--- _id: '2856' abstract: - lang: eng text: 'G protein–coupled receptors (GPCRs), the largest family of membrane signaling proteins, respond to neurotransmitters, hormones and small environmental molecules. The neuronal function of many GPCRs has been difficult to resolve because of an inability to gate them with subtype specificity, spatial precision, speed and reversibility. To address this, we developed an approach for opto-chemical engineering of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs) to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized LimGluR2, on which we focused, was fast, bistable and supported multiple rounds of on/off switching. Light gated two of the primary neuronal functions of mGluR2: suppression of excitability and inhibition of neurotransmitter release. We found that the light-antagonized tool LimGluR2-block was able to manipulate negative feedback of synaptically released glutamate on transmitter release. We generalized the optical control to two additional family members: mGluR3 and mGluR6. This system worked in rodent brain slices and in zebrafish in vivo, where we found that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs pave the way for determining the roles of mGluRs in synaptic plasticity, memory and disease.' acknowledgement: National Science Foundation grants CHE-0233882 and CHE-0840505 (to the College of Chemistry at the University of California, Berkeley), a postdoctoral fellowship of the European Molecular Biology Organization (H.J.) author: - first_name: Joshua full_name: Levitz, Joshua last_name: Levitz - first_name: Carlos full_name: Pantoja, Carlos last_name: Pantoja - first_name: Benjamin full_name: Gaub, Benjamin last_name: Gaub - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Andreas full_name: Reiner, Andreas last_name: Reiner - first_name: Adam full_name: Hoagland, Adam last_name: Hoagland - first_name: David full_name: Schoppik, David last_name: Schoppik - first_name: Brian full_name: Kane, Brian last_name: Kane - first_name: Philipp full_name: Stawski, Philipp last_name: Stawski - first_name: Alexander full_name: Schier, Alexander last_name: Schier - first_name: Dirk full_name: Trauner, Dirk last_name: Trauner - first_name: Ehud full_name: Isacoff, Ehud last_name: Isacoff citation: ama: Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate receptors. Nature Neuroscience. 2013;16:507-516. doi:10.1038/nn.3346 apa: Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A., … Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3346 chicago: Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic Glutamate Receptors.” Nature Neuroscience. Nature Publishing Group, 2013. https://doi.org/10.1038/nn.3346. ieee: J. Levitz et al., “Optical control of metabotropic glutamate receptors,” Nature Neuroscience, vol. 16. Nature Publishing Group, pp. 507–516, 2013. ista: Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D, Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic glutamate receptors. Nature Neuroscience. 16, 507–516. mla: Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.” Nature Neuroscience, vol. 16, Nature Publishing Group, 2013, pp. 507–16, doi:10.1038/nn.3346. short: J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D. Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience 16 (2013) 507–516. date_created: 2018-12-11T11:59:57Z date_published: 2013-03-03T00:00:00Z date_updated: 2021-01-12T07:00:16Z day: '03' department: - _id: HaJa doi: 10.1038/nn.3346 external_id: pmid: - '23455609' intvolume: ' 16' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/ month: '03' oa: 1 oa_version: Submitted Version page: 507 - 516 pmid: 1 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '3936' quality_controlled: '1' scopus_import: 1 status: public title: Optical control of metabotropic glutamate receptors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2013' ... --- _id: '2859' abstract: - lang: eng text: Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization. author: - first_name: Paul full_name: Bendich, Paul id: 43F6EC54-F248-11E8-B48F-1D18A9856A87 last_name: Bendich - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Amit full_name: Patel, Amit id: 34A254A0-F248-11E8-B48F-1D18A9856A87 last_name: Patel citation: ama: Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 2013;15(1):51-72. doi:10.4310/HHA.2013.v15.n1.a3 apa: Bendich, P., Edelsbrunner, H., Morozov, D., & Patel, A. (2013). Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2013.v15.n1.a3 chicago: Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications. International Press, 2013. https://doi.org/10.4310/HHA.2013.v15.n1.a3. ieee: P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” Homology, Homotopy and Applications, vol. 15, no. 1. International Press, pp. 51–72, 2013. ista: Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72. mla: Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications, vol. 15, no. 1, International Press, 2013, pp. 51–72, doi:10.4310/HHA.2013.v15.n1.a3. short: P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72. date_created: 2018-12-11T11:59:58Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T07:00:18Z day: '01' department: - _id: HeEd doi: 10.4310/HHA.2013.v15.n1.a3 external_id: arxiv: - '1102.3389' intvolume: ' 15' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1102.3389v1 month: '05' oa: 1 oa_version: Preprint page: 51 - 72 publication: Homology, Homotopy and Applications publication_status: published publisher: International Press publist_id: '3930' quality_controlled: '1' scopus_import: 1 status: public title: Homology and robustness of level and interlevel sets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2863' abstract: - lang: eng text: Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population. article_number: e1002922 author: - first_name: Einat full_name: Granot Atedgi, Einat last_name: Granot Atedgi - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Ronen full_name: Segev, Ronen last_name: Segev - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman citation: ama: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 2013;9(3). doi:10.1371/journal.pcbi.1002922 apa: Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922 chicago: Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922. ieee: E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3. Public Library of Science, 2013. ista: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 9(3), e1002922. mla: Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922. short: E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013). date_created: 2018-12-11T12:00:00Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T07:00:20Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1002922 file: - access_level: open_access checksum: 5a30876c193209fa05b26db71845dd16 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:45Z date_updated: 2020-07-14T12:45:52Z file_id: '5099' file_name: IST-2013-120-v1+1_journal.pcbi.1002922.pdf file_size: 1548120 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 9' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '3926' pubrep_id: '120' quality_controlled: '1' scopus_import: 1 status: public title: Stimulus-dependent maximum entropy models of neural population codes 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '2862' abstract: - lang: eng text: Motile cilia perform crucial functions during embryonic development and throughout adult life. Development of organs containing motile cilia involves regulation of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis) in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis is not yet fully understood, and it remains unclear whether these processes are coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently in ciliated organs. Lgl proteins are involved in establishing cell polarity and have been implicated in vesicle trafficking. Here, we identified a role for Lgl2 in development of ciliated epithelia in Kupffer's vesicle, which directs left-right asymmetry of the embryo; the otic vesicles, which give rise to the inner ear; and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed loss of the adherens junction component E-cadherin at lateral membranes. Genetic interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin and mediate lumen formation that is uncoupled from cilia formation. These results uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis and ciliogenesis and indicate that these processes are genetically separable in zebrafish. acknowledgement: Deposited in PMC for release after 12 months. We thank members of the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents. author: - first_name: Hwee full_name: Tay, Hwee last_name: Tay - first_name: Sabrina full_name: Schulze, Sabrina last_name: Schulze - first_name: Julien full_name: Compagnon, Julien id: 2E3E0988-F248-11E8-B48F-1D18A9856A87 last_name: Compagnon - first_name: Fiona full_name: Foley, Fiona last_name: Foley - 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: H Joseph full_name: Yost, H Joseph last_name: Yost - first_name: Salim full_name: Abdelilah Seyfried, Salim last_name: Abdelilah Seyfried - first_name: Jeffrey full_name: Amack, Jeffrey last_name: Amack citation: ama: Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. 2013;140(7):1550-1559. doi:10.1242/dev.087130 apa: Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost, H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. Company of Biologists. https://doi.org/10.1242/dev.087130 chicago: Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.087130. ieee: H. Tay et al., “Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company of Biologists, pp. 1550–1559, 2013. ista: Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559. mla: Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” Development, vol. 140, no. 7, Company of Biologists, 2013, pp. 1550–59, doi:10.1242/dev.087130. short: H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost, S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559. date_created: 2018-12-11T11:59:59Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T07:00:20Z day: '01' department: - _id: CaHe doi: 10.1242/dev.087130 external_id: pmid: - '23482490' intvolume: ' 140' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/ month: '04' oa: 1 oa_version: Submitted Version page: 1550 - 1559 pmid: 1 publication: Development publication_status: published publisher: Company of Biologists publist_id: '3927' quality_controlled: '1' scopus_import: 1 status: public title: Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 140 year: '2013' ... --- _id: '2861' abstract: - lang: eng text: We consider a two-parameter family of piecewise linear maps in which the moduli of the two slopes take different values. We provide numerical evidence of the existence of some parameter regions in which the Lyapunov exponent and the topological entropy remain constant. Analytical proof of this phenomenon is also given for certain cases. Surprisingly however, the systems with that property are not conjugate as we prove by using kneading theory. article_number: '125101' author: - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: José full_name: Oteo, José last_name: Oteo - first_name: Javier full_name: Ros, Javier last_name: Ros - first_name: Paul full_name: Glendinning, Paul last_name: Glendinning citation: ama: 'Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 2013;46(12). doi:10.1088/1751-8113/46/12/125101' apa: 'Botella Soler, V., Oteo, J., Ros, J., & Glendinning, P. (2013). Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. IOP Publishing Ltd. https://doi.org/10.1088/1751-8113/46/12/125101' chicago: 'Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1751-8113/46/12/125101.' ieee: 'V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent and topological entropy plateaus in piecewise linear maps,” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing Ltd., 2013.' ista: 'Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 46(12), 125101.' mla: 'Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12, 125101, IOP Publishing Ltd., 2013, doi:10.1088/1751-8113/46/12/125101.' short: 'V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).' date_created: 2018-12-11T11:59:59Z date_published: 2013-03-29T00:00:00Z date_updated: 2021-01-12T07:00:19Z day: '29' department: - _id: GaTk doi: 10.1088/1751-8113/46/12/125101 intvolume: ' 46' issue: '12' language: - iso: eng month: '03' oa_version: None publication: 'Journal of Physics A: Mathematical and Theoretical' publication_status: published publisher: IOP Publishing Ltd. publist_id: '3928' quality_controlled: '1' scopus_import: 1 status: public title: Lyapunov exponent and topological entropy plateaus in piecewise linear maps type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2013' ... --- _id: '2877' abstract: - lang: eng text: 'Premise of the study: To reach favorable conditions for photosynthesis, seedlings grow upward when deprived of light upon underground germination. To direct their growth, they use their negative gravitropic capacity. Negative gravitropism is under tight control of multiple hormones. • Methods: By counting the number of standing plants in a population or by real time monitoring of the reorientation of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis of transcriptomic data on AUX / IAA genes was gathered, and subsequent mutant analysis was performed. • Key results: Ethylene and BR have opposite effects in regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in 2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX / IAA genes. BRs regulate a wider range of auxin signaling components than ethylene. • Conclusions: Upward growth in seedlings depends strongly on the internal hormonal balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism in a manner that depends on the function of different, yet overlapping sets of auxin signaling components.' author: - first_name: Filip full_name: Vandenbussche, Filip last_name: Vandenbussche - first_name: Pieter full_name: Callebert, Pieter last_name: Callebert - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Eva full_name: Eva Benková 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: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. 2013;100(1):215-225. doi:10.3732/ajb.1200264 apa: Vandenbussche, F., Callebert, P., Žádníková, P., Benková, E., & Van Der Straeten, D. (2013). Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. Botanical Society of America. https://doi.org/10.3732/ajb.1200264 chicago: Vandenbussche, Filip, Pieter Callebert, Petra Žádníková, Eva Benková, and Dominique Van Der Straeten. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” American Journal of Botany. Botanical Society of America, 2013. https://doi.org/10.3732/ajb.1200264. ieee: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, and D. Van Der Straeten, “Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components,” American Journal of Botany, vol. 100, no. 1. Botanical Society of America, pp. 215–225, 2013. ista: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. 2013. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. 100(1), 215–225. mla: Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” American Journal of Botany, vol. 100, no. 1, Botanical Society of America, 2013, pp. 215–25, doi:10.3732/ajb.1200264. short: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten, American Journal of Botany 100 (2013) 215–225. date_created: 2018-12-11T12:00:06Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:25Z day: '01' doi: 10.3732/ajb.1200264 extern: 1 intvolume: ' 100' issue: '1' month: '01' page: 215 - 225 publication: American Journal of Botany publication_status: published publisher: Botanical Society of America publist_id: '3883' quality_controlled: 0 status: public title: Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components type: journal_article volume: 100 year: '2013' ... --- _id: '2883' abstract: - lang: eng text: Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1 (TWD1), although underlying mechanisms are unclear. By genetic manipulation of TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and, thus, downstream developmental traits, such as epidermal twisting and gravitropism of the root. Using immunological assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1. In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root apoplast into the cytoplasm. acknowledgement: We would thank Vincent Vincenzetti and Laurence Charrier for excellent technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data were partially collected at the Center for Advanced Bioimaging, University of Copenhagen, Denmark. This work was supported by grants from the Novartis Foundation (to M.G.), from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit of the University of Zurich (to A.B.), from the Pool de Recherche of the University of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates this work to his father, who passed away during the resubmission process. author: - first_name: Bangjun full_name: Wang, Bangjun last_name: Wang - first_name: Aurélien full_name: Bailly, Aurélien last_name: Bailly - first_name: Marta full_name: Zwiewk, Marta last_name: Zwiewk - first_name: Sina full_name: Henrichs, Sina last_name: Henrichs - first_name: Elisa full_name: Azzarello, Elisa last_name: Azzarello - first_name: Stefano full_name: Mancuso, Stefano last_name: Mancuso - first_name: Masayoshi full_name: Maeshima, Masayoshi last_name: Maeshima - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Alexander full_name: Schulz, Alexander last_name: Schulz - first_name: Markus full_name: Geisler, Markus last_name: Geisler citation: ama: Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 2013;25(1):202-214. doi:10.1105/tpc.112.105999 apa: Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S., … Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.105999 chicago: Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello, Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.112.105999. ieee: B. Wang et al., “Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane,” Plant Cell, vol. 25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013. ista: Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M, Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214. mla: Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell, vol. 25, no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:10.1105/tpc.112.105999. short: B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M. Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214. date_created: 2018-12-11T12:00:08Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:28Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.112.105999 external_id: pmid: - '23321285' intvolume: ' 25' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/ month: '01' oa: 1 oa_version: Submitted Version page: 202 - 214 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3878' quality_controlled: '1' scopus_import: 1 status: public title: Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '2880' abstract: - lang: eng text: Lateral root (LR) formation is initiated when pericycle cells accumulate auxin, thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions, giving rise to a new primordium. How this auxin maximum in pericycle cells builds up and remains focused is not understood. We report that the endodermis plays an active role in the regulation of auxin accumulation and is instructive for FCs to progress during the LR initiation (LRI) phase. We describe the functional importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux pathway causes dramatic defects in the progress of FCs towards the next initiation phase. Our data identify an unexpected regulatory function for the endodermis in LRI as part of the fine-tuning mechanism that appears to act as a check point in LR organogenesis after FCs are specified. author: - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Ding full_name: Zhaojun, Ding last_name: Zhaojun - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. 