z date_published: 2014-06-22T00:00:00Z date_updated: 2023-09-07T12:00:25Z day: '22' department: - _id: ToBo doi: 10.1111/1758-2229.12190 ec_funded: 1 intvolume: ' 6' issue: '6' language: - iso: eng month: '06' oa_version: None page: 545 - 557 project: - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics publication: Environmental Microbiology Reports publication_status: published publisher: Wiley publist_id: '5076' quality_controlled: '1' related_material: record: - id: '818' relation: dissertation_contains status: public scopus_import: 1 status: public title: Bacterial responses to antibiotics and their combinations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2014' ... --- _id: '2082' abstract: - lang: eng 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].' alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2014-08-21 location: Santa Barbara, USA name: 'CRYPTO: International Cryptology Conference' start_date: 2014-08-17 date_created: 2018-12-11T11:55:36Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-09-07T12:02:27Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-662-44371-2_7 ec_funded: 1 editor: - first_name: Juan full_name: Garay, Juan last_name: Garay - first_name: Rosario full_name: Gennaro, Rosario last_name: Gennaro file: - access_level: open_access checksum: dab6ab36a5f6af94f2b597e6404ed11d content_type: application/pdf creator: system date_created: 2018-12-12T10:13:17Z date_updated: 2020-07-14T12:45:28Z file_id: '4999' file_name: IST-2016-682-v1+1_578.pdf file_size: 492310 relation: main_file file_date_updated: 2020-07-14T12:45:28Z has_accepted_license: '1' intvolume: ' 8616' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 113 - 130 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '4955' pubrep_id: '682' quality_controlled: '1' related_material: record: - id: '838' relation: dissertation_contains status: public status: public title: The exact PRF-security of NMAC and HMAC type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8616 year: '2014' ... --- _id: '1912' abstract: - lang: eng 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. 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. article_processing_charge: No author: - first_name: Julien full_name: Compagnon, Julien id: 2E3E0988-F248-11E8-B48F-1D18A9856A87 last_name: Compagnon - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Srivarsha full_name: Rajshekar, Srivarsha last_name: Rajshekar - first_name: Rita full_name: Kottmeier, Rita last_name: Kottmeier - first_name: Kornelija full_name: Pranjic-Ferscha, Kornelija id: 4362B3C2-F248-11E8-B48F-1D18A9856A87 last_name: Pranjic-Ferscha - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:41Z date_published: 2014-12-22T00:00:00Z date_updated: 2023-09-07T12:05:08Z day: '22' department: - _id: CaHe doi: 10.1016/j.devcel.2014.11.003 external_id: pmid: - '25535919' intvolume: ' 31' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/25535919 month: '12' oa: 1 oa_version: Published Version page: 774 - 783 pmid: 1 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '5182' quality_controlled: '1' related_material: record: - id: '961' relation: dissertation_contains status: public scopus_import: '1' status: public title: The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2014' ... --- _id: '2084' 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. acknowledgement: European Union Seventh Framework Programme; Human Frontier Science Program; Oesterreichische Nationalbank Anniversary Fund 14211; Austrian Research Promotion Agency; FemTech author: - first_name: Michael full_name: Grusch, Michael last_name: Grusch - first_name: Karin full_name: Schelch, Karin last_name: Schelch - first_name: Robert full_name: Riedler, Robert last_name: Riedler - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 - first_name: Christopher full_name: Differ, Christopher last_name: Differ - first_name: Walter full_name: Berger, Walter last_name: Berger - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:55:37Z date_published: 2014-07-01T00:00:00Z date_updated: 2023-09-07T12:49:09Z day: '01' department: - _id: HaJa doi: 10.15252/embj.201387695 intvolume: ' 33' issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194103/ month: '07' oa: 1 oa_version: Submitted Version page: 1713 - 1726 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '4953' quality_controlled: '1' related_material: record: - id: '418' relation: dissertation_contains status: public scopus_import: 1 status: public title: Spatio-temporally precise activation of engineered receptor tyrosine kinases by light type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2014' ... --- _id: '2157' abstract: - lang: eng 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.' acknowledgement: ERC Advanced Grant No. 267165; Grant GRADR Eurogiga GIG/11/E023 (SNSF-PP00P2-138948); Swiss National Science Foundation (SNSF-200020-138230). author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Eric full_name: Sedgwick, Eric last_name: Sedgwick - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: 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' 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. 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.' 