--- _id: '11836' abstract: - lang: eng text: "Given a graph where vertices are partitioned into k terminals and non-terminals, the goal is to compress the graph (i.e., reduce the number of non-terminals) using minor operations while preserving terminal distances approximately. The distortion of a compressed graph is the maximum multiplicative blow-up of distances between all pairs of terminals. We study the trade-off between the number of non-terminals and the distortion. This problem generalizes the Steiner Point Removal (SPR) problem, in which all non-terminals must be removed.\r\n\r\nWe introduce a novel black-box reduction to convert any lower bound on distortion for the SPR problem into a super-linear lower bound on the number of non-terminals, with the same distortion, for our problem. This allows us to show that there exist graphs such that every minor with distortion less than 2 / 2.5 / 3 must have Omega(k^2) / Omega(k^{5/4}) / Omega(k^{6/5}) non-terminals, plus more trade-offs in between. The black-box reduction has an interesting consequence: if the tight lower bound on distortion for the SPR problem is super-constant, then allowing any O(k) non-terminals will not help improving the lower bound to a constant.\r\n\r\nWe also build on the existing results on spanners, distance oracles and connected 0-extensions to show a number of upper bounds for general graphs, planar graphs, graphs that exclude a fixed minor and bounded treewidth graphs. Among others, we show that any graph admits a minor with O(log k) distortion and O(k^2) non-terminals, and any planar graph admits a minor with\r\n1 + epsilon distortion and ~O((k/epsilon)^2) non-terminals." alternative_title: - LIPIcs article_number: '131' article_processing_charge: No arxiv: 1 author: - first_name: Yun Kuen full_name: Cheung, Yun Kuen last_name: Cheung - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Cheung YK, Goranci G, Henzinger M. Graph minors for preserving terminal distances approximately - lower and upper bounds. In: 43rd International Colloquium on Automata, Languages, and Programming. Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ICALP.2016.131' apa: 'Cheung, Y. K., Goranci, G., & Henzinger, M. (2016). Graph minors for preserving terminal distances approximately - lower and upper bounds. In 43rd International Colloquium on Automata, Languages, and Programming (Vol. 55). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2016.131' chicago: Cheung, Yun Kuen, Gramoz Goranci, and Monika Henzinger. “Graph Minors for Preserving Terminal Distances Approximately - Lower and Upper Bounds.” In 43rd International Colloquium on Automata, Languages, and Programming, Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPICS.ICALP.2016.131. ieee: Y. K. Cheung, G. Goranci, and M. Henzinger, “Graph minors for preserving terminal distances approximately - lower and upper bounds,” in 43rd International Colloquium on Automata, Languages, and Programming, Rome, Italy, 2016, vol. 55. ista: 'Cheung YK, Goranci G, Henzinger M. 2016. Graph minors for preserving terminal distances approximately - lower and upper bounds. 43rd International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 55, 131.' mla: Cheung, Yun Kuen, et al. “Graph Minors for Preserving Terminal Distances Approximately - Lower and Upper Bounds.” 43rd International Colloquium on Automata, Languages, and Programming, vol. 55, 131, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ICALP.2016.131. short: Y.K. Cheung, G. Goranci, M. Henzinger, in:, 43rd International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. conference: end_date: 2016-07-15 location: Rome, Italy name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2016-07-12 date_created: 2022-08-12T11:16:01Z date_published: 2016-08-23T00:00:00Z date_updated: 2024-11-06T11:58:15Z day: '23' doi: 10.4230/LIPICS.ICALP.2016.131 extern: '1' external_id: arxiv: - '1604.08342' intvolume: ' 55' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.ICALP.2016.131 month: '08' oa: 1 oa_version: Published Version publication: 43rd International Colloquium on Automata, Languages, and Programming publication_identifier: isbn: - 978-3-95977-013-2 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Graph minors for preserving terminal distances approximately - lower and upper bounds type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2016' ... --- _id: '1184' abstract: - lang: eng text: Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival. acknowledgement: 'German Science Foundation. Grant Number: SCHR 1135/2-1. We thank M. Adam for handling part of the setups and J. Zoellner for behavioral observations.' article_processing_charge: No author: - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler orcid: 0000-0002-9547-2494 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf citation: ama: Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474 apa: Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474 chicago: Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474. ieee: S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,” Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906, 2016. ista: Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males. Ecology and Evolution. 6(24), 8903–8906. mla: Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution, vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474. short: S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906. date_created: 2018-12-11T11:50:36Z date_published: 2016-12-01T00:00:00Z date_updated: 2025-09-22T09:47:16Z day: '01' ddc: - '576' - '592' department: - _id: SyCr doi: 10.1002/ece3.2474 external_id: isi: - '000392063300022' file: - access_level: open_access checksum: 789026eb9e1be2a0da08376f29f569cf content_type: application/pdf creator: system date_created: 2018-12-12T10:14:12Z date_updated: 2020-07-14T12:44:37Z file_id: '5062' file_name: IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf file_size: 328414 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '24' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version page: 8903 - 8906 publication: Ecology and Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '6169' pubrep_id: '736' quality_controlled: '1' scopus_import: '1' status: public title: Mating and longevity in ant males 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2016' ... --- _id: '1185' abstract: - lang: eng text: The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk. acknowledgement: M.C. was funded by a PhD fellowship from the Università degli Studi di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would like to thank Andrew MacCabe and Edward Kiegle for editing the paper. article_processing_charge: No author: - first_name: Mara full_name: Cucinotta, Mara last_name: Cucinotta - first_name: Silvia full_name: Manrique, Silvia last_name: Manrique - first_name: Andrea full_name: Guazzotti, Andrea last_name: Guazzotti - first_name: Nadia full_name: Quadrelli, Nadia last_name: Quadrelli - first_name: Marta full_name: Mendes, Marta last_name: Mendes - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Lucia