[{"year":"2016","oa_version":"Preprint","publist_id":"6035","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:36Z","scopus_import":1,"issue":"2","date_published":"2016-10-01T00:00:00Z","_id":"1281","abstract":[{"lang":"eng","text":"Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue."}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/"}],"oa":1,"publication_status":"published","volume":172,"title":"Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor","citation":{"mla":"Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” <i>Plant Physiology</i>, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:<a href=\"https://doi.org/10.1104/pp.16.01047\">10.1104/pp.16.01047</a>.","chicago":"Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1104/pp.16.01047\">https://doi.org/10.1104/pp.16.01047</a>.","ieee":"E. Bouguyon <i>et al.</i>, “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” <i>Plant Physiology</i>, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.","ista":"Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248.","ama":"Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. <i>Plant Physiology</i>. 2016;172(2):1237-1248. doi:<a href=\"https://doi.org/10.1104/pp.16.01047\">10.1104/pp.16.01047</a>","apa":"Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.16.01047\">https://doi.org/10.1104/pp.16.01047</a>","short":"E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248."},"author":[{"last_name":"Bouguyon","full_name":"Bouguyon, Eléonore","first_name":"Eléonore"},{"first_name":"Francine","full_name":"Perrine Walker, Francine","last_name":"Perrine Walker"},{"first_name":"Marjorie","full_name":"Pervent, Marjorie","last_name":"Pervent"},{"last_name":"Rochette","full_name":"Rochette, Juliette","first_name":"Juliette"},{"orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","full_name":"Cuesta, Candela","last_name":"Cuesta"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martinière","full_name":"Martinière, Alexandre","first_name":"Alexandre"},{"last_name":"Bach","full_name":"Bach, Lien","first_name":"Lien"},{"full_name":"Krouk, Gabriel","first_name":"Gabriel","last_name":"Krouk"},{"full_name":"Gojon, Alain","first_name":"Alain","last_name":"Gojon"},{"last_name":"Nacry","first_name":"Philippe","full_name":"Nacry, Philippe"}],"type":"journal_article","day":"01","acknowledgement":"This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility.","doi":"10.1104/pp.16.01047","language":[{"iso":"eng"}],"page":"1237 - 1248","date_created":"2018-12-11T11:51:07Z","month":"10","publisher":"American Society of Plant Biologists","intvolume":"       172","status":"public","quality_controlled":"1","department":[{"_id":"EvBe"}],"publication":"Plant Physiology"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:36Z","language":[{"iso":"eng"}],"scopus_import":1,"doi":"10.1007/s11856-016-1419-1","citation":{"mla":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>.","ista":"Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582.","ieee":"A. Gundert and U. Wagner, “On eigenvalues of random complexes,” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2. Springer, pp. 545–582, 2016.","chicago":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” <i>Israel Journal of Mathematics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>.","apa":"Gundert, A., &#38; Wagner, U. (2016). On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-016-1419-1\">https://doi.org/10.1007/s11856-016-1419-1</a>","ama":"Gundert A, Wagner U. On eigenvalues of random complexes. <i>Israel Journal of Mathematics</i>. 2016;216(2):545-582. doi:<a href=\"https://doi.org/10.1007/s11856-016-1419-1\">10.1007/s11856-016-1419-1</a>","short":"A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582."},"title":"On eigenvalues of random complexes","day":"01","publist_id":"6034","oa_version":"Preprint","year":"2016","author":[{"first_name":"Anna","full_name":"Gundert, Anna","last_name":"Gundert"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner"}],"type":"journal_article","publisher":"Springer","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.4906"}],"oa":1,"department":[{"_id":"UlWa"}],"quality_controlled":"1","publication":"Israel Journal of Mathematics","volume":216,"intvolume":"       216","status":"public","page":"545 - 582","issue":"2","month":"10","_id":"1282","abstract":[{"text":"We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k.","lang":"eng"}],"date_created":"2018-12-11T11:51:07Z","date_published":"2016-10-01T00:00:00Z"},{"month":"10","date_created":"2018-12-11T11:51:08Z","page":"809 - 811","publication":"Trends in Plant Science","department":[{"_id":"EvBe"}],"quality_controlled":"1","intvolume":"        21","status":"public","publisher":"Cell Press","day":"01","author":[{"first_name":"Qiang","full_name":"Zhu, Qiang","last_name":"Zhu","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"type":"journal_article","citation":{"ista":"Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 21(10), 809–811.","ieee":"Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” <i>Trends in Plant Science</i>, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.","chicago":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>.","mla":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” <i>Trends in Plant Science</i>, vol. 21, no. 10, Cell Press, 2016, pp. 809–11, doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>.","short":"Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811.","apa":"Zhu, Q., &#38; Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">https://doi.org/10.1016/j.tplants.2016.08.003</a>","ama":"Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. <i>Trends in Plant Science</i>. 2016;21(10):809-811. doi:<a href=\"https://doi.org/10.1016/j.tplants.2016.08.003\">10.1016/j.tplants.2016.08.003</a>"},"title":"Seedlings’ strategy to overcome a soil barrier","language":[{"iso":"eng"}],"ddc":["575"],"doi":"10.1016/j.tplants.2016.08.003","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF01_I1774S) to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript.","file":[{"date_created":"2018-12-12T10:08:19Z","content_type":"application/pdf","file_id":"4679","relation":"main_file","date_updated":"2020-07-14T12:44:42Z","access_level":"local","checksum":"4d569977fad7a7f22b7e3424003d2ab1","file_name":"IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf","file_size":229094,"creator":"system"}],"_id":"1283","date_published":"2016-10-01T00:00:00Z","abstract":[{"text":"The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil.","lang":"eng"}],"issue":"10","file_date_updated":"2020-07-14T12:44:42Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"pubrep_id":"1018","volume":21,"publication_status":"published","article_type":"original","publist_id":"6033","oa_version":"Submitted Version","year":"2016","has_accepted_license":"1","scopus_import":1,"date_updated":"2021-01-12T06:49:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"E5982 - E5991","month":"10","extern":"1","date_created":"2018-12-11T11:51:08Z","publisher":"National Academy of Sciences","publication":"PNAS","quality_controlled":"1","intvolume":"       113","status":"public","citation":{"ama":"Eremina M, Unterholzner S, Rathnayake A, et al. Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. <i>PNAS</i>. 2016;113(40):E5982-E5991. doi:<a href=\"https://doi.org/10.1073/pnas.1611477113\">10.1073/pnas.1611477113</a>","apa":"Eremina, M., Unterholzner, S., Rathnayake, A., Castellanos, M., Khan-Djamei, M., Kügler, K., … Poppenberger, B. (2016). Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1611477113\">https://doi.org/10.1073/pnas.1611477113</a>","short":"M. Eremina, S. Unterholzner, A. Rathnayake, M. Castellanos, M. Khan-Djamei, K. Kügler, S. May, K. Mayer, W. Rozhon, B. Poppenberger, PNAS 113 (2016) E5982–E5991.","mla":"Eremina, Marina, et al. “Brassinosteroids Participate in the Control of Basal and Acquired Freezing Tolerance of Plants.” <i>PNAS</i>, vol. 113, no. 40, National Academy of Sciences, 2016, pp. E5982–91, doi:<a href=\"https://doi.org/10.1073/pnas.1611477113\">10.1073/pnas.1611477113</a>.","chicago":"Eremina, Marina, Simon Unterholzner, Ajith Rathnayake, Marcos Castellanos, Mamoona Khan-Djamei, Karl Kügler, Sean May, Klaus Mayer, Wilfried Rozhon, and Brigitte Poppenberger. “Brassinosteroids Participate in the Control of Basal and Acquired Freezing Tolerance of Plants.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1611477113\">https://doi.org/10.1073/pnas.1611477113</a>.","ista":"Eremina M, Unterholzner S, Rathnayake A, Castellanos M, Khan-Djamei M, Kügler K, May S, Mayer K, Rozhon W, Poppenberger B. 2016. Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. PNAS. 113(40), E5982–E5991.","ieee":"M. Eremina <i>et al.</i>, “Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants,” <i>PNAS</i>, vol. 113, no. 40. National Academy of Sciences, pp. E5982–E5991, 2016."},"title":"Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants","day":"04","author":[{"first_name":"Marina","full_name":"Eremina, Marina","last_name":"Eremina"},{"last_name":"Unterholzner","full_name":"Unterholzner, Simon","first_name":"Simon"},{"first_name":"Ajith","full_name":"Rathnayake, Ajith","last_name":"Rathnayake"},{"full_name":"Castellanos, Marcos","first_name":"Marcos","last_name":"Castellanos"},{"id":"391B5BBC-F248-11E8-B48F-1D18A9856A87","full_name":"Khan-Djamei, Mamoona","first_name":"Mamoona","last_name":"Khan-Djamei"},{"last_name":"Kügler","full_name":"Kügler, Karl","first_name":"Karl"},{"last_name":"May","full_name":"May, Sean","first_name":"Sean"},{"last_name":"Mayer","first_name":"Klaus","full_name":"Mayer, Klaus"},{"first_name":"Wilfried","full_name":"Rozhon, Wilfried","last_name":"Rozhon"},{"full_name":"Poppenberger, Brigitte","first_name":"Brigitte","last_name":"Poppenberger"}],"type":"journal_article","pmid":1,"acknowledgement":"We thank Joanne Chory for seeds of the bee1 bee2 bee3, bes1-D, and bzr1-1D mutants and the 35S:BRI1-GFP line; Irene Ziegler, Clarissa Fahrig, and Renata Milcevicova for technical assistance; and the horticultural staff of the TUMs Gewächshauslaborzentrum Dürnast for plant care. This work was supported by funds from the Austrian Science Fund (Project P22734 to B.P.), the Deutsche Forschungsgemeinschaft (Project PO1640/4 to B.P. and SFB924 to B.P. and K.F.X.M.), and a TUM doctoral fellowship (to M.E.). M.E. and S.J.U. were members of the TUM graduate school. ","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1611477113","article_processing_charge":"No","issue":"40","date_published":"2016-10-04T00:00:00Z","_id":"1284","abstract":[{"lang":"eng","text":"Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix-loop-helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the post-translational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation."}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056081/"}],"oa":1,"volume":113,"publist_id":"6032","oa_version":"Submitted Version","year":"2016","scopus_import":"1","external_id":{"pmid":["27489342"]},"date_updated":"2022-02-18T13:41:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"10","date_created":"2018-12-11T11:51:08Z","_id":"1285","date_published":"2016-10-06T00:00:00Z","abstract":[{"lang":"eng","text":"Cell migration is central to a multitude of physiological processes, including embryonic development, immune surveillance, and wound healing, and deregulated migration is key to cancer dissemination. Decades of investigations have uncovered many of the molecular and physical mechanisms underlying cell migration. Together with protrusion extension and cell body retraction, adhesion to the substrate via specific focal adhesion points has long been considered an essential step in cell migration. Although this is true for cells moving on two-dimensional substrates, recent studies have demonstrated that focal adhesions are not required for cells moving in three dimensions, in which confinement is sufficient to maintain a cell in contact with its substrate. Here, we review the investigations that have led to challenging the requirement of specific adhesions for migration, discuss the physical mechanisms proposed for cell body translocation during focal adhesion-independent migration, and highlight the remaining open questions for the future."}],"page":"469 - 490","department":[{"_id":"MiSi"}],"quality_controlled":"1","publication":"Annual Review of Cell and Developmental Biology","volume":32,"intvolume":"        32","status":"public","publisher":"Annual Reviews","publication_status":"published","day":"06","publist_id":"6031","oa_version":"None","year":"2016","author":[{"first_name":"Ewa","full_name":"Paluch, Ewa","last_name":"Paluch"},{"first_name":"Irene","full_name":"Aspalter, Irene","last_name":"Aspalter"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"type":"journal_article","ec_funded":1,"citation":{"short":"E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental Biology 32 (2016) 469–490.","apa":"Paluch, E., Aspalter, I., &#38; Sixt, M. K. (2016). Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>","ama":"Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. <i>Annual Review of Cell and Developmental Biology</i>. 2016;32:469-490. doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>","ieee":"E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32. Annual Reviews, pp. 469–490, 2016.","ista":"Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 32, 469–490.","chicago":"Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">https://doi.org/10.1146/annurev-cellbio-111315-125341</a>.","mla":"Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 32, Annual Reviews, 2016, pp. 469–90, doi:<a href=\"https://doi.org/10.1146/annurev-cellbio-111315-125341\">10.1146/annurev-cellbio-111315-125341</a>."},"title":"Focal adhesion-independent cell migration","date_updated":"2021-01-12T06:49:37Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"doi":"10.1146/annurev-cellbio-111315-125341","acknowledgement":"We would like to thank Dani Bodor for critical comments on the manuscript and Guillaume Salbreux for discussions. The authors are supported by the United Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian Science Foundation (M.S.).","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"}]},{"publist_id":"6030","oa_version":"Preprint","year":"2016","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:37Z","article_number":"041601","date_published":"2016-10-13T00:00:00Z","_id":"1286","abstract":[{"text":"We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.","lang":"eng"}],"issue":"4","volume":94,"publication_status":"published","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1607.06092","open_access":"1"}],"day":"13","type":"journal_article","author":[{"last_name":"Midya","full_name":"Midya, Bikashkali","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tomza","first_name":"Michał","full_name":"Tomza, Michał"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"citation":{"apa":"Midya, B., Tomza, M., Schmidt, R., &#38; Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>","ama":"Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;94(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>","short":"B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 94 (2016).","mla":"Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>.","ista":"Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 94(4), 041601.","ieee":"B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 94, no. 4. American Physical Society, 2016.","chicago":"Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>."},"ec_funded":1,"title":"Rotation of cold molecular ions inside a Bose-Einstein condensate","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.94.041601","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.","month":"10","date_created":"2018-12-11T11:51:09Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","department":[{"_id":"MiLe"}],"quality_controlled":"1","status":"public","intvolume":"        94","publisher":"American Physical Society"},{"publist_id":"6029","year":"2016","oa_version":"Preprint","date_updated":"2023-10-17T12:16:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","issue":"20","article_processing_charge":"No","date_published":"2016-10-15T00:00:00Z","_id":"1287","abstract":[{"lang":"eng","text":"A planar waveguide with an impedance boundary, composed of nonperfect metallic plates, and with passive or active dielectric filling, is considered. We show the possibility of selective mode guiding and amplification when a homogeneous pump is added to the dielectric and analyze differences in TE and TM mode propagation. Such a non-conservative system is also shown to feature exceptional points for specific and experimentally tunable parameters, which are described for a particular case of transparent dielectric."}],"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.02863"}],"volume":41,"ec_funded":1,"citation":{"short":"B. Midya, V. Konotop, Optics Letters 41 (2016) 4621–4624.","apa":"Midya, B., &#38; Konotop, V. (2016). Modes and exceptional points in waveguides with impedance boundary conditions. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.41.004621\">https://doi.org/10.1364/OL.41.004621</a>","ama":"Midya B, Konotop V. Modes and exceptional points in waveguides with impedance boundary conditions. <i>Optics Letters</i>. 2016;41(20):4621-4624. doi:<a href=\"https://doi.org/10.1364/OL.41.004621\">10.1364/OL.41.004621</a>","ieee":"B. Midya and V. Konotop, “Modes and exceptional points in waveguides with impedance boundary conditions,” <i>Optics Letters</i>, vol. 41, no. 20. Optica Publishing Group, pp. 4621–4624, 2016.","ista":"Midya B, Konotop V. 2016. Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. 41(20), 4621–4624.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” <i>Optics Letters</i>. Optica Publishing Group, 2016. <a href=\"https://doi.org/10.1364/OL.41.004621\">https://doi.org/10.1364/OL.41.004621</a>.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” <i>Optics Letters</i>, vol. 41, no. 20, Optica Publishing Group, 2016, pp. 4621–24, doi:<a href=\"https://doi.org/10.1364/OL.41.004621\">10.1364/OL.41.004621</a>."},"title":"Modes and exceptional points in waveguides with impedance boundary conditions","day":"15","author":[{"id":"456187FC-F248-11E8-B48F-1D18A9856A87","first_name":"Bikashkali","full_name":"Midya, Bikashkali","last_name":"Midya"},{"last_name":"Konotop","full_name":"Konotop, Vladimir","first_name":"Vladimir"}],"type":"journal_article","acknowledgement":"The research of B.M. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant No. [291734].","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"doi":"10.1364/OL.41.004621","page":"4621 - 4624","month":"10","date_created":"2018-12-11T11:51:09Z","publisher":"Optica Publishing Group","department":[{"_id":"MiLe"}],"quality_controlled":"1","publication":"Optics Letters","intvolume":"        41","status":"public"},{"acknowledgement":"This work was funded by the UK Medical Research Council.","doi":"10.1016/j.bbabio.2016.08.008","date_updated":"2021-01-12T06:49:38Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"title":"Reversible FMN dissociation from Escherichia coli respiratory complex I","citation":{"mla":"Holt, Peter, et al. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 11, Elsevier, 2016, pp. 1777–85, doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">10.1016/j.bbabio.2016.08.008</a>.","ieee":"P. Holt, R. Efremov, E. Nakamaru Ogiso, and L. A. Sazanov, “Reversible FMN dissociation from Escherichia coli respiratory complex I,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 11. Elsevier, pp. 1777–1785, 2016.","ista":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. 2016. Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(11), 1777–1785.","chicago":"Holt, Peter, Rouslan Efremov, Eiko Nakamaru Ogiso, and Leonid A Sazanov. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">https://doi.org/10.1016/j.bbabio.2016.08.008</a>.","apa":"Holt, P., Efremov, R., Nakamaru Ogiso, E., &#38; Sazanov, L. A. (2016). Reversible FMN dissociation from Escherichia coli respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">https://doi.org/10.1016/j.bbabio.2016.08.008</a>","ama":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. Reversible FMN dissociation from Escherichia coli respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2016;1857(11):1777-1785. doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.08.008\">10.1016/j.bbabio.2016.08.008</a>","short":"P. Holt, R. Efremov, E. Nakamaru Ogiso, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 1777–1785."},"oa_version":"None","year":"2016","author":[{"first_name":"Peter","full_name":"Holt, Peter","last_name":"Holt"},{"last_name":"Efremov","full_name":"Efremov, Rouslan","first_name":"Rouslan"},{"last_name":"Nakamaru Ogiso","first_name":"Eiko","full_name":"Nakamaru Ogiso, Eiko"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A"}],"type":"journal_article","day":"01","publist_id":"6028","publisher":"Elsevier","publication_status":"published","volume":1857,"status":"public","intvolume":"      1857","quality_controlled":"1","department":[{"_id":"LeSa"}],"publication":"Biochimica et Biophysica Acta - Bioenergetics","issue":"11","page":"1777 - 1785","date_created":"2018-12-11T11:51:09Z","_id":"1288","date_published":"2016-11-01T00:00:00Z","abstract":[{"text":"Respiratory complex I transfers electrons from NADH to quinone, utilizing the reaction energy to translocate protons across the membrane. It is a key enzyme of the respiratory chain of many prokaryotic and most eukaryotic organisms. The reversible NADH oxidation reaction is facilitated in complex I by non-covalently bound flavin mononucleotide (FMN). Here we report that the catalytic activity of E. coli complex I with artificial electron acceptors potassium ferricyanide (FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar range in oxidized complex I to the nanomolar range in the NADH reduced enzyme, with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex I, rather than that of FMN, proved critical to the dissociation. Such dissociation is not observed with the T. thermophilus enzyme and our analysis suggests that the difference may be due to the unusually high redox potential of Fe-S cluster N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo by releasing FMN under highly reducing conditions.","lang":"eng"}],"month":"11"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:04:40Z","scopus_import":1,"publist_id":"6027","has_accepted_license":"1","year":"2016","oa_version":"Submitted Version","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:44:42Z","volume":83,"pubrep_id":"975","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"issue":"1","article_processing_charge":"No","file":[{"content_type":"application/pdf","file_id":"6334","relation":"main_file","date_created":"2019-04-17T07:55:51Z","file_name":"2016-Edelsbrunner_The_classification.pdf","creator":"dernst","file_size":1921113,"date_updated":"2020-07-14T12:44:42Z","access_level":"open_access","checksum":"33458bbb8c32a339e1adeca6d5a1112d"}],"abstract":[{"lang":"eng","text":"Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI) magnifying endoscopic (ME) images of the stomach, we combine methods from image processing, topology, geometry, and machine learning to classify patterns into three classes: oval, tubular and irregular. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions."}],"_id":"1289","date_published":"2016-11-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"1568","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"doi":"10.1016/j.patrec.2015.12.012","ddc":["004","514"],"citation":{"ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy images with persistent homology. <i>Pattern Recognition Letters</i>. 2016;83(1):13-22. doi:<a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">10.1016/j.patrec.2015.12.012</a>","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev, R., &#38; Kashin, S. (2016). The classification of endoscopy images with persistent homology. <i>Pattern Recognition Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">https://doi.org/10.1016/j.patrec.2015.12.012</a>","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev, S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” <i>Pattern Recognition Letters</i>, vol. 83, no. 1, Elsevier, 2016, pp. 13–22, doi:<a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">10.1016/j.patrec.2015.12.012</a>.","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images with Persistent Homology.” <i>Pattern Recognition Letters</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.patrec.2015.12.012\">https://doi.org/10.1016/j.patrec.2015.12.012</a>.","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin S. 2016. The classification of endoscopy images with persistent homology. Pattern Recognition Letters. 83(1), 13–22.","ieee":"O. Dunaeva <i>et al.</i>, “The classification of endoscopy images with persistent homology,” <i>Pattern Recognition Letters</i>, vol. 83, no. 1. Elsevier, pp. 13–22, 2016."},"title":"The classification of endoscopy images with persistent homology","day":"01","author":[{"first_name":"Olga","full_name":"Dunaeva, Olga","last_name":"Dunaeva"},{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"last_name":"Lukyanov","first_name":"Anton","full_name":"Lukyanov, Anton"},{"last_name":"Machin","full_name":"Machin, Michael","first_name":"Michael"},{"last_name":"Malkova","full_name":"Malkova, Daria","first_name":"Daria"},{"first_name":"Roman","full_name":"Kuvaev, Roman","last_name":"Kuvaev"},{"first_name":"Sergey","full_name":"Kashin, Sergey","last_name":"Kashin"}],"type":"journal_article","publisher":"Elsevier","quality_controlled":"1","department":[{"_id":"HeEd"}],"publication":"Pattern Recognition Letters","intvolume":"        83","status":"public","page":"13 - 22","month":"11","date_created":"2018-12-11T11:51:10Z"},{"publisher":"Nature Publishing Group","publication":"Nature Chemical Biology","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"quality_controlled":"1","intvolume":"        12","status":"public","page":"902 - 904","month":"11","date_created":"2018-12-11T11:51:10Z","acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","language":[{"iso":"eng"}],"doi":"10.1038/nchembio.2176","citation":{"chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>.","ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” <i>Nature Chemical Biology</i>, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.","ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. 