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. short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84. conference: end_date: 2014-06-11 location: Kyoto, Japan name: 'SoCG: Symposium on Computational Geometry' start_date: 2014-06-08 date_created: 2018-12-11T11:56:02Z date_published: 2014-06-01T00:00:00Z date_updated: 2023-09-11T13:38:49Z day: '01' department: - _id: UlWa doi: 10.1145/2582112.2582137 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0815 month: '06' oa: 1 oa_version: Submitted Version page: 78 - 84 publication: Proceedings of the Annual Symposium on Computational Geometry publication_status: published publisher: ACM publist_id: '4849' quality_controlled: '1' related_material: record: - id: '425' relation: later_version status: public scopus_import: 1 status: public title: Embeddability in the 3 sphere is decidable type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '10894' 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. article_processing_charge: No author: - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Michael full_name: Kerber, Michael last_name: Kerber - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Hubert full_name: Wagner, Hubert last_name: Wagner 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' 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' 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.' 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.' 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.' 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.' 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.' conference: end_date: 2014-08-09 location: Seoul, South Korea name: 'ICMS: International Congress on Mathematical Software' start_date: 2014-08-05 date_created: 2022-03-21T07:12:16Z date_published: 2014-09-01T00:00:00Z date_updated: 2023-09-20T09:42:40Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-662-44199-2_24 intvolume: ' 8592' language: - iso: eng month: '09' oa_version: None page: 137-143 place: Berlin, Heidelberg publication: 'ICMS 2014: International Congress on Mathematical Software' publication_identifier: eisbn: - '9783662441992' eissn: - 1611-3349 isbn: - '9783662441985' issn: - 0302-9743 publication_status: published publisher: Springer Berlin Heidelberg quality_controlled: '1' related_material: record: - id: '1433' relation: later_version status: public scopus_import: '1' series_title: LNCS status: public title: PHAT – Persistent Homology Algorithms Toolbox type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8592 year: '2014' ... --- _id: '5428' 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: 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 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 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. ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair simulation games. IST Austria, 2014. ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p. mla: Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST Austria, 2014, doi: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. date_created: 2018-12-12T11:39:16Z date_published: 2014-12-05T00:00:00Z date_updated: 2023-09-20T12:07:48Z day: '05' ddc: - '004' department: - _id: ToHe - _id: KrCh doi: 10.15479/AT:IST-2014-315-v1-1 file: - access_level: open_access checksum: b1d573bc04365625ff9974880c0aa807 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:59Z date_updated: 2020-07-14T12:46:52Z file_id: '5521' file_name: IST-2014-315-v1+1_report.pdf file_size: 531046 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '26' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '315' related_material: record: - id: '1066' relation: later_version status: public status: public title: Quantitative fair simulation games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1887' article_processing_charge: No article_type: original author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie. 2014:23-30. apa: Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie. Deutsche Zoologische Gesellschaft. chicago: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie. Deutsche Zoologische Gesellschaft, 2014. 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. mla: Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie, Deutsche Zoologische Gesellschaft, 2014, pp. 23–30. short: S. Cremer, Zoologie (2014) 23–30. date_created: 2018-12-11T11:54:33Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-10-17T07:54:57Z day: '01' department: - _id: SyCr language: - iso: eng main_file_link: - open_access: '1' url: https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf month: '01' oa: 1 oa_version: Published Version page: 23 - 30 publication: Zoologie publication_status: published publisher: Deutsche Zoologische Gesellschaft publist_id: '5208' quality_controlled: '1' status: public title: Gemeinsame Krankheitsabwehr in Ameisengesellschaften type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2175' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: 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' 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' 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.' 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.' ista: 'Postiglione MP, Hippenmeyer S. 2014. Monitoring neurogenesis in the cerebral cortex: an update. Future Neurology. 