full_name: Colombo, Lucia last_name: Colombo citation: ama: Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 2016;143(23):4419-4424. doi:10.1242/dev.143545 apa: Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková, E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. Company of Biologists. https://doi.org/10.1242/dev.143545 chicago: Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.143545. ieee: M. Cucinotta et al., “Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development,” Development, vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016. ista: Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 143(23), 4419–4424. mla: Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development, vol. 143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545. short: M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková, L. Colombo, Development 143 (2016) 4419–4424. date_created: 2018-12-11T11:50:36Z date_published: 2016-12-01T00:00:00Z date_updated: 2025-09-22T09:46:43Z day: '01' department: - _id: EvBe doi: 10.1242/dev.143545 external_id: isi: - '000393454100012' intvolume: ' 143' isi: 1 issue: '23' language: - iso: eng month: '12' oa_version: None page: 4419 - 4424 publication: Development publication_status: published publisher: Company of Biologists publist_id: '6168' quality_controlled: '1' scopus_import: '1' status: public title: Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 143 year: '2016' ... --- _id: '1186' abstract: - lang: eng text: The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus. acknowledgement: We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann, for technical assistance and Lothar Petruschka for in silico analysis (all Dept. of Genetics, University of Greifswald). We are further grateful to the staff from SLS synchrotron beamline for help in data collection. This work was supported by grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to JAH and FG). article_number: '38094' article_processing_charge: No author: - first_name: Javier full_name: Gutierrez-Fernandez, Javier id: 3D9511BA-F248-11E8-B48F-1D18A9856A87 last_name: Gutierrez-Fernandez - first_name: Malek full_name: Saleh, Malek last_name: Saleh - first_name: Martín full_name: Alcorlo, Martín last_name: Alcorlo - first_name: Alejandro full_name: Gómez Mejóa, Alejandro last_name: Gómez Mejóa - first_name: David full_name: Pantoja Uceda, David last_name: Pantoja Uceda - first_name: Miguel full_name: Treviño, Miguel last_name: Treviño - first_name: Franziska full_name: Vob, Franziska last_name: Vob - first_name: Mohammed full_name: Abdullah, Mohammed last_name: Abdullah - first_name: Sergio full_name: Galán Bartual, Sergio last_name: Galán Bartual - first_name: Jolien full_name: Seinen, Jolien last_name: Seinen - first_name: Pedro full_name: Sánchez Murcia, Pedro last_name: Sánchez Murcia - first_name: Federico full_name: Gago, Federico last_name: Gago - first_name: Marta full_name: Bruix, Marta last_name: Bruix - first_name: Sven full_name: Hammerschmidt, Sven last_name: Hammerschmidt - first_name: Juan full_name: Hermoso, Juan last_name: Hermoso citation: ama: Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094 apa: Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda, D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094 chicago: Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38094. ieee: J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016. ista: Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D, Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 6, 38094. mla: Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group, 2016, doi:10.1038/srep38094. short: J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6 (2016). date_created: 2018-12-11T11:50:36Z date_published: 2016-12-05T00:00:00Z date_updated: 2025-09-22T09:46:12Z day: '05' ddc: - '576' - '610' department: - _id: LeSa doi: 10.1038/srep38094 external_id: isi: - '000389129100001' file: - access_level: open_access checksum: e007d78b483bc59bf5ab98e9d42a6ec1 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:18Z date_updated: 2020-07-14T12:44:37Z file_id: '4804' file_name: IST-2017-735-v1+1_srep38094.pdf file_size: 2716045 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '6167' pubrep_id: '735' quality_controlled: '1' scopus_import: '1' status: public title: Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2016' ... --- _id: '11866' abstract: - lang: eng text: "We present a deterministic (1+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for solving the single-source shortest paths problem on distributed weighted networks (the CONGEST model); here n is the number of nodes in the network and D is its (hop) diameter. This is the first non-trivial deterministic algorithm for this problem. It also improves (i) the running time of the randomized (1+o(1))-approximation Õ(n1/2D1/4+D)-time algorithm of Nanongkai [STOC 2014] by a factor of as large as n1/8, and (ii) the O(є−1logє−1)-approximation factor of Lenzen and Patt-Shamir’s Õ(n1/2+є+D)-time algorithm [STOC 2013] within the same running time. Our running time matches the known time lower bound of Ω(n1/2/logn + D) [Das Sarma et al. STOC 2011] modulo some lower-order terms, thus essentially settling the status of this problem which was raised at least a decade ago [Elkin SIGACT News 2004]. It also implies a (2+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for approximating a network’s weighted diameter which almost matches the lower bound by Holzer et al. [PODC 2012].\r\n\r\nIn achieving this result, we develop two techniques which might be of independent interest and useful in other settings: (i) a deterministic process that replaces the “hitting set argument” commonly used for shortest paths computation in various settings, and (ii) a simple, deterministic, construction of an (no(1), o(1))-hop set of size O(n1+o(1)). We combine these techniques with many distributed algorithmic techniques, some of which from problems that are not directly related to shortest paths, e.g. ruling sets [Goldberg et al. STOC 1987], source detection [Lenzen, Peleg PODC 2013], and partial distance estimation [Lenzen, Patt-Shamir PODC 2015]. Our hop set construction also leads to single-source shortest paths algorithms in two other settings: (i) a (1+o(1))-approximation O(no(1))-time algorithm on congested cliques, and (ii) a (1+o(1))-approximation O(no(1)logW)-pass O(n1+o(1)logW)-space streaming algorithm, when edge weights are in {1, 2, …, W}. The first result answers an open problem in [Nanongkai, STOC 2014]. The second result partially answers an open problem raised by McGregor in 2006 [
sublinear.info