2016;12(11):902-904. doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>","apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., &#38; Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>"},"title":"Compounds that select against the tetracycline-resistance efflux pump","day":"01","author":[{"full_name":"Stone, Laura","first_name":"Laura","last_name":"Stone"},{"last_name":"Baym","first_name":"Michael","full_name":"Baym, Michael"},{"last_name":"Lieberman","full_name":"Lieberman, Tami","first_name":"Tami"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","last_name":"Chait","first_name":"Remy P","full_name":"Chait, Remy P"},{"last_name":"Clardy","full_name":"Clardy, Jon","first_name":"Jon"},{"last_name":"Kishony","full_name":"Kishony, Roy","first_name":"Roy"}],"type":"journal_article","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"volume":12,"issue":"11","_id":"1290","abstract":[{"text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.","lang":"eng"}],"date_published":"2016-11-01T00:00:00Z","scopus_import":1,"date_updated":"2021-01-12T06:49:39Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6026","year":"2016","oa_version":"Preprint"},{"article_processing_charge":"No","page":"37","_id":"12903","date_published":"2016-02-24T00:00:00Z","date_created":"2023-05-05T12:54:47Z","file":[{"file_name":"2016_AHPC_Schloegl.pdf","creator":"dernst","file_size":1073523,"date_updated":"2023-05-16T07:03:56Z","access_level":"open_access","checksum":"4a7b00362e81358d568f5e216fa03c3e","content_type":"application/pdf","file_id":"12968","relation":"main_file","success":1,"date_created":"2023-05-16T07:03:56Z"}],"month":"02","oa":1,"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf"}],"publication_status":"published","publisher":"VSC - Vienna Scientific Cluster","status":"public","quality_controlled":"1","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2023-05-16T07:03:56Z","publication":"AHPC16 - Austrian HPC Meeting 2016","conference":{"location":"Grundlsee, Austria","start_date":"2016-02-22","end_date":"2016-02-24","name":"AHPC: Austrian HPC Meeting"},"title":"High performance computing at IST Austria: Modelling the human hippocampus","citation":{"chicago":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” In <i>AHPC16 - Austrian HPC Meeting 2016</i>, 37. VSC - Vienna Scientific Cluster, 2016.","ista":"Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria: Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian HPC Meeting, 37.","ieee":"A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria: Modelling the human hippocampus,” in <i>AHPC16 - Austrian HPC Meeting 2016</i>, Grundlsee, Austria, 2016, p. 37.","mla":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” <i>AHPC16 - Austrian HPC Meeting 2016</i>, VSC - Vienna Scientific Cluster, 2016, p. 37.","short":"A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC - Vienna Scientific Cluster, 2016, p. 37.","ama":"Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling the human hippocampus. In: <i>AHPC16 - Austrian HPC Meeting 2016</i>. VSC - Vienna Scientific Cluster; 2016:37.","apa":"Schlögl, A., &#38; Stadlbauer, S. (2016). High performance computing at IST Austria: Modelling the human hippocampus. In <i>AHPC16 - Austrian HPC Meeting 2016</i> (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster."},"year":"2016","has_accepted_license":"1","oa_version":"Published Version","type":"conference_abstract","author":[{"last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer"}],"day":"24","ddc":["000"],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-05-16T07:15:14Z"},{"project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The\r\nresearch leading to these results has received funding from the European Research Council under the European\r\nUnion’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN National Grant Geometric and analytic theory of Hamiltonian systems in finite and infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27. Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems, random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully acknowledged.","language":[{"iso":"eng"}],"doi":"10.1007/s00220-016-2665-0","ddc":["510","530"],"citation":{"mla":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” <i>Communications in Mathematical Physics</i>, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:<a href=\"https://doi.org/10.1007/s00220-016-2665-0\">10.1007/s00220-016-2665-0</a>.","chicago":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” <i>Communications in Mathematical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00220-016-2665-0\">https://doi.org/10.1007/s00220-016-2665-0</a>.","ieee":"A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models with competing interactions,” <i>Communications in Mathematical Physics</i>, vol. 347, no. 3. Springer, pp. 983–1007, 2016.","ista":"Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007.","ama":"Giuliani A, Seiringer R. Periodic striped ground states in Ising models with competing interactions. <i>Communications in Mathematical Physics</i>. 2016;347(3):983-1007. doi:<a href=\"https://doi.org/10.1007/s00220-016-2665-0\">10.1007/s00220-016-2665-0</a>","apa":"Giuliani, A., &#38; Seiringer, R. (2016). Periodic striped ground states in Ising models with competing interactions. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-016-2665-0\">https://doi.org/10.1007/s00220-016-2665-0</a>","short":"A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016) 983–1007."