9(3), 323–340.' 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. date_created: 2018-12-11T11:56:09Z date_published: 2014-05-01T00:00:00Z date_updated: 2023-10-17T08:34:27Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.2217/fnl.14.18 ec_funded: 1 file: - access_level: open_access checksum: ba06659ecadabceec9a37dd8c4586dce content_type: application/pdf creator: system date_created: 2018-12-12T10:10:25Z date_updated: 2020-07-14T12:45:31Z file_id: '4812' file_name: IST-2016-528-v1+1_fnl.14.18.pdf file_size: 3848424 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' intvolume: ' 9' issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 323 - 340 project: - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development publication: Future Neurology publication_identifier: eissn: - 1748-6971 issn: - 1479-6708 publication_status: published publisher: Future Science Group publist_id: '4806' pubrep_id: '528' quality_controlled: '1' scopus_import: '1' status: public title: 'Monitoring neurogenesis in the cerebral cortex: an update' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '1913' 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.' acknowledgement: This study was supported by the European Commission’s 7th Framework Programme under GA No. 278486, ‘DEVELAGE’. article_processing_charge: No article_type: original author: - first_name: Ivan full_name: Milenković, Ivan last_name: Milenković - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 - first_name: Gábor full_name: Kovács, Gábor last_name: Kovács citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:41Z date_published: 2014-11-07T00:00:00Z date_updated: 2023-10-17T10:21:17Z day: '07' department: - _id: CaGu doi: 10.1159/000365548 external_id: pmid: - '25195847' intvolume: ' 38' issue: 5-6 language: - iso: eng main_file_link: - open_access: '1' url: https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf month: '11' oa: 1 oa_version: Published Version page: 375 - 388 pmid: 1 publication: Dementia and Geriatric Cognitive Disorders publication_identifier: issn: - 1420-8008 publication_status: published publisher: Karger Publishers publist_id: '5181' quality_controlled: '1' scopus_import: '1' status: public title: Patterns of hippocampal tau pathology differentiate neurodegenerative dementias type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2014' ... --- _id: '1507' 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. acknowledgement: The author is partially supported by SFB-TR 12 Grant of the German Research Council. article_processing_charge: No author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: 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.' 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.' 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. 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. 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.' 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. conference: end_date: 2014-08-21 location: Seoul, Korea name: 'ICM: International Congress of Mathematicians' start_date: 2014-08-13 date_created: 2018-12-11T11:52:25Z date_published: 2014-08-01T00:00:00Z date_updated: 2023-10-17T11:12:55Z day: '01' department: - _id: LaEr ec_funded: 1 intvolume: ' 3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.5752 month: '08' oa: 1 oa_version: Submitted Version page: 214 - 236 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Proceedings of the International Congress of Mathematicians publication_status: published publisher: International Congress of Mathematicians publist_id: '5670' quality_controlled: '1' scopus_import: '1' status: public title: Random matrices, log-gases and Hölder regularity type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2014' ... --- _id: '8044' abstract: - lang: eng text: Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system. article_processing_charge: No author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: Proceeding of the International Congress of Mathematicans. Vol 3. International Congress of Mathematicians; 2014:1175-1194.' apa: 'Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In Proceeding of the International Congress of Mathematicans (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.' chicago: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In Proceeding of the International Congress of Mathematicans, 3:1175–94. International Congress of Mathematicians, 2014. ieee: R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in Proceeding of the International Congress of Mathematicans, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194. ista: 'Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194.' mla: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” Proceeding of the International Congress of Mathematicans, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94. short: R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194. conference: end_date: 2014-08-21 location: Seoul, South Korea name: 'ICM: International Congress of Mathematicans' start_date: 2014-08-13 date_created: 2020-06-29T07:59:35Z date_published: 2014-08-01T00:00:00Z date_updated: 2023-10-17T11:12:33Z day: '01' department: - _id: RoSe intvolume: ' 