, Problem 14]." article_processing_charge: No arxiv: 1 author: - 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: 'Henzinger M, Krinninger S, Nanongkai D. A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. In: 48th Annual ACM SIGACT Symposium on Theory of Computing. Association for Computing Machinery; 2016:489-498. doi:10.1145/2897518.2897638' apa: 'Henzinger, M., Krinninger, S., & Nanongkai, D. (2016). A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. In 48th Annual ACM SIGACT Symposium on Theory of Computing (pp. 489–498). Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/2897518.2897638' chicago: Henzinger, Monika, Sebastian Krinninger, and Danupon Nanongkai. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” In 48th Annual ACM SIGACT Symposium on Theory of Computing, 489–98. Association for Computing Machinery, 2016. https://doi.org/10.1145/2897518.2897638. ieee: M. Henzinger, S. Krinninger, and D. Nanongkai, “A deterministic almost-tight distributed algorithm for approximating single-source shortest paths,” in 48th Annual ACM SIGACT Symposium on Theory of Computing, Cambridge, MA, United States, 2016, pp. 489–498. ista: 'Henzinger M, Krinninger S, Nanongkai D. 2016. A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. 48th Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 489–498.' mla: Henzinger, Monika, et al. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–98, doi:10.1145/2897518.2897638. short: M. Henzinger, S. Krinninger, D. Nanongkai, in:, 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–498. conference: end_date: 2016-06-21 location: Cambridge, MA, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2016-06-19 date_created: 2022-08-16T09:19:31Z date_published: 2016-06-01T00:00:00Z date_updated: 2024-11-06T12:19:26Z day: '01' doi: 10.1145/2897518.2897638 extern: '1' external_id: arxiv: - '1504.07056' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.07056 month: '06' oa: 1 oa_version: Preprint page: 489 - 498 publication: 48th Annual ACM SIGACT Symposium on Theory of Computing publication_identifier: isbn: - 978-145034132-5 issn: - 0737-8017 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: A deterministic almost-tight distributed algorithm for approximating single-source shortest paths type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '11867' abstract: - lang: eng text: We present two deterministic dynamic algorithms for the maximum matching problem. (1) An algorithm that maintains a (2+є)-approximate maximum matching in general graphs with O(poly(logn, 1/є)) update time. (2) An algorithm that maintains an αK approximation of the value of the maximum matching with O(n2/K) update time in bipartite graphs, for every sufficiently large constant positive integer K. Here, 1≤ αK < 2 is a constant determined by the value of K. Result (1) is the first deterministic algorithm that can maintain an o(logn)-approximate maximum matching with polylogarithmic update time, improving the seminal result of Onak et al. [STOC 2010]. Its approximation guarantee almost matches the guarantee of the best randomized polylogarithmic update time algorithm [Baswana et al. FOCS 2011]. Result (2) achieves a better-than-two approximation with arbitrarily small polynomial update time on bipartite graphs. Previously the best update time for this problem was O(m1/4) [Bernstein et al. ICALP 2015], where m is the current number of edges in the graph. article_processing_charge: No arxiv: 1 author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - 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: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Bhattacharya S, Henzinger M, Nanongkai D. New deterministic approximation algorithms for fully dynamic matching. In: 48th Annual ACM SIGACT Symposium on Theory of Computing. Association for Computing Machinery; 2016:398-411. doi:10.1145/2897518.2897568' apa: 'Bhattacharya, S., Henzinger, M., & Nanongkai, D. (2016). New deterministic approximation algorithms for fully dynamic matching. In 48th Annual ACM SIGACT Symposium on Theory of Computing (pp. 398–411). Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/2897518.2897568' chicago: Bhattacharya, Sayan, Monika Henzinger, and Danupon Nanongkai. “New Deterministic Approximation Algorithms for Fully Dynamic Matching.” In 48th Annual ACM SIGACT Symposium on Theory of Computing, 398–411. Association for Computing Machinery, 2016. https://doi.org/10.1145/2897518.2897568. ieee: S. Bhattacharya, M. Henzinger, and D. Nanongkai, “New deterministic approximation algorithms for fully dynamic matching,” in 48th Annual ACM SIGACT Symposium on Theory of Computing, Cambridge, MA, United States, 2016, pp. 398–411. ista: 'Bhattacharya S, Henzinger M, Nanongkai D. 2016. New deterministic approximation algorithms for fully dynamic matching. 48th Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 398–411.' mla: Bhattacharya, Sayan, et al. “New Deterministic Approximation Algorithms for Fully Dynamic Matching.” 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 398–411, doi:10.1145/2897518.2897568. short: S. Bhattacharya, M. Henzinger, D. Nanongkai, in:, 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 398–411. conference: end_date: 2016-06-21 location: Cambridge, MA, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2016-06-19 date_created: 2022-08-16T09:27:35Z date_published: 2016-06-01T00:00:00Z date_updated: 2024-11-06T12:19:37Z day: '01' doi: 10.1145/2897518.2897568 extern: '1' external_id: arxiv: - '1604.05765' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.05765 month: '06' oa: 1 oa_version: Preprint page: 398 - 411 publication: 48th Annual ACM SIGACT Symposium on Theory of Computing publication_identifier: isbn: - 978-145034132-5 issn: - 0737-8017 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: New deterministic approximation algorithms for fully dynamic matching type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1188' abstract: - lang: eng text: "We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations." acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night. article_number: '123502' article_processing_charge: No arxiv: 1 author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Davide full_name: Masoero, Davide last_name: Masoero citation: ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f' apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/aa4e8f' chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &amp; Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.' ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOP Publishing, 2016.' ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.' mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &amp; Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:10.1088/1742-5468/aa4e8f.' short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).' date_created: 2018-12-11T11:50:37Z date_published: 2016-12-30T00:00:00Z date_updated: 2025-09-22T09:45:38Z day: '30' department: - _id: GaTk doi: 10.1088/1742-5468/aa4e8f ec_funded: 1 external_id: arxiv: - '1606.09048' isi: - '000391973900001' intvolume: ' 2016' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.09048 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Journal of Statistical Mechanics: Theory and Experiment' publication_status: published publisher: IOP Publishing publist_id: '6165' quality_controlled: '1' scopus_import: '1' status: public title: Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 2016 year: '2016' ... --- _id: '1189' abstract: - lang: eng text: "Within the scope of this thesis, we show that a driven-dissipative system with\r\nfew ultracold atoms can exhibit dissipatively bound states, even if the atom-atom\r\ninteraction is purely repulsive. This bond arises due to the dipole-dipole inter-\r\naction, which is restricted to one of the lower electronic energy states, resulting\r\nin the distance-dependent coherent population trapping. The quality of this al-\r\nready established method of dissipative binding is improved and the application\r\nis extended to higher dimensions and a larger number of atoms. \ Here, we simu-\r\nlate two- and three-atom systems using an adapted approach to the Monte Carlo\r\nwave-function method and analyse the results. Finally, \ we examine the possi-\r\nbility of finding a setting allowing trimer \ states but prohibiting dimer states.