--- _id: '1908' abstract: - lang: eng text: In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations. author: - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Oskar full_name: Hallatschek, Oskar last_name: Hallatschek citation: ama: Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705 apa: Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705 chicago: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705. ieee: D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014. ista: Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183. mla: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705. short: D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183. date_created: 2018-12-11T11:54:39Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:53:59Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.113.160705 ec_funded: 1 intvolume: ' 196' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.0737 month: '04' oa: 1 oa_version: Submitted Version page: 1167 - 1183 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5187' quality_controlled: '1' scopus_import: 1 status: public title: The rate of adaptation in large sexual populations with linear chromosomes type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 196 year: '2014' ... --- _id: '1911' abstract: - lang: eng text: The topological Tverberg theorem has been generalized in several directions by setting extra restrictions on the Tverberg partitions. Restricted Tverberg partitions, defined by the idea that certain points cannot be in the same part, are encoded with graphs. When two points are adjacent in the graph, they are not in the same part. If the restrictions are too harsh, then the topological Tverberg theorem fails. The colored Tverberg theorem corresponds to graphs constructed as disjoint unions of small complete graphs. Hell studied the case of paths and cycles. In graph theory these partitions are usually viewed as graph colorings. As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections between several notions of graph colorings and topological combinatorics. For ordinary graph colorings it is enough to require that the number of colors q satisfy q>Δ, where Δ is the maximal degree of the graph. It was proven by the first author using equivariant topology that if q>Δ 2 then the topological Tverberg theorem still works. It is conjectured that q>KΔ is also enough for some constant K, and in this paper we prove a fixed-parameter version of that conjecture. The required topological connectivity results are proven with shellability, which also strengthens some previous partial results where the topological connectivity was proven with the nerve lemma. acknowledgement: Patrik Norén gratefully acknowledges support from the Wallenberg foundation author: - first_name: Alexander full_name: Engström, Alexander last_name: Engström - first_name: Patrik full_name: Noren, Patrik id: 46870C74-F248-11E8-B48F-1D18A9856A87 last_name: Noren citation: ama: Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3 apa: Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3 chicago: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3. ieee: A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete & Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014. ista: Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 51(1), 207–220. mla: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014, pp. 207–20, doi:10.1007/s00454-013-9556-3. short: A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220. date_created: 2018-12-11T11:54:40Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:01Z day: '01' department: - _id: CaUh doi: 10.1007/s00454-013-9556-3 intvolume: ' 51' issue: '1' language: - iso: eng month: '01' oa_version: None page: 207 - 220 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5183' scopus_import: 1 status: public title: Tverberg's Theorem and Graph Coloring type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2014' ... --- _id: '1916' abstract: - lang: eng text: Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease. acknowledgement: Supported by the Deutsche Forschungsgemeinschaft (G.N.) article_processing_charge: No article_type: original author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Ali full_name: Fenstermaker, Ali last_name: Fenstermaker - first_name: Maha full_name: Zaki, Maha last_name: Zaki - first_name: Matan full_name: Hofree, Matan last_name: Hofree - first_name: Jennifer full_name: Silhavy, Jennifer last_name: Silhavy - first_name: Andrew full_name: Heiberg, Andrew last_name: Heiberg - first_name: Mostafa full_name: Abdellateef, Mostafa last_name: Abdellateef - first_name: Başak full_name: Rosti, Başak last_name: Rosti - first_name: Eric full_name: Scott, Eric last_name: Scott - first_name: Lobna full_name: Mansour, Lobna last_name: Mansour - first_name: Amira full_name: Masri, Amira last_name: Masri - first_name: Hülya full_name: Kayserili, Hülya last_name: Kayserili - first_name: Jumana full_name: Al Aama, Jumana last_name: Al Aama - first_name: Ghada full_name: Abdel Salam, Ghada last_name: Abdel Salam - first_name: Ariana full_name: Karminejad, Ariana last_name: Karminejad - first_name: Majdi full_name: Kara, Majdi last_name: Kara - first_name: Bülent full_name: Kara, Bülent last_name: Kara - first_name: Bita full_name: Bozorgmehri, Bita last_name: Bozorgmehri - first_name: Tawfeg full_name: Ben Omran, Tawfeg last_name: Ben Omran - first_name: Faezeh full_name: Mojahedi, Faezeh last_name: Mojahedi - first_name: Iman full_name: Mahmoud, Iman last_name: Mahmoud - first_name: Naïma full_name: Bouslam, Naïma last_name: Bouslam - first_name: Ahmed full_name: Bouhouche, Ahmed last_name: Bouhouche - first_name: Ali full_name: Benomar, Ali last_name: Benomar - first_name: Sylvain full_name: Hanein, Sylvain last_name: Hanein - first_name: Laure full_name: Raymond, Laure last_name: Raymond - first_name: Sylvie full_name: Forlani, Sylvie last_name: Forlani - first_name: Massimo full_name: Mascaro, Massimo last_name: Mascaro - first_name: Laila full_name: Selim, Laila last_name: Selim - first_name: Nabil full_name: Shehata, Nabil last_name: Shehata - first_name: Nasir full_name: Al Allawi, Nasir last_name: Al Allawi - first_name: Parayil full_name: Bindu, Parayil last_name: Bindu - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Murat full_name: Günel, Murat last_name: Günel - first_name: Ahmet full_name: Caglayan, Ahmet last_name: Caglayan - first_name: Kaya full_name: Bilgüvar, Kaya last_name: Bilgüvar - first_name: Aslihan full_name: Tolun, Aslihan last_name: Tolun - first_name: Mahmoud full_name: Issa, Mahmoud last_name: Issa - first_name: Jana full_name: Schroth, Jana last_name: Schroth - first_name: Emily full_name: Spencer, Emily last_name: Spencer - first_name: Rasim full_name: Rosti, Rasim last_name: Rosti - first_name: Naiara full_name: Akizu, Naiara last_name: Akizu - first_name: Keith full_name: Vaux, Keith last_name: Vaux - first_name: Anide full_name: Johansen, Anide last_name: Johansen - first_name: Alice full_name: Koh, Alice last_name: Koh - first_name: Hisham full_name: Megahed, Hisham last_name: Megahed - first_name: Alexandra full_name: Dürr, Alexandra last_name: Dürr - first_name: Alexis full_name: Brice, Alexis last_name: Brice - first_name: Giovanni full_name: Stévanin, Giovanni last_name: Stévanin - first_name: Stacy full_name: Gabriel, Stacy last_name: Gabriel - first_name: Trey full_name: Ideker, Trey last_name: Ideker - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson citation: ama: Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511. doi:10.1126/science.1247363 apa: Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg, A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1247363 chicago: Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy, Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363. ieee: G. Novarino et al., “Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders,” Science, vol. 343, no. 6170. American Association for the Advancement of Science, pp. 506–511, 2014. ista: Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A, Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J. 2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 343(6170), 506–511. mla: Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363. short: G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg, M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein, L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu, M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E. Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr, A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511. date_created: 2018-12-11T11:54:42Z date_published: 2014-01-31T00:00:00Z date_updated: 2021-01-12T06:54:03Z day: '31' department: - _id: GaNo doi: 10.1126/science.1247363 external_id: pmid: - '24482476' intvolume: ' 343' issue: '6170' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/ month: '01' oa: 1 oa_version: Submitted Version page: 506 - 511 pmid: 1 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5178' quality_controlled: '1' scopus_import: 1 status: public title: Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 343 year: '2014' ... --- _id: '1917' abstract: - lang: eng text: Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was shown to be essential for plant development and morphogenesis, but its mode of action remains unclear. Here, we report that the plasma membrane-localized transmembrane kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases (GTPase) from plants], leading to changes in the cytoskeleton and the shape of leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings show that TMK proteins and ABP1 form a cell surface auxin perception complex that activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses and associated fundamental processes. acknowledgement: Supported by the intramural research program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and by its Laboratory Animal Care and Use Section and Flow Cytometry Group, Office of Science and Technology article_processing_charge: No article_type: original author: - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Ning full_name: Dai, Ning last_name: Dai - first_name: Jisheng full_name: Chen, Jisheng last_name: Chen - first_name: Shingo full_name: Nagawa, Shingo last_name: Nagawa - first_name: Min full_name: Cao, Min last_name: Cao - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Zimin full_name: Zhou, Zimin last_name: Zhou - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Wen full_name: Wang, Wen last_name: Wang - first_name: Alan full_name: Jones, Alan last_name: Jones - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Sara full_name: Patterson, Sara last_name: Patterson - first_name: Anthony full_name: Bleecker, Anthony last_name: Bleecker - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang citation: ama: Xu T, Dai N, Chen J, et al. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 2014;343(6174):1025-1028. doi:10.1126/science.1245125 apa: Xu, T., Dai, N., Chen, J., Nagawa, S., Cao, M., Li, H., … Yang, Z. (2014). Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1245125 chicago: Xu, Tongda, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1245125. ieee: T. Xu et al., “Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling,” Science, vol. 343, no. 6174. American Association for the Advancement of Science, pp. 1025–1028, 2014. ista: Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones A, Friml J, Patterson S, Bleecker A, Yang Z. 2014. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 343(6174), 1025–1028. mla: Xu, Tongda, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science, vol. 343, no. 6174, American Association for the Advancement of Science, 2014, pp. 1025–28, doi:10.1126/science.1245125. short: T. Xu, N. Dai, J. Chen, S. Nagawa, M. Cao, H. Li, Z. Zhou, X. Chen, R. De Rycke, H. Rakusová, W. Wang, A. Jones, J. Friml, S. Patterson, A. Bleecker, Z. Yang, Science 343 (2014) 1025–1028. date_created: 2018-12-11T11:54:42Z date_published: 2014-02-28T00:00:00Z date_updated: 2021-01-12T06:54:03Z day: '28' department: - _id: JiFr doi: 10.1126/science.1245125 external_id: pmid: - '24578577' intvolume: ' 343' issue: '6174' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166562/ month: '02' oa: 1 oa_version: Submitted Version page: 1025 - 1028 pmid: 1 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5177' quality_controlled: '1' scopus_import: 1 status: public title: Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 343 year: '2014' ... --- _id: '1920' abstract: - lang: eng text: Cerebellar motor learning is suggested to be caused by long-term plasticity of excitatory parallel fiber-Purkinje cell (PF-PC) synapses associated with changes in the number of synaptic AMPA-type glutamate receptors (AMPARs). However, whether the AMPARs decrease or increase in individual PF-PC synapses occurs in physiological motor learning and accounts for memory that lasts over days remains elusive. We combined quantitative SDS-digested freeze-fracture replica labeling for AMPAR and physical dissector electron microscopy with a simple model of cerebellar motor learning, adaptation of horizontal optokinetic response (HOKR) in mouse. After 1-h training of HOKR, short-term adaptation (STA) was accompanied with transient decrease in AMPARs by 28% in target PF-PC synapses. STA was well correlated with AMPAR decrease in individual animals and both STA and AMPAR decrease recovered to basal levels within 24 h. Surprisingly, long-termadaptation (LTA) after five consecutive daily trainings of 1-h HOKR did not alter the number of AMPARs in PF-PC synapses but caused gradual and persistent synapse elimination by 45%, with corresponding PC spine loss by the fifth training day. Furthermore, recovery of LTA after 2 wk was well correlated with increase of PF-PC synapses to the control level. Our findings indicate that the AMPARs decrease in PF-PC synapses and the elimination of these synapses are in vivo engrams in short- and long-term motor learning, respectively, showing a unique type of synaptic plasticity that may contribute to memory consolidation. acknowledgement: This work was supported by Solution-Oriented Research for Science and Technology from the Japan Science and Technology Agency; Ministry of Education, Culture, Sports, Science and Technology of Japan Grant 16300114 (to R.S.). author: - first_name: Wen full_name: Wang, Wen last_name: Wang - first_name: Kazuhiko full_name: Nakadate, Kazuhiko last_name: Nakadate - first_name: Miwako full_name: Masugi Tokita, Miwako last_name: Masugi Tokita - first_name: Fumihiro full_name: Shutoh, Fumihiro last_name: Shutoh - first_name: Wajeeha full_name: Aziz, Wajeeha last_name: Aziz - first_name: Etsuko full_name: Tarusawa, Etsuko last_name: Tarusawa - first_name: Andrea full_name: Lörincz, Andrea last_name: Lörincz - first_name: Elek full_name: Molnár, Elek last_name: Molnár - first_name: Sebnem full_name: Kesaf, Sebnem id: 401AB46C-F248-11E8-B48F-1D18A9856A87 last_name: Kesaf - first_name: Yunqing full_name: Li, Yunqing last_name: Li - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Soichi full_name: Nagao, Soichi last_name: Nagao - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Wang W, Nakadate K, Masugi Tokita M, et al. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 2014;111(1):E188-E193. doi:10.1073/pnas.1315541111 apa: Wang, W., Nakadate, K., Masugi Tokita, M., Shutoh, F., Aziz, W., Tarusawa, E., … Shigemoto, R. (2014). Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315541111 chicago: Wang, Wen, Kazuhiko Nakadate, Miwako Masugi Tokita, Fumihiro Shutoh, Wajeeha Aziz, Etsuko Tarusawa, Andrea Lörincz, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1315541111. ieee: W. Wang et al., “Distinct cerebellar engrams in short-term and long-term motor learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E188–E193, 2014. ista: Wang W, Nakadate K, Masugi Tokita M, Shutoh F, Aziz W, Tarusawa E, Lörincz A, Molnár E, Kesaf S, Li Y, Fukazawa Y, Nagao S, Shigemoto R. 2014. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 111(1), E188–E193. mla: Wang, Wen, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E188–93, doi:10.1073/pnas.1315541111. short: W. Wang, K. Nakadate, M. Masugi Tokita, F. Shutoh, W. Aziz, E. Tarusawa, A. Lörincz, E. Molnár, S. Kesaf, Y. Li, Y. Fukazawa, S. Nagao, R. Shigemoto, PNAS 111 (2014) E188–E193. date_created: 2018-12-11T11:54:43Z date_published: 2014-01-07T00:00:00Z date_updated: 2021-01-12T06:54:05Z day: '07' department: - _id: RySh doi: 10.1073/pnas.1315541111 intvolume: ' 111' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890858/ month: '01' oa: 1 oa_version: Submitted Version page: E188 - E193 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5174' scopus_import: 1 status: public title: Distinct cerebellar engrams in short-term and long-term motor learning type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1915' abstract: - lang: eng text: ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity. acknowledgement: This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czec article_processing_charge: No article_type: original author: - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269 apa: Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130269 chicago: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions. Portland Press, 2014. https://doi.org/10.1042/BST20130269. ieee: X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press, pp. 212–218, 2014. ista: Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 42(1), 212–218. mla: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland Press, 2014, pp. 212–18, doi:10.1042/BST20130269. short: X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218. date_created: 2018-12-11T11:54:41Z date_published: 2014-02-01T00:00:00Z date_updated: 2022-06-07T11:20:56Z day: '01' department: - _id: JiFr doi: 10.1042/BST20130269 ec_funded: 1 external_id: pmid: - '24450654' intvolume: ' 42' issue: '1' language: - iso: eng month: '02' oa_version: None page: 212 - 218 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Biochemical Society Transactions publication_identifier: eissn: - 1470-8752 issn: - 0300-5127 publication_status: published publisher: Portland Press publist_id: '5179' quality_controlled: '1' scopus_import: '1' status: public title: Rho-GTPase-regulated vesicle trafficking in plant cell polarity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2014' ... --- _id: '1919' abstract: - lang: eng text: Long-lasting memories are formed when the stimulus is temporally distributed (spacing effect). However, the synaptic mechanisms underlying this robust phenomenon and the precise time course of the synaptic modifications that occur during learning remain unclear. Here we examined the adaptation of horizontal optokinetic response in mice that underwent 1 h of massed and spaced training at varying intervals. Despite similar acquisition by all training protocols, 1 h of spacing produced the highest memory retention at 24 h, which lasted for 1 mo. The distinct kinetics of memory are strongly correlated with the reduction of floccular parallel fiber-Purkinje cell synapses but not with AMPA receptor (AMPAR) number and synapse size. After the spaced training, we observed 25%, 23%, and 12% reduction in AMPAR density, synapse size, and synapse number, respectively. Four hours after the spaced training, half of the synapses and Purkinje cell spines had been eliminated, whereas AMPAR density and synapse size were recovered in remaining synapses. Surprisingly, massed training also produced long-term memory and halving of synapses; however, this occurred slowly over days, and the memory lasted for only 1 wk. This distinct kinetics of structural plasticity may serve as a basis for unique temporal profiles in the formation and decay of memory with or without intervals. acknowledgement: his work was supported by Solution Oriented Research for Science and Technology (R.S.), Core Research for Evolutional Science and Technology, Japan Science and Technology Agency (Y.F.), and Grants-in-Aid for Scientific Research on Priority Areas-Molecular Brain Sciences 16300114 (to R.S.) and 18022043 (to Y.F.). author: - first_name: Wajeeha full_name: Aziz, Wajeeha last_name: Aziz - first_name: Wen full_name: Wang, Wen last_name: Wang - first_name: Sebnem full_name: Kesaf, Sebnem id: 401AB46C-F248-11E8-B48F-1D18A9856A87 last_name: Kesaf - first_name: Alsayed full_name: Mohamed, Alsayed last_name: Mohamed - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 2014;111(1):E194-E202. doi:10.1073/pnas.1303317110 apa: Aziz, W., Wang, W., Kesaf, S., Mohamed, A., Fukazawa, Y., & Shigemoto, R. (2014). Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1303317110 chicago: Aziz, Wajeeha, Wen Wang, Sebnem Kesaf, Alsayed Mohamed, Yugo Fukazawa, and Ryuichi Shigemoto. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1303317110. ieee: W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, and R. Shigemoto, “Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E194–E202, 2014. ista: Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. 2014. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 111(1), E194–E202. mla: Aziz, Wajeeha, et al. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E194–202, doi:10.1073/pnas.1303317110. short: W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, R. Shigemoto, PNAS 111 (2014) E194–E202. date_created: 2018-12-11T11:54:43Z date_published: 2014-01-07T00:00:00Z date_updated: 2021-01-12T06:54:04Z day: '07' department: - _id: RySh doi: 10.1073/pnas.1303317110 intvolume: ' 111' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890840/ month: '01' oa: 1 oa_version: Submitted Version page: E194 - E202 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5175' scopus_import: 1 status: public title: Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1918' abstract: - lang: eng text: As the nuclear charge Z is continuously decreased an N-electron atom undergoes a binding-unbinding transition. We investigate whether the electrons remain bound and whether the radius of the system stays finite as the critical value Zc is approached. Existence of a ground state at Zc is shown under the condition Zc < N-K, where K is the maximal number of electrons that can be removed at Zc without changing the energy. article_number: '1350021' author: - first_name: Jacopo full_name: Bellazzini, Jacopo last_name: Bellazzini - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Bellazzini J, Frank R, Lieb É, Seiringer R. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 2014;26(1). doi:10.1142/S0129055X13500219 apa: Bellazzini, J., Frank, R., Lieb, É., & Seiringer, R. (2014). Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X13500219 chicago: Bellazzini, Jacopo, Rupert Frank, Élliott Lieb, and Robert Seiringer. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X13500219. ieee: J. Bellazzini, R. Frank, É. Lieb, and R. Seiringer, “Existence of ground states for negative ions at the binding threshold,” Reviews in Mathematical Physics, vol. 26, no. 1. World Scientific Publishing, 2014. ista: Bellazzini J, Frank R, Lieb É, Seiringer R. 2014. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 26(1), 1350021. mla: Bellazzini, Jacopo, et al. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics, vol. 26, no. 1, 1350021, World Scientific Publishing, 2014, doi:10.1142/S0129055X13500219. short: J. Bellazzini, R. Frank, É. Lieb, R. Seiringer, Reviews in Mathematical Physics 26 (2014). date_created: 2018-12-11T11:54:42Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:54:04Z day: '01' department: - _id: RoSe doi: 10.1142/S0129055X13500219 intvolume: ' 26' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1301.5370 month: '02' oa: 1 oa_version: Submitted Version project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '5176' quality_controlled: '1' scopus_import: 1 status: public title: Existence of ground states for negative ions at the binding threshold type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1914' abstract: - lang: eng text: Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants. author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019' apa: 'Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019' chicago: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019.' ieee: 'M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.' ista: 'Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 24(1), R27–R29.' mla: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014, pp. R27–29, doi:10.1016/j.cub.2013.11.019.' short: M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29. date_created: 2018-12-11T11:54:41Z date_published: 2014-01-06T00:00:00Z date_updated: 2021-01-12T06:54:02Z day: '06' department: - _id: JiFr doi: 10.1016/j.cub.2013.11.019 intvolume: ' 24' issue: '1' language: - iso: eng month: '01' oa_version: None page: R27 - R29 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5180' quality_controlled: '1' scopus_import: 1 status: public title: 'Plant biology: Gatekeepers of the road to protein perdition' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1925' abstract: - lang: eng text: In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity. acknowledgement: "This work was supported by EC grant Marie Curie RTN-CT-2006-035616, CARBIO 'Carbon nanotubes for biomedical applications' and Austrian FFG grant mnt-era.net 823980, 'IntelliTip'.\r\n" article_number: '125704' article_processing_charge: No article_type: original author: - first_name: Constanze full_name: Lamprecht, Constanze last_name: Lamprecht - first_name: Birgit full_name: Plochberger, Birgit last_name: Plochberger - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Christian full_name: Rankl, Christian last_name: Rankl - first_name: Elena full_name: Heister, Elena last_name: Heister - first_name: Barbara full_name: Unterauer, Barbara last_name: Unterauer - first_name: Mario full_name: Brameshuber, Mario last_name: Brameshuber - first_name: Jürgen full_name: Danzberger, Jürgen last_name: Danzberger - first_name: Petar full_name: Lukanov, Petar last_name: Lukanov - first_name: Emmanuel full_name: Flahaut, Emmanuel last_name: Flahaut - first_name: Gerhard full_name: Schütz, Gerhard last_name: Schütz - first_name: Peter full_name: Hinterdorfer, Peter last_name: Hinterdorfer - first_name: Andreas full_name: Ebner, Andreas last_name: Ebner citation: ama: Lamprecht C, Plochberger B, Ruprecht V, et al. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 2014;25(12). doi:10.1088/0957-4484/25/12/125704 apa: Lamprecht, C., Plochberger, B., Ruprecht, V., Wieser, S., Rankl, C., Heister, E., … Ebner, A. (2014). A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. IOP Publishing. https://doi.org/10.1088/0957-4484/25/12/125704 chicago: Lamprecht, Constanze, Birgit Plochberger, Verena Ruprecht, Stefan Wieser, Christian Rankl, Elena Heister, Barbara Unterauer, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology. IOP Publishing, 2014. https://doi.org/10.1088/0957-4484/25/12/125704. ieee: C. Lamprecht et al., “A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes,” Nanotechnology, vol. 25, no. 12. IOP Publishing, 2014. ista: Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. 2014. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 25(12), 125704. mla: Lamprecht, Constanze, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology, vol. 25, no. 12, 125704, IOP Publishing, 2014, doi:10.1088/0957-4484/25/12/125704. short: C. Lamprecht, B. Plochberger, V. Ruprecht, S. Wieser, C. Rankl, E. Heister, B. Unterauer, M. Brameshuber, J. Danzberger, P. Lukanov, E. Flahaut, G. Schütz, P. Hinterdorfer, A. Ebner, Nanotechnology 25 (2014). date_created: 2018-12-11T11:54:45Z date_published: 2014-03-28T00:00:00Z date_updated: 2021-01-12T06:54:07Z day: '28' ddc: - '570' department: - _id: CaHe - _id: MiSi doi: 10.1088/0957-4484/25/12/125704 file: - access_level: open_access checksum: df4e03d225a19179e7790f6d87a12332 content_type: application/pdf creator: dernst date_created: 2020-05-15T09:21:19Z date_updated: 2020-07-14T12:45:21Z file_id: '7856' file_name: 2014_Nanotechnology_Lamprecht.pdf file_size: 3804152 relation: main_file file_date_updated: 2020-07-14T12:45:21Z has_accepted_license: '1' intvolume: ' 25' issue: '12' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version publication: Nanotechnology publication_status: published publisher: IOP Publishing publist_id: '5169' scopus_import: 1 status: public title: A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2014' ... --- _id: '1923' abstract: - lang: eng text: We derive the equations for a thin, axisymmetric elastic shell subjected to an internal active stress giving rise to active tension and moments within the shell. We discuss the stability of a cylindrical elastic shell and its response to a localized change in internal active stress. This description is relevant to describe the cellular actomyosin cortex, a thin shell at the cell surface behaving elastically at a short timescale and subjected to active internal forces arising from myosin molecular motor activity. We show that the recent observations of cell deformation following detachment of adherent cells (Maître J-L et al 2012 Science 338 253-6) are well accounted for by this mechanical description. The actin cortex elastic and bending moduli can be obtained from a quantitative analysis of cell shapes observed in these experiments. Our approach thus provides a non-invasive, imaging-based method for the extraction of cellular physical parameters. article_number: '065005' author: - first_name: Hélène full_name: Berthoumieux, Hélène last_name: Berthoumieux - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Ewa full_name: Paluch, Ewa last_name: Paluch - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Guillaume full_name: Salbreux, Guillaume last_name: Salbreux citation: ama: Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 2014;16. doi:10.1088/1367-2630/16/6/065005 apa: Berthoumieux, H., Maître, J.