},"title":"Periodic striped ground states in Ising models with competing interactions","day":"01","author":[{"full_name":"Giuliani, Alessandro","first_name":"Alessandro","last_name":"Giuliani"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","publisher":"Springer","publication":"Communications in Mathematical Physics","quality_controlled":"1","department":[{"_id":"RoSe"}],"status":"public","intvolume":"       347","page":"983 - 1007","month":"11","date_created":"2018-12-11T11:51:11Z","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:40Z","publist_id":"6025","year":"2016","oa_version":"Published Version","has_accepted_license":"1","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:44:42Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"688","volume":347,"issue":"3","file":[{"date_created":"2018-12-12T10:09:02Z","content_type":"application/pdf","relation":"main_file","file_id":"4725","date_updated":"2020-07-14T12:44:42Z","access_level":"open_access","checksum":"3c6e08c048fc462e312788be72874bb1","file_name":"IST-2016-688-v1+1_s00220-016-2665-0.pdf","creator":"system","file_size":794983}],"abstract":[{"text":"We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p &gt; 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity.","lang":"eng"}],"_id":"1291","date_published":"2016-11-01T00:00:00Z"},{"citation":{"ama":"Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in open books. <i>Acta Mathematica Hungarica</i>. 2016;150(2):441-455. doi:<a href=\"https://doi.org/10.1007/s10474-016-0648-4\">10.1007/s10474-016-0648-4</a>","apa":"Durst, S., Kegel, M., &#38; Klukas, M. D. (2016). Computing the Thurston–Bennequin invariant in open books. <i>Acta Mathematica Hungarica</i>. Springer. <a href=\"https://doi.org/10.1007/s10474-016-0648-4\">https://doi.org/10.1007/s10474-016-0648-4</a>","short":"S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455.","mla":"Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open Books.” <i>Acta Mathematica Hungarica</i>, vol. 150, no. 2, Springer, 2016, pp. 441–55, doi:<a href=\"https://doi.org/10.1007/s10474-016-0648-4\">10.1007/s10474-016-0648-4</a>.","chicago":"Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin Invariant in Open Books.” <i>Acta Mathematica Hungarica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s10474-016-0648-4\">https://doi.org/10.1007/s10474-016-0648-4</a>.","ieee":"S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant in open books,” <i>Acta Mathematica Hungarica</i>, vol. 150, no. 2. Springer, pp. 441–455, 2016.","ista":"Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 150(2), 441–455."},"title":"Computing the Thurston–Bennequin invariant in open books","day":"01","author":[{"last_name":"Durst","first_name":"Sebastian","full_name":"Durst, Sebastian"},{"first_name":"Marc","full_name":"Kegel, Marc","last_name":"Kegel"},{"first_name":"Mirko D","full_name":"Klukas, Mirko D","last_name":"Klukas","id":"34927512-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","acknowledgement":"The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful discussions and advice and Christian Evers for helpful remarks on a draft version.","language":[{"iso":"eng"}],"doi":"10.1007/s10474-016-0648-4","page":"441 - 455","month":"12","date_created":"2018-12-11T11:51:11Z","publisher":"Springer","publication":"Acta Mathematica Hungarica","quality_controlled":"1","department":[{"_id":"HeEd"}],"intvolume":"       150","status":"public","publist_id":"6023","year":"2016","oa_version":"Preprint","scopus_import":1,"date_updated":"2021-01-12T06:49:40Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"2","date_published":"2016-12-01T00:00:00Z","_id":"1292","abstract":[{"text":"We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds.","lang":"eng"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.00794"}],"oa":1,"volume":150},{"volume":509,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/pdf/1506.06702.pdf","open_access":"1"}],"oa":1,"_id":"1293","date_published":"2016-11-15T00:00:00Z","abstract":[{"text":"For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T06:49:40Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6024","year":"2016","oa_version":"Preprint","publication":"Linear Algebra and Its Applications","department":[{"_id":"CaUh"}],"quality_controlled":"1","intvolume":"       509","status":"public","publisher":"Elsevier","month":"11","date_created":"2018-12-11T11:51:11Z","page":"247 - 275","language":[{"iso":"eng"}],"doi":"10.1016/j.laa.2016.07.026","project":[{"name":"Gaussian Graphical Models: Theory and Applications","grant_number":"Y 903-N35","call_identifier":"FWF","_id":"2530CA10-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We wish to thank Alexander Engström and Bernd Sturmfels for various valuable discussions and insights. We also thank the two anonymous referees for their thoughtful feedback on the paper. CU was partially supported by the Austrian Science Fund (FWF) Y 903-N35.","day":"15","author":[{"id":"2AADA620-F248-11E8-B48F-1D18A9856A87","full_name":"Solus, Liam T","first_name":"Liam T","last_name":"Solus"},{"full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216"},{"last_name":"Yoshida","full_name":"Yoshida, Ruriko","first_name":"Ruriko"}],"type":"journal_article","citation":{"ista":"Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 509, 247–275.","ieee":"L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors,” <i>Linear Algebra and Its Applications</i>, vol. 509. Elsevier, pp. 247–275, 2016.","chicago":"Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">https://doi.org/10.1016/j.laa.2016.07.026</a>.","mla":"Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” <i>Linear Algebra and Its Applications</i>, vol. 509, Elsevier, 2016, pp. 247–75, doi:<a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">10.1016/j.laa.2016.07.026</a>.","short":"L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509 (2016) 247–275.","apa":"Solus, L. T., Uhler, C., &#38; Yoshida, R. (2016). Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">https://doi.org/10.1016/j.laa.2016.07.026</a>","ama":"Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. <i>Linear Algebra and Its Applications</i>. 2016;509:247-275. doi:<a href=\"https://doi.org/10.1016/j.laa.2016.07.026\">10.1016/j.laa.2016.07.026</a>"},"title":"Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors"},{"citation":{"apa":"Edelsbrunner, H., &#38; Iglesias Ham, M. (2016). Multiple covers with balls II: Weighted averages. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">https://doi.org/10.1016/j.endm.2016.09.030</a>","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls II: Weighted averages. <i>Electronic Notes in Discrete Mathematics</i>. 2016;54:169-174. doi:<a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">10.1016/j.endm.2016.09.030</a>","short":"H. Edelsbrunner, M. Iglesias Ham, Electronic Notes in Discrete Mathematics 54 (2016) 169–174.