2013;32(1):149-158. doi:10.1038/emboj.2012.303 apa: Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman, T., & Benková, E. (2013). Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.303 chicago: Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.303. ieee: P. Marhavý et al., “Auxin reflux between the endodermis and pericycle promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp. 149–158, 2013. ista: Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. 32(1), 149–158. mla: Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 149–58, doi:10.1038/emboj.2012.303. short: P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman, E. Benková, EMBO Journal 32 (2013) 149–158. date_created: 2018-12-11T12:00:07Z date_published: 2013-01-09T00:00:00Z date_updated: 2021-01-12T07:00:27Z day: '09' department: - _id: EvBe doi: 10.1038/emboj.2012.303 ec_funded: 1 external_id: pmid: - '23178590' intvolume: ' 32' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/ month: '01' oa: 1 oa_version: Submitted Version page: 149 - 158 pmid: 1 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3882' quality_controlled: '1' scopus_import: 1 status: public title: Auxin reflux between the endodermis and pericycle promotes lateral root initiation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2882' abstract: - lang: eng text: Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots. author: - first_name: Christian full_name: Löfke, Christian last_name: Löfke - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Marc full_name: Van Montagu, Marc last_name: Van Montagu - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. 2013;110(9):3627-3632. doi:10.1073/pnas.1300107110 apa: Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., & Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1300107110 chicago: Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1300107110. ieee: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml, “Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism,” PNAS, vol. 110, no. 9. National Academy of Sciences, pp. 3627–3632, 2013. ista: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. 110(9), 3627–3632. mla: Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS, vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:10.1073/pnas.1300107110. short: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632. date_created: 2018-12-11T12:00:07Z date_published: 2013-02-26T00:00:00Z date_updated: 2021-01-12T07:00:27Z day: '26' department: - _id: JiFr doi: 10.1073/pnas.1300107110 external_id: pmid: - '23391733' intvolume: ' 110' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/ month: '02' oa: 1 oa_version: Submitted Version page: 3627 - 3632 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3879' quality_controlled: '1' scopus_import: 1 status: public title: Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2885' abstract: - lang: eng text: 'This volume contains the post-proceedings of the 8th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were carefully selected out of 31 submissions and are presented together with 6 invited papers. The topics covered by the papers include: computer-aided analysis and verification, applications of game theory in computer science, networks and security, modern trends of graph theory in computer science, electronic systems design and testing, and quantum information processing.' acknowledgement: Red Hat Czech Republic, Y Soft alternative_title: - LNCS citation: ama: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D, eds. Mathematical and Engineering Methods in Computer Science. Vol 7721. Springer; 2013:1-228. doi:10.1007/978-3-642-36046-6 apa: 'Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., & Antos, D. (Eds.). (2013). Mathematical and Engineering Methods in Computer Science (Vol. 7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods in computer science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6' chicago: Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and David Antos, eds. Mathematical and Engineering Methods in Computer Science. Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6. ieee: A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., Mathematical and Engineering Methods in Computer Science, vol. 7721. Springer, 2013, pp. 1–228. ista: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical and Engineering Methods in Computer Science, Springer,p. mla: Kucera, Antonin, et al., editors. Mathematical and Engineering Methods in Computer Science. Vol. 7721, Springer, 2013, pp. 1–228, doi:10.1007/978-3-642-36046-6. short: A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical and Engineering Methods in Computer Science, Springer, 2013. conference: end_date: 2012-10-28 location: Znojmo, Czech Republic name: 'MEMICS: Mathematical and Engineering methods in computer science' start_date: 2012-10-25 date_created: 2018-12-11T12:00:08Z date_published: 2013-01-09T00:00:00Z date_updated: 2019-08-02T12:37:55Z day: '09' department: - _id: ToHe doi: 10.1007/978-3-642-36046-6 editor: - first_name: Antonin full_name: Kucera, Antonin last_name: Kucera - 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: Jaroslav full_name: Nesetril, Jaroslav last_name: Nesetril - first_name: Tomas full_name: Vojnar, Tomas last_name: Vojnar - first_name: David full_name: Antos, David last_name: Antos intvolume: ' 7721' language: - iso: eng month: '01' oa_version: None page: 1 - 228 publication_status: published publisher: Springer publist_id: '3874' quality_controlled: '1' series_title: Lecture Notes in Computer Science status: public title: Mathematical and Engineering Methods in Computer Science type: conference_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7721 year: '2013' ... --- _id: '2881' abstract: - lang: eng text: The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated lobes and indents is a good model system to investigate the mechanisms that coordinate cell polarity and shape formation within a tissue. Auxin has been shown to coordinate the interdigitation by activating ROP GTPase-dependent signaling pathways. To identify additional components or mechanisms, we screened for mutants with abnormal PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling (such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant, and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas over-production of cytokinin and over-activation of cytokinin signaling in an ARR20 over-expression line delayed or abolished PC interdigitation throughout the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling acts upstream of ROPs to suppress the formation of interdigitated pattern. Our results provide novel mechanistic understanding of the pathways controlling PC shape and uncover a new role for cytokinin signaling in cell morphogenesis. acknowledgement: is work was supported by grants from the US National Institute of General Medical Sciences (GM081451 and GM081451-03S2) to ZY. We thank National Science Foundation grant (IOS-1147250) to GVR and MX. HL and DL were partially supported by the Chinese Scholarship Council. author: - first_name: Hongjiang full_name: Hongjiang Li id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Deshu full_name: Lin, Deshu last_name: Lin - first_name: Mingzhang full_name: Wen, Mingzhang last_name: Wen - first_name: Mingtang full_name: Xie, Mingtang last_name: Xie - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Jungmook full_name: Kim, Jungmook last_name: Kim - first_name: G Venugopala full_name: Reddy, G Venugopala last_name: Reddy - first_name: Jianru full_name: Zuo, Jianru last_name: Zuo - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Hongwei full_name: Guo, Hongwei last_name: Guo - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang citation: ama: Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. 2013;23(2):290-299. doi:10.1038/cr.2012.146 apa: Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013). Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2012.146 chicago: Li, Hongjiang, Tongda Xu, Deshu Lin, Mingzhang Wen, Mingtang Xie, Jérôme Duclercq, Agnieszka Bielach, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis in Arabidopsis.” Cell Research. Nature Publishing Group, 2013. https://doi.org/10.1038/cr.2012.146. ieee: H. Li et al., “Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis,” Cell Research, vol. 23, no. 2. Nature Publishing Group, pp. 290–299, 2013. ista: Li H, Xu T, Lin D, Wen M, Xie M, Duclercq J, Bielach A, Kim J, Reddy GV, Zuo J, Benková E, Friml J, Guo H, Yang Z. 2013. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. 23(2), 290–299. mla: Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis in Arabidopsis.” Cell Research, vol. 23, no. 2, Nature Publishing Group, 2013, pp. 290–99, doi:10.1038/cr.2012.146. short: H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V. Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013) 290–299. date_created: 2018-12-11T12:00:07Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T07:00:27Z day: '01' doi: 10.1038/cr.2012.146 extern: 1 intvolume: ' 23' issue: '2' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/ month: '02' oa: 1 page: 290 - 299 publication: Cell Research publication_status: published publisher: Nature Publishing Group publist_id: '3881' quality_controlled: 0 status: public title: Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis type: journal_article volume: 23 year: '2013' ... --- _id: '2884' author: - 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: Hélène full_name: Berthoumieux, Hélène last_name: Berthoumieux - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Guillaume full_name: Salbreux, Guillaume last_name: Salbreux - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Ewa full_name: Paluch, Ewa last_name: Paluch - 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 citation: ama: Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 2013;29(2):147-150. doi:10.1051/medsci/2013292011 apa: Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., & Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. Éditions Médicales et Scientifiques. https://doi.org/10.1051/medsci/2013292011 chicago: Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” Medecine Sciences. Éditions Médicales et Scientifiques, 2013. https://doi.org/10.1051/medsci/2013292011. ieee: J.-L. Maître et al., “Cell adhesion mechanics of zebrafish gastrulation,” Medecine Sciences, vol. 29, no. 2. Éditions Médicales et Scientifiques, pp. 147–150, 2013. ista: Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2013. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 29(2), 147–150. mla: Maître, Jean-Léon, et al. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” Medecine Sciences, vol. 29, no. 2, Éditions Médicales et Scientifiques, 2013, pp. 147–50, doi:10.1051/medsci/2013292011. short: J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150. date_created: 2018-12-11T12:00:08Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T07:00:28Z day: '01' department: - _id: CaHe doi: 10.1051/medsci/2013292011 intvolume: ' 29' issue: '2' language: - iso: eng month: '02' oa_version: None page: 147 - 150 project: - _id: 252064B8-B435-11E9-9278-68D0E5697425 grant_number: HE_3231/6-1 name: Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo - _id: 2527D5CC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 812-B12 name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation publication: Medecine Sciences publication_status: published publisher: Éditions Médicales et Scientifiques publist_id: '3877' quality_controlled: '1' scopus_import: 1 status: public title: Cell adhesion mechanics of zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '2886' abstract: - lang: eng text: We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization. alternative_title: - LNCS author: - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Vojtěch full_name: Řehák, Vojtěch last_name: Řehák citation: ama: Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130. doi:10.1007/978-3-642-36046-6_12 apa: 'Chmelik, M., & Řehák, V. (2013). Controllable-choice message sequence graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6_12' chicago: Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence Graphs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6_12. ieee: M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013. ista: Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130. mla: Chmelik, Martin, and Vojtěch Řehák. Controllable-Choice Message Sequence Graphs. Vol. 7721, Springer, 2013, pp. 118–30, doi:10.1007/978-3-642-36046-6_12. short: M. Chmelik, V. Řehák, 7721 (2013) 118–130. conference: end_date: 2012-10-28 location: Znojmo, Czech Republic name: 'MEMICS: Mathematical and Engineering Methods in Computer Science' start_date: 2012-10-25 date_created: 2018-12-11T12:00:09Z date_published: 2013-01-09T00:00:00Z date_updated: 2020-08-11T10:09:52Z day: '09' department: - _id: KrCh doi: 10.1007/978-3-642-36046-6_12 ec_funded: 1 intvolume: ' 7721' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.4499 month: '01' oa: 1 oa_version: Submitted Version page: 118 - 130 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '3873' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Controllable-choice message sequence graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7721 year: '2013' ... --- _id: '2887' abstract: - lang: eng text: 'Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.' article_processing_charge: No article_type: original author: - first_name: Suqin full_name: Fang, Suqin last_name: Fang - first_name: Randy full_name: Clark, Randy last_name: Clark - first_name: Ying full_name: Zheng, Ying last_name: Zheng - first_name: Anjali full_name: Iyer Pascuzzi, Anjali last_name: Iyer Pascuzzi - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz - first_name: Leon full_name: Kochian, Leon last_name: Kochian - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Hong full_name: Liao, Hong last_name: Liao - first_name: Philip full_name: Benfey, Philip last_name: Benfey citation: ama: Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses by rice roots. PNAS. 2013;110(7):2670-2675. doi:10.1073/pnas.1222821110 apa: Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L., … Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1222821110 chicago: Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz, Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition and Spatial Responses by Rice Roots.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1222821110. ieee: S. Fang et al., “Genotypic recognition and spatial responses by rice roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013. ista: Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice roots. PNAS. 110(7), 2670–2675. mla: Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75, doi:10.1073/pnas.1222821110. short: S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner, H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675. date_created: 2018-12-11T12:00:09Z date_published: 2013-02-12T00:00:00Z date_updated: 2021-01-12T07:00:29Z day: '12' department: - _id: HeEd doi: 10.1073/pnas.1222821110 external_id: pmid: - '23362379' intvolume: ' 110' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/ month: '02' oa: 1 oa_version: Published Version page: 2670 - 2675 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3872' quality_controlled: '1' scopus_import: 1 status: public title: Genotypic recognition and spatial responses by rice roots type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2901' abstract: - lang: eng text: ' We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. ' alternative_title: - ' JMLR: W&CP' author: - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Zhu full_name: Yan, Zhu last_name: Yan - first_name: Dimitris full_name: Metaxas, Dimitris last_name: Metaxas - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable modes of a graphical model. In: Vol 31. JMLR; 2013:161-169.' apa: 'Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., & Lampert, C. (2013). Computing the M most probable modes of a graphical model (Vol. 31, pp. 161–169). Presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States: JMLR.' chicago: Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph Lampert. “Computing the M Most Probable Modes of a Graphical Model,” 31:161–69. JMLR, 2013. ieee: 'C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the M most probable modes of a graphical model,” presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States, 2013, vol. 31, pp. 161–169.' ista: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M most probable modes of a graphical model. AISTATS: Conference on Uncertainty in Artificial Intelligence, JMLR: W&CP, vol. 31, 161–169.' mla: Chen, Chao, et al. Computing the M Most Probable Modes of a Graphical Model. Vol. 31, JMLR, 2013, pp. 161–69. short: C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013, pp. 161–169. conference: end_date: 2013-05-01 location: Scottsdale, AZ, United States name: ' AISTATS: Conference on Uncertainty in Artificial Intelligence' start_date: 2013-04-29 date_created: 2018-12-11T12:00:14Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:35Z day: '01' department: - _id: HeEd - _id: VlKo - _id: ChLa intvolume: ' 31' language: - iso: eng main_file_link: - open_access: '1' url: http://jmlr.org/proceedings/papers/v31/chen13a.html month: '01' oa: 1 oa_version: None page: 161 - 169 publication_status: published publisher: JMLR publist_id: '3846' quality_controlled: '1' scopus_import: 1 status: public title: Computing the M most probable modes of a graphical model type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2013' ... --- _id: '2900' author: - first_name: Ricardo full_name: Azevedo, Ricardo B last_name: Azevedo - first_name: Rolf full_name: Lohaus, Rolf last_name: Lohaus - first_name: Tiago full_name: Tiago Paixao id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development. 2013;10(5):514-515. apa: Azevedo, R., Lohaus, R., & Paixao, T. (2013). Networking networks. Evolution & Development. Wiley-Blackwell. chicago: Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” Evolution & Development. Wiley-Blackwell, 2013. ieee: R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013. ista: Azevedo R, Lohaus R, Paixao T. 2013. Networking networks. Evolution & Development. 10(5), 514–515. mla: Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development, vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15. short: R. Azevedo, R. Lohaus, T. Paixao, Evolution & Development 10 (2013) 514–515. date_created: 2018-12-11T12:00:14Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:34Z day: '01' extern: 1 intvolume: ' 10' issue: '5' main_file_link: - open_access: '0' url: http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract month: '01' page: 514 - 515 publication: Evolution & Development publication_status: published publisher: Wiley-Blackwell publist_id: '3858' quality_controlled: 0 status: public title: Networking networks type: journal_article volume: 10 year: '2013' ... --- _id: '2906' abstract: - lang: eng text: "Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact geometric computation paradigm. We report on several\r\ntechniques to accelerate the computation that turn our implementation applicable to the underlying biological\r\nproblem." alternative_title: - ALENEX author: - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation. In: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments. Society of Industrial and Applied Mathematics; 2013:70-77. doi:10.1137/1.9781611972931.6' apa: 'Kerber, M., & Edelsbrunner, H. (2013). 