\r\nIn the context of open quantum systems, such a three-body bound states corre-\r\nsponds to the driven-dissipative analogue of a Borromean state. These states can\r\nbe detected in modern experiments with dipolar and Rydberg-dressed ultracold\r\natomic gases.\r\n" article_processing_charge: No author: - first_name: Clemens full_name: Jochum, Clemens last_name: Jochum citation: ama: Jochum C. Dissipative Few-Body Quantum Systems. 2016. apa: Jochum, C. (2016). Dissipative Few-Body Quantum Systems. Technical University Vienna. chicago: Jochum, Clemens. “Dissipative Few-Body Quantum Systems.” Technical University Vienna, 2016. ieee: C. Jochum, “Dissipative Few-Body Quantum Systems,” Technical University Vienna, 2016. ista: Jochum C. 2016. Dissipative Few-Body Quantum Systems. Technical University Vienna. mla: Jochum, Clemens. Dissipative Few-Body Quantum Systems. Technical University Vienna, 2016. short: C. Jochum, Dissipative Few-Body Quantum Systems, Technical University Vienna, 2016. date_created: 2018-12-11T11:50:37Z date_published: 2016-11-28T00:00:00Z date_updated: 2021-01-12T06:48:57Z day: '28' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://repositum.tuwien.ac.at/obvutwhs/content/titleinfo/1517088 month: '11' oa: 1 oa_version: Published Version page: '94' publication_status: published publisher: Technical University Vienna publist_id: '6164' status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Peter full_name: Rabl, Peter last_name: Rabl title: Dissipative Few-Body Quantum Systems type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '11891' abstract: - lang: eng text: "We study dynamic (1+\U0001D716)-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected \U0001D45B-node \U0001D45A-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with a total update time of \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716) and constant query time by Roditty and Zwick [SIAM J. Comput., 41 (2012), pp. 670--683]. The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach [J. ACM, 28 (1981), pp. 1--4]; it has a total update time of \U0001D442(\U0001D45A\U0001D45B2) and constant query time. We improve these results as follows: (1) We present an algorithm with a total update time of \U0001D442̃ (\U0001D45B5/2/\U0001D716) and constant query time that has an additive error of 2 in addition to the 1+\U0001D716 multiplicative error. This beats the previous \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716) time when \U0001D45A=Ω(\U0001D45B3/2). Note that the additive error is unavoidable since, even in the static case, an \U0001D442(\U0001D45B3−\U0001D6FF)-time (a so-called truly subcubic) combinatorial algorithm with 1+\U0001D716 multiplicative error cannot have an additive error less than 2−\U0001D716, unless we make a major breakthrough for Boolean matrix multiplication [D. Dor, S. Halrepin, and U. Zwick, SIAM J. Comput., 29 (2000), pp. 1740--1759] and many other long-standing problems [V. Vassilevska Williams and R. Williams, Proceedings of the 2010 IEEE 51st Annual Symposium on Foundations of Computer Science, 2010, pp. 645--654]. The algorithm can also be turned into a (2+\U0001D716)-approximation algorithm (without an additive error) with the same time guarantees, improving the recent (3+\U0001D716)-approximation algorithm with \U0001D442̃ (\U0001D45B5/2+\U0001D442(log(1/\U0001D716)/log\U0001D45B√)) running time of Bernstein and Roditty [Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, 2011, pp. 1355--1365] in terms of both approximation and time guarantees. (2) We present a deterministic algorithm with a total update time of \U0001D442̃ (\U0001D45A\U0001D45B/\U0001D716) and a query time of \U0001D442(loglog\U0001D45B). The algorithm has a multiplicative error of 1+\U0001D716 and gives the first improved deterministic algorithm since 1981. It also answers an open question raised by Bernstein in [Proceedings of the Forty-Fifth Annual ACM Symposium on Theory of Computing, 2013, pp. 725--734]. The deterministic algorithm can be turned into a deterministic fully dynamic (1+\U0001D716)-approximation with an amortized update time of \U0001D442̃ (\U0001D45A\U0001D45B/(\U0001D716\U0001D461)) and a query time of \U0001D442̃ (\U0001D461) for every \U0001D461≤\U0001D45B√. In order to achieve our results, we introduce two new techniques: (i) A monotone Even--Shiloach tree algorithm which maintains a bounded-distance shortest-paths tree on a certain type of emulator called a locally persevering emulator. (ii) A derandomization technique based on moving Even--Shiloach trees as a way to derandomize the standard random set argument. These techniques might be of independent interest." article_processing_charge: No article_type: original arxiv: 1 author: - 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: 'Henzinger M, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing. 2016;45(3):947-1006. doi:10.1137/140957299' apa: 'Henzinger, M., Krinninger, S., & Nanongkai, D. (2016). Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140957299' chicago: 'Henzinger, Monika, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2016. https://doi.org/10.1137/140957299.' ieee: 'M. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization,” SIAM Journal on Computing, vol. 45, no. 3. Society for Industrial & Applied Mathematics, pp. 947–1006, 2016.' ista: 'Henzinger M, Krinninger S, Nanongkai D. 2016. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing. 45(3), 947–1006.' mla: 'Henzinger, Monika, et al. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” SIAM Journal on Computing, vol. 45, no. 3, Society for Industrial & Applied Mathematics, 2016, pp. 947–1006, doi:10.1137/140957299.' short: M. Henzinger, S. Krinninger, D. Nanongkai, SIAM Journal on Computing 45 (2016) 947–1006. date_created: 2022-08-17T08:37:00Z date_published: 2016-05-01T00:00:00Z date_updated: 2024-11-06T12:23:06Z day: '01' doi: 10.1137/140957299 extern: '1' external_id: arxiv: - '1308.0776' intvolume: ' 45' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1308.0776 month: '05' oa: 1 oa_version: Preprint page: 947-1006 publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: 'Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2016' ... --- _id: '1193' abstract: - lang: eng text: We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid "bad features", or "flaws". It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and "resamples" it using a "resampling oracle" provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new "commutativity" condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately. acknowledgement: European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160 article_number: '7782993' article_processing_charge: No arxiv: 1 author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings - Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December. IEEE; 2016. doi:10.1109/FOCS.2016.88' apa: 'Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma. In Proceedings - Annual IEEE Symposium on Foundations of Computer Science (Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88' chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” In Proceedings - Annual IEEE Symposium on Foundations of Computer Science, Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88. ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings - Annual IEEE Symposium on Foundations of Computer Science, New Brunswick, NJ, USA , 2016, vol. 2016–December. ista: 'Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma. Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science vol. 2016–December, 7782993.' mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” Proceedings - Annual IEEE Symposium on Foundations of Computer Science, vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88. short: V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2016. conference: end_date: 2016-09-11 location: 'New Brunswick, NJ, USA ' name: 'FOCS: Foundations of Computer Science' start_date: 2016-09-09 date_created: 2018-12-11T11:50:38Z date_published: 2016-12-15T00:00:00Z date_updated: 2025-09-22T09:44:20Z day: '15' department: - _id: VlKo doi: 10.1109/FOCS.2016.88 ec_funded: 1 external_id: arxiv: - '1506.08547' isi: - '000391198500082' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1506.08547v7 month: '12' oa: 1 oa_version: Preprint project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Proceedings - Annual IEEE Symposium on Foundations of Computer Science publication_status: published publisher: IEEE publist_id: '6158' quality_controlled: '1' related_material: record: - id: '5975' relation: later_version status: public scopus_import: '1' status: public title: Commutativity in the algorithmic Lovasz local lemma type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 2016-December year: '2016' ... --- _id: '1195' abstract: - lang: eng text: 'The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. ' acknowledgement: "The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported \ by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”." article_processing_charge: No author: - first_name: Susan full_name: Franssen, Susan last_name: Franssen - 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: Christian full_name: Schlötterer, Christian last_name: Schlötterer citation: ama: Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210 apa: Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210 chicago: Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210. ieee: S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016. ista: Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184. mla: Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210. short: S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184. date_created: 2018-12-11T11:50:39Z date_published: 2016-10-03T00:00:00Z date_updated: 2025-09-22T09:43:41Z day: '03' ddc: - '576' department: - _id: NiBa doi: 10.1093/molbev/msw210 ec_funded: 1 external_id: isi: - '000396772000009' file: - access_level: open_access checksum: 1e78d3aaffcb40dc8b02b7b4666019e0 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:35Z date_updated: 2020-07-14T12:44:38Z file_id: '5223' file_name: IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf file_size: 295274 relation: main_file - access_level: open_access checksum: e13171843283774404c936c581b4543e content_type: application/pdf creator: system date_created: 2018-12-12T10:16:36Z date_updated: 2020-07-14T12:44:38Z file_id: '5224' file_name: IST-2017-770-v1+2_Fig1.pdf file_size: 10902625 relation: main_file - access_level: open_access checksum: 63bc6e6e61f347594d8c00c37f874a0b content_type: application/pdf creator: system date_created: 2018-12-12T10:16:37Z date_updated: 2020-07-14T12:44:38Z file_id: '5225' file_name: IST-2017-770-v1+3_Fig2.pdf file_size: 21437 relation: main_file - access_level: open_access checksum: da87cc7c78808837f22a3dae1c8397f9 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:38Z date_updated: 2020-07-14T12:44:38Z file_id: '5226' file_name: IST-2017-770-v1+4_Fig3.pdf file_size: 1172194 relation: main_file - access_level: open_access checksum: e47b2a0c32142f423b3100150c0294f8 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:38Z date_updated: 2020-07-14T12:44:38Z file_id: '5227' file_name: IST-2017-770-v1+5_Fig4.pdf file_size: 50045 relation: main_file - access_level: open_access checksum: a5a7d6b32e7e17d35d337d7ec2a9f6c9 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:39Z date_updated: 2020-07-14T12:44:38Z file_id: '5228' file_name: IST-2017-770-v1+6_Fig5.pdf file_size: 50705 relation: main_file file_date_updated: 2020-07-14T12:44:38Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 174 - 184 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6155' pubrep_id: '770' quality_controlled: '1' scopus_import: '1' status: public title: Reconstruction of haplotype-blocks selected during experimental evolution. type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 34 year: '2016' ... --- _id: '1197' abstract: - lang: eng text: Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina. acknowledgement: JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript. article_number: e1005855 article_processing_charge: No author: - first_name: Jason full_name: Prentice, Jason last_name: Prentice - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Mark full_name: Ioffe, Mark last_name: Ioffe - first_name: Adrianna full_name: Loback, Adrianna last_name: Loback - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. PLoS Computational Biology. 