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 54, Elsevier, 2016, pp. 169–74, doi:<a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">10.1016/j.endm.2016.09.030</a>.","ista":"Edelsbrunner H, Iglesias Ham M. 2016. Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. 54, 169–174.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls II: Weighted averages,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 54. Elsevier, pp. 169–174, 2016.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.endm.2016.09.030\">https://doi.org/10.1016/j.endm.2016.09.030</a>."},"ec_funded":1,"title":"Multiple covers with balls II: Weighted averages","publist_id":"5976","day":"01","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel","first_name":"Mabel","last_name":"Iglesias Ham"}],"type":"journal_article","year":"2016","oa_version":"None","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"acknowledgement":"This work is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.","scopus_import":1,"date_updated":"2021-01-12T06:49:41Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.endm.2016.09.030","page":"169 - 174","month":"10","_id":"1295","abstract":[{"lang":"eng","text":"Voronoi diagrams and Delaunay triangulations have been extensively used to represent and compute geometric features of point configurations. We introduce a generalization to poset diagrams and poset complexes, which contain order-k and degree-k Voronoi diagrams and their duals as special cases. Extending a result of Aurenhammer from 1990, we show how to construct poset diagrams as weighted Voronoi diagrams of average balls."}],"date_published":"2016-10-01T00:00:00Z","date_created":"2018-12-11T11:51:12Z","publisher":"Elsevier","publication_status":"published","publication":"Electronic Notes in Discrete Mathematics","department":[{"_id":"HeEd"}],"quality_controlled":"1","intvolume":"        54","status":"public","volume":54},{"day":"14","publist_id":"5966","year":"2016","type":"journal_article","author":[{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Maximilian Jösch","first_name":"Maximilian A","last_name":"Jösch"},{"full_name":"Meister, Markus","first_name":"Markus","last_name":"Meister"}],"citation":{"short":"M.A. Jösch, M. Meister, Nature 532 (2016) 236–239.","ama":"Jösch MA, Meister M. A neuronal circuit for colour vision based on rod-cone opponency. <i>Nature</i>. 2016;532(7598):236-239. doi:<a href=\"https://doi.org/10.1038/nature17158\">10.1038/nature17158</a>","apa":"Jösch, M. A., &#38; Meister, M. (2016). A neuronal circuit for colour vision based on rod-cone opponency. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature17158\">https://doi.org/10.1038/nature17158</a>","chicago":"Jösch, Maximilian A, and Markus Meister. “A Neuronal Circuit for Colour Vision Based on Rod-Cone Opponency.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature17158\">https://doi.org/10.1038/nature17158</a>.","ieee":"M. A. Jösch and M. Meister, “A neuronal circuit for colour vision based on rod-cone opponency,” <i>Nature</i>, vol. 532, no. 7598. Nature Publishing Group, pp. 236–239, 2016.","ista":"Jösch MA, Meister M. 2016. A neuronal circuit for colour vision based on rod-cone opponency. Nature. 532(7598), 236–239.","mla":"Jösch, Maximilian A., and Markus Meister. “A Neuronal Circuit for Colour Vision Based on Rod-Cone Opponency.” <i>Nature</i>, vol. 532, no. 7598, Nature Publishing Group, 2016, pp. 236–39, doi:<a href=\"https://doi.org/10.1038/nature17158\">10.1038/nature17158</a>."},"title":"A neuronal circuit for colour vision based on rod-cone opponency","date_updated":"2021-01-12T06:49:45Z","doi":"10.1038/nature17158","acknowledgement":"This work was supported by grants to M.M. from the NIH and to M.J. from The International Human Frontier Science Program Organization.","extern":1,"month":"04","date_published":"2016-04-14T00:00:00Z","_id":"1303","abstract":[{"text":"In bright light, cone-photoreceptors are active and colour vision derives from a comparison of signals in cones with different visual pigments. This comparison begins in the retina, where certain retinal ganglion cells have 'colour-opponent' visual responses-excited by light of one colour and suppressed by another colour. In dim light, rod-photoreceptors are active, but colour vision is impossible because they all use the same visual pigment. Instead, the rod signals are thought to splice into retinal circuits at various points, in synergy with the cone signals. Here we report a new circuit for colour vision that challenges these expectations. A genetically identified type of mouse retinal ganglion cell called JAMB (J-RGC), was found to have colour-opponent responses, OFF to ultraviolet (UV) light and ON to green light. Although the mouse retina contains a green-sensitive cone, the ON response instead originates in rods. Rods and cones both contribute to the response over several decades of light intensity. Remarkably, the rod signal in this circuit is antagonistic to that from cones. For rodents, this UV-green channel may play a role in social communication, as suggested by spectral measurements from the environment. In the human retina, all of the components for this circuit exist as well, and its function can explain certain experiences of colour in dim lights, such as a 'blue shift' in twilight. The discovery of this genetically defined pathway will enable new targeted studies of colour processing in the brain.","lang":"eng"}],"date_created":"2018-12-11T11:51:15Z","page":"236 - 239","issue":"7598","quality_controlled":0,"publication":"Nature","volume":532,"intvolume":"       532","status":"public","publisher":"Nature Publishing Group","publication_status":"published"},{"_id":"9704","date_created":"2021-07-23T08:30:38Z","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"date_published":"2016-05-06T00:00:00Z","month":"05","article_processing_charge":"No","status":"public","department":[{"_id":"SyCr"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.cq7t1","open_access":"1"}],"publisher":"Dryad","author":[{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini","first_name":"Myrsini"},{"last_name":"Doublet","first_name":"Vincent","full_name":"Doublet, Vincent"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias","full_name":"Fürst, Matthias"},{"full_name":"Weging, Silvio","first_name":"Silvio","last_name":"Weging"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"full_name":"Gogol Döring, Andreas","first_name":"Andreas","last_name":"Gogol Döring"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"}],"type":"research_data_reference","oa_version":"Published Version","year":"2016","day":"06","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","citation":{"short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>."