3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.icm2014.org/en/vod/proceedings.html month: '08' oa: 1 oa_version: Published Version page: 1175-1194 publication: Proceeding of the International Congress of Mathematicans publication_identifier: isbn: - '9788961058063' publication_status: published publisher: International Congress of Mathematicians quality_controlled: '1' scopus_import: '1' status: public title: Structure of the excitation spectrum for many-body quantum systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2014' ... --- _id: '2160' abstract: - lang: eng text: Transfer learning has received a lot of attention in the machine learning community over the last years, and several effective algorithms have been developed. However, relatively little is known about their theoretical properties, especially in the setting of lifelong learning, where the goal is to transfer information to tasks for which no data have been observed so far. In this work we study lifelong learning from a theoretical perspective. Our main result is a PAC-Bayesian generalization bound that offers a unified view on existing paradigms for transfer learning, such as the transfer of parameters or the transfer of low-dimensional representations. We also use the bound to derive two principled lifelong learning algorithms, and we show that these yield results comparable with existing methods. article_processing_charge: No author: - first_name: Anastasia full_name: Pentina, Anastasia id: 42E87FC6-F248-11E8-B48F-1D18A9856A87 last_name: Pentina - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Pentina A, Lampert C. A PAC-Bayesian bound for Lifelong Learning. In: Vol 32. ML Research Press; 2014:991-999.' apa: 'Pentina, A., & Lampert, C. (2014). A PAC-Bayesian bound for Lifelong Learning (Vol. 32, pp. 991–999). Presented at the ICML: International Conference on Machine Learning, Beijing, China: ML Research Press.' chicago: Pentina, Anastasia, and Christoph Lampert. “A PAC-Bayesian Bound for Lifelong Learning,” 32:991–99. ML Research Press, 2014. ieee: 'A. Pentina and C. Lampert, “A PAC-Bayesian bound for Lifelong Learning,” presented at the ICML: International Conference on Machine Learning, Beijing, China, 2014, vol. 32, pp. 991–999.' ista: 'Pentina A, Lampert C. 2014. A PAC-Bayesian bound for Lifelong Learning. ICML: International Conference on Machine Learning vol. 32, 991–999.' mla: Pentina, Anastasia, and Christoph Lampert. A PAC-Bayesian Bound for Lifelong Learning. Vol. 32, ML Research Press, 2014, pp. 991–99. short: A. Pentina, C. Lampert, in:, ML Research Press, 2014, pp. 991–999. conference: end_date: 2014-06-26 location: Beijing, China name: 'ICML: International Conference on Machine Learning' start_date: 2014-06-21 date_created: 2018-12-11T11:56:03Z date_published: 2014-05-10T00:00:00Z date_updated: 2023-10-17T11:54:24Z day: '10' department: - _id: ChLa intvolume: ' 32' language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/citation.cfm?id=3045003 month: '05' oa: 1 oa_version: Submitted Version page: 991 - 999 publication_status: published publisher: ML Research Press publist_id: '4844' quality_controlled: '1' scopus_import: '1' status: public title: A PAC-Bayesian bound for Lifelong Learning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2014' ... --- _id: '1403' abstract: - lang: eng text: A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis. acknowledged_ssus: - _id: SSU alternative_title: - IST Austria Thesis author: - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt citation: ama: Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014. apa: Behrndt, M. (2014). Forces driving epithelial spreading in zebrafish epiboly. IST Austria. chicago: Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.” IST Austria, 2014. ieee: M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST Austria, 2014. ista: Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly. IST Austria. mla: Behrndt, Martin. Forces Driving Epithelial Spreading in Zebrafish Epiboly. IST Austria, 2014. short: M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST Austria, 2014. date_created: 2018-12-11T11:51:49Z date_published: 2014-08-01T00:00:00Z date_updated: 2023-10-17T12:16:58Z day: '01' department: - _id: CaHe language: - iso: eng month: '08' oa_version: None page: '91' publication_status: published publisher: IST Austria publist_id: '5804' related_material: record: - id: '2282' relation: part_of_dissertation status: public - id: '2950' relation: part_of_dissertation status: public - id: '3373' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Forces driving epithelial spreading in zebrafish epiboly type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1888' abstract: - lang: ger text: 'Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig? Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen ergänzt werden.' alternative_title: - Rundgespräche der Kommission für Ökologie article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Cremer S. Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In: Soziale Insekten in Einer Sich Wandelnden Welt. Vol 43. Verlag Dr. Friedrich Pfeil; 2014:65-72.' apa: 'Cremer, S. (2014). Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In Soziale Insekten in einer sich wandelnden Welt (Vol. 43, pp. 65–72). Verlag Dr. Friedrich Pfeil.' chicago: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt  Bayerische Akademie Der Wissenschaften.” In Soziale Insekten in Einer Sich Wandelnden Welt, 43:65–72. Verlag Dr. Friedrich Pfeil, 2014.' ieee: 'S. Cremer, “Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften,” in Soziale Insekten in einer sich wandelnden Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.' ista: 'Cremer S. 2014.Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In: Soziale Insekten in einer sich wandelnden Welt. Rundgespräche der Kommission für Ökologie, vol. 43, 65–72.' mla: 'Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt  Bayerische Akademie Der Wissenschaften.” Soziale Insekten in Einer Sich Wandelnden Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.' short: S. Cremer, in:, Soziale Insekten in Einer Sich Wandelnden Welt, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72. date_created: 2018-12-11T11:54:33Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-10-17T12:28:45Z day: '01' department: - _id: SyCr intvolume: ' 43' language: - iso: eng month: '01' oa_version: None page: 65 - 72 publication: Soziale Insekten in einer sich wandelnden Welt publication_identifier: issn: - 2366-2875 publication_status: published publisher: Verlag Dr. Friedrich Pfeil publist_id: '5207' quality_controlled: '1' status: public title: 'Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2014' ... --- _id: '2012' abstract: - lang: eng text: The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice. acknowledgement: We thank Herbert Edelsbrunner for his valuable discussions and ideas on the topic of this paper. The second author has been supported by the Max Planck Center for Visual Computing and Communication article_number: '1401.0468' article_processing_charge: No author: - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham - first_name: Michael full_name: Kerber, Michael last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv. doi:10.48550/arXiv.1401.0468 apa: Iglesias Ham, M., Kerber, M., & Uhler, C. (n.d.). Sphere packing with limited overlap. arXiv. https://doi.org/10.48550/arXiv.1401.0468 chicago: Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing with Limited Overlap.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1401.0468. ieee: M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,” arXiv. . ista: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv, 1401.0468. mla: Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” ArXiv, 1401.0468, doi:10.48550/arXiv.1401.0468. short: M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.). date_created: 2018-12-11T11:55:12Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-10-18T08:06:45Z day: '01' department: - _id: HeEd - _id: CaUh doi: 10.48550/arXiv.1401.0468 external_id: arxiv: - '1401.0468' language: - iso: eng main_file_link: - open_access: '1' url: http://cccg.ca/proceedings/2014/papers/paper23.pdf month: '01' oa: 1 oa_version: Submitted Version publication: arXiv publication_status: submitted publist_id: '5064' status: public title: Sphere packing with limited overlap type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '14301' abstract: - lang: eng text: DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects. article_processing_charge: No article_type: original author: - first_name: Evi full_name: Stahl, Evi last_name: Stahl - first_name: Thomas full_name: Martin, Thomas last_name: Martin - first_name: Florian M full_name: Praetorius, Florian M id: dfec9381-4341-11ee-8fd8-faa02bba7d62 last_name: Praetorius - first_name: Hendrik full_name: Dietz, Hendrik last_name: Dietz citation: ama: Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 2014;126(47):12949-12954. doi:10.1002/ange.201405991 apa: Stahl, E., Martin, T., Praetorius, F. M., & Dietz, H. (2014). Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/ange.201405991 chicago: Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/ange.201405991. ieee: E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable preparation of pure and dense DNA origami solutions,” Angewandte Chemie International Edition, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014. ista: Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 126(47), 12949–12954. mla: Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition, vol. 126, no. 47, Wiley, 2014, pp. 12949–54, doi:10.1002/ange.201405991. short: E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International Edition 126 (2014) 12949–12954. date_created: 2023-09-06T12:51:14Z date_published: 2014-11-17T00:00:00Z date_updated: 2023-11-07T12:14:30Z day: '17' doi: 10.1002/ange.201405991 extern: '1' external_id: pmid: - '25346175' intvolume: ' 126' issue: '47' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/ange.201405991 month: '11' oa: 1 oa_version: Published Version page: 12949-12954 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Facile and scalable preparation of pure and dense DNA origami solutions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 126 year: '2014' ... --- _id: '7699' article_processing_charge: No article_type: original author: - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 - first_name: Darcy B full_name: Kelley, Darcy B last_name: Kelley citation: ama: Sweeney LB, Kelley DB. Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. 2014;28(10):34-41. doi:10.1016/j.conb.2014.06.006 apa: Sweeney, L. B., & Kelley, D. B. (2014). Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2014.06.006 chicago: Sweeney, Lora B., and Darcy B Kelley. “Harnessing Vocal Patterns for Social Communication.” Current Opinion in Neurobiology. Elsevier, 2014. https://doi.org/10.1016/j.conb.2014.06.006. ieee: L. B. Sweeney and D. B. Kelley, “Harnessing vocal patterns for social communication,” Current Opinion in Neurobiology, vol. 28, no. 10. Elsevier, pp. 34–41, 2014. ista: Sweeney LB, Kelley DB. 2014. Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. 28(10), 34–41. mla: Sweeney, Lora B., and Darcy B. Kelley. “Harnessing Vocal Patterns for Social Communication.” Current Opinion in Neurobiology, vol. 28, no. 10, Elsevier, 2014, pp. 34–41, doi:10.1016/j.conb.2014.06.006. short: L.B. Sweeney, D.B. Kelley, Current Opinion in Neurobiology 28 (2014) 34–41. date_created: 2020-04-30T10:35:39Z date_published: 2014-10-01T00:00:00Z date_updated: 2024-01-31T10:14:08Z day: '01' doi: 10.1016/j.conb.2014.06.006 extern: '1' intvolume: ' 28' issue: '10' language: - iso: eng month: '10' oa_version: None page: 34-41 publication: Current Opinion in Neurobiology publication_identifier: issn: - 0959-4388 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Harnessing vocal patterns for social communication type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2014' ... --- _id: '2281' abstract: - lang: eng text: We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential. article_processing_charge: No article_type: original author: - first_name: Yujin full_name: Guo, Yujin last_name: Guo - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Guo Y, Seiringer R. On the mass concentration for Bose-Einstein condensates with attractive interactions. Letters in Mathematical Physics. 2014;104(2):141-156. doi:10.1007/s11005-013-0667-9 apa: Guo, Y., & Seiringer, R. (2014). On the mass concentration for Bose-Einstein condensates with attractive interactions. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-013-0667-9 chicago: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein Condensates with Attractive Interactions.” Letters in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s11005-013-0667-9. ieee: Y. Guo and R. Seiringer, “On the mass concentration for Bose-Einstein condensates with attractive interactions,” Letters in Mathematical Physics, vol. 104, no. 2. Springer, pp. 141–156, 2014. ista: Guo Y, Seiringer R. 2014. On the mass concentration for Bose-Einstein condensates with attractive interactions. Letters in Mathematical Physics. 104(2), 141–156. mla: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein Condensates with Attractive Interactions.” Letters in Mathematical Physics, vol. 104, no. 2, Springer, 2014, pp. 141–56, doi:10.1007/s11005-013-0667-9. short: Y. Guo, R. Seiringer, Letters in Mathematical Physics 104 (2014) 141–156. date_created: 2018-12-11T11:56:44Z date_published: 2014-02-01T00:00:00Z date_updated: 2024-02-14T12:19:42Z day: '01' department: - _id: RoSe doi: 10.1007/s11005-013-0667-9 external_id: arxiv: - '1301.5682' intvolume: ' 104' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1301.5682 month: '02' oa: 1 oa_version: Preprint page: 141 - 156 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '4653' quality_controlled: '1' scopus_import: '1' status: public title: On the mass concentration for Bose-Einstein condensates with attractive interactions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 104 year: '2014' ... --- _id: '2257' abstract: - lang: eng text: 'Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population''s capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction.' acknowledgement: "\r\n\r\n\r\n\r\nThis work was funded by NSF grant IIS-0613435, NSF grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508, the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation, ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES: ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651." article_number: e1003408 author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Dario full_name: Amodei, Dario last_name: Amodei - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 2014;10(1). doi:10.1371/journal.pcbi.1003408 apa: Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003408 chicago: Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003408. ieee: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” PLoS Computational Biology, vol. 10, no. 1. Public Library of Science, 2014. ista: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 10(1), e1003408. mla: Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408. short: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014). date_created: 2018-12-11T11:56:36Z date_published: 2014-01-02T00:00:00Z date_updated: 2024-02-21T13:46:14Z day: '02' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1003408 file: - access_level: open_access checksum: c720222c5e924a4acb17f23b9381a6ca content_type: application/pdf creator: system date_created: 2018-12-12T10:12:46Z date_updated: 2020-07-14T12:45:35Z file_id: '4965' file_name: IST-2016-436-v1+1_journal.pcbi.1003408.pdf file_size: 