2016;12(11). doi:10.1371/journal.pcbi.1005148 apa: Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148 chicago: Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148. ieee: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016. ista: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855. mla: Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148. short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016). date_created: 2018-12-11T11:50:40Z date_published: 2016-11-17T00:00:00Z date_updated: 2025-09-22T09:43:12Z day: '17' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1005148 external_id: isi: - '000391230900008' file: - access_level: open_access checksum: 47b08cbd4dbf32b25ba161f5f4b262cc content_type: application/pdf creator: kschuh date_created: 2019-01-25T10:35:00Z date_updated: 2020-07-14T12:44:38Z file_id: '5884' file_name: 2016_PLOS_Prentice.pdf file_size: 4492021 relation: main_file file_date_updated: 2020-07-14T12:44:38Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '6153' quality_controlled: '1' related_material: record: - id: '9709' relation: research_data status: public scopus_import: '1' status: public title: Error-robust modes of the retinal population code 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 12 year: '2016' ... --- _id: '11983' abstract: - lang: eng text: A continuous process for the synthesis and inline separation of anhydrous trifluoromethyl diazomethane in a single continuous flow process is presented. The diazo building block is generated from the corresponding amine and NaNO2 under acidic, aqueous conditions and subsequently diffuses through a gas-permeable membrane into an organic stream. To avoid storage and transportation of the hazardous compound, a representative downstream process in a packed-bed reactor yielding highly functionalized building blocks was developed. article_processing_charge: No article_type: letter_note author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Pieber B, Kappe CO. Generation and synthetic application of trifluoromethyl diazomethane utilizing continuous flow technologies. Organic Letters. 2016;18(5):1076-1079. doi:10.1021/acs.orglett.6b00194 apa: Pieber, B., & Kappe, C. O. (2016). Generation and synthetic application of trifluoromethyl diazomethane utilizing continuous flow technologies. Organic Letters. American Chemical Society. https://doi.org/10.1021/acs.orglett.6b00194 chicago: Pieber, Bartholomäus, and C. Oliver Kappe. “Generation and Synthetic Application of Trifluoromethyl Diazomethane Utilizing Continuous Flow Technologies.” Organic Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.orglett.6b00194. ieee: B. Pieber and C. O. Kappe, “Generation and synthetic application of trifluoromethyl diazomethane utilizing continuous flow technologies,” Organic Letters, vol. 18, no. 5. American Chemical Society, pp. 1076–1079, 2016. ista: Pieber B, Kappe CO. 2016. Generation and synthetic application of trifluoromethyl diazomethane utilizing continuous flow technologies. Organic Letters. 18(5), 1076–1079. mla: Pieber, Bartholomäus, and C. Oliver Kappe. “Generation and Synthetic Application of Trifluoromethyl Diazomethane Utilizing Continuous Flow Technologies.” Organic Letters, vol. 18, no. 5, American Chemical Society, 2016, pp. 1076–79, doi:10.1021/acs.orglett.6b00194. short: B. Pieber, C.O. Kappe, Organic Letters 18 (2016) 1076–1079. date_created: 2022-08-25T11:22:20Z date_published: 2016-03-04T00:00:00Z date_updated: 2024-10-14T12:07:21Z day: '04' doi: 10.1021/acs.orglett.6b00194 extern: '1' external_id: pmid: - '26902154' intvolume: ' 18' issue: '5' language: - iso: eng month: '03' oa_version: None page: 1076-1079 pmid: 1 publication: Organic Letters publication_identifier: eissn: - 1523-7052 issn: - 1523-7060 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Generation and synthetic application of trifluoromethyl diazomethane utilizing continuous flow technologies type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2016' ... --- _id: '11985' abstract: - lang: eng text: Hydrocodone, a high value active pharmaceutical ingredient (API), is usually produced in a semisynthetic pathway from morphine, codeine or thebaine. The latter alkaloid is an attractive precursor as it is not used as a remedy itself. The key step in this production route is a selective olefin reduction forming 8,14-dihydrothebaine which can be subsequently hydrolyzed to yield hydrocodone. Unfortunately, standard hydrogenation procedures cannot be applied due to severe selectivity problems. A transfer hydrogenation using in situ generated diimide is the only known alternative to achieve a selective transformation. The most (atom) economic generation of this highly unstable reducing agent is by oxidizing hydrazine hydrate (N2H4·H2O) with O2. In the past, this route was “forbidden” on an industrial scale due to its enormous explosion potential in batch. A continuous high-temperature/high-pressure methodology allows an efficient, safe, and scalable processing of the hazardous reaction mixture. The industrially relevant reduction was achieved by using four consecutive liquid feeds (of N2H4·H2O) and residence time units, resulting in a highly selective reduction within less than 1 h. article_processing_charge: No article_type: original author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: D. Phillip full_name: Cox, D. Phillip last_name: Cox - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Pieber B, Cox DP, Kappe CO. Selective olefin reduction in thebaine using hydrazine hydrate and O₂ under intensified continuous flow conditions. Organic Process Research and Development. 2016;20(2):376-385. doi:10.1021/acs.oprd.5b00370 apa: Pieber, B., Cox, D. P., & Kappe, C. O. (2016). Selective olefin reduction in thebaine using hydrazine hydrate and O₂ under intensified continuous flow conditions. Organic Process Research and Development. American Chemical Society. https://doi.org/10.1021/acs.oprd.5b00370 chicago: Pieber, Bartholomäus, D. Phillip Cox, and C. Oliver Kappe. “Selective Olefin Reduction in Thebaine Using Hydrazine Hydrate and O₂ under Intensified Continuous Flow Conditions.” Organic Process Research and Development. American Chemical Society, 2016. https://doi.org/10.1021/acs.oprd.5b00370. ieee: B. Pieber, D. P. Cox, and C. O. Kappe, “Selective olefin reduction in thebaine using hydrazine hydrate and O₂ under intensified continuous flow conditions,” Organic Process Research and Development, vol. 20, no. 2. American Chemical Society, pp. 376–385, 2016. ista: Pieber B, Cox DP, Kappe CO. 2016. Selective olefin reduction in thebaine using hydrazine hydrate and O₂ under intensified continuous flow conditions. Organic Process Research and Development. 20(2), 376–385. mla: Pieber, Bartholomäus, et al. “Selective Olefin Reduction in Thebaine Using Hydrazine Hydrate and O₂ under Intensified Continuous Flow Conditions.” Organic Process Research and Development, vol. 20, no. 2, American Chemical Society, 2016, pp. 376–85, doi:10.1021/acs.oprd.5b00370. short: B. Pieber, D.P. Cox, C.O. Kappe, Organic Process Research and Development 20 (2016) 376–385. date_created: 2022-08-25T11:34:28Z date_published: 2016-02-19T00:00:00Z date_updated: 2023-02-21T10:10:26Z day: '19' doi: 10.1021/acs.oprd.5b00370 extern: '1' intvolume: ' 20' issue: '2' language: - iso: eng month: '02' oa_version: None page: 376-385 publication: Organic Process Research and Development publication_identifier: eissn: - 1520-586X issn: - 1083-6160 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Selective olefin reduction in thebaine using hydrazine hydrate and O₂ under intensified continuous flow conditions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2016' ... --- _id: '11988' abstract: - lang: eng text: A continuous Bucherer–Bergs hydantoin synthesis utilizing intensified conditions is reported. The methodology is characterized by a two-feed flow approach to independently feed the organic substrate and the aqueous reagent solution. The increased interfacial area of the biphasic reaction mixture and the lack of headspace enabled almost quantitative conversions within ca. 30 minutes at 120 °C and 20 bar even for unpolar starting materials. In addition, a selective N(3)-monoalkylation of the resulting heterocycles under batch microwave conditions is reported yielding potential acetylcholinesterase inhibitors. article_processing_charge: No article_type: letter_note author: - first_name: C. full_name: Kappe, C. last_name: Kappe - first_name: Julia full_name: Monteiro, Julia last_name: Monteiro - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Arlene full_name: Corrêa, Arlene last_name: Corrêa citation: ama: 'Kappe C, Monteiro J, Pieber B, Corrêa A. Continuous synthesis of hydantoins: Intensifying the Bucherer–Bergs reaction. Synlett. 