--- _id: '10384' abstract: - lang: eng text: 'Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.' acknowledgement: This work was supported by the ERC Advanced Grant 227758, the National Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3 of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941 ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support from the Alexander von Humboldt Foundation. article_number: '245702' article_processing_charge: No article_type: original author: - first_name: B. M. full_name: Mognetti, B. M. last_name: Mognetti - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: S. full_name: Angioletti-Uberti, S. last_name: Angioletti-Uberti - first_name: A. full_name: Cacciuto, A. last_name: Cacciuto - first_name: C. full_name: Valeriani, C. last_name: Valeriani - first_name: D. full_name: Frenkel, D. last_name: Frenkel citation: ama: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 2013;111(24). doi:10.1103/physrevlett.111.245702 apa: Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani, C., & Frenkel, D. (2013). Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.111.245702 chicago: Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/physrevlett.111.245702. ieee: B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel, “Living clusters and crystals from low-density suspensions of active colloids,” Physical Review Letters, vol. 111, no. 24. American Physical Society, 2013. ista: Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. 2013. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 111(24), 245702. mla: Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” Physical Review Letters, vol. 111, no. 24, 245702, American Physical Society, 2013, doi:10.1103/physrevlett.111.245702. short: B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013). date_created: 2021-11-29T13:29:31Z date_published: 2013-12-11T00:00:00Z date_updated: 2021-11-29T14:05:19Z day: '11' doi: 10.1103/physrevlett.111.245702 extern: '1' external_id: arxiv: - '1311.4681' pmid: - '24483677' intvolume: ' 111' issue: '24' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.4681 month: '12' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Living clusters and crystals from low-density suspensions of active colloids type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 111 year: '2013' ... --- _id: '10386' abstract: - lang: eng text: In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface. acknowledgement: This work was supported by the National Science Foundation under Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions on the subject. article_number: '6677' article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 2013;9(29). doi:10.1039/c3sm50188d apa: Šarić, A., & Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm50188d chicago: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm50188d. ieee: A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” Soft Matter, vol. 9, no. 29. Royal Society of Chemistry, 2013. ista: Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677. mla: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” Soft Matter, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:10.1039/c3sm50188d. short: A. Šarić, A. Cacciuto, Soft Matter 9 (2013). date_created: 2021-11-29T14:06:32Z date_published: 2013-05-03T00:00:00Z date_updated: 2021-11-29T14:29:31Z day: '03' doi: 10.1039/c3sm50188d extern: '1' intvolume: ' 9' issue: '29' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - url: https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d month: '05' oa_version: None publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Self-assembly of nanoparticles adsorbed on fluid and elastic membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9 year: '2013' ... --- _id: '10385' abstract: - lang: eng text: We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials. acknowledgement: This work was supported by the National Science Foundation under Career Grant no. DMR-0846426. article_processing_charge: No article_type: original author: - first_name: Joseph A. full_name: Napoli, Joseph A. last_name: Napoli - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. Soft Matter. 2013;9(37):8881-8886. doi:10.1039/c3sm51495a apa: Napoli, J. A., Šarić, A., & Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51495a chicago: Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51495a. ieee: J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” Soft Matter, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013. ista: Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886. mla: Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” Soft Matter, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:10.1039/c3sm51495a. short: J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886. date_created: 2021-11-29T13:31:24Z date_published: 2013-08-08T00:00:00Z date_updated: 2021-11-29T14:05:23Z day: '08' doi: 10.1039/c3sm51495a extern: '1' intvolume: ' 9' issue: '37' keyword: - condensed matter physics - general chemistry language: - iso: eng month: '08' oa_version: None page: 8881-8886 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Collapsing nanoparticle-laden nanotubes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9 year: '2013' ... --- _id: '10396' abstract: - lang: eng text: Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable. article_number: '000010151520134181' article_processing_charge: No article_type: original author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: C. full_name: Schmidt-Hieber, C. last_name: Schmidt-Hieber - first_name: S. J. full_name: Guzman, S. J. last_name: Guzman citation: ama: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181' apa: 'Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter. https://doi.org/10.1515/bmt-2013-4181' chicago: 'Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.' ieee: 'A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” Biomedical Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.' ista: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.' mla: 'Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.' short: A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013). conference: end_date: 2013-09-21 location: Graz, Austria name: 'BMT: Biomedizinische Technik ' start_date: 2013-09-19 date_created: 2021-12-01T14:35:35Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-12-02T12:51:12Z day: '01' ddc: - '005' - '610' department: - _id: PeJo doi: 10.1515/bmt-2013-4181 external_id: pmid: - '24042795' file: - access_level: open_access checksum: cdfc5339b530a25d6079f7223f0b1f16 content_type: application/pdf creator: schloegl date_created: 2021-12-01T14:38:08Z date_updated: 2021-12-01T14:38:08Z file_id: '10397' file_name: Schloegl_Abstract-BMT2013.pdf file_size: 149825 relation: main_file success: 1 file_date_updated: 2021-12-01T14:38:08Z has_accepted_license: '1' intvolume: ' 58' issue: SI-1-Track-G keyword: - biomedical engineering - data analysis - free software language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version pmid: 1 publication: Biomedical Engineering / Biomedizinische Technik publication_identifier: eissn: - 1862-278X issn: - 0013-5585 publication_status: published publisher: De Gruyter quality_controlled: '1' status: public title: 'Stimfit: A fast visualization and analysis environment for cellular neurophysiology' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 58 year: '2013' ... --- _id: '10749' abstract: - lang: eng text: Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures. acknowledgement: This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the US DOE, Office of Science. alternative_title: - Bulletin of the American Physical Society article_number: N36.00001 article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian - first_name: Genda full_name: Gu, Genda last_name: Gu citation: ama: 'Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In: APS March Meeting 2013. Vol 58. American Physical Society; 2013.' apa: 'Polshyn, H., Budakian, R., & Gu, G. (2013). Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In APS March Meeting 2013 (Vol. 58). Baltimore, MD, United States: American Physical Society.' chicago: Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” In APS March Meeting 2013, Vol. 58. American Physical Society, 2013. ieee: H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic Bi2212 samples,” in APS March Meeting 2013, Baltimore, MD, United States, 2013, vol. 58, no. 1. ista: 'Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin of the American Physical Society, vol. 58, N36.00001.' mla: Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” APS March Meeting 2013, vol. 58, no. 1, N36.00001, American Physical Society, 2013. short: H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical Society, 2013. conference: end_date: 2013-03-22 location: Baltimore, MD, United States name: 'APS: American Physical Society' start_date: 2013-03-18 date_created: 2022-02-08T10:34:29Z date_published: 2013-03-01T00:00:00Z date_updated: 2022-02-08T10:48:06Z day: '01' extern: '1' intvolume: ' 58' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR13/Event/186873 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2013 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Cantilever micro-susceptometry of mesoscopic Bi2212 samples type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 58 year: '2013' ... --- _id: '10895' abstract: - lang: eng text: 'Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. ' article_processing_charge: No article_type: original author: - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants. 2013;2(4):650-675. doi:10.3390/plants2040650' apa: 'Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action. Plants. MDPI. https://doi.org/10.3390/plants2040650' chicago: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.' ieee: 'S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants, vol. 2, no. 4. MDPI, pp. 650–675, 2013.' ista: 'Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.' mla: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.' short: S. Vanneste, J. Friml, Plants 2 (2013) 650–675. date_created: 2022-03-21T07:13:49Z date_published: 2013-10-21T00:00:00Z date_updated: 2022-03-21T12:15:29Z day: '21' ddc: - '580' department: - _id: JiFr doi: 10.3390/plants2040650 external_id: pmid: - '27137397' file: - access_level: open_access checksum: fb4ff2e820e344e253c9197544610be6 content_type: application/pdf creator: dernst date_created: 2022-03-21T12:12:56Z date_updated: 2022-03-21T12:12:56Z file_id: '10916' file_name: 2013_Plants_Vanneste.pdf file_size: 670188 relation: main_file success: 1 file_date_updated: 2022-03-21T12:12:56Z has_accepted_license: '1' intvolume: ' 2' issue: '4' keyword: - Plant Science - Ecology - Ecology - Evolution - Behavior and Systematics language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '10' oa: 1 oa_version: Published Version page: 650-675 pmid: 1 publication: Plants publication_identifier: issn: - 2223-7747 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: 'Calcium: The missing link in auxin action' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2013' ... --- _id: '10898' abstract: - lang: eng text: A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered. article_number: '17' article_processing_charge: No author: - first_name: Andreas full_name: Haas, Andreas last_name: Haas - first_name: Michael full_name: Lippautz, Michael last_name: Lippautz - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Hannes full_name: Payer, Hannes last_name: Payer - first_name: Ana full_name: Sokolova, Ana last_name: Sokolova - first_name: Christoph M. full_name: Kirsch, Christoph M. last_name: Kirsch - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: 'Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. ACM Press; 2013. doi:10.1145/2482767.2482789' apa: 'Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., & Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. Ischia, Italy: ACM Press. https://doi.org/10.1145/2482767.2482789' chicago: 'Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. ACM Press, 2013. https://doi.org/10.1145/2482767.2482789.' ieee: 'A. Haas et al., “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, Ischia, Italy, 2013, no. 5.' ista: 'Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.' mla: 'Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, no. 5, 17, ACM Press, 2013, doi:10.1145/2482767.2482789.' short: A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM Press, 2013. conference: end_date: 2013-05-16 location: Ischia, Italy name: 'CF: Conference on Computing Frontiers' start_date: 2013-05-14 date_created: 2022-03-21T07:33:22Z date_published: 2013-05-01T00:00:00Z date_updated: 2022-06-21T08:01:19Z day: '01' department: - _id: ToHe doi: 10.1145/2482767.2482789 issue: '5' language: - iso: eng month: '05' oa_version: None publication: Proceedings of the ACM International Conference on Computing Frontiers - CF '13 publication_identifier: isbn: - 978-145032053-5 publication_status: published publisher: ACM Press quality_controlled: '1' scopus_import: '1' status: public title: 'Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '10899' article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed. Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9' apa: Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity (2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9 chicago: Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity, 2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9. ieee: N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515. ista: 'Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.' mla: Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9. short: N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515. date_created: 2022-03-21T07:46:22Z date_published: 2013-01-01T00:00:00Z date_updated: 2022-06-20T09:18:06Z day: '01' department: - _id: NiBa doi: 10.1016/b978-0-12-384719-5.00031-9 edition: '2' keyword: - Adaptive landscape - Cline - Coalescent process - Gene flow - Hybrid zone - Local adaptation - Natural selection - Neutral theory - Population structure - Speciation language: - iso: eng month: '01' oa_version: None page: 508-515 publication: Encyclopedia of Biodiversity publication_identifier: isbn: - 978-0-12-384720-1 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Differentiation type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '11086' abstract: - lang: eng text: Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs. article_number: e1003308 article_processing_charge: No article_type: original author: - first_name: Yun full_name: Liang, Yun last_name: Liang - first_name: Tobias M. full_name: Franks, Tobias M. last_name: Franks - first_name: Maria C. full_name: Marchetto, Maria C. last_name: Marchetto - first_name: Fred H. full_name: Gage, Fred H. last_name: Gage - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of NUP98 with the human genome. PLoS Genetics. 2013;9(2). doi:10.1371/journal.pgen.1003308 apa: Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., & Hetzer, M. (2013). Dynamic association of NUP98 with the human genome. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003308 chicago: Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin Hetzer. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003308. ieee: Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic association of NUP98 with the human genome,” PLoS Genetics, vol. 9, no. 2. Public Library of Science, 2013. ista: Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308. mla: Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003308. short: Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics 9 (2013). date_created: 2022-04-07T07:50:59Z date_published: 2013-02-28T00:00:00Z date_updated: 2022-07-18T08:45:58Z day: '28' doi: 10.1371/journal.pgen.1003308 extern: '1' external_id: pmid: - '23468646' intvolume: ' 9' issue: '2' keyword: - Cancer Research - Genetics (clinical) - Genetics - Molecular Biology - Ecology - Evolution - Behavior and Systematics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1003308 month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Dynamic association of NUP98 with the human genome type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 9 year: '2013' ... --- _id: '11087' abstract: - lang: eng text: Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process. article_processing_charge: No article_type: original author: - first_name: Brandon H. full_name: Toyama, Brandon H. last_name: Toyama - first_name: Jeffrey N. full_name: Savas, Jeffrey N. last_name: Savas - first_name: Sung Kyu full_name: Park, Sung Kyu last_name: Park - first_name: Michael S. full_name: Harris, Michael S. last_name: Harris - first_name: Nicholas T. full_name: Ingolia, Nicholas T. last_name: Ingolia - first_name: John R. full_name: Yates, John R. last_name: Yates - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982. doi:10.1016/j.cell.2013.07.037 apa: Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.07.037 chicago: Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037. ieee: B. H. Toyama et al., “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” Cell, vol. 154, no. 5. Elsevier, pp. 971–982, 2013. ista: Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982. mla: Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037. short: B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982. date_created: 2022-04-07T07:51:08Z date_published: 2013-08-29T00:00:00Z date_updated: 2022-07-18T08:50:47Z day: '29' doi: 10.1016/j.cell.2013.07.037 extern: '1' external_id: pmid: - '23993091' intvolume: ' 154' issue: '5' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2013.07.037 month: '08' oa: 1 oa_version: Published Version page: 971-982 pmid: 1 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Identification of long-lived proteins reveals exceptional stability of essential cellular structures type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 154 year: '2013' ...