3D kinetic alpha complexes and their implementation. In 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments (pp. 70–77). New Orleans, LA, United States: Society of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611972931.6' chicago: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” In 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, 70–77. Society of Industrial and Applied Mathematics, 2013. https://doi.org/10.1137/1.9781611972931.6. ieee: M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,” in 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, New Orleans, LA, United States, 2013, pp. 70–77. ista: 'Kerber M, Edelsbrunner H. 2013. 3D kinetic alpha complexes and their implementation. 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, ALENEX, , 70–77.' mla: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2013, pp. 70–77, doi:10.1137/1.9781611972931.6. short: M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2013, pp. 70–77. conference: end_date: 2013-01-07 location: New Orleans, LA, United States name: 'ALENEX: Algorithm Engineering and Experiments' start_date: 2013-01-07 date_created: 2018-12-11T12:00:16Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:36Z day: '01' ddc: - '500' department: - _id: HeEd doi: 10.1137/1.9781611972931.6 file: - access_level: open_access checksum: a15a3ba22df9445731507f3e06c9fcee content_type: application/pdf creator: system date_created: 2018-12-12T10:08:57Z date_updated: 2020-07-14T12:45:52Z file_id: '4720' file_name: IST-2016-547-v1+1_2013-P-08-MedusaII.pdf file_size: 403013 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 70 - 77 publication: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments publication_status: published publisher: Society of Industrial and Applied Mathematics publist_id: '3841' pubrep_id: '547' quality_controlled: '1' scopus_import: 1 status: public title: 3D kinetic alpha complexes and their implementation type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2910' abstract: - lang: eng text: "Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module." author: - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067 apa: Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067 chicago: Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” Bioinformatics. Oxford University Press, 2013. https://doi.org/10.1093/bioinformatics/btt067. ieee: J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013. ista: Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956. mla: Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067. short: J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956. date_created: 2018-12-11T12:00:17Z date_published: 2013-02-07T00:00:00Z date_updated: 2021-01-12T07:00:38Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1093/bioinformatics/btt067 ec_funded: 1 file: - access_level: open_access checksum: a3b54d7477fac923815ac082403d9bd0 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:04Z date_updated: 2020-07-14T12:45:52Z file_id: '5189' file_name: IST-2016-556-v1+1_bioinformatics-2013.pdf file_size: 170197 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 29' issue: '7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 955 - 956 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Bioinformatics publication_status: published publisher: Oxford University Press publist_id: '3833' pubrep_id: '556' quality_controlled: '1' scopus_import: 1 status: public title: Coalescent simulation in continuous space type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '2909' abstract: - lang: eng text: "We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research." 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 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002 apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002 chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002. ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. IOP Publishing Ltd., 2013. ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1). mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002. short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013). date_created: 2018-12-11T12:00:17Z date_published: 2013-01-16T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '16' ddc: - '570' department: - _id: NiBa doi: 10.1088/1742-5468/2013/01/P01002 ec_funded: 1 file: - access_level: open_access checksum: ce8a4424385b3086138a1e054e16e0e3 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:52Z date_updated: 2020-07-14T12:45:52Z file_id: '5242' file_name: IST-2016-557-v1+1_BEVrevised.pdf file_size: 702583 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 2013' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Journal of Statistical Mechanics Theory and Experiment publication_status: published publisher: IOP Publishing Ltd. publist_id: '3834' pubrep_id: '557' quality_controlled: '1' scopus_import: 1 status: public title: Modelling evolution in a spatial continuum type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2013 year: '2013' ... --- _id: '2908' abstract: - lang: eng text: 'Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence.' 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. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015 apa: Barton, N. H. (2013). Does hybridisation influence speciation?  . Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015 chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” Journal of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015. ieee: N. H. Barton, “Does hybridisation influence speciation?  ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013. ista: Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269. mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” Journal of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:10.1111/jeb.12015. short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269. date_created: 2018-12-11T12:00:17Z date_published: 2013-01-17T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '17' ddc: - '576' department: - _id: NiBa doi: 10.1111/jeb.12015 file: - access_level: open_access checksum: 716e88714c3411cd0bd70928b14ea692 content_type: text/rtf creator: system date_created: 2018-12-12T10:09:38Z date_updated: 2020-07-14T12:45:52Z file_id: '4762' file_name: IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf file_size: 13339 relation: main_file - access_level: open_access checksum: 957fd07c71c1b1eac2c65ae3311aca78 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:39Z date_updated: 2020-07-14T12:45:52Z file_id: '4763' file_name: IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf file_size: 103437 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 26' issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 267 - 269 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley-Blackwell publist_id: '3835' pubrep_id: '111' quality_controlled: '1' scopus_import: 1 status: public title: 'Does hybridisation influence speciation? ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2013' ... --- _id: '2907' abstract: - lang: eng text: 'Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.' 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. Recombination and sex. In: The Princeton Guide to Evolution. Princeton University Press; 2013:328-333.' apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution (pp. 328–333). Princeton University Press. chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide to Evolution, 328–33. Princeton University Press, 2013. ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333. ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.' mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–33. short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333. date_created: 2018-12-11T12:00:16Z date_published: 2013-11-04T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '04' ddc: - '576' department: - _id: NiBa file: - access_level: open_access checksum: 8332ca9cb40f7e66d1006b175ce36b60 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: system date_created: 2018-12-12T10:16:47Z date_updated: 2020-07-14T12:45:52Z file_id: '5237' file_name: IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx file_size: 79838 relation: main_file - access_level: open_access checksum: 849f418620fb78d6ba23bb4f488ee93f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:48Z date_updated: 2020-07-14T12:45:52Z file_id: '5238' file_name: IST-2017-119-v1+2_Barton_Recombination_Sex.pdf file_size: 144131 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 328 - 333 publication: The Princeton Guide to Evolution publication_identifier: isbn: - '9780691149776' publication_status: published publisher: Princeton University Press publist_id: '3839' pubrep_id: '119' quality_controlled: '1' status: public title: Recombination and sex type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2913' abstract: - lang: eng text: 'The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this "neural metric" tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.' article_number: '058104' author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Einat full_name: Granot Atedgi, Einat last_name: Granot Atedgi - first_name: Ronen full_name: Segev, Ronen last_name: Segev - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman citation: ama: 'Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 2013;110(5). doi:10.1103/PhysRevLett.110.058104' apa: 'Tkačik, G., Granot Atedgi, E., Segev, R., & Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.058104' chicago: 'Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.058104.' ieee: 'G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” Physical Review Letters, vol. 110, no. 5. American Physical Society, 2013.' ista: 'Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 110(5), 058104.' mla: 'Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.' short: G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013). date_created: 2018-12-11T12:00:18Z date_published: 2013-01-28T00:00:00Z date_updated: 2021-01-12T07:00:39Z day: '28' department: - _id: GaTk doi: 10.1103/PhysRevLett.110.058104 intvolume: ' 110' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1205.6598 month: '01' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3830' quality_controlled: '1' scopus_import: 1 status: public title: 'Retinal metric: a stimulus distance measure derived from population neural responses' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2918' abstract: - lang: eng text: "Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n" acknowledgement: This work was supported by the SNSF, the Swiss SystemsX.ch initiative and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers in Genetics and Chemical Biology programmes and the Polish–Swiss research program (M.G-G.). author: - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Laurence full_name: Abrami, Laurence last_name: Abrami - first_name: Laurent full_name: Holtzer, Laurent last_name: Holtzer - 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: Françoise full_name: Van Der Goot, Françoise last_name: Van Der Goot - first_name: Marcos full_name: González Gaitán, Marcos last_name: González Gaitán citation: ama: Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 2013;15(1):28-39. doi:10.1038/ncb2632 apa: Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot, F., & González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2632 chicago: Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg, Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” Nature Cell Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/ncb2632. ieee: I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” Nature Cell Biology, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013. ista: Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 15(1), 28–39. mla: Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” Nature Cell Biology, vol. 15, no. 1, Nature Publishing Group, 2013, pp. 28–39, doi:10.1038/ncb2632. short: I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot, M. González Gaitán, Nature Cell Biology 15 (2013) 28–39. date_created: 2018-12-11T12:00:20Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:41Z day: '01' department: - _id: CaHe doi: 10.1038/ncb2632 intvolume: ' 15' issue: '1' language: - iso: eng month: '01' oa_version: None page: 28 - 39 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '3819' quality_controlled: '1' scopus_import: 1 status: public title: Anthrax toxin receptor 2a controls mitotic spindle positioning type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2919' abstract: - lang: eng text: The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth. author: - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Urszula full_name: Kania, Urszula id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 2013;32(2):260-274. doi:10.1038/emboj.2012.310 apa: Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.310 chicago: Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.310. ieee: P. Baster et al., “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” EMBO Journal, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013. ista: Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274. mla: Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” EMBO Journal, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:10.1038/emboj.2012.310. short: P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274. date_created: 2018-12-11T12:00:20Z date_published: 2013-01-23T00:00:00Z date_updated: 2021-01-12T07:00:41Z day: '23' department: - _id: JiFr doi: 10.1038/emboj.2012.310 external_id: pmid: - '23211744' intvolume: ' 32' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/ month: '01' oa: 1 oa_version: Submitted Version page: 260 - 274 pmid: 1 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3818' quality_controlled: '1' scopus_import: 1 status: public title: SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2920' abstract: - lang: eng text: Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen. author: - first_name: Julien full_name: Compagnon, Julien id: 2E3E0988-F248-11E8-B48F-1D18A9856A87 last_name: Compagnon - 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 citation: ama: Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 2013;32(1):1-3. doi:10.1038/emboj.2012.325 apa: Compagnon, J., & Heisenberg, C.-P. J. (2013). Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.325 chicago: Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.325. ieee: J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013. ista: Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 32(1), 1–3. mla: Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 1–3, doi:10.1038/emboj.2012.325. short: J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3. date_created: 2018-12-11T12:00:20Z date_published: 2013-01-09T00:00:00Z date_updated: 2021-01-12T07:00:42Z day: '09' department: - _id: CaHe doi: 10.1038/emboj.2012.325 external_id: pmid: - '23211745' intvolume: ' 32' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/ month: '01' oa: 1 oa_version: Submitted Version page: 1 - 3 pmid: 1 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3817' quality_controlled: '1' scopus_import: 1 status: public title: Neurulation coordinating cell polarisation and lumen formation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2940' abstract: - lang: eng text: "A chain rule for an entropy notion H(.) states that the entropy H(X) of a variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)>= H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)>= H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability entropy and several variants of HILL entropy) satisfy the chain rule for conditional entropy, though here not only the quantity decreases by l, but also the quality of the entropy decreases exponentially in l. However, for \r\nthe standard notion of conditional HILL entropy (the computational equivalent of min-entropy) the existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that for conditional HILL entropy no meaningful chain rule exists, assuming the existence of one-way permutations: there exist distributions X,Y,A, where A is a distribution over a single bit, but $H(X|Y)>>H(X|Y,A)$, even if we simultaneously allow for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying our construction is based on a surprising connection between the chain rule for HILL entropy and deniable encryption. " alternative_title: - LNCS author: - first_name: Stephan full_name: Krenn, Stephan id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Akshay full_name: Wadia, Akshay last_name: Wadia citation: ama: 'Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed. Vol 7785. Springer; 2013:23-39. doi:10.1007/978-3-642-36594-2_2' apa: 'Krenn, S., Pietrzak, K. Z., & Wadia, A. (2013). A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-642-36594-2_2' chicago: Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. https://doi.org/10.1007/978-3-642-36594-2_2. ieee: 'S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it,” presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol. 7785, pp. 23–39.' ista: 'Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. TCC: Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.' mla: Krenn, Stephan, et al. A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It. Edited by Amit Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:10.1007/978-3-642-36594-2_2. short: S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp. 23–39. conference: end_date: 2013-03-06 location: Tokyo, Japan name: 'TCC: Theory of Cryptography Conference' start_date: 2013-03-03 date_created: 2018-12-11T12:00:27Z date_published: 2013-01-29T00:00:00Z date_updated: 2023-02-23T10:00:43Z day: '29' ddc: - '000' department: - _id: KrPi doi: 10.1007/978-3-642-36594-2_2 ec_funded: 1 editor: - first_name: Amit full_name: Sahai, Amit last_name: Sahai file: - access_level: open_access checksum: beb0cc1c0579da2d2e84394230a5da78 content_type: application/pdf creator: dernst date_created: 2019-01-22T14:11:11Z date_updated: 2020-07-14T12:45:54Z file_id: '5875' file_name: 2013_LNCS_Krenn.pdf file_size: 414823 relation: main_file file_date_updated: 2020-07-14T12:45:54Z has_accepted_license: '1' intvolume: ' 7785' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 23 - 39 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '3795' quality_controlled: '1' related_material: record: - id: '1479' relation: later_version status: public scopus_import: 1 status: public title: A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7785 year: '2013' ... --- _id: '2948' abstract: - lang: eng text: 'Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.' acknowledgement: This work was supported by the PASCAL 2 Network of Excellence (TT) and by the Newton International Fellowship (NQ) alternative_title: - LNCS author: - first_name: Tatiana full_name: Tommasi, Tatiana last_name: Tommasi - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto - first_name: Barbara full_name: Caputo, Barbara last_name: Caputo - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 2013;7724:1-15. doi:10.1007/978-3-642-37331-2_1' apa: 'Tommasi, T., Quadrianto, N., Caputo, B., & Lampert, C. (2013). Beyond dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. https://doi.org/10.1007/978-3-642-37331-2_1' chicago: 'Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert. “Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-37331-2_1.' ieee: 'T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013.' ista: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 7724, 1–15.' mla: 'Tommasi, Tatiana, et al. Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer. Vol. 7724, Springer, 2013, pp. 1–15, doi:10.1007/978-3-642-37331-2_1.' short: T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15. conference: end_date: 2012-11-09 location: Daejeon, Korea name: 'ACCV: Asian Conference on Computer Vision' start_date: 2012-11-05 date_created: 2018-12-11T12:00:30Z date_published: 2013-04-04T00:00:00Z date_updated: 2020-08-11T10:09:54Z day: '04' ddc: - '000' department: - _id: ChLa doi: 10.1007/978-3-642-37331-2_1 file: - access_level: open_access checksum: a0a7234a89e2192af655b0d0ae3bf445 content_type: application/pdf creator: dernst date_created: 2019-01-22T14:03:11Z date_updated: 2020-07-14T12:45:55Z file_id: '5874' file_name: 2012_ACCV_Tommasi.pdf file_size: 1513620 relation: main_file file_date_updated: 2020-07-14T12:45:55Z has_accepted_license: '1' intvolume: ' 7724' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 1 - 15 publication_status: published publisher: Springer publist_id: '3784' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: 'Beyond dataset bias: Multi-task unaligned shared knowledge transfer' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7724 year: '2013' ... --- _id: '2973' abstract: - lang: eng text: "Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building blocks of many practical cryptographic applications such as identification schemes, group signatures, and secure multiparty computation. Currently, first applications that critically rely on ZK-PoKs are being deployed in the real world. The most prominent example is Direct Anonymous Attestation (DAA), which was adopted by the Trusted Computing Group (TCG) and implemented as one of the functionalities of the cryptographic Trusted Platform Module (TPM) chip.\n\nImplementing systems using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking, significantly more complex than standard crypto primitives, such as encryption and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming and error-prone, in particular for developers with minor or no cryptographic skills. \n\nIn this paper we report on our ongoing and future research vision with the goal to bring ZK-PoK to practice by making them accessible to crypto and security engineers. To this end we are developing compilers and related tools that support and partially automate the design, implementation, verification and secure implementation of ZK-PoK protocols." acknowledgement: This work is being performed within the FP7 EU project CACE (Computer Aided Cryptography Engineering). alternative_title: - LNCS author: - first_name: Endre full_name: Bangerter, Endre last_name: Bangerter - first_name: Stefania full_name: Barzan, Stefania last_name: Barzan - first_name: Stephan full_name: Stephan Krenn id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 - first_name: Ahmad full_name: Sadeghi, Ahmad-Reza last_name: Sadeghi - first_name: Thomas full_name: Schneider, Thomas last_name: Schneider - first_name: Joe full_name: Tsay, Joe-Kai last_name: Tsay citation: ama: 'Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. Bringing Zero-Knowledge Proofs of Knowledge to Practice. In: Christianson B, Malcolm J, Matyas V, Roe M, eds. Vol 7028. Springer; 2013:51-62. doi:10.1007/978-3-642-36213-2_9' apa: 'Bangerter, E., Barzan, S., Krenn, S., Sadeghi, A., Schneider, T., & Tsay, J. (2013). Bringing Zero-Knowledge Proofs of Knowledge to Practice. In B. Christianson, J. Malcolm, V. Matyas, & M. Roe (Eds.) (Vol. 7028, pp. 51–62). Presented at the SPW: Security Protocols Workshop, Springer. https://doi.org/10.1007/978-3-642-36213-2_9' chicago: Bangerter, Endre, Stefania Barzan, Stephan Krenn, Ahmad Sadeghi, Thomas Schneider, and Joe Tsay. “Bringing Zero-Knowledge Proofs of Knowledge to Practice.” edited by Bruce Christianson, James Malcolm, Vashek Matyas, and Michael Roe, 7028:51–62. Springer, 2013. https://doi.org/10.1007/978-3-642-36213-2_9. ieee: 'E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, and J. Tsay, “Bringing Zero-Knowledge Proofs of Knowledge to Practice,” presented at the SPW: Security Protocols Workshop, 2013, vol. 7028, pp. 51–62.' ista: 'Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. 2013. Bringing Zero-Knowledge Proofs of Knowledge to Practice. SPW: Security Protocols Workshop, LNCS, vol. 7028, 51–62.' mla: Bangerter, Endre, et al. Bringing Zero-Knowledge Proofs of Knowledge to Practice. Edited by Bruce Christianson et al., vol. 7028, Springer, 2013, pp. 51–62, doi:10.1007/978-3-642-36213-2_9. short: E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, J. Tsay, in:, B. Christianson, J. Malcolm, V. Matyas, M. Roe (Eds.), Springer, 2013, pp. 51–62. conference: name: 'SPW: Security Protocols Workshop' date_created: 2018-12-11T12:00:38Z date_published: 2013-01-08T00:00:00Z date_updated: 2021-01-12T07:40:10Z day: '08' doi: 10.1007/978-3-642-36213-2_9 editor: - first_name: Bruce full_name: Christianson, Bruce last_name: Christianson - first_name: James full_name: Malcolm, James A. last_name: Malcolm - first_name: Vashek full_name: Matyas, Vashek last_name: Matyas - first_name: Michael full_name: Roe, Michael last_name: Roe extern: 1 intvolume: ' 7028' main_file_link: - open_access: '1' url: http://eprint.iacr.org/2009/211.pdf month: '01' oa: 1 page: 51 - 62 publication_status: published publisher: Springer publist_id: '3732' quality_controlled: 0 status: public title: Bringing Zero-Knowledge Proofs of Knowledge to Practice type: conference volume: 7028 year: '2013' ... --- _id: '3116' abstract: - lang: eng text: Multithreaded programs coordinate their interaction through synchronization primitives like mutexes and semaphores, which are managed by an OS-provided resource manager. We propose algorithms for the automatic construction of code-aware resource managers for multithreaded embedded applications. Such managers use knowledge about the structure and resource usage (mutex and semaphore usage) of the threads to guarantee deadlock freedom and progress while managing resources in an efficient way. Our algorithms compute managers as winning strategies in certain infinite games, and produce a compact code description of these strategies. We have implemented the algorithms in the tool Cynthesis. Given a multithreaded program in C, the tool produces C code implementing a code-aware resource manager. We show in experiments that Cynthesis produces compact resource managers within a few minutes on a set of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business Media, LLC. acknowledgement: This research was supported in part by the National Science Foundation CAREER award CCR-0132780, by the ONR grant N00014-02-1-0671, by the National Science Foundation grants CCR-0427202 and CCR-0234690, and by the ARP award TO.030.MM.D. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Marco full_name: Faella, Marco last_name: Faella - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Vishwanath full_name: Raman, Vishwanath last_name: Raman citation: ama: Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. Code aware resource management. Formal Methods in System Design. 2013;42(2):142-174. doi:10.1007/s10703-012-0170-4 apa: Chatterjee, K., De Alfaro, L., Faella, M., Majumdar, R., & Raman, V. (2013). Code aware resource management. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0170-4 chicago: Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Ritankar Majumdar, and Vishwanath Raman. “Code Aware Resource Management.” Formal Methods in System Design. Springer, 2013. https://doi.org/10.1007/s10703-012-0170-4. ieee: K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware resource management,” Formal Methods in System Design, vol. 42, no. 2. Springer, pp. 142–174, 2013. ista: Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. 2013. Code aware resource management. Formal Methods in System Design. 42(2), 142–174. mla: Chatterjee, Krishnendu, et al. “Code Aware Resource Management.” Formal Methods in System Design, vol. 42, no. 2, Springer, 2013, pp. 142–74, doi:10.1007/s10703-012-0170-4. short: K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, V. Raman, Formal Methods in System Design 42 (2013) 142–174. date_created: 2018-12-11T12:01:29Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T07:41:10Z day: '01' department: - _id: KrCh doi: 10.1007/s10703-012-0170-4 intvolume: ' 42' issue: '2' language: - iso: eng month: '04' oa_version: None page: 142 - 174 publication: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '3583' quality_controlled: '1' scopus_import: 1 status: public title: Code aware resource management type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2013' ... --- _id: '2815' abstract: - lang: eng text: The fact that a sum of isotropic Gaussian kernels can have more modes than kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally not well studied in higher dimensions. We study a configuration of n+1 Gaussian kernels for which there are exactly n+2 modes. We show that all modes lie on a finite set of lines, which we call axes, and study the restriction of the Gaussian mixture to these axes in order to discover that there are an exponential number of critical points in this configuration. Although the existence of ghost modes remained unknown due to the difficulty of finding examples in ℝ2, we show that the resilience of ghost modes grows like the square root of the dimension. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. acknowledgement: This research is partially supported by the National Science Foundation (NSF) under Grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053. article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Brittany Terese full_name: Fasy, Brittany Terese id: F65D502E-E68D-11E9-9252-C644099818F6 last_name: Fasy - first_name: Günter full_name: Rote, Günter last_name: Rote citation: ama: 'Edelsbrunner H, Fasy BT, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Discrete & Computational Geometry. 2013;49(4):797-822. doi:10.1007/s00454-013-9517-x' apa: 'Edelsbrunner, H., Fasy, B. T., & Rote, G. (2013). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9517-x' chicago: 'Edelsbrunner, Herbert, Brittany Terese Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” Discrete & Computational Geometry. Springer, 2013. https://doi.org/10.1007/s00454-013-9517-x.' ieee: 'H. Edelsbrunner, B. T. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” Discrete & Computational Geometry, vol. 49, no. 4. Springer, pp. 797–822, 2013.' ista: 'Edelsbrunner H, Fasy BT, Rote G. 2013. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Discrete & Computational Geometry. 49(4), 797–822.' mla: 'Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” Discrete & Computational Geometry, vol. 49, no. 4, Springer, 2013, pp. 797–822, doi:10.1007/s00454-013-9517-x.' short: H. Edelsbrunner, B.T. Fasy, G. Rote, Discrete & Computational Geometry 49 (2013) 797–822. date_created: 2018-12-11T11:59:44Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-02-23T11:13:49Z day: '01' department: - _id: HeEd doi: 10.1007/s00454-013-9517-x intvolume: ' 49' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00454-013-9517-x month: '06' oa: 1 oa_version: Published Version page: 797 - 822 publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer publist_id: '3991' quality_controlled: '1' related_material: record: - id: '3134' relation: earlier_version status: public scopus_import: '1' status: public title: 'Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2013' ... --- _id: '2939' abstract: - lang: eng text: In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ > 0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number of homology classes with persistence at least (1 - δ) Γ, n is the total number of simplices in the complex, d its dimension, and R d (n) is the complexity of computing the rank of an n × n matrix with O (d n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ) Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C (1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} > 0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n log n). acknowledgement: The authors thank Herbert Edelsbrunner for many helpful discussions and suggestions. Moreover, they are grateful for the careful reviews that helped to improve the quality of the paper. author: - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 citation: ama: 'Chen C, Kerber M. An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. 2013;46(4):435-447. doi:10.1016/j.comgeo.2012.02.010' apa: 'Chen, C., & Kerber, M. (2013). An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2012.02.010' chicago: 'Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” Computational Geometry: Theory and Applications. Elsevier, 2013. https://doi.org/10.1016/j.comgeo.2012.02.010.' ieee: 'C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” Computational Geometry: Theory and Applications, vol. 46, no. 4. Elsevier, pp. 435–447, 2013.' ista: 'Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. 46(4), 435–447.' mla: 'Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” Computational Geometry: Theory and Applications, vol. 46, no. 4, Elsevier, 2013, pp. 435–47, doi:10.1016/j.comgeo.2012.02.010.' short: 'C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013) 435–447.' date_created: 2018-12-11T12:00:27Z date_published: 2013-05-01T00:00:00Z date_updated: 2023-02-23T11:24:10Z day: '01' department: - _id: HeEd doi: 10.1016/j.comgeo.2012.02.010 intvolume: ' 46' issue: '4' language: - iso: eng month: '05' oa_version: None page: 435 - 447 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '3796' quality_controlled: '1' related_material: record: - id: '3367' relation: earlier_version status: public scopus_import: 1 status: public title: An output sensitive algorithm for persistent homology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2013' ... --- _id: '344' abstract: - lang: eng text: Copper-based selenides are attracting increasing interest due to their outstanding optoelectronic and thermoelectric properties. Herein a novel colloidal synthetic route to prepare Cu2SnSe3 nanocrystals with controlled size, shape and composition is presented. The high yield of the developed procedure allowed its up-scaling to the production of grams of colloidal Cu2SnSe3 nanocrystals. These nanocrystals were used as building blocks for the production of Cu2SnSe3 bulk nanostructured materials by spark plasma sintering. The thermoelectric properties of the prepared nanocrystalline Cu2SnSe3 pellets were characterized in the temperature range from 300 to 720 K. The obtained results show the bottom-up production of nanocrystalline materials from solution-processed nanocrystals to be a potentially advantageous alternative to conventional methods of production of efficient thermoelectric materials. article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Umberto full_name: Anselmi Tamburini, Umberto last_name: Anselmi Tamburini - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Stéphane full_name: Gorsse, Stéphane last_name: Gorsse - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Antonio full_name: López, Antonio last_name: López - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Ibáñez M, Cadavid D, Anselmi Tamburini U, et al. Colloidal synthesis and thermoelectric properties of Cu 2SnSe3 nanocrystals. Journal of Materials Chemistry A. 2013;1(4):1421-1426. doi:10.1039/C2TA00419D apa: Ibáñez, M., Cadavid, D., Anselmi Tamburini, U., Zamani, R., Gorsse, S., Li, W., … Cabot, A. (2013). Colloidal synthesis and thermoelectric properties of Cu 2SnSe3 nanocrystals. Journal of Materials Chemistry A. Royal Society of Chemistry. https://doi.org/10.1039/C2TA00419D chicago: Ibáñez, Maria, Doris Cadavid, Umberto Anselmi Tamburini, Reza Zamani, Stéphane Gorsse, Wenhua Li, Antonio López, Joan Morante, Jordi Arbiol, and Andreu Cabot. “Colloidal Synthesis and Thermoelectric Properties of Cu 2SnSe3 Nanocrystals.” Journal of Materials Chemistry A. Royal Society of Chemistry, 2013. https://doi.org/10.1039/C2TA00419D. ieee: M. Ibáñez et al., “Colloidal synthesis and thermoelectric properties of Cu 2SnSe3 nanocrystals,” Journal of Materials Chemistry A, vol. 1, no. 4. Royal Society of Chemistry, pp. 1421–1426, 2013. ista: Ibáñez M, Cadavid D, Anselmi Tamburini U, Zamani R, Gorsse S, Li W, López A, Morante J, Arbiol J, Cabot A. 2013. Colloidal synthesis and thermoelectric properties of Cu 2SnSe3 nanocrystals. Journal of Materials Chemistry A. 1(4), 1421–1426. mla: Ibáñez, Maria, et al. “Colloidal Synthesis and Thermoelectric Properties of Cu 2SnSe3 Nanocrystals.” Journal of Materials Chemistry A, vol. 1, no. 4, Royal Society of Chemistry, 2013, pp. 1421–26, doi:10.1039/C2TA00419D. short: M. Ibáñez, D. Cadavid, U. Anselmi Tamburini, R. Zamani, S. Gorsse, W. Li, A. López, J. Morante, J. Arbiol, A. Cabot, Journal of Materials Chemistry A 1 (2013) 1421–1426. date_created: 2018-12-11T11:45:56Z date_published: 2013-01-28T00:00:00Z date_updated: 2021-01-12T07:43:28Z day: '28' doi: 10.1039/C2TA00419D extern: '1' intvolume: ' 1' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-00917429/ month: '01' oa: 1 oa_version: Submitted Version page: 1421 - 1426 publication: Journal of Materials Chemistry A publication_status: published publisher: Royal Society of Chemistry publist_id: '7484' quality_controlled: '1' status: public title: Colloidal synthesis and thermoelectric properties of Cu 2SnSe3 nanocrystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '352' abstract: - lang: eng text: The presence of organic ligands on the surface of colloidal nanoparticles strongly limits their performance in technological applications where charge carrier transfer/transport plays an important role. We use metal salts, matched with the nanoparticle composition, to eliminate the surface organic ligands without introducing extrinsic impurities in the final nanomaterial. The potential of the simple, general and scalable processes presented here is demonstrated by characterizing the thermoelectric properties of nanostructured Ag2Te produced by the bottom up assembly of Ag2Te nanocrystals. A 6-fold increase of the thermoelectric figure of merit of Ag2Te was obtained when organic ligands were displaced by AgNO3. The same procedure can enhance the performance of nanocrystals and nanocrystal-based devices in a broad range of applications, from photovoltaics and thermoelectrics to catalysis. article_processing_charge: No article_type: original author: - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Oscar full_name: Durá, Oscar last_name: Durá - first_name: Marco full_name: López De La Torre, Marco last_name: López De La Torre - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Cadavid D, Ibáñez M, Shavel A, Durá O, López De La Torre M, Cabot A. Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials Chemistry A. 2013;1(15):4864-4870. doi:10.1039/C3TA01455J' apa: 'Cadavid, D., Ibáñez, M., Shavel, A., Durá, O., López De La Torre, M., & Cabot, A. (2013). Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials Chemistry A. Royal Society of Chemistry. https://doi.org/10.1039/C3TA01455J' chicago: 'Cadavid, Doris, Maria Ibáñez, Alexey Shavel, Oscar Durá, Marco López De La Torre, and Andreu Cabot. “Organic Ligand Displacement by Metal Salts to Enhance Nanoparticle Functionality: Thermoelectric Properties of Ag Inf 2 Inf Te.” Journal of Materials Chemistry A. Royal Society of Chemistry, 2013. https://doi.org/10.1039/C3TA01455J.' ieee: 'D. Cadavid, M. Ibáñez, A. Shavel, O. Durá, M. López De La Torre, and A. Cabot, “Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te,” Journal of Materials Chemistry A, vol. 1, no. 15. Royal Society of Chemistry, pp. 4864–4870, 2013.' ista: 'Cadavid D, Ibáñez M, Shavel A, Durá O, López De La Torre M, Cabot A. 2013. Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials Chemistry A. 1(15), 4864–4870.' mla: 'Cadavid, Doris, et al. “Organic Ligand Displacement by Metal Salts to Enhance Nanoparticle Functionality: Thermoelectric Properties of Ag Inf 2 Inf Te.” Journal of Materials Chemistry A, vol. 1, no. 15, Royal Society of Chemistry, 2013, pp. 4864–70, doi:10.1039/C3TA01455J.' short: D. Cadavid, M. Ibáñez, A. Shavel, O. Durá, M. López De La Torre, A. Cabot, Journal of Materials Chemistry A 1 (2013) 4864–4870. date_created: 2018-12-11T11:45:58Z date_published: 2013-02-13T00:00:00Z date_updated: 2021-01-12T07:44:02Z day: '13' doi: 10.1039/C3TA01455J extern: '1' intvolume: ' 1' issue: '15' language: - iso: eng month: '02' oa_version: None page: 4864 - 4870 publication: Journal of Materials Chemistry A publication_status: published publisher: Royal Society of Chemistry publist_id: '7481' quality_controlled: '1' status: public title: 'Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '378' abstract: - lang: eng text: Until recently, to prepare nanocrystals of a new material, scientists searched their shelves for the appropriate molecular precursors, surfactants, and solvents. They then optimized the reaction conditions for the atoms to self-assemble into monodisperse nanocrystals (1). This approach is being replaced by a simpler strategy, in which preformed nanocrystals serve as templates to produce nanoparticles with a different composition through chemical transformation. On page 964 of this issue, Oh et al. (2) report a powerful mechanism that allows the composition of oxide nanoparticles to be transformed in solution and at low temperatures. article_processing_charge: No author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Ibáñez M, Cabot A. All change for nanocrystals. Science. 2013;340(6135):935-936. doi:10.1126/science.1239221 apa: Ibáñez, M., & Cabot, A. (2013). All change for nanocrystals. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1239221 chicago: Ibáñez, Maria, and Andreu Cabot. “All Change for Nanocrystals.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239221. ieee: M. Ibáñez and A. Cabot, “All change for nanocrystals,” Science, vol. 340, no. 6135. American Association for the Advancement of Science, pp. 935–936, 2013. ista: Ibáñez M, Cabot A. 2013. All change for nanocrystals. Science. 340(6135), 935–936. mla: Ibáñez, Maria, and Andreu Cabot. “All Change for Nanocrystals.” Science, vol. 340, no. 6135, American Association for the Advancement of Science, 2013, pp. 935–36, doi:10.1126/science.1239221. short: M. Ibáñez, A. Cabot, Science 340 (2013) 935–936. date_created: 2018-12-11T11:46:08Z date_published: 2013-05-24T00:00:00Z date_updated: 2021-01-12T07:52:09Z day: '24' doi: 10.1126/science.1239221 extern: '1' intvolume: ' 340' issue: '6135' language: - iso: eng month: '05' oa_version: None page: 935 - 936 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '7451' status: public title: All change for nanocrystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 340 year: '2013' ... --- _id: '3261' abstract: - lang: eng text: Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network. author: - first_name: Julien full_name: Dubuis, Julien last_name: Dubuis - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Eric full_name: Wieschaus, Eric last_name: Wieschaus - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. PNAS. 2013;110(41):16301-16308. doi:10.1073/pnas.1315642110 apa: Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., & Bialek, W. (2013). Positional information, in bits. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315642110 chicago: Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1315642110. ieee: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013. ista: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308. mla: Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110. short: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308. date_created: 2018-12-11T12:02:19Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T07:42:13Z day: '08' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.1315642110 external_id: pmid: - '24089448' file: - access_level: open_access checksum: ecd859fe52a562193027d428b5524a8d content_type: application/pdf creator: dernst date_created: 2019-01-22T13:53:23Z date_updated: 2020-07-14T12:46:06Z file_id: '5873' file_name: 2013_PNAS_Dubuis.pdf file_size: 1670548 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 110' issue: '41' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 16301 - 16308 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3387' quality_controlled: '1' scopus_import: 1 status: public title: Positional information, in bits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '331' abstract: - lang: eng text: We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents. article_processing_charge: No article_type: original author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Pilar full_name: Rivera Gil, Pilar last_name: Rivera Gil - first_name: Beatriz full_name: Pelaz, Beatriz last_name: Pelaz - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Ramon full_name: Alvarez Puebla, Ramon last_name: Alvarez Puebla - first_name: Wolfgang full_name: Parak, Wolfgang last_name: Parak - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 2013;135(19):7098-7101. doi:10.1021/ja401428e' apa: 'Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., … Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja401428e' chicago: 'Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez, Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society. ACS, 2013. https://doi.org/10.1021/ja401428e.' ieee: 'W. Li et al., “CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents,” Journal of the American Chemical Society, vol. 135, no. 19. ACS, pp. 7098–7101, 2013.' ista: 'Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 135(19), 7098–7101.' mla: 'Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society, vol. 135, no. 19, ACS, 2013, pp. 7098–101, doi:10.1021/ja401428e.' short: W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel, R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 7098–7101. date_created: 2018-12-11T11:45:51Z date_published: 2013-04-30T00:00:00Z date_updated: 2021-01-12T07:42:33Z day: '30' doi: 10.1021/ja401428e extern: '1' intvolume: ' 135' issue: '19' language: - iso: eng month: '04' oa_version: None page: 7098 - 7101 publication: Journal of the American Chemical Society publication_status: published publisher: ACS publist_id: '7521' quality_controlled: '1' status: public title: 'CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '3321' author: - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H, eds. Encyclopedia of Systems Biology. Vol 3. Springer; 2013:1069-1069. doi:10.1007/978-1-4419-9863-7_604' apa: Quadrianto, N., & Lampert, C. (2013). Kernel based learning. In W. Dubitzky, O. Wolkenhauer, K. Cho, & H. Yokota (Eds.), Encyclopedia of Systems Biology (Vol. 3, pp. 1069–1069). Springer. https://doi.org/10.1007/978-1-4419-9863-7_604 chicago: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In Encyclopedia of Systems Biology, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho, and Hiroki Yokota, 3:1069–1069. Springer, 2013. https://doi.org/10.1007/978-1-4419-9863-7_604. ieee: N. Quadrianto and C. Lampert, “Kernel based learning,” in Encyclopedia of Systems Biology, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Eds. Springer, 2013, pp. 1069–1069. ista: 'Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of Systems Biology. vol. 3, 1069–1069.' mla: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” Encyclopedia of Systems Biology, edited by Werner Dubitzky et al., vol. 3, Springer, 2013, pp. 1069–1069, doi:10.1007/978-1-4419-9863-7_604. short: N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069. date_created: 2018-12-11T12:02:39Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:42:38Z day: '01' department: - _id: ChLa doi: 10.1007/978-1-4419-9863-7_604 editor: - first_name: Werner full_name: Dubitzky, Werner last_name: Dubitzky - first_name: Olaf full_name: Wolkenhauer, Olaf last_name: Wolkenhauer - first_name: Kwang full_name: Cho, Kwang last_name: Cho - first_name: Hiroki full_name: Yokota, Hiroki last_name: Yokota intvolume: ' 3' language: - iso: eng month: '01' oa_version: None page: 1069 - 1069 publication: Encyclopedia of Systems Biology publication_status: published publisher: Springer publist_id: '3314' quality_controlled: '1' status: public title: Kernel based learning type: encyclopedia_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2831' abstract: - lang: eng text: 'We consider Markov decision processes (MDPs) with Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning states from where the objective can be ensured with probability 1. Our contributions are as follows: First, we present the first subquadratic symbolic algorithm to compute the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes O(n · √ m) symbolic steps as compared to the previous known algorithm that takes O(n 2) symbolic steps, where n is the number of states and m is the number of edges of the MDP. In practice MDPs have constant out-degree, and then our symbolic algorithm takes O(n · √ n) symbolic steps, as compared to the previous known O(n 2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose algorithm, with the following two properties: (a) the algorithm iteratively computes subsets of the almost-sure winning set and its complement, as compared to all previous algorithms that discover the almost-sure winning set upon termination; and (b) requires O(n · √ K) symbolic steps, where K is the maximal number of edges of strongly connected components (scc''s) of the MDP. The win-lose algorithm requires symbolic computation of scc''s. Third, we improve the algorithm for symbolic scc computation; the previous known algorithm takes linear symbolic steps, and our new algorithm improves the constants associated with the linear number of steps. In the worst case the previous known algorithm takes 5×n symbolic steps, whereas our new algorithm takes 4×n symbolic steps.' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Manas full_name: Joglekar, Manas last_name: Joglekar - first_name: Nisarg full_name: Shah, Nisarg last_name: Shah citation: ama: Chatterjee K, Henzinger MH, Joglekar M, Shah N. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. Formal Methods in System Design. 2013;42(3):301-327. doi:10.1007/s10703-012-0180-2 apa: Chatterjee, K., Henzinger, M. H., Joglekar, M., & Shah, N. (2013). Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0180-2 chicago: Chatterjee, Krishnendu, Monika H Henzinger, Manas Joglekar, and Nisarg Shah. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” Formal Methods in System Design. Springer, 2013. https://doi.org/10.1007/s10703-012-0180-2. ieee: K. Chatterjee, M. H. Henzinger, M. Joglekar, and N. Shah, “Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives,” Formal Methods in System Design, vol. 42, no. 3. Springer, pp. 301–327, 2013. ista: Chatterjee K, Henzinger MH, Joglekar M, Shah N. 2013. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. Formal Methods in System Design. 42(3), 301–327. mla: Chatterjee, Krishnendu, et al. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” Formal Methods in System Design, vol. 42, no. 3, Springer, 2013, pp. 301–27, doi:10.1007/s10703-012-0180-2. short: K. Chatterjee, M.H. Henzinger, M. Joglekar, N. Shah, Formal Methods in System Design 42 (2013) 301–327. date_created: 2018-12-11T11:59:49Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-02-23T11:23:04Z day: '01' department: - _id: KrCh doi: 10.1007/s10703-012-0180-2 ec_funded: 1 external_id: arxiv: - '1104.3348' intvolume: ' 42' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.3348 month: '06' oa: 1 oa_version: Preprint page: 301 - 327 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '3968' quality_controlled: '1' related_material: record: - id: '3342' relation: earlier_version status: public scopus_import: '1' status: public title: Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 42 year: '2013' ... --- _id: '342' abstract: - lang: eng text: Morphology is a key parameter in the design of novel nanocrystals and nanomaterials with controlled functional properties. Here, we demonstrate the potential of foreign metal ions to tune the morphology of colloidal semiconductor nanoparticles. We illustrate the underlying mechanism by preparing copper selenide nanocubes in the presence of Al ions. We further characterize the plasmonic properties of the obtained nanocrystals and demonstrate their potential as a platform to produce cubic nanoparticles with different composition by cation exchange. © 2013 American Chemical Society. acknowledgement: The research was supported by the European Regional Development Funds. M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge MAT2010-15138. article_processing_charge: No article_type: original author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Zamani R, Ibáñez M, et al. Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. Journal of the American Chemical Society. 2013;135(12):4664-4667. doi:10.1021/ja400472m' apa: 'Li, W., Zamani, R., Ibáñez, M., Cadavid, D., Shavel, A., Morante, J., … Cabot, A. (2013). Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja400472m' chicago: 'Li, Wenhua, Reza Zamani, Maria Ibáñez, Doris Cadavid, Alexey Shavel, Joan Morante, Jordi Arbiol, and Andreu Cabot. “Metal Ions to Control the Morphology of Semiconductor Nanoparticles: Copper Selenide Nanocubes.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja400472m.' ieee: 'W. Li et al., “Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes,” Journal of the American Chemical Society, vol. 135, no. 12. American Chemical Society, pp. 4664–4667, 2013.' ista: 'Li W, Zamani R, Ibáñez M, Cadavid D, Shavel A, Morante J, Arbiol J, Cabot A. 2013. Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. Journal of the American Chemical Society. 135(12), 4664–4667.' mla: 'Li, Wenhua, et al. “Metal Ions to Control the Morphology of Semiconductor Nanoparticles: Copper Selenide Nanocubes.” Journal of the American Chemical Society, vol. 135, no. 12, American Chemical Society, 2013, pp. 4664–67, doi:10.1021/ja400472m.' short: W. Li, R. Zamani, M. Ibáñez, D. Cadavid, A. Shavel, J. Morante, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 4664–4667. date_created: 2018-12-11T11:45:55Z date_published: 2013-03-07T00:00:00Z date_updated: 2021-01-12T07:43:21Z day: '07' doi: 10.1021/ja400472m extern: '1' intvolume: ' 135' issue: '12' language: - iso: eng month: '03' oa_version: None page: 4664 - 4667 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7482' quality_controlled: '1' status: public title: 'Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '343' abstract: - lang: eng text: The bottom-up assembly of nanocrystals provides access to a three-dimensional composition control at the nanoscale not attainable by any other technology. In particular, colloidal nanoheterostructures, with intrinsic multiphase organization, are especially appealing building blocks for the bottom-up production of nanocomposites. In the present work, we use PbTe-PbS as the model material system and thermoelectricity as the paradigmatic application to investigate the potential of the bottom-up assembly of core-shell nanoparticles to produce functional nanocomposites. With this goal in mind, a rapid, high-yield and scalable colloidal synthetic route to prepare grams of PbTe@PbS core-shell nanoparticles with unprecedented narrow size distributions and exceptional composition control is detailed. PbTe@PbS nanoparticles were used as building blocks for the bottom-up production of PbTe-PbS nanocomposites with tuned composition. In such PbTe-PbS nanocomposites, synergistic nanocrystal doping effects result in up to 10-fold higher electrical conductivities than in pure PbTe and PbS nanomaterials. At the same time, the acoustic impedance mismatch between PbTe and PbS phases and a partial phase alloying provide PbTe-PbS nanocomposites with strongly reduced thermal conductivities. As a result, record thermoelectric figures of merit (ZT) of ∼1.1 were obtained from undoped PbTe and PbS phases at 710 K. These high ZT values prove the potential of the proposed processes to produce efficient functional nanomaterials with programmable properties. © 2013 American Chemical Society. acknowledgement: "The research was supported by the European Regional Development Funds (ERDF, “FEDER Programa Competitivitat de Catalunya 2007-2013”) and the Spanish MICINN Projects MAT2008-05779, MAT2010-15138, CSD2009-00050, and CSD2009-00013. M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE.\r\n\r\nThe authors declare no competing financial interest." article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Stéphane full_name: Gorsse, Stéphane last_name: Gorsse - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Silvia full_name: Ortega, Silvia last_name: Ortega - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Ibáñez M, Zamani R, Gorsse S, et al. Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties. ACS Nano. 2013;7(3):2573-2586. doi:10.1021/nn305971v' apa: 'Ibáñez, M., Zamani, R., Gorsse, S., Fan, J., Ortega, S., Cadavid, D., … Cabot, A. (2013). Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn305971v' chicago: 'Ibáñez, Maria, Reza Zamani, Stéphane Gorsse, Jiandong Fan, Silvia Ortega, Doris Cadavid, Joan Morante, Jordi Arbiol, and Andreu Cabot. “Core Shell Nanoparticles as Building Blocks for the Bottom-up Production of Functional Nanocomposites: PbTe PbS Thermoelectric Properties.” ACS Nano. American Chemical Society, 2013. https://doi.org/10.1021/nn305971v.' ieee: 'M. Ibáñez et al., “Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties,” ACS Nano, vol. 7, no. 3. American Chemical Society, pp. 2573–2586, 2013.' ista: 'Ibáñez M, Zamani R, Gorsse S, Fan J, Ortega S, Cadavid D, Morante J, Arbiol J, Cabot A. 2013. Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties. ACS Nano. 7(3), 2573–2586.' mla: 'Ibáñez, Maria, et al. “Core Shell Nanoparticles as Building Blocks for the Bottom-up Production of Functional Nanocomposites: PbTe PbS Thermoelectric Properties.” ACS Nano, vol. 7, no. 3, American Chemical Society, 2013, pp. 2573–86, doi:10.1021/nn305971v.' short: M. Ibáñez, R. Zamani, S. Gorsse, J. Fan, S. Ortega, D. Cadavid, J. Morante, J. Arbiol, A. Cabot, ACS Nano 7 (2013) 2573–2586. date_created: 2018-12-11T11:45:55Z date_published: 2013-02-28T00:00:00Z date_updated: 2021-01-12T07:43:25Z day: '28' doi: 10.1021/nn305971v extern: '1' intvolume: ' 7' issue: '3' language: - iso: eng month: '02' oa_version: None page: 2573 - 2586 publication: ACS Nano publication_status: published publisher: American Chemical Society publist_id: '7483' quality_controlled: '1' status: public title: 'Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2013' ... --- _id: '351' abstract: - lang: eng text: 'A multistrategy approach to overcome the main challenges of nanoparticle-based solution-processed Cu2ZnSnSe4 thin film solar cells is presented. We developed an efficient ligand exchange strategy, using an antimony salt, to displace organic ligands from the surface of Cu 2ZnSnS4 nanoparticles. An automated pulsed spray-deposition system was used to deposit the nanoparticles into homogeneous and crack-free films with controlled thickness. After annealing the film in a Se-rich atmosphere, carbon-free and crystalline Cu2ZnSnSe4 absorber layers were obtained. Not only was crystallization promoted by the complete removal of organics, but also Sb itself played a critical role. The Sb-assisted crystal growth is associated with the formation of a Sb-based compound at the grain boundaries, which locally reduces the melting point, thus promoting the film diffusion-limited crystallization. ' acknowledgement: This work was supported by the European Regional Development Funds and the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486). E.S. thanks the Spanish government for the “Ramon y Cajal” fellowship (RYC-2011-09212). article_processing_charge: No article_type: original author: - first_name: Alex full_name: Carrete, Alex last_name: Carrete - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Xavier full_name: Fontané, Xavier last_name: Fontané - first_name: Joana full_name: Montserrat, Joana last_name: Montserrat - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Edgardo full_name: Saucedo, Edgardo last_name: Saucedo - first_name: Alejandro full_name: Pérez Rodríguez, Alejandro last_name: Pérez Rodríguez - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Carrete A, Shavel A, Fontané X, et al. Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical Society. 