2194790 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' intvolume: ' 10' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://repository.ist.ac.at/id/eprint/436 month: '01' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_identifier: issn: - 1553734X publication_status: published publisher: Public Library of Science publist_id: '4689' pubrep_id: '436' quality_controlled: '1' related_material: record: - id: '5562' relation: popular_science status: public scopus_import: 1 status: public title: Searching for collective behavior in a large network of sensory neurons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2014' ... --- _id: '15161' abstract: - lang: eng text: The copper-catalyzed diboration of ketones followed by an acid-catalyzed elimination leads to the formation of 1,1-disubstituted and trisubstituted vinyl boronate esters with moderate to good yields and selectivity. Addition of tosic acid to the crude diboration products provides the corresponding vinyl boronate esters upon elimination. The trisubstituted vinyl boronate esters are formed as the (Z)-olefin isomer, which was established by subjecting the products to a Suzuki–Miyaura coupling reaction to obtain alkenes of known geometry. article_processing_charge: No article_type: letter_note author: - first_name: Weiye full_name: Guan, Weiye last_name: Guan - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Melissa L. full_name: McIntosh, Melissa L. last_name: McIntosh - first_name: Liza full_name: Koren-Selfridge, Liza last_name: Koren-Selfridge - first_name: John P. full_name: Scott, John P. last_name: Scott - first_name: Timothy B. full_name: Clark, Timothy B. last_name: Clark citation: ama: Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. 2014;79(15):7199-7204. doi:10.1021/jo500773t apa: Guan, W., Michael, A. K., McIntosh, M. L., Koren-Selfridge, L., Scott, J. P., & Clark, T. B. (2014). Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/jo500773t chicago: Guan, Weiye, Alicia K. Michael, Melissa L. McIntosh, Liza Koren-Selfridge, John P. Scott, and Timothy B. Clark. “Stereoselective Formation of Trisubstituted Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” The Journal of Organic Chemistry. American Chemical Society, 2014. https://doi.org/10.1021/jo500773t. ieee: W. Guan, A. K. Michael, M. L. McIntosh, L. Koren-Selfridge, J. P. Scott, and T. B. Clark, “Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters,” The Journal of Organic Chemistry, vol. 79, no. 15. American Chemical Society, pp. 7199–7204, 2014. ista: Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. 2014. Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. 79(15), 7199–7204. mla: Guan, Weiye, et al. “Stereoselective Formation of Trisubstituted Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” The Journal of Organic Chemistry, vol. 79, no. 15, American Chemical Society, 2014, pp. 7199–204, doi:10.1021/jo500773t. short: W. Guan, A.K. Michael, M.L. McIntosh, L. Koren-Selfridge, J.P. Scott, T.B. Clark, The Journal of Organic Chemistry 79 (2014) 7199–7204. date_created: 2024-03-21T07:58:31Z date_published: 2014-06-10T00:00:00Z date_updated: 2024-03-25T11:50:01Z day: '10' doi: 10.1021/jo500773t extern: '1' intvolume: ' 79' issue: '15' keyword: - Organic Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/jo500773t month: '06' oa: 1 oa_version: Published Version page: 7199-7204 publication: The Journal of Organic Chemistry publication_identifier: eissn: - 1520-6904 issn: - 0022-3263 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2014' ... --- _id: '1999' abstract: - lang: eng text: Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses. author: - first_name: Nathalie full_name: Stroeymeyt, Nathalie last_name: Stroeymeyt - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. Current Opinion in Insect Science. 2014;5(1):1-15. doi:10.1016/j.cois.2014.09.001 apa: Stroeymeyt, N., Casillas Perez, B. E., & Cremer, S. (2014). Organisational immunity in social insects. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2014.09.001 chicago: Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science. Elsevier, 2014. https://doi.org/10.1016/j.cois.2014.09.001. ieee: N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” Current Opinion in Insect Science, vol. 5, no. 1. Elsevier, pp. 1–15, 2014. ista: Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15. mla: Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:10.1016/j.cois.2014.09.001. short: N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15. date_created: 2018-12-11T11:55:08Z date_published: 2014-11-01T00:00:00Z date_updated: 2024-03-28T23:30:05Z day: '01' department: - _id: SyCr doi: 10.1016/j.cois.2014.09.001 ec_funded: 1 intvolume: ' 5' issue: '1' language: - iso: eng month: '11' oa_version: None page: 1 - 15 project: - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' publication: Current Opinion in Insect Science publication_status: published publisher: Elsevier publist_id: '5080' quality_controlled: '1' related_material: record: - id: '6383' relation: dissertation_contains - id: '6435' relation: dissertation_contains status: public scopus_import: 1 status: public title: Organisational immunity in social insects type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2014' ...