-L., Heisenberg, C.-P. J., Paluch, E., Julicher, F., & Salbreux, G. (2014). Active elastic thin shell theory for cellular deformations. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/16/6/065005 chicago: Berthoumieux, Hélène, Jean-Léon Maître, Carl-Philipp J Heisenberg, Ewa Paluch, Frank Julicher, and Guillaume Salbreux. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics. IOP Publishing Ltd., 2014. https://doi.org/10.1088/1367-2630/16/6/065005. ieee: H. Berthoumieux, J.-L. Maître, C.-P. J. Heisenberg, E. Paluch, F. Julicher, and G. Salbreux, “Active elastic thin shell theory for cellular deformations,” New Journal of Physics, vol. 16. IOP Publishing Ltd., 2014. ista: Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. 2014. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 16, 065005. mla: Berthoumieux, Hélène, et al. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics, vol. 16, 065005, IOP Publishing Ltd., 2014, doi:10.1088/1367-2630/16/6/065005. short: H. Berthoumieux, J.-L. Maître, C.-P.J. Heisenberg, E. Paluch, F. Julicher, G. Salbreux, New Journal of Physics 16 (2014). date_created: 2018-12-11T11:54:44Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:54:06Z day: '01' ddc: - '570' department: - _id: CaHe doi: 10.1088/1367-2630/16/6/065005 file: - access_level: open_access checksum: 8dbe81ec656bf1264d8889bda9b2b985 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:16Z date_updated: 2020-07-14T12:45:21Z file_id: '5202' file_name: IST-2016-429-v1+1_document.pdf file_size: 941387 relation: main_file file_date_updated: 2020-07-14T12:45:21Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '5171' pubrep_id: '429' quality_controlled: '1' scopus_import: 1 status: public title: Active elastic thin shell theory for cellular deformations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1921' abstract: - lang: eng text: Cell polarity manifested by asymmetric distribution of cargoes, such as receptors and transporters, within the plasma membrane (PM) is crucial for essential functions in multicellular organisms. In plants, cell polarity (re)establishment is intimately linked to patterning processes. Despite the importance of cell polarity, its underlying mechanisms are still largely unknown, including the definition and distinctiveness of the polar domains within the PM. Here, we show in Arabidopsis thaliana that the signaling membrane components, the phosphoinositides phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4, 5-bisphosphate [PtdIns(4, 5)P2] as well as PtdIns4P 5-kinases mediating their interconversion, are specifically enriched at apical and basal polar plasma membrane domains. The PtdIns4P 5-kinases PIP5K1 and PIP5K2 are redundantly required for polar localization of specifically apical and basal cargoes, such as PIN-FORMED transporters for the plant hormone auxin. As a consequence of the polarity defects, instructive auxin gradients as well as embryonic and postembryonic patterning are severely compromised. Furthermore, auxin itself regulates PIP5K transcription and PtdIns4P and PtdIns(4, 5)P2 levels, in particular their association with polar PM domains. Our results provide insight into the polar domain-delineating mechanisms in plant cells that depend on apical and basal distribution of membrane lipids and are essential for embryonic and postembryonic patterning. acknowledgement: This work was supported by grants from the Odysseus program of the Research Foundation-Flanders (to J.F.). author: - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: 'MiriamPalacios ' full_name: 'Palacios-Gomez, MiriamPalacios ' last_name: Palacios-Gomez - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Mareike full_name: Heilmann, Mareike last_name: Heilmann - first_name: Ringo full_name: Van Wijk, Ringo last_name: Van Wijk - first_name: Joop full_name: Vermeer, Joop last_name: Vermeer - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Teun full_name: Munnik, Teun last_name: Munnik - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tejos R, Sauer M, Vanneste S, et al. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 2014;26(5):2114-2128. doi:10.1105/tpc.114.126185 apa: Tejos, R., Sauer, M., Vanneste, S., Palacios-Gomez, M., Li, H., Heilmann, M., … Friml, J. (2014). Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.126185 chicago: Tejos, Ricardo, Michael Sauer, Steffen Vanneste, MiriamPalacios Palacios-Gomez, Hongjiang Li, Mareike Heilmann, Ringo Van Wijk, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.126185. ieee: R. Tejos et al., “Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis,” Plant Cell, vol. 26, no. 5. American Society of Plant Biologists, pp. 2114–2128, 2014. ista: Tejos R, Sauer M, Vanneste S, Palacios-Gomez M, Li H, Heilmann M, Van Wijk R, Vermeer J, Heilmann I, Munnik T, Friml J. 2014. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 26(5), 2114–2128. mla: Tejos, Ricardo, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell, vol. 26, no. 5, American Society of Plant Biologists, 2014, pp. 2114–28, doi:10.1105/tpc.114.126185. short: R. Tejos, M. Sauer, S. Vanneste, M. Palacios-Gomez, H. Li, M. Heilmann, R. Van Wijk, J. Vermeer, I. Heilmann, T. Munnik, J. Friml, Plant Cell 26 (2014) 2114–2128. date_created: 2018-12-11T11:54:43Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T06:54:05Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.114.126185 ec_funded: 1 intvolume: ' 26' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079372/ month: '05' oa: 1 oa_version: Submitted Version page: 2114 - 2128 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '5173' scopus_import: 1 status: public title: Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1922' abstract: - lang: eng text: Germination of Arabidopsis seeds in darkness induces apical hook development, based on a tightly regulated differential growth coordinated by a multiple hormone cross-talk. Here, we endeavoured to clarify the function of brassinosteroids (BRs) and cross-talk with ethylene in hook development. An automated infrared imaging system was developed to study the kinetics of hook development in etiolated Arabidopsis seedlings. To ascertain the photomorphogenic control of hook opening, the system was equipped with an automatic light dimmer. We demonstrate that ethylene and BRs are indispensable for hook formation and maintenance. Ethylene regulation