2016;27(01):83-87. doi:10.1055/s-0035-1560317' apa: 'Kappe, C., Monteiro, J., Pieber, B., & Corrêa, A. (2016). Continuous synthesis of hydantoins: Intensifying the Bucherer–Bergs reaction. Synlett. Georg Thieme Verlag. https://doi.org/10.1055/s-0035-1560317' chicago: 'Kappe, C., Julia Monteiro, Bartholomäus Pieber, and Arlene Corrêa. “Continuous Synthesis of Hydantoins: Intensifying the Bucherer–Bergs Reaction.” Synlett. Georg Thieme Verlag, 2016. https://doi.org/10.1055/s-0035-1560317.' ieee: 'C. Kappe, J. Monteiro, B. Pieber, and A. Corrêa, “Continuous synthesis of hydantoins: Intensifying the Bucherer–Bergs reaction,” Synlett, vol. 27, no. 01. Georg Thieme Verlag, pp. 83–87, 2016.' ista: 'Kappe C, Monteiro J, Pieber B, Corrêa A. 2016. Continuous synthesis of hydantoins: Intensifying the Bucherer–Bergs reaction. Synlett. 27(01), 83–87.' mla: 'Kappe, C., et al. “Continuous Synthesis of Hydantoins: Intensifying the Bucherer–Bergs Reaction.” Synlett, vol. 27, no. 01, Georg Thieme Verlag, 2016, pp. 83–87, doi:10.1055/s-0035-1560317.' short: C. Kappe, J. Monteiro, B. Pieber, A. Corrêa, Synlett 27 (2016) 83–87. date_created: 2022-08-25T11:52:22Z date_published: 2016-01-04T00:00:00Z date_updated: 2023-02-21T10:10:33Z day: '04' doi: 10.1055/s-0035-1560317 extern: '1' intvolume: ' 27' issue: '01' language: - iso: eng month: '01' oa_version: None page: 83-87 publication: Synlett publication_identifier: eissn: - 1437-2096 issn: - 0936-5214 publication_status: published publisher: Georg Thieme Verlag quality_controlled: '1' scopus_import: '1' status: public title: 'Continuous synthesis of hydantoins: Intensifying the Bucherer–Bergs reaction' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2016' ... --- _id: '1200' acknowledgement: C.H. acknowledges generous support from the ISTFELLOW program. article_processing_charge: No author: - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Arne full_name: Traulsen, Arne last_name: Traulsen citation: ama: 'Hilbe C, Traulsen A. Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. 2016;19:29-31. doi:10.1016/j.plrev.2016.10.004' apa: 'Hilbe, C., & Traulsen, A. (2016). Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.10.004' chicago: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling: Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J. Schossau and A. Hintze.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.10.004.' ieee: 'C. Hilbe and A. Traulsen, “Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on ‘Evolutionary game theory using agent-based methods’ by C. Adami, J. Schossau and A. Hintze,” Physics of Life Reviews, vol. 19. Elsevier, pp. 29–31, 2016.' ista: 'Hilbe C, Traulsen A. 2016. Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. 19, 29–31.' mla: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling: Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J. Schossau and A. Hintze.” Physics of Life Reviews, vol. 19, Elsevier, 2016, pp. 29–31, doi:10.1016/j.plrev.2016.10.004.' short: C. Hilbe, A. Traulsen, Physics of Life Reviews 19 (2016) 29–31. date_created: 2018-12-11T11:50:40Z date_published: 2016-12-01T00:00:00Z date_updated: 2025-09-22T09:42:11Z day: '01' ddc: - '530' department: - _id: KrCh doi: 10.1016/j.plrev.2016.10.004 ec_funded: 1 external_id: isi: - '000390640200003' file: - access_level: open_access checksum: 95e6dc78278334b99dacbf8822509364 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:02Z date_updated: 2020-07-14T12:44:39Z file_id: '4855' file_name: IST-2017-798-v1+1_comment_adami.pdf file_size: 171352 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Submitted Version page: 29 - 31 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physics of Life Reviews publication_status: published publisher: Elsevier publist_id: '6150' pubrep_id: '798' quality_controlled: '1' scopus_import: '1' status: public title: 'Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze' 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 19 year: '2016' ... --- _id: '1201' abstract: - lang: eng text: In this issue of Cell, Skau et al. show that the formin FMN2 organizes a perinuclear actin cytoskeleton that protects the nucleus and its genomic content of migrating cells squeezing through small spaces. article_processing_charge: No author: - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Renkawitz J, Sixt MK. Formin’ a nuclear protection. Cell. 2016;167(6):1448-1449. doi:10.1016/j.cell.2016.11.024 apa: Renkawitz, J., & Sixt, M. K. (2016). Formin’ a nuclear protection. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.024 chicago: Renkawitz, Jörg, and Michael K Sixt. “Formin’ a Nuclear Protection.” Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.024. ieee: J. Renkawitz and M. K. Sixt, “Formin’ a nuclear protection,” Cell, vol. 167, no. 6. Cell Press, pp. 1448–1449, 2016. ista: Renkawitz J, Sixt MK. 2016. Formin’ a nuclear protection. Cell. 167(6), 1448–1449. mla: Renkawitz, Jörg, and Michael K. Sixt. “Formin’ a Nuclear Protection.” Cell, vol. 167, no. 6, Cell Press, 2016, pp. 1448–49, doi:10.1016/j.cell.2016.11.024. short: J. Renkawitz, M.K. Sixt, Cell 167 (2016) 1448–1449. date_created: 2018-12-11T11:50:41Z date_published: 2016-12-01T00:00:00Z date_updated: 2025-09-22T09:41:33Z day: '01' department: - _id: MiSi doi: 10.1016/j.cell.2016.11.024 external_id: isi: - '000389470500007' intvolume: ' 167' isi: 1 issue: '6' language: - iso: eng month: '12' oa_version: None page: 1448 - 1449 publication: Cell publication_status: published publisher: Cell Press publist_id: '6149' quality_controlled: '1' scopus_import: '1' status: public title: Formin’ a nuclear protection type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 167 year: '2016' ... --- _id: '1202' acknowledgement: The authors thank Sophie A.O. Armitage and Jan N. Offenborn for helpful comments on the figures, and two anonymous reviewers for their helpful comments. The project was funded by the Deutsche Forschungsgemeinschaft (DFG, KU 1929/4-2) within the priority programme SPP 1399 “Host–Parasite Coevolution”. article_processing_charge: No author: - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Robert full_name: Peuß, Robert last_name: Peuß - first_name: Kevin full_name: Ferro, Kevin last_name: Ferro - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: 'Milutinovic B, Peuß R, Ferro K, Kurtz J. Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . 2016;119(4):254-261. doi:10.1016/j.zool.2016.03.006' apa: 'Milutinovic, B., Peuß, R., Ferro, K., & Kurtz, J. (2016). Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . Elsevier. https://doi.org/10.1016/j.zool.2016.03.006' chicago: 'Milutinovic, Barbara, Robert Peuß, Kevin Ferro, and Joachim Kurtz. “Immune Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology . Elsevier, 2016. https://doi.org/10.1016/j.zool.2016.03.006.' ieee: 'B. Milutinovic, R. Peuß, K. Ferro, and J. Kurtz, “Immune priming in arthropods: an update focusing on the red flour beetle,” Zoology , vol. 119, no. 4. Elsevier, pp. 254–261, 2016.' ista: 'Milutinovic B, Peuß R, Ferro K, Kurtz J. 2016. Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . 119(4), 254–261.' mla: 'Milutinovic, Barbara, et al. “Immune Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology , vol. 119, no. 4, Elsevier, 2016, pp. 254–61, doi:10.1016/j.zool.2016.03.006.' short: B. Milutinovic, R. Peuß, K. Ferro, J. Kurtz, Zoology 119 (2016) 254–261. date_created: 2018-12-11T11:50:41Z date_published: 2016-08-01T00:00:00Z date_updated: 2025-09-22T09:41:02Z day: '01' ddc: - '570' department: - _id: SyCr doi: 10.1016/j.zool.2016.03.006 external_id: isi: - '000384958500003' file: - access_level: open_access checksum: 8396d5bd95f9c4295857162f902afabf content_type: application/pdf creator: kschuh date_created: 2019-01-25T13:00:20Z date_updated: 2020-07-14T12:44:39Z file_id: '5885' file_name: 2016_Elsevier_Milutinovic.pdf file_size: 1473211 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 119' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 254 - 261 project: - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution publication: 'Zoology ' publication_status: published publisher: Elsevier publist_id: '6147' quality_controlled: '1' scopus_import: '1' status: public title: 'Immune priming in arthropods: an update focusing on the red flour beetle' 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 119 year: '2016' ... --- _id: '1203' abstract: - lang: eng text: Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae. acknowledgement: We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support. article_processing_charge: No author: - first_name: Fang full_name: Hu, Fang last_name: Hu - first_name: Lavanya full_name: Rishishwar, Lavanya last_name: Rishishwar - first_name: Ambily full_name: Sivadas, Ambily last_name: Sivadas - first_name: Gabriel full_name: Mitchell, Gabriel id: 315BCD80-F248-11E8-B48F-1D18A9856A87 last_name: Mitchell - first_name: Jordan full_name: King, Jordan last_name: King - first_name: Timothy full_name: Murphy, Timothy last_name: Murphy - first_name: Janet full_name: Gilsdorf, Janet last_name: Gilsdorf - first_name: Leonard full_name: Mayer, Leonard last_name: Mayer - first_name: Xin full_name: Wang, Xin last_name: Wang citation: ama: Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017. doi:10.1128/JCM.01511-16 apa: Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16 chicago: Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology. American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16. ieee: F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016. ista: Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017. mla: Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16. short: F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017. date_created: 2018-12-11T11:50:41Z date_published: 2016-12-01T00:00:00Z date_updated: 2025-09-22T09:40:28Z day: '01' department: - _id: GaTk doi: 10.1128/JCM.01511-16 external_id: isi: - '000389209600026' intvolume: ' 54' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/ month: '12' oa: 1 oa_version: Submitted Version page: 3010 - 3017 publication: Journal of Clinical Microbiology publication_status: published publisher: American Society for Microbiology publist_id: '6146' quality_controlled: '1' scopus_import: '1' status: public title: Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 54 year: '2016' ... --- _id: '1204' abstract: - lang: eng text: In science, as in life, "surprises" can be adequately appreciated only in the presence of a null model, what we expect a priori. In physics, theories sometimes express the values of dimensionless physical constants as combinations of mathematical constants like π or e. The inverse problem also arises, whereby the measured value of a physical constant admits a "surprisingly" simple approximation in terms of well-known mathematical constants. Can we estimate the probability for this to be a mere coincidence, rather than an inkling of some theory? We answer the question in the most naive form. article_processing_charge: No arxiv: 1 author: - first_name: Ariel full_name: Amir, Ariel last_name: Amir - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Tadashi full_name: Tokieda, Tadashi last_name: Tokieda citation: ama: Amir A, Lemeshko M, Tokieda T. Surprises in numerical expressions of physical constants. American Mathematical Monthly. 2016;123(6):609-612. doi:10.4169/amer.math.monthly.123.6.609 apa: Amir, A., Lemeshko, M., & Tokieda, T. (2016). Surprises in numerical expressions of physical constants. American Mathematical Monthly. Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.123.6.609 chicago: Amir, Ariel, Mikhail Lemeshko, and Tadashi Tokieda. “Surprises in Numerical Expressions of Physical Constants.” American Mathematical Monthly. Mathematical Association of America, 2016. https://doi.org/10.4169/amer.math.monthly.123.6.609. ieee: A. Amir, M. Lemeshko, and T. Tokieda, “Surprises in numerical expressions of physical constants,” American Mathematical Monthly, vol. 123, no. 6. Mathematical Association of America, pp. 609–612, 2016. ista: Amir A, Lemeshko M, Tokieda T. 2016. Surprises in numerical expressions of physical constants. American Mathematical Monthly. 123(6), 609–612. mla: Amir, Ariel, et al. “Surprises in Numerical Expressions of Physical Constants.” American Mathematical Monthly, vol. 123, no. 6, Mathematical Association of America, 2016, pp. 609–12, doi:10.4169/amer.math.monthly.123.6.609. short: A. Amir, M. Lemeshko, T. Tokieda, American Mathematical Monthly 123 (2016) 609–612. date_created: 2018-12-11T11:50:42Z date_published: 2016-06-01T00:00:00Z date_updated: 2025-09-22T09:39:09Z day: '01' department: - _id: MiLe doi: 10.4169/amer.math.monthly.123.6.609 external_id: arxiv: - '1603.00299' isi: - '000381754900010' intvolume: ' 123' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1603.00299 month: '06' oa: 1 oa_version: Preprint page: 609 - 612 publication: American Mathematical Monthly publication_status: published publisher: Mathematical Association of America publist_id: '6143' quality_controlled: '1' scopus_import: '1' status: public title: Surprises in numerical expressions of physical constants type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 123 year: '2016' ...