},"doi":"10.5061/dryad.cq7t1","date_updated":"2023-02-21T16:54:31Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","id":"1262","status":"public"}]}},{"status":"public","department":[{"_id":"NiBa"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}],"publisher":"Dryad","_id":"9710","date_created":"2021-07-23T11:45:47Z","date_published":"2016-09-23T00:00:00Z","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}],"month":"09","article_processing_charge":"No","doi":"10.5061/dryad.s5s7r","date_updated":"2025-05-28T11:57:03Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","id":"1199","relation":"used_in_publication"}]},"oa_version":"Published Version","year":"2016","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"type":"research_data_reference","day":"23","title":"Data from: How does epistasis influence the response to selection?","citation":{"ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>","short":"N.H. Barton, (2016).","mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016."}},{"related_material":{"record":[{"id":"1855","relation":"used_in_publication","status":"public"}]},"doi":"10.5061/dryad.4b565","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:17:25Z","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","citation":{"short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, <a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016.","mla":"Mcmahon, Dino, et al. <i>Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>."},"author":[{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias","full_name":"Fürst, Matthias"},{"first_name":"Jesicca","full_name":"Caspar, Jesicca","last_name":"Caspar"},{"last_name":"Theodorou","full_name":"Theodorou, Panagiotis","first_name":"Panagiotis"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"}],"type":"research_data_reference","year":"2016","oa_version":"Published Version","day":"22","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"publisher":"Dryad","status":"public","department":[{"_id":"SyCr"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"_id":"9720","date_created":"2021-07-26T09:14:19Z","date_published":"2016-01-22T00:00:00Z","month":"01"},{"issue":"3","date_published":"2016-01-01T00:00:00Z","_id":"983","date_created":"2018-12-11T11:49:32Z","abstract":[{"lang":"eng","text":"The half-filled Landau level is expected to be approximately particle-hole symmetric, which requires an extension of the Halperin-Lee-Read (HLR) theory of the compressible state observed at this filling. Recent work indicates that, when particle-hole symmetry is preserved, the composite fermions experience a quantized π-Berry phase upon winding around the composite Fermi surface, analogous to Dirac fermions at the surface of a 3D topological insulator. In contrast, the effective low-energy theory of the composite fermion liquid originally proposed by HLR lacks particle-hole symmetry and has vanishing Berry phase. In this paper, we explain how thermoelectric transport measurements can be used to test the Dirac nature of the composite fermions by quantitatively extracting this Berry phase. First, we point out that longitudinal thermopower (Seebeck effect) is nonvanishing because of the unusual nature of particle-hole symmetry in this context and is not sensitive to the Berry phase. In contrast, we find that off-diagonal thermopower (Nernst effect) is directly related to the topological structure of the composite Fermi surface, vanishing for zero Berry phase and taking its maximal value for π Berry phase. In contrast, in purely electrical transport signatures, the Berry phase contributions appear as small corrections to a large background signal, making the Nernst effect a promising diagnostic of the Dirac nature of composite fermions."}],"month":"01","extern":1,"main_file_link":[{"url":"https://arxiv.org/abs/1512.06852","open_access":"1"}],"oa":1,"publisher":"American Physical Society","publication_status":"published","status":"public","intvolume":"         6","volume":6,"publication":"Physical Review X","quality_controlled":0,"title":"Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level","citation":{"mla":"Potter, Andrew, et al. “Thermoelectric Transport Signatures of Dirac Composite Fermions in the Half-Filled Landau Level.” <i>Physical Review X</i>, vol. 6, no. 3, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">10.1103/PhysRevX.6.031026</a>.","ieee":"A. Potter, M. Serbyn, and A. Vishwanath, “Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level,” <i>Physical Review X</i>, vol. 6, no. 3. American Physical Society, 2016.","ista":"Potter A, Serbyn M, Vishwanath A. 2016. Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level. Physical Review X. 6(3).","chicago":"Potter, Andrew, Maksym Serbyn, and Ashvin Vishwanath. “Thermoelectric Transport Signatures of Dirac Composite Fermions in the Half-Filled Landau Level.” <i>Physical Review X</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">https://doi.org/10.1103/PhysRevX.6.031026</a>.","apa":"Potter, A., Serbyn, M., &#38; Vishwanath, A. (2016). Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">https://doi.org/10.1103/PhysRevX.6.031026</a>","ama":"Potter A, Serbyn M, Vishwanath A. Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level. <i>Physical Review X</i>. 2016;6(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031026\">10.1103/PhysRevX.6.031026</a>","short":"A. Potter, M. Serbyn, A. Vishwanath, Physical Review X 6 (2016)."},"type":"journal_article","author":[{"last_name":"Potter","full_name":"Potter, Andrew C","first_name":"Andrew"},{"first_name":"Maksym","full_name":"Maksym Serbyn","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"first_name":"Ashvin","full_name":"Vishwanath, Ashvin K","last_name":"Vishwanath"}],"year":"2016","publist_id":"6417","day":"01","acknowledgement":"We thank B. I. Halperin, N. Cooper, C. Wang, J. Alicea, and M. Zaletel for insightful conversations. A. C. P. and M. S. were supported by the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant No. GBMF4307. A. V. was supported by a Simons Investigator grant.","doi":"10.1103/PhysRevX.6.031026","date_updated":"2021-01-12T08:22:25Z"}]