2013;135(43):15982-15985. doi:10.1021/ja4068639 apa: Carrete, A., Shavel, A., Fontané, X., Montserrat, J., Fan, J., Ibáñez, M., … Cabot, A. (2013). Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja4068639 chicago: Carrete, Alex, Alexey Shavel, Xavier Fontané, Joana Montserrat, Jiandong Fan, Maria Ibáñez, Edgardo Saucedo, Alejandro Pérez Rodríguez, and Andreu Cabot. “Antimony-Based Ligand Exchange to Promote Crystallization in Spray-Deposited Cu2ZnSnSe4 Solar Cells.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja4068639. ieee: A. Carrete et al., “Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells,” Journal of the American Chemical Society, vol. 135, no. 43. American Chemical Society, pp. 15982–15985, 2013. ista: Carrete A, Shavel A, Fontané X, Montserrat J, Fan J, Ibáñez M, Saucedo E, Pérez Rodríguez A, Cabot A. 2013. Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical Society. 135(43), 15982–15985. mla: Carrete, Alex, et al. “Antimony-Based Ligand Exchange to Promote Crystallization in Spray-Deposited Cu2ZnSnSe4 Solar Cells.” Journal of the American Chemical Society, vol. 135, no. 43, American Chemical Society, 2013, pp. 15982–85, doi:10.1021/ja4068639. short: A. Carrete, A. Shavel, X. Fontané, J. Montserrat, J. Fan, M. Ibáñez, E. Saucedo, A. Pérez Rodríguez, A. Cabot, Journal of the American Chemical Society 135 (2013) 15982–15985. date_created: 2018-12-11T11:45:58Z date_published: 2013-10-30T00:00:00Z date_updated: 2021-01-12T07:43:57Z day: '30' doi: 10.1021/ja4068639 extern: '1' intvolume: ' 135' issue: '43' language: - iso: eng month: '10' oa_version: None page: 15982 - 15985 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7479' quality_controlled: '1' status: public title: Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '353' abstract: - lang: eng text: We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents. acknowledgement: This research was supported by the European Regional Development Funds. J.A. and R.Z. acknowledge MAT2010-15138. Part of this work was supported by HFSP grant RGP0052/2012 to W.J.P. article_processing_charge: No article_type: original author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Pilar full_name: Rivera Gil, Pilar last_name: Rivera Gil - first_name: Beatriz full_name: Pelaz, Beatriz last_name: Pelaz - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Ramon full_name: Alvarez Puebla, Ramon last_name: Alvarez Puebla - first_name: Wolfgang full_name: Parak, Wolfgang last_name: Parak - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 2013;135(19):7098-7101. doi:10.1021/ja401428e' apa: 'Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., … Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja401428e' chicago: 'Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez, Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja401428e.' ieee: 'W. Li et al., “CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents,” Journal of the American Chemical Society, vol. 135, no. 19. American Chemical Society, pp. 7098–7101, 2013.' ista: 'Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 135(19), 7098–7101.' mla: 'Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society, vol. 135, no. 19, American Chemical Society, 2013, pp. 7098–101, doi:10.1021/ja401428e.' short: W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel, R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 7098–7101. date_created: 2018-12-11T11:45:59Z date_published: 2013-04-30T00:00:00Z date_updated: 2021-01-12T07:44:06Z day: '30' doi: 10.1021/ja401428e extern: '1' intvolume: ' 135' issue: '19' language: - iso: eng month: '04' oa_version: None page: 7098 - 7101 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7480' quality_controlled: '1' status: public title: 'CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '376' abstract: - lang: eng text: The compositional versatility of I2–II–IV–VI4 tetrahedrally-coordinated compounds allows for accommodating their functional properties to numerous technological applications. Among them, Cu2ZnSnSe4 is an emerging photovoltaic material and Cu2CdSnSe4 displays excellent thermoelectric properties. The third compound of this family, Cu2HgSnSe4, remains relatively unexplored. Herein, a synthetic route to produce Cu2HgSnSe4 nanoparticles with narrow size distribution and controlled composition is presented. Cu2HgSnSe4 nanoparticles were subsequently used as building blocks to produce bulk nanocrystalline materials, whose thermoelectric properties were analyzed. A very preliminary adjustment of the material composition yielded Seebeck coefficients up to 160 μV K−1, electrical conductivities close to 104 S m−1 and thermal conductivities down to 0.5 W m−1 K−1. author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Nuria full_name: García Castelló, Nuria last_name: García Castelló - first_name: Grosse full_name: Stéphane, Grosse last_name: Stéphane - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Joan full_name: Prades, Joan last_name: Prades - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Ibáñez M, Zamani R, et al. Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties. CrystEngComm. 2013;44:8966-8971. doi:10.1039/C3CE41583J' apa: 'Li, W., Ibáñez, M., Zamani, R., García Castelló, N., Stéphane, G., Cadavid, D., … Cabot, A. (2013). Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties. CrystEngComm. Royal Society of Chemistry. https://doi.org/10.1039/C3CE41583J' chicago: 'Li, Wenhua, Maria Ibáñez, Reza Zamani, Nuria García Castelló, Grosse Stéphane, Doris Cadavid, Joan Prades, Jordi Arbiol, and Andreu Cabot. “Cu2HgSnSe4 Nanoparticles: Synthesis and Thermoelectric Properties.” CrystEngComm. Royal Society of Chemistry, 2013. https://doi.org/10.1039/C3CE41583J.' ieee: 'W. Li et al., “Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties,” CrystEngComm, vol. 44. Royal Society of Chemistry, pp. 8966–8971, 2013.' ista: 'Li W, Ibáñez M, Zamani R, García Castelló N, Stéphane G, Cadavid D, Prades J, Arbiol J, Cabot A. 2013. Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties. CrystEngComm. 44, 8966–8971.' mla: 'Li, Wenhua, et al. “Cu2HgSnSe4 Nanoparticles: Synthesis and Thermoelectric Properties.” CrystEngComm, vol. 44, Royal Society of Chemistry, 2013, pp. 8966–71, doi:10.1039/C3CE41583J.' short: W. Li, M. Ibáñez, R. Zamani, N. García Castelló, G. Stéphane, D. Cadavid, J. Prades, J. Arbiol, A. Cabot, CrystEngComm 44 (2013) 8966–8971. date_created: 2018-12-11T11:46:07Z date_published: 2013-09-23T00:00:00Z date_updated: 2021-01-12T07:52:00Z day: '23' doi: 10.1039/C3CE41583J extern: '1' intvolume: ' 44' language: - iso: eng month: '09' oa_version: None page: 8966 - 8971 publication: CrystEngComm publication_status: published publisher: Royal Society of Chemistry publist_id: '7453' quality_controlled: '1' status: public title: 'Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2013' ... --- _id: '450' abstract: - lang: eng text: Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations. article_number: '2058' author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: David full_name: Rowell, David last_name: Rowell - first_name: Andrew full_name: Young, Andrew last_name: Young citation: ama: Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1750). doi:10.1098/rspb.2012.2058 apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058 chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058. ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750. Royal Society, The, 2013. ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058. mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058. short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013). date_created: 2018-12-11T11:46:32Z date_published: 2013-01-07T00:00:00Z date_updated: 2021-01-12T07:57:25Z day: '07' department: - _id: NiBa doi: 10.1098/rspb.2012.2058 external_id: pmid: - '23173202' intvolume: ' 280' issue: '1750' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/ month: '01' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '7372' quality_controlled: '1' status: public title: Source population characteristics affect heterosis following genetic rescue of fragmented plant populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 280 year: '2013' ... --- _id: '476' abstract: - lang: eng text: 'Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. ' author: - first_name: Desiree full_name: Dickerson, Desiree id: 444EB89E-F248-11E8-B48F-1D18A9856A87 last_name: Dickerson - first_name: David full_name: Bilkey, David last_name: Bilkey citation: ama: 'Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217' apa: 'Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217' chicago: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.' ieee: 'D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research Foundation, 2013.' ista: 'Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 7(DEC).' mla: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research Foundation, 2013, doi:10.3389/fnbeh.2013.00217.' short: D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013). date_created: 2018-12-11T11:46:41Z date_published: 2013-12-27T00:00:00Z date_updated: 2021-01-12T08:00:53Z day: '27' ddc: - '571' department: - _id: JoCs doi: 10.3389/fnbeh.2013.00217 file: - access_level: open_access checksum: cd7183121e56251176100ccac165c95c content_type: application/pdf creator: system date_created: 2018-12-12T10:15:10Z date_updated: 2020-07-14T12:46:35Z file_id: '5128' file_name: IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf file_size: 530134 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 7' issue: DEC language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Frontiers in Behavioral Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '7346' pubrep_id: '953' quality_controlled: '1' status: public title: 'Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2013' ... --- _id: '499' abstract: - lang: eng text: Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing "persisters." Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure. author: - first_name: Yurichi full_name: Wakamoto, Yurichi last_name: Wakamoto - first_name: Neraaj full_name: Dhar, Neraaj last_name: Dhar - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Katrin full_name: Schneider, Katrin last_name: Schneider - first_name: François full_name: Signorino Gelo, François last_name: Signorino Gelo - first_name: Stanislas full_name: Leibler, Stanislas last_name: Leibler - first_name: John full_name: Mckinney, John last_name: Mckinney citation: ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858 apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858 chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1229858. ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,” Science, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013. ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95. mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:10.1126/science.1229858. short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95. date_created: 2018-12-11T11:46:48Z date_published: 2013-01-04T00:00:00Z date_updated: 2021-01-12T08:01:06Z day: '04' department: - _id: CaGu - _id: GaTk doi: 10.1126/science.1229858 intvolume: ' 339' issue: '6115' language: - iso: eng month: '01' oa_version: None page: 91 - 95 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '7321' quality_controlled: '1' scopus_import: 1 status: public title: Dynamic persistence of antibiotic-stressed mycobacteria type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2013' ... --- _id: '500' abstract: - lang: eng text: 'Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.' acknowledgement: "This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n" article_number: '222' author: - first_name: Melissa full_name: Ward, Melissa last_name: Ward - first_name: Samantha full_name: Lycett, Samantha last_name: Lycett - first_name: Dorita full_name: Avila, Dorita last_name: Avila - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Andrew full_name: Leigh Brown, Andrew last_name: Leigh Brown citation: ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-222 apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222 chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222. ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013. ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222. mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no. 1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222. short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013). date_created: 2018-12-11T11:46:49Z date_published: 2013-10-09T00:00:00Z date_updated: 2021-01-12T08:01:08Z day: '09' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-222 file: - access_level: open_access checksum: 52cf48a7c1794676ae8b0029573a84a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4722' file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf file_size: 1150052 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '7320' pubrep_id: '941' quality_controlled: '1' scopus_import: 1 status: public title: Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '501' abstract: - lang: eng text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.' author: - first_name: Mario full_name: Cozzuol, Mario last_name: Cozzuol - first_name: Camila full_name: Clozato, Camila last_name: Clozato - first_name: Elizete full_name: Holanda, Elizete last_name: Holanda - first_name: Flávio full_name: Rodrigues, Flávio last_name: Rodrigues - first_name: Samuel full_name: Nienow, Samuel last_name: Nienow - first_name: Benoit full_name: De Thoisy, Benoit last_name: De Thoisy - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Fabrício full_name: Santos, Fabrício last_name: Santos citation: ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1 apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1 chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1. ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013. ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345. mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:10.1644/12-MAMM-A-169.1. short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345. date_created: 2018-12-11T11:46:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T08:01:09Z day: '01' ddc: - '570' department: - _id: JoBo doi: 10.1644/12-MAMM-A-169.1 file: - access_level: open_access checksum: 8007815078dccac21ecd1cf73a269dc6 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4980' file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf file_size: 1040765 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 94' issue: '6' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1331 - 1345 publication: Journal of Mammalogy publication_status: published publisher: Oxford University Press publist_id: '7319' pubrep_id: '940' quality_controlled: '1' scopus_import: 1 status: public title: A new species of tapir from the Amazon tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 94 year: '2013' ... --- _id: '505' abstract: - lang: eng text: Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts. acknowledgement: "This study was performed within the Austrian Centre of Indus-\r\ntrial Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology Agency of the \ City of Vienna through the\r\nCOMET-Funding Program managed by the Austrian Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with the CLSM measurements." author: - first_name: Katrin full_name: Greimel, Katrin last_name: Greimel - first_name: Veronika full_name: Perz, Veronika last_name: Perz - first_name: Klaus full_name: Koren, Klaus id: 382FBD6A-F248-11E8-B48F-1D18A9856A87 last_name: Koren - first_name: Roland full_name: Feola, Roland last_name: Feola - first_name: Armin full_name: Temel, Armin last_name: Temel - first_name: Christian full_name: Sohar, Christian last_name: Sohar - first_name: Enrique full_name: Herrero Acero, Enrique last_name: Herrero Acero - first_name: Ingo full_name: Klimant, Ingo last_name: Klimant - first_name: Georg full_name: Guebitz, Georg last_name: Guebitz citation: ama: 'Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 2013;15(2):381-388. doi:10.1039/c2gc36666e' apa: 'Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz, G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36666e' chicago: 'Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel, Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36666e.' ieee: 'K. Greimel et al., “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.' ista: 'Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.' mla: 'Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 381–88, doi:10.1039/c2gc36666e.' short: K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero, I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388. date_created: 2018-12-11T11:46:51Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T08:01:11Z day: '01' department: - _id: HaJa doi: 10.1039/c2gc36666e intvolume: ' 15' issue: '2' language: - iso: eng month: '02' oa_version: None page: 381 - 388 publication: Green Chemistry publication_status: published publisher: Royal Society of Chemistry publist_id: '7313' quality_controlled: '1' scopus_import: 1 status: public title: 'Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '502' abstract: - lang: eng text: 'Blind signatures allow users to obtain signatures on messages hidden from the signer; moreover, the signer cannot link the resulting message/signature pair to the signing session. This paper presents blind signature schemes, in which the number of interactions between the user and the signer is minimal and whose blind signatures are short. Our schemes are defined over bilinear groups and are proved secure in the common-reference-string model without random oracles and under standard assumptions: CDH and the decision-linear assumption. (We also give variants over asymmetric groups based on similar assumptions.) The blind signatures are Waters signatures, which consist of 2 group elements. Moreover, we instantiate partially blind signatures, where the message consists of a part hidden from the signer and a commonly known public part, and schemes achieving perfect blindness. We propose new variants of blind signatures, such as signer-friendly partially blind signatures, where the public part can be chosen by the signer without prior agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated messages provided by independent sources. We also extend Waters signatures to non-binary alphabets by proving a new result on the underlying hash function. ' author: - first_name: Olivier full_name: Blazy, Olivier last_name: Blazy - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: David full_name: Pointcheval, David last_name: Pointcheval - first_name: Damien full_name: Vergnaud, Damien last_name: Vergnaud citation: ama: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. Journal of Computer Security. 2013;21(5):627-661. doi:10.3233/JCS-130477 apa: Blazy, O., Fuchsbauer, G., Pointcheval, D., & Vergnaud, D. (2013). Short blind signatures. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-130477 chicago: Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud. “Short Blind Signatures.” Journal of Computer Security. IOS Press, 2013. https://doi.org/10.3233/JCS-130477. ieee: O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,” Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013. ista: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures. Journal of Computer Security. 