--- _id: '1181' abstract: - lang: eng text: 'This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.' acknowledgement: This work was supported by National Institutes of Health Grants R01NS089795 and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777 to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444 and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent to L.N. The authors apologize to colleagues whose work could not be cited due to space limitations. author: - first_name: Noelle full_name: Dwyer, Noelle last_name: Dwyer - first_name: Bin full_name: Chen, Bin last_name: Chen - first_name: Shen full_name: Chou, Shen last_name: Chou - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Laurent full_name: Nguyen, Laurent last_name: Nguyen - first_name: Troy full_name: Ghashghaei, Troy last_name: Ghashghaei citation: ama: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 2016;36(45):11394-11401. doi:10.1523/JNEUROSCI.2359-16.2016' apa: 'Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., & Ghashghaei, T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2359-16.2016' chicago: 'Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen, and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience. Society for Neuroscience, 2016. https://doi.org/10.1523/JNEUROSCI.2359-16.2016.' ieee: 'N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei, “Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity,” Journal of Neuroscience, vol. 36, no. 45. Society for Neuroscience, pp. 11394–11401, 2016.' ista: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 36(45), 11394–11401.' mla: 'Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience, vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:10.1523/JNEUROSCI.2359-16.2016.' short: N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal of Neuroscience 36 (2016) 11394–11401. date_created: 2018-12-11T11:50:35Z date_published: 2016-11-09T00:00:00Z date_updated: 2021-01-12T06:48:54Z day: '09' department: - _id: SiHi doi: 10.1523/JNEUROSCI.2359-16.2016 intvolume: ' 36' issue: '45' language: - iso: eng month: '11' oa_version: None page: 11394 - 11401 project: - _id: 25D7962E-B435-11E9-9278-68D0E5697425 grant_number: RGP0053/2014 name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '6172' quality_controlled: '1' scopus_import: 1 status: public title: 'Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2016' ... --- _id: '1182' abstract: - lang: eng text: 'Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 citation: ama: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.' apa: 'Chatterjee, K., Ibsen-Jensen, R., & Tkadlec, J. (2016). Robust draws in balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA: AAAI Press.' chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016. ieee: 'K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced knockout tournaments,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.' ista: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout tournaments. IJCAI: International Joint Conference on Artificial Intelligence vol. 2016–January, 172–179.' mla: Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments. Vol. 2016–January, AAAI Press, 2016, pp. 172–79. short: K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179. conference: end_date: 2016-07-15 location: New York, NY, USA name: 'IJCAI: International Joint Conference on Artificial Intelligence' start_date: 2016-07-09 date_created: 2018-12-11T11:50:35Z date_published: 2016-01-01T00:00:00Z date_updated: 2023-02-21T10:04:26Z day: '01' department: - _id: KrCh ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.05090v1 month: '01' oa: 1 oa_version: Preprint page: 172 - 179 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: AAAI Press publist_id: '6171' quality_controlled: '1' related_material: link: - relation: table_of_contents url: https://www.ijcai.org/proceedings/2016 scopus_import: 1 status: public title: Robust draws in balanced knockout tournaments type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2016-January 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.' author: - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler - 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: 2021-01-12T06:48:55Z day: '01' ddc: - '576' - '592' department: - _id: SyCr doi: 10.1002/ece3.2474 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' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 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. 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: 2021-01-12T06:48:56Z day: '01' department: - _id: EvBe doi: 10.1242/dev.143545 intvolume: ' 143' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 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' 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: 2021-01-12T06:48:56Z day: '05' ddc: - '576' - '610' department: - _id: LeSa doi: 10.1038/srep38094 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' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 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' 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 & 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 & growth. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f' chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 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 & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.' ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & 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 & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 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: 2021-01-12T06:48:57Z day: '30' department: - _id: GaTk doi: 10.1088/1742-5468/aa4e8f ec_funded: 1 intvolume: ' 2016' 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: IOPscience 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016 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”." 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: 2021-01-12T06:49:00Z day: '03' ddc: - '576' department: - _id: NiBa doi: 10.1093/molbev/msw210 ec_funded: 1 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' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2016' ... --- _id: '1200' acknowledgement: C.H. acknowledges generous support from the ISTFELLOW program. 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: 2021-01-12T06:49:03Z day: '01' ddc: - '530' department: - _id: KrCh doi: 10.1016/j.plrev.2016.10.004 ec_funded: 1 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' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 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. 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: 2021-01-12T06:49:03Z day: '01' department: - _id: MiSi doi: 10.1016/j.cell.2016.11.024 intvolume: ' 167' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 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”. 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: 2021-01-12T06:49:03Z day: '01' ddc: - '570' department: - _id: SyCr doi: 10.1016/j.zool.2016.03.006 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' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2016' ...