of hook formation functions partly through BRs, with BR feedback inhibition of ethylene action. Conversely, BR-mediated extension of hook maintenance functions partly through ethylene. Furthermore, we revealed that a short light pulse is sufficient to induce rapid hook opening. Our dynamic infrared imaging system allows high-resolution, kinetic imaging of up to 112 seedlings in a single experimental run. At this high throughput, it is ideally suited to rapidly gain insight in pathway networks. We demonstrate that BRs and ethylene cooperatively regulate apical hook development in a phase-dependent manner. Furthermore, we show that light is a predominant regulator of hook opening, inhibiting ethylene- and BR-mediated postponement of hook opening. acknowledgement: 'Funded by Ghent University; Research Foundation Flanders Grant Number: G065613N European Research Council Grant Number: CZ.1.07/2.3.00/20.0043' author: - first_name: Dajo full_name: Smet, Dajo last_name: Smet - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Filip full_name: Vandenbussche, Filip last_name: Vandenbussche - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten citation: ama: 'Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 2014;202(4):1398-1411. doi:10.1111/nph.12751' apa: 'Smet, D., Žádníková, P., Vandenbussche, F., Benková, E., & Van Der Straeten, D. (2014). Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.12751' chicago: 'Smet, Dajo, Petra Žádníková, Filip Vandenbussche, Eva Benková, and Dominique Van Der Straeten. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist. Wiley-Blackwell, 2014. https://doi.org/10.1111/nph.12751.' ieee: 'D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, and D. Van Der Straeten, “Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids,” New Phytologist, vol. 202, no. 4. Wiley-Blackwell, pp. 1398–1411, 2014.' ista: 'Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. 2014. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 202(4), 1398–1411.' mla: 'Smet, Dajo, et al. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist, vol. 202, no. 4, Wiley-Blackwell, 2014, pp. 1398–411, doi:10.1111/nph.12751.' short: D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, D. Van Der Straeten, New Phytologist 202 (2014) 1398–1411. date_created: 2018-12-11T11:54:44Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:54:05Z day: '01' department: - _id: EvBe doi: 10.1111/nph.12751 ec_funded: 1 intvolume: ' 202' issue: '4' language: - iso: eng month: '06' oa_version: None page: 1398 - 1411 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: New Phytologist publication_status: published publisher: Wiley-Blackwell publist_id: '5172' scopus_import: 1 status: public title: 'Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2014' ... --- _id: '1927' abstract: - lang: eng text: Constrained pseudorandom functions have recently been introduced independently by Boneh and Waters (Asiacrypt’13), Kiayias et al. (CCS’13), and Boyle et al. (PKC’14). In a standard pseudorandom function (PRF) a key k is used to evaluate the PRF on all inputs in the domain. Constrained PRFs additionally offer the functionality to delegate “constrained” keys kS which allow to evaluate the PRF only on a subset S of the domain. The three above-mentioned papers all show that the classical GGM construction (J.ACM’86) of a PRF from a pseudorandom generator (PRG) directly yields a constrained PRF where one can compute constrained keys to evaluate the PRF on all inputs with a given prefix. This constrained PRF has already found many interesting applications. Unfortunately, the existing security proofs only show selective security (by a reduction to the security of the underlying PRG). To achieve full security, one has to use complexity leveraging, which loses an exponential factor 2N in security, where N is the input length. The first contribution of this paper is a new reduction that only loses a quasipolynomial factor qlog N, where q is the number of adversarial queries. For this we develop a new proof technique which constructs a distinguisher by interleaving simple guessing steps and hybrid arguments a small number of times. This approach might be of interest also in other contexts where currently the only technique to achieve full security is complexity leveraging. Our second contribution is concerned with another constrained PRF, due to Boneh and Waters, which allows for constrained keys for the more general class of bit-fixing functions. Their security proof also suffers from a 2N loss, which we show is inherent. We construct a meta-reduction which shows that any “simple” reduction of full security from a noninteractive hardness assumption must incur an exponential security loss. acknowledgement: We are grateful to Mihir Bellare for his feedback on earlier versions of this paper. We are indebted to Vanishree Rao for her generous assistance in preparing this proceedings version. author: - first_name: Georg full_name: Georg Fuchsbauer id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Momchil full_name: Konstantinov, Momchil last_name: Konstantinov - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Vanishree full_name: Rao, Vanishree last_name: Rao citation: ama: 'Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. Adaptive security of constrained PRFs. In: Vol 8874. Springer; 2014:173-192. doi:10.1145/2591796.2591825' apa: Fuchsbauer, G., Konstantinov, M., Pietrzak, K. Z., & Rao, V. (2014). Adaptive security of constrained PRFs (Vol. 8874, pp. 173–192). Presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer. https://doi.org/10.1145/2591796.2591825 chicago: Fuchsbauer, Georg, Momchil Konstantinov, Krzysztof Z Pietrzak, and Vanishree Rao. “Adaptive Security of Constrained PRFs,” 8874:173–92. Springer, 2014. https://doi.org/10.1145/2591796.2591825. ieee: G. Fuchsbauer, M. Konstantinov, K. Z. Pietrzak, and V. Rao, “Adaptive security of constrained PRFs,” presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014, vol. 8874, pp. 173–192. ista: Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. 2014. Adaptive security of constrained PRFs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) vol. 8874, 173–192. mla: Fuchsbauer, Georg, et al. Adaptive Security of Constrained PRFs. Vol. 8874, Springer, 2014, pp. 173–92, doi:10.1145/2591796.2591825. short: G. Fuchsbauer, M. Konstantinov, K.Z. Pietrzak, V. Rao, in:, Springer, 2014, pp. 173–192. conference: name: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) date_created: 2018-12-11T11:54:45Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:08Z day: '01' doi: 10.1145/2591796.2591825 extern: 1 intvolume: ' 8874' main_file_link: - open_access: '1' url: http://eprint.iacr.org/2014/416 month: '01' oa: 1 page: 173 - 192 publication_status: published publisher: Springer publist_id: '5167' quality_controlled: 0 status: public title: Adaptive security of constrained PRFs type: conference volume: 8874 year: '2014' ... --- _id: '1926' abstract: - lang: eng text: We consider cross products of finite graphs with a class of trees that have arbitrarily but finitely long line segments, such as the Fibonacci tree. Such cross products are called tree-strips. We prove that for small disorder random Schrödinger operators on such tree-strips have purely absolutely continuous spectrum in a certain set. article_processing_charge: No article_type: original author: - first_name: Christian full_name: Sadel, Christian id: 4760E9F8-F248-11E8-B48F-1D18A9856A87 last_name: Sadel orcid: 0000-0001-8255-3968 citation: ama: Sadel C. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):409-440. doi:10.1007/s11040-014-9163-4 apa: Sadel, C. (2014). Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9163-4 chicago: Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9163-4. ieee: C. Sadel, “Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 409–440, 2014. ista: Sadel C. 2014. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 17(3–4), 409–440. mla: Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 409–40, doi:10.1007/s11040-014-9163-4. short: C. Sadel, Mathematical Physics, Analysis and Geometry 17 (2014) 409–440. date_created: 2018-12-11T11:54:45Z date_published: 2014-12-17T00:00:00Z date_updated: 2021-01-12T06:54:07Z day: '17' department: - _id: LaEr doi: 10.1007/s11040-014-9163-4 ec_funded: 1 external_id: arxiv: - '1304.3862' intvolume: ' 17' issue: 3-4 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1304.3862 month: '12' oa: 1 oa_version: Preprint page: 409 - 440 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Mathematical Physics, Analysis and Geometry publication_status: published publisher: Springer publist_id: '5168' quality_controlled: '1' scopus_import: 1 status: public title: Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2014' ... --- _id: '1924' abstract: - lang: eng text: Stomata are two-celled valves that control epidermal pores whose spacing optimizes shoot-atmosphere gas exchange. They develop from protodermal cells after unequal divisions followed by an equal division and differentiation. The concentration of the hormone auxin, a master plant developmental regulator, is tightly controlled in time and space, but its role, if any, in stomatal formation is obscure. Here dynamic changes of auxin activity during stomatal development are monitored using auxin input (DII-VENUS) and output (DR5:VENUS) markers by time-lapse imaging. A decrease in auxin levels in the smaller daughter cell after unequal division presages the acquisition of a guard mother cell fate whose equal division produces the two guard cells. Thus, stomatal patterning requires auxin pathway control of stem cell compartment size, as well as auxin depletion that triggers a developmental switch from unequal to equal division. article_number: '3090' author: - first_name: Jie full_name: Le, Jie last_name: Le - first_name: Xuguang full_name: Liu, Xuguang last_name: Liu - first_name: Kezhen full_name: Yang, Kezhen last_name: Yang - first_name: Xiaolan full_name: Chen, Xiaolan last_name: Chen - first_name: Lingling full_name: Zhu, Lingling last_name: Zhu - first_name: Hongzhe full_name: Wang, Hongzhe last_name: Wang - first_name: Ming full_name: Wang, Ming last_name: Wang - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Miyo full_name: Morita, Miyo last_name: Morita - first_name: Masao full_name: Tasaka, Masao last_name: Tasaka - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Fred full_name: Sack, Fred last_name: Sack citation: ama: Le J, Liu X, Yang K, et al. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 2014;5. doi:10.1038/ncomms4090 apa: Le, J., Liu, X., Yang, K., Chen, X., Zhu, L., Wang, H., … Sack, F. (2014). Auxin transport and activity regulate stomatal patterning and development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4090 chicago: Le, Jie, Xuguang Liu, Kezhen Yang, Xiaolan Chen, Lingling Zhu, Hongzhe Wang, Ming Wang, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4090. ieee: J. Le et al., “Auxin transport and activity regulate stomatal patterning and development,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Le J, Liu X, Yang K, Chen X, Zhu L, Wang H, Wang M, Vanneste S, Morita M, Tasaka M, Ding Z, Friml J, Beeckman T, Sack F. 2014. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 5, 3090. mla: Le, Jie, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications, vol. 5, 3090, Nature Publishing Group, 2014, doi:10.1038/ncomms4090. short: J. Le, X. Liu, K. Yang, X. Chen, L. Zhu, H. Wang, M. Wang, S. Vanneste, M. Morita, M. Tasaka, Z. Ding, J. Friml, T. Beeckman, F. Sack, Nature Communications 5 (2014). date_created: 2018-12-11T11:54:44Z date_published: 2014-01-27T00:00:00Z date_updated: 2021-01-12T06:54:06Z day: '27' department: - _id: JiFr doi: 10.1038/ncomms4090 intvolume: ' 5' language: - iso: eng month: '01' oa_version: None publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5170' quality_controlled: '1' scopus_import: 1 status: public title: Auxin transport and activity regulate stomatal patterning and development type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2014' ... --- _id: '1928' abstract: - lang: eng text: In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen. acknowledgement: J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague. author: - first_name: Jan full_name: Humplik, Jan id: 2E9627A8-F248-11E8-B48F-1D18A9856A87 last_name: Humplik - first_name: Alison full_name: Hill, Alison last_name: Hill - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039 apa: Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039 chicago: Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology. Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039. ieee: J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014. ista: Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162. mla: Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039. short: J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162. date_created: 2018-12-11T11:54:46Z date_published: 2014-11-07T00:00:00Z date_updated: 2021-01-12T06:54:08Z day: '07' department: - _id: GaTk doi: 10.1016/j.jtbi.2014.06.039 intvolume: ' 360' language: - iso: eng month: '11' oa_version: None page: 149 - 162 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '5166' scopus_import: 1 status: public title: Evolutionary dynamics of infectious diseases in finite populations type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 360 year: '2014' ... --- _id: '1929' abstract: - lang: eng text: We propose an algorithm for the generalization of cartographic objects that can be used to represent maps on different scales. acknowledgement: We would like to offer our special thanks to students of the Department of Mathematics of Demidov Yaroslavl State University A. A. Gorokhov and V. N. Knyazev for participation in developing the program and assistance in preparation of test data. This work was supported by grant 11.G34.31.0053 from the government of the Russian Federation. article_processing_charge: No article_type: original author: - first_name: V V full_name: Alexeev, V V last_name: Alexeev - first_name: V G full_name: Bogaevskaya, V G last_name: Bogaevskaya - first_name: M M full_name: Preobrazhenskaya, M M last_name: Preobrazhenskaya - first_name: A Y full_name: Ukhalov, A Y last_name: Ukhalov - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Olga full_name: Yakimova, Olga last_name: Yakimova citation: ama: Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 2014;203(6):754-760. doi:10.1007/s10958-014-2165-8 apa: Alexeev, V. V., Bogaevskaya, V. G., Preobrazhenskaya, M. M., Ukhalov, A. Y., Edelsbrunner, H., & Yakimova, O. (2014). An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. Springer. https://doi.org/10.1007/s10958-014-2165-8 chicago: Alexeev, V V, V G Bogaevskaya, M M Preobrazhenskaya, A Y Ukhalov, Herbert Edelsbrunner, and Olga Yakimova. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences. Springer, 2014. https://doi.org/10.1007/s10958-014-2165-8. ieee: V. V. Alexeev, V. G. Bogaevskaya, M. M. Preobrazhenskaya, A. Y. Ukhalov, H. Edelsbrunner, and O. Yakimova, “An algorithm for cartographic generalization that preserves global topology,” Journal of Mathematical Sciences, vol. 203, no. 6. Springer, pp. 754–760, 2014. ista: Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. 2014. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 203(6), 754–760. mla: Alexeev, V. V., et al. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences, vol. 203, no. 6, Springer, 2014, pp. 754–60, doi:10.1007/s10958-014-2165-8. short: V.V. Alexeev, V.G. Bogaevskaya, M.M. Preobrazhenskaya, A.Y. Ukhalov, H. Edelsbrunner, O. Yakimova, Journal of Mathematical Sciences 203 (2014) 754–760. date_created: 2018-12-11T11:54:46Z date_published: 2014-11-16T00:00:00Z date_updated: 2022-05-24T10:39:06Z day: '16' department: - _id: HeEd doi: 10.1007/s10958-014-2165-8 intvolume: ' 203' issue: '6' language: - iso: eng month: '11' oa_version: None page: 754 - 760 publication: Journal of Mathematical Sciences publication_identifier: eissn: - 1573-8795 issn: - 1072-3374 publication_status: published publisher: Springer publist_id: '5165' quality_controlled: '1' scopus_import: '1' status: public title: An algorithm for cartographic generalization that preserves global topology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 203 year: '2014' ... --- _id: '1935' abstract: - lang: eng text: 'We consider Ising models in d = 2 and d = 3 dimensions with nearest neighbor ferromagnetic and long-range antiferromagnetic interactions, the latter decaying as (distance)-p, p > 2d, at large distances. If the strength J of the ferromagnetic interaction is larger than a critical value J c, then the ground state is homogeneous. It has been conjectured that when J is smaller than but close to J c, the ground state is periodic and striped, with stripes of constant width h = h(J), and h → ∞ as J → Jc -. (In d = 3 stripes mean slabs, not columns.) Here we rigorously prove that, if we normalize the energy in such a way that the energy of the homogeneous state is zero, then the ratio e 0(J)/e S(J) tends to 1 as J → Jc -, with e S(J) being the energy per site of the optimal periodic striped/slabbed state and e 0(J) the actual ground state energy per site of the system. Our proof comes with explicit bounds on the difference e 0(J)-e S(J) at small but positive J c-J, and also shows that in this parameter range the ground state is striped/slabbed in a certain sense: namely, if one looks at a randomly chosen window, of suitable size ℓ (very large compared to the optimal stripe size h(J)), one finds a striped/slabbed state with high probability.' acknowledgement: "2014 by the authors. This paper may be reproduced, in its entirety, for non-commercial purposes.\r\n\r\nThe research leading to these results has received funding from the European Research\r\nCouncil under the European Union’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694; A.G. and R.S.), the U.S. National Science Foundation (Grant PHY 0965859; E.H.L.), the Simons Foundation (Grant # 230207; E.H.L) and the NSERC (R.S.). The work is part of a project started in collaboration with Joel Lebowitz, whom we thank for many useful discussions and for his constant encouragement." article_processing_charge: No article_type: original author: - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Giuliani A, Lieb É, Seiringer R. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 2014;331:333-350. doi:10.1007/s00220-014-1923-2 apa: Giuliani, A., Lieb, É., & Seiringer, R. (2014). Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-1923-2 chicago: Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-1923-2. ieee: A. Giuliani, É. Lieb, and R. Seiringer, “Formation of stripes and slabs near the ferromagnetic transition,” Communications in Mathematical Physics, vol. 331. Springer, pp. 333–350, 2014. ista: Giuliani A, Lieb É, Seiringer R. 2014. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 331, 333–350. mla: Giuliani, Alessandro, et al. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics, vol. 331, Springer, 2014, pp. 333–50, doi:10.1007/s00220-014-1923-2. short: A. Giuliani, É. Lieb, R. Seiringer, Communications in Mathematical Physics 331 (2014) 333–350. date_created: 2018-12-11T11:54:48Z date_published: 2014-10-01T00:00:00Z date_updated: 2022-05-24T08:32:50Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00220-014-1923-2 external_id: arxiv: - '1304.6344' file: - access_level: open_access checksum: c8423271cd1e1ba9e44c47af75efe7b6 content_type: application/pdf creator: dernst date_created: 2022-05-24T08:30:40Z date_updated: 2022-05-24T08:30:40Z file_id: '11409' file_name: 2014_CommMathPhysics_Giuliani.pdf file_size: 334064 relation: main_file success: 1 file_date_updated: 2022-05-24T08:30:40Z has_accepted_license: '1' intvolume: ' 331' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 333 - 350 publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer publist_id: '5159' quality_controlled: '1' scopus_import: '1' status: public title: Formation of stripes and slabs near the ferromagnetic transition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 331 year: '2014' ... --- _id: '1936' abstract: - lang: eng text: 'The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race''s plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures.' author: - first_name: Michal full_name: Arbilly, Michal last_name: Arbilly - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Marcus full_name: Feldman, Marcus last_name: Feldman - first_name: Uri full_name: Grodzinski, Uri last_name: Grodzinski citation: ama: Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 2014;25(3):487-495. doi:10.1093/beheco/aru002 apa: Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002 chicago: Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002. ieee: M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” Behavioral Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014. ista: Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495. mla: Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002. short: M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495. date_created: 2018-12-11T11:54:48Z date_published: 2014-02-13T00:00:00Z date_updated: 2021-01-12T06:54:11Z day: '13' department: - _id: NiBa doi: 10.1093/beheco/aru002 ec_funded: 1 intvolume: ' 25' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/ month: '02' oa: 1 oa_version: Submitted Version page: 487 - 495 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Behavioral Ecology publication_status: published publisher: Oxford University Press publist_id: '5157' quality_controlled: '1' scopus_import: 1 status: public title: An arms race between producers and scroungers can drive the evolution of social cognition type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2014' ...