21(5), 627–661. mla: Blazy, Olivier, et al. “Short Blind Signatures.” Journal of Computer Security, vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:10.3233/JCS-130477. short: O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer Security 21 (2013) 627–661. date_created: 2018-12-11T11:46:50Z date_published: 2013-11-22T00:00:00Z date_updated: 2021-01-12T08:01:09Z day: '22' department: - _id: KrPi doi: 10.3233/JCS-130477 intvolume: ' 21' issue: '5' language: - iso: eng month: '11' oa_version: None page: 627 - 661 publication: Journal of Computer Security publication_status: published publisher: IOS Press publist_id: '7318' quality_controlled: '1' scopus_import: 1 status: public title: Short blind signatures type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2013' ... --- _id: '508' abstract: - lang: eng text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases. author: - first_name: Eduardo full_name: Tarazona Santos, Eduardo last_name: Tarazona Santos - first_name: Moara full_name: Machado, Moara last_name: Machado - first_name: Wagner full_name: Magalhães, Wagner last_name: Magalhães - first_name: Renee full_name: Chen, Renee last_name: Chen - first_name: Fernanda full_name: Lyon, Fernanda last_name: Lyon - first_name: Laurie full_name: Burdett, Laurie last_name: Burdett - first_name: Andrew full_name: Crenshaw, Andrew last_name: Crenshaw - first_name: Cristina full_name: Fabbri, Cristina last_name: Fabbri - first_name: Latife full_name: Pereira, Latife last_name: Pereira - first_name: Laelia full_name: Pinto, Laelia last_name: Pinto - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Ben full_name: Sestanovich, Ben last_name: Sestanovich - first_name: Meredith full_name: Yeager, Meredith last_name: Yeager - first_name: Stephen full_name: Chanock, Stephen last_name: Chanock citation: ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119' apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119' chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.' ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.' ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.' mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:10.1093/molbev/mst119.' short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167. date_created: 2018-12-11T11:46:52Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:01:12Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst119 external_id: pmid: - '23821607' intvolume: ' 30' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/ month: '09' oa: 1 oa_version: Submitted Version page: 2157 - 2167 pmid: 1 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '7310' quality_controlled: '1' scopus_import: 1 status: public title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2013' ... --- _id: '509' abstract: - lang: eng text: 'Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. ' author: - first_name: Simone full_name: Di Rubbo, Simone last_name: Di Rubbo - first_name: Niloufer full_name: Irani, Niloufer last_name: Irani - first_name: Soo full_name: Kim, Soo last_name: Kim - first_name: Zheng full_name: Xu, Zheng last_name: Xu - first_name: Astrid full_name: Gadeyne, Astrid last_name: Gadeyne - first_name: Wim full_name: Dejonghe, Wim last_name: Dejonghe - first_name: Isabelle full_name: Vanhoutte, Isabelle last_name: Vanhoutte - first_name: Geert full_name: Persiau, Geert last_name: Persiau - first_name: Dominique full_name: Eeckhout, Dominique last_name: Eeckhout - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Kyungyoung full_name: Song, Kyungyoung last_name: Song - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Daniël full_name: Van Damme, Daniël last_name: Van Damme - first_name: Inhwan full_name: Hwang, Inhwan last_name: Hwang - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 2013;25(8):2986-2997. doi:10.1105/tpc.113.114058 apa: Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova, E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114058 chicago: Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114058. ieee: S. Di Rubbo et al., “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013. ista: Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997. mla: Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:10.1105/tpc.113.114058. short: S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte, G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger, D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997. date_created: 2018-12-11T11:46:52Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:01:13Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.113.114058 external_id: pmid: - '23975899' intvolume: ' 25' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/ month: '08' oa: 1 oa_version: Submitted Version page: 2986 - 2997 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '7311' quality_controlled: '1' scopus_import: 1 status: public title: The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '507' abstract: - lang: eng text: Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs. author: - first_name: Soo full_name: Kim, Soo last_name: Kim - first_name: Zheng full_name: Xu, Zheng last_name: Xu - first_name: Kyungyoung full_name: Song, Kyungyoung last_name: Song - first_name: Dae full_name: Kim, Dae last_name: Kim - first_name: Hyangju full_name: Kang, Hyangju last_name: Kang - first_name: Ilka full_name: Reichardt, Ilka last_name: Reichardt - first_name: Eun full_name: Sohn, Eun last_name: Sohn - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Gerd full_name: Juergens, Gerd last_name: Juergens - first_name: Inhwan full_name: Hwang, Inhwan last_name: Hwang citation: ama: Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 2013;25(8):2970-2985. doi:10.1105/tpc.113.114264 apa: Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114264 chicago: Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114264. ieee: S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013. ista: Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985. mla: Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” Plant Cell, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:10.1105/tpc.113.114264. short: S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985. date_created: 2018-12-11T11:46:52Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:01:12Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.113.114264 external_id: pmid: - '23975898' intvolume: ' 25' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/ month: '08' oa: 1 oa_version: Submitted Version page: 2970 - 2985 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '7312' quality_controlled: '1' scopus_import: 1 status: public title: Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '511' abstract: - lang: eng text: The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms. author: - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Biljana full_name: Simonovik, Biljana last_name: Simonovik - first_name: Sara full_name: Petersson, Sara last_name: Petersson - first_name: Eva full_name: Henyková, Eva last_name: Henyková - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Kathleen full_name: Greenham, Kathleen last_name: Greenham - first_name: Yi full_name: Zhang, Yi last_name: Zhang - first_name: Mariusz full_name: Kowalczyk, Mariusz last_name: Kowalczyk - first_name: Mark full_name: Estelle, Mark last_name: Estelle - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Göran full_name: Sandberg, Göran last_name: Sandberg - first_name: Karin full_name: Ljung, Karin last_name: Ljung citation: ama: Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 2013;25(10):3858-3870. doi:10.1105/tpc.113.114421 apa: Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham, K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114421 chicago: Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon, Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114421. ieee: A. Pěnčík et al., “Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid,” Plant Cell, vol. 25, no. 10. American Society of Plant Biologists, pp. 3858–3870, 2013. ista: Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10), 3858–3870. mla: Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” Plant Cell, vol. 25, no. 10, American Society of Plant Biologists, 2013, pp. 3858–70, doi:10.1105/tpc.113.114421. short: A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham, Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung, Plant Cell 25 (2013) 3858–3870. date_created: 2018-12-11T11:46:53Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T08:01:15Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.113.114421 external_id: pmid: - '24163311' intvolume: ' 25' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: www.doi.org/10.1105/tpc.113.114421 month: '10' oa: 1 oa_version: Published Version page: 3858 - 3870 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '7309' quality_controlled: '1' scopus_import: 1 status: public title: Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '516' abstract: - lang: eng text: In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development. article_number: '688' article_processing_charge: No author: - first_name: Bastiaan full_name: Bargmann, Bastiaan last_name: Bargmann - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Gabriel full_name: Krouk, Gabriel last_name: Krouk - first_name: Tal full_name: Nawy, Tal last_name: Nawy - first_name: Idan full_name: Efroni, Idan last_name: Efroni - first_name: Eilon full_name: Shani, Eilon last_name: Shani - first_name: Goh full_name: Choe, Goh last_name: Choe - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dominique full_name: Bergmann, Dominique last_name: Bergmann - first_name: Mark full_name: Estelle, Mark last_name: Estelle - first_name: Kenneth full_name: Birnbaum, Kenneth last_name: Birnbaum citation: ama: Bargmann B, Vanneste S, Krouk G, et al. A map of cell type‐specific auxin responses. Molecular Systems Biology. 2013;9(1). doi:10.1038/msb.2013.40 apa: Bargmann, B., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., … Birnbaum, K. (2013). A map of cell type‐specific auxin responses. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2013.40 chicago: Bargmann, Bastiaan, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.40. ieee: B. Bargmann et al., “A map of cell type‐specific auxin responses,” Molecular Systems Biology, vol. 9, no. 1. Nature Publishing Group, 2013. ista: Bargmann B, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann D, Estelle M, Birnbaum K. 2013. A map of cell type‐specific auxin responses. Molecular Systems Biology. 9(1), 688. mla: Bargmann, Bastiaan, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular Systems Biology, vol. 9, no. 1, 688, Nature Publishing Group, 2013, doi:10.1038/msb.2013.40. short: B. Bargmann, S. Vanneste, G. Krouk, T. Nawy, I. Efroni, E. Shani, G. Choe, J. Friml, D. Bergmann, M. Estelle, K. Birnbaum, Molecular Systems Biology 9 (2013). date_created: 2018-12-11T11:46:55Z date_published: 2013-09-10T00:00:00Z date_updated: 2021-01-12T08:01:17Z day: '10' ddc: - '581' department: - _id: JiFr doi: 10.1038/msb.2013.40 file: - access_level: open_access checksum: 9c4fbe793af4bb22b3fe50cc677a39bf content_type: application/pdf creator: system date_created: 2018-12-12T10:07:46Z date_updated: 2020-07-14T12:46:36Z file_id: '4644' file_name: IST-2018-936-v1+1_2008_Barton_A_map.pdf file_size: 3257692 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '09' oa: 1 oa_version: Published Version publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '7303' pubrep_id: '936' quality_controlled: '1' scopus_import: 1 status: public title: A map of cell type‐specific auxin responses tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '522' abstract: - lang: eng text: Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic endothelial cells and responsible for separation of blood and lymphatic circulation through activation of platelets. Here we show that podoplanin is also expressed by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell type associated with thymic conduits, and involved in development of natural regulatory T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes in the medulla. This might be due to CCL21 that delocalizes upon deletion of the CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not remain devoid of nTreg but generate them delayed within the first month resulting in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype of Foxp3-deficient Scurfy mice. author: - first_name: Elke full_name: Fuertbauer, Elke last_name: Fuertbauer - first_name: Jan full_name: Zaujec, Jan last_name: Zaujec - first_name: Pavel full_name: Uhrin, Pavel last_name: Uhrin - first_name: Ingrid full_name: Raab, Ingrid last_name: Raab - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Helga full_name: Schachner, Helga last_name: Schachner - first_name: Miroslav full_name: Bauer, Miroslav last_name: Bauer - first_name: Gerhard full_name: Schütz, Gerhard last_name: Schütz - first_name: Bernd full_name: Binder, Bernd last_name: Binder - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Dontscho full_name: Kerjaschki, Dontscho last_name: Kerjaschki - first_name: Hannes full_name: Stockinger, Hannes last_name: Stockinger citation: ama: Fuertbauer E, Zaujec J, Uhrin P, et al. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 2013;154(1-2):31-41. doi:10.1016/j.imlet.2013.07.007 apa: Fuertbauer, E., Zaujec, J., Uhrin, P., Raab, I., Weber, M., Schachner, H., … Stockinger, H. (2013). Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. Elsevier. https://doi.org/10.1016/j.imlet.2013.07.007 chicago: Fuertbauer, Elke, Jan Zaujec, Pavel Uhrin, Ingrid Raab, Michele Weber, Helga Schachner, Miroslav Bauer, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” Immunology Letters. Elsevier, 2013. https://doi.org/10.1016/j.imlet.2013.07.007. ieee: E. Fuertbauer et al., “Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells,” Immunology Letters, vol. 154, no. 1–2. Elsevier, pp. 31–41, 2013. ista: Fuertbauer E, Zaujec J, Uhrin P, Raab I, Weber M, Schachner H, Bauer M, Schütz G, Binder B, Sixt MK, Kerjaschki D, Stockinger H. 2013. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 154(1–2), 31–41. mla: Fuertbauer, Elke, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” Immunology Letters, vol. 154, no. 1–2, Elsevier, 2013, pp. 31–41, doi:10.1016/j.imlet.2013.07.007. short: E. Fuertbauer, J. Zaujec, P. Uhrin, I. Raab, M. Weber, H. Schachner, M. Bauer, G. Schütz, B. Binder, M.K. Sixt, D. Kerjaschki, H. Stockinger, Immunology Letters 154 (2013) 31–41. date_created: 2018-12-11T11:46:57Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:01:22Z day: '01' department: - _id: MiSi doi: 10.1016/j.imlet.2013.07.007 intvolume: ' 154' issue: 1-2 language: - iso: eng month: '07' oa_version: None page: 31 - 41 publication: Immunology Letters publication_status: published publisher: Elsevier publist_id: '7300' quality_controlled: '1' scopus_import: 1 status: public title: Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 154 year: '2013' ... --- _id: '2279' abstract: - lang: eng text: We consider two-player games played on weighted directed graphs with mean-payoff and total-payoff objectives, two classical quantitative objectives. While for single-dimensional games the complexity and memory bounds for both objectives coincide, we show that in contrast to multi-dimensional mean-payoff games that are known to be coNP-complete, multi-dimensional total-payoff games are undecidable. We introduce conservative approximations of these objectives, where the payoff is considered over a local finite window sliding along a play, instead of the whole play. For single dimension, we show that (i) if the window size is polynomial, deciding the winner takes polynomial time, and (ii) the existence of a bounded window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff games. For multiple dimensions, we show that (i) the problem with fixed window size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to decide the existence of a bounded window. acknowledgement: 279307; ERC; Fonds National de la Reserche Luxembourg; 279499; ERC; Fonds National de la Reserche Luxembourg alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Mickael full_name: Randour, Mickael last_name: Randour - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff through windows. 2013;8172:118-132. doi:10.1007/978-3-319-02444-8_10 apa: 'Chatterjee, K., Doyen, L., Randour, M., & Raskin, J. (2013). Looking at mean-payoff and total-payoff through windows. Presented at the ATVA: Automated Technology for Verification and Analysis, Hanoi, Vietnam: Springer. https://doi.org/10.1007/978-3-319-02444-8_10' chicago: Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin. “Looking at Mean-Payoff and Total-Payoff through Windows.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-319-02444-8_10. ieee: K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff and total-payoff through windows,” vol. 8172. Springer, pp. 118–132, 2013. ista: Chatterjee K, Doyen L, Randour M, Raskin J. 2013. Looking at mean-payoff and total-payoff through windows. 8172, 118–132. mla: Chatterjee, Krishnendu, et al. Looking at Mean-Payoff and Total-Payoff through Windows. Vol. 8172, Springer, 2013, pp. 118–32, doi:10.1007/978-3-319-02444-8_10. short: K. Chatterjee, L. Doyen, M. Randour, J. Raskin, 8172 (2013) 118–132. conference: end_date: 2013-10-18 location: Hanoi, Vietnam name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2013-10-15 date_created: 2018-12-11T11:56:44Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-23T12:22:51Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-319-02444-8_10 ec_funded: 1 intvolume: ' 8172' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1302.4248 month: '01' oa: 1 oa_version: Preprint page: 118 - 132 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '4656' quality_controlled: '1' related_material: record: - id: '523' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Looking at mean-payoff and total-payoff through windows type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8172 year: '2013' ... --- _id: '528' abstract: - lang: eng text: Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin [1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal axis [3-6]. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis [9-12]. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life [13, 14]. author: - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Anna full_name: Stepanova, Anna last_name: Stepanova - first_name: Linda full_name: Robles, Linda last_name: Robles - first_name: Annemarie full_name: Lokerse, Annemarie last_name: Lokerse - first_name: Jose full_name: Alonso, Jose last_name: Alonso - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Robert H, Grones P, Stepanova A, et al. Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. 2013;23(24):2506-2512. doi:10.1016/j.cub.2013.09.039 apa: Robert, H., Grones, P., Stepanova, A., Robles, L., Lokerse, A., Alonso, J., … Friml, J. (2013). Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.09.039 chicago: Robert, Hélène, Peter Grones, Anna Stepanova, Linda Robles, Annemarie Lokerse, Jose Alonso, Dolf Weijers, and Jiří Friml. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.09.039. ieee: H. Robert et al., “Local auxin sources orient the apical basal axis in arabidopsis embryos,” Current Biology, vol. 23, no. 24. Cell Press, pp. 2506–2512, 2013. ista: Robert H, Grones P, Stepanova A, Robles L, Lokerse A, Alonso J, Weijers D, Friml J. 2013. Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. 23(24), 2506–2512. mla: Robert, Hélène, et al. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” Current Biology, vol. 23, no. 24, Cell Press, 2013, pp. 2506–12, doi:10.1016/j.cub.2013.09.039. short: H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D. Weijers, J. Friml, Current Biology 23 (2013) 2506–2512. date_created: 2018-12-11T11:46:59Z date_published: 2013-12-16T00:00:00Z date_updated: 2021-01-12T08:01:25Z day: '16' department: - _id: JiFr doi: 10.1016/j.cub.2013.09.039 ec_funded: 1 intvolume: ' 23' issue: '24' language: - iso: eng month: '12' oa_version: None page: 2506 - 2512 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Current Biology publication_status: published publisher: Cell Press publist_id: '7291' quality_controlled: '1' scopus_import: 1 status: public title: Local auxin sources orient the apical basal axis in arabidopsis embryos type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '527' abstract: - lang: eng text: The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development. author: - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Richard full_name: Smith, Richard last_name: Smith - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 2013;23(24):2513-2518. doi:10.1016/j.cub.2013.10.038 apa: Wabnik, K. T., Robert, H., Smith, R., & Friml, J. (2013). Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.10.038 chicago: Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.10.038. ieee: K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the establishment of the apical-basal embryonic axis in plants,” Current Biology, vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013. ista: Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518. mla: Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” Current Biology, vol. 23, no. 24, Cell Press, 2013, pp. 2513–18, doi:10.1016/j.cub.2013.10.038. short: K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518. date_created: 2018-12-11T11:46:58Z date_published: 2013-12-16T00:00:00Z date_updated: 2021-01-12T08:01:24Z day: '16' department: - _id: EvBe - _id: JiFr doi: 10.1016/j.cub.2013.10.038 ec_funded: 1 intvolume: ' 23' issue: '24' language: - iso: eng month: '12' oa_version: None page: 2513 - 2518 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Current Biology publication_status: published publisher: Cell Press publist_id: '7292' quality_controlled: '1' scopus_import: 1 status: public title: Modeling framework for the establishment of the apical-basal embryonic axis in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '5399' abstract: - lang: eng text: In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics. alternative_title: - IST Austria Technical Report author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Ivana full_name: Bozic, Ivana last_name: Bozic - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: 'Reiter J, Bozic I, Chatterjee K, Nowak M. TTP: Tool for Tumor Progression. IST Austria; 2013. doi:10.15479/AT:IST-2013-104-v1-1' apa: 'Reiter, J., Bozic, I., Chatterjee, K., & Nowak, M. (2013). TTP: Tool for Tumor Progression. IST Austria. https://doi.org/10.15479/AT:IST-2013-104-v1-1' chicago: 'Reiter, Johannes, Ivana Bozic, Krishnendu Chatterjee, and Martin Nowak. TTP: Tool for Tumor Progression. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-104-v1-1.' ieee: 'J. Reiter, I. Bozic, K. Chatterjee, and M. Nowak, TTP: Tool for Tumor Progression. IST Austria, 2013.' ista: 'Reiter J, Bozic I, Chatterjee K, Nowak M. 2013. TTP: Tool for Tumor Progression, IST Austria, 17p.' mla: 'Reiter, Johannes, et al. TTP: Tool for Tumor Progression. IST Austria, 2013, doi:10.15479/AT:IST-2013-104-v1-1.' short: 'J. Reiter, I. Bozic, K. Chatterjee, M. Nowak, TTP: Tool for Tumor Progression, IST Austria, 2013.' date_created: 2018-12-12T11:39:07Z date_published: 2013-01-11T00:00:00Z date_updated: 2023-02-23T10:23:57Z day: '11' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2013-104-v1-1 file: - access_level: open_access checksum: 2cc8c6e157eca1271128db80bb3dec80 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:20Z date_updated: 2020-07-14T12:46:44Z file_id: '5542' file_name: IST-2013-104-v1+1_tumortool.pdf file_size: 1471954 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '17' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '104' related_material: record: - id: '2000' relation: later_version status: public status: public title: 'TTP: Tool for Tumor Progression' type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2295' abstract: - lang: eng text: We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal EXPTIME-complete complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite-memory strategies. We also establish asymptotically optimal (exponential) memory bounds. alternative_title: - LIPIcs author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Mathieu full_name: Tracol, Mathieu id: 3F54FA38-F248-11E8-B48F-1D18A9856A87 last_name: Tracol citation: ama: Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with omega-regular objectives. 2013;23:165-180. doi:10.4230/LIPIcs.CSL.2013.165 apa: 'Chatterjee, K., Chmelik, M., & Tracol, M. (2013). What is decidable about partially observable Markov decision processes with omega-regular objectives. Presented at the CSL: Computer Science Logic, Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2013.165' chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with Omega-Regular Objectives.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.165. ieee: K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with omega-regular objectives,” vol. 23. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 165–180, 2013. ista: Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with omega-regular objectives. 23, 165–180. mla: Chatterjee, Krishnendu, et al. What Is Decidable about Partially Observable Markov Decision Processes with Omega-Regular Objectives. Vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 165–80, doi:10.4230/LIPIcs.CSL.2013.165. short: K. Chatterjee, M. Chmelik, M. Tracol, 23 (2013) 165–180. conference: end_date: 2013-09-05 location: Torino, Italy name: 'CSL: Computer Science Logic' start_date: 2013-09-02 date_created: 2018-12-11T11:56:50Z date_published: 2013-08-27T00:00:00Z date_updated: 2023-02-23T12:24:38Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPIcs.CSL.2013.165 ec_funded: 1 file: - access_level: open_access checksum: ba2828322955574d9283bea0e17a37a6 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:42Z date_updated: 2020-07-14T12:45:37Z file_id: '4766' file_name: IST-2017-756-v1+1_2.pdf file_size: 345171 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 23' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 165 - 180 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4633' pubrep_id: '756' quality_controlled: '1' related_material: record: - id: '1477' relation: later_version status: public - id: '5400' relation: earlier_version status: public scopus_import: 1 series_title: Leibniz International Proceedings in Informatics status: public title: What is decidable about partially observable Markov decision processes with omega-regular objectives 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '5403' abstract: - lang: eng text: 'We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of mean-payoff games) that is not known to be in polynomial time.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 citation: ama: Chatterjee K, Ibsen-Jensen R. Qualitative Analysis of Concurrent Mean-Payoff Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-126-v1-1 apa: Chatterjee, K., & Ibsen-Jensen, R. (2013). Qualitative analysis of concurrent mean-payoff games. IST Austria. https://doi.org/10.15479/AT:IST-2013-126-v1-1 chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. Qualitative Analysis of Concurrent Mean-Payoff Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-126-v1-1. ieee: K. Chatterjee and R. Ibsen-Jensen, Qualitative analysis of concurrent mean-payoff games. IST Austria, 2013. ista: Chatterjee K, Ibsen-Jensen R. 2013. Qualitative analysis of concurrent mean-payoff games, IST Austria, 33p. mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. Qualitative Analysis of Concurrent Mean-Payoff Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-126-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, Qualitative Analysis of Concurrent Mean-Payoff Games, IST Austria, 2013. date_created: 2018-12-12T11:39:08Z date_published: 2013-07-03T00:00:00Z date_updated: 2023-02-23T12:22:53Z day: '03' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-126-v1-1 file: - access_level: open_access checksum: 063868c665beec37bf28160e2a695746 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:49Z date_updated: 2020-07-14T12:46:45Z file_id: '5510' file_name: IST-2013-126-v1+1_soda_full.pdf file_size: 434523 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '33' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '126' related_material: record: - id: '524' relation: later_version status: public status: public title: Qualitative analysis of concurrent mean-payoff games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5402' abstract: - lang: eng text: "Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element. \r\nIn this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention." alternative_title: - IST Austria Technical Report author: - 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: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: Henzinger TA, Sezgin A. How Free Is Your Linearizable Concurrent Data Structure? IST Austria; 2013. doi:10.15479/AT:IST-2013-123-v1-1 apa: Henzinger, T. A., & Sezgin, A. (2013). How free is your linearizable concurrent data structure? IST Austria. https://doi.org/10.15479/AT:IST-2013-123-v1-1 chicago: Henzinger, Thomas A, and Ali Sezgin. How Free Is Your Linearizable Concurrent Data Structure? IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-123-v1-1. ieee: T. A. Henzinger and A. Sezgin, How free is your linearizable concurrent data structure? IST Austria, 2013. ista: Henzinger TA, Sezgin A. 2013. How free is your linearizable concurrent data structure?, IST Austria, 16p. mla: Henzinger, Thomas A., and Ali Sezgin. How Free Is Your Linearizable Concurrent Data Structure? IST Austria, 2013, doi:10.15479/AT:IST-2013-123-v1-1. short: T.A. Henzinger, A. Sezgin, How Free Is Your Linearizable Concurrent Data Structure?, IST Austria, 2013. date_created: 2018-12-12T11:39:07Z date_published: 2013-06-12T00:00:00Z date_updated: 2020-07-14T23:04:47Z day: '12' ddc: - '000' - '004' department: - _id: ToHe doi: 10.15479/AT:IST-2013-123-v1-1 file: - access_level: open_access checksum: ce580605ae9756a8c99d7b403ebb8eed content_type: application/pdf creator: system date_created: 2018-12-12T11:53:19Z date_updated: 2020-07-14T12:46:45Z file_id: '5480' file_name: IST-2013-123-v1+1_main-concur2013.pdf file_size: 249790 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '16' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '123' status: public title: How free is your linearizable concurrent data structure? type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5400' abstract: - lang: eng text: We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Mathieu full_name: Tracol, Mathieu id: 3F54FA38-F248-11E8-B48F-1D18A9856A87 last_name: Tracol citation: ama: Chatterjee K, Chmelik M, Tracol M. What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives. IST Austria; 2013. doi:10.15479/AT:IST-2013-109-v1-1 apa: Chatterjee, K., Chmelik, M., & Tracol, M. (2013). What is decidable about partially observable Markov decision processes with ω-regular objectives. IST Austria. https://doi.org/10.15479/AT:IST-2013-109-v1-1 chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-109-v1-1. ieee: K. Chatterjee, M. Chmelik, and M. Tracol, What is decidable about partially observable Markov decision processes with ω-regular objectives. IST Austria, 2013. ista: Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with ω-regular objectives, IST Austria, 41p. mla: Chatterjee, Krishnendu, et al. What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives. IST Austria, 2013, doi:10.15479/AT:IST-2013-109-v1-1. short: K. Chatterjee, M. Chmelik, M. Tracol, What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives, IST Austria, 2013. date_created: 2018-12-12T11:39:07Z date_published: 2013-02-20T00:00:00Z date_updated: 2023-02-23T10:36:45Z day: '20' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-109-v1-1 file: - access_level: open_access checksum: cbba40210788a1b22c6cf06433b5ed6f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:06Z date_updated: 2020-07-14T12:46:44Z file_id: '5467' file_name: IST-2013-109-v1+1_What_is_Decidable_about_Partially_Observable_Markov_Decision_Processes_with_ω-Regular_Objectives.pdf file_size: 483407 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '41' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '109' related_material: record: - id: '1477' relation: later_version status: public - id: '2295' relation: later_version status: public status: public title: What is decidable about partially observable Markov decision processes with ω-regular objectives type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5404' abstract: - lang: eng text: 'We study finite-state two-player (zero-sum) concurrent mean-payoff games played on a graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lie in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP and coNP is the long-standing best known bound). We show that the exact value can be expressed in the existential theory of the reals, and also establish square-root sum hardness for a related class of games.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 citation: ama: Chatterjee K, Ibsen-Jensen R. The Complexity of Ergodic Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-127-v1-1 apa: Chatterjee, K., & Ibsen-Jensen, R. (2013). The complexity of ergodic games. IST Austria. https://doi.org/10.15479/AT:IST-2013-127-v1-1 chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-127-v1-1. ieee: K. Chatterjee and R. Ibsen-Jensen, The complexity of ergodic games. IST Austria, 2013. ista: Chatterjee K, Ibsen-Jensen R. 2013. The complexity of ergodic games, IST Austria, 29p. mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-127-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, The Complexity of Ergodic Games, IST Austria, 2013. date_created: 2018-12-12T11:39:08Z date_published: 2013-07-03T00:00:00Z date_updated: 2023-02-23T10:30:55Z day: '03' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-127-v1-1 file: - access_level: open_access checksum: 79ee5e677a82611ce06e0360c69d494a content_type: application/pdf creator: system date_created: 2018-12-12T11:53:35Z date_updated: 2020-07-14T12:46:45Z file_id: '5496' file_name: IST-2013-127-v1+1_ergodic.pdf file_size: 517275 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '29' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '127' related_material: record: - id: '2162' relation: later_version status: public status: public title: The complexity of ergodic games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5401' abstract: - lang: eng text: This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the actual initiatives, projects and standards related to the project. It supports the preparation of standards and specifications for the project, which should be considered and followed to ensure interoperability and visibility of the uploaded data. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Initiatives and Projects Related to RD. IST Austria; 2013. apa: Porsche, J. (2013). Initiatives and projects related to RD. IST Austria. chicago: Porsche, Jana. Initiatives and Projects Related to RD. IST Austria, 2013. ieee: J. Porsche, Initiatives and projects related to RD. IST Austria, 2013. ista: Porsche J. 2013. Initiatives and projects related to RD, IST Austria,p. mla: Porsche, Jana. Initiatives and Projects Related to RD. IST Austria, 2013. short: J. Porsche, Initiatives and Projects Related to RD, IST Austria, 2013. date_created: 2018-12-12T11:39:07Z date_published: 2013-03-20T00:00:00Z date_updated: 2020-07-14T23:04:47Z day: '20' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: d68712db838432ecdacf9ffb1de8f8a6 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:14Z date_updated: 2020-07-14T12:46:45Z file_id: '5536' file_name: IST-2013-113-v1+1_Initiatives_and_projects_related_to_RD.pdf file_size: 151208 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria pubrep_id: '113' status: public title: Initiatives and projects related to RD type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5405' abstract: - lang: eng text: "The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2-1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2-1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic) with only parity objectives, or with only mean-payoff objectives. We present an algorithm running\r\nin time O(d · n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the objective\r\ncan be ensured with probability 1, where n is the number of states of the game, d the number of priorities\r\nof the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states\r\nin 2-1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems\r\nwith both functional requirement (given as a qualitative objective) and performance requirement (given\r\nas a quantitative objective)." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Hugo full_name: Gimbert, Hugo last_name: Gimbert - first_name: Youssouf full_name: Oualhadj, Youssouf last_name: Oualhadj citation: ama: Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-Information Stochastic Mean-Payoff Parity Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-128-v1-1 apa: Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2013). Perfect-information stochastic mean-payoff parity games. IST Austria. https://doi.org/10.15479/AT:IST-2013-128-v1-1 chicago: Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. Perfect-Information Stochastic Mean-Payoff Parity Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-128-v1-1. ieee: K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, Perfect-information stochastic mean-payoff parity games. IST Austria, 2013. ista: Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2013. Perfect-information stochastic mean-payoff parity games, IST Austria, 22p. mla: Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff Parity Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-128-v1-1. short: K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, Perfect-Information Stochastic Mean-Payoff Parity Games, IST Austria, 2013. date_created: 2018-12-12T11:39:09Z date_published: 2013-07-08T00:00:00Z date_updated: 2023-02-23T10:33:08Z day: '08' ddc: - '000' - '005' - '510' department: - _id: KrCh doi: 10.15479/AT:IST-2013-128-v1-1 file: - access_level: open_access checksum: ede787a10e74e4f7db302fab8f12f3ca content_type: application/pdf creator: system date_created: 2018-12-12T11:53:54Z date_updated: 2020-07-14T12:46:45Z file_id: '5516' file_name: IST-2013-128-v1+1_full_stoch_mpp.pdf file_size: 387467 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '22' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '128' related_material: record: - id: '2212' relation: later_version status: public status: public title: Perfect-information stochastic mean-payoff parity games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5409' abstract: - lang: eng text: "The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. \r\nIn this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in timestamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than delta away from the parameter, for delta>0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and we show analogous decidability results for rectangular automata." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar citation: ama: Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit Distance for Timed Automata. IST Austria; 2013. doi:10.15479/AT:IST-2013-144-v1-1 apa: Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2013). Edit distance for timed automata. IST Austria. https://doi.org/10.15479/AT:IST-2013-144-v1-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Rupak Majumdar. Edit Distance for Timed Automata. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-144-v1-1. ieee: K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, Edit distance for timed automata. IST Austria, 2013. ista: Chatterjee K, Ibsen-Jensen R, Majumdar R. 2013. Edit distance for timed automata, IST Austria, 12p. mla: Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. IST Austria, 2013, doi:10.15479/AT:IST-2013-144-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, Edit Distance for Timed Automata, IST Austria, 2013. date_created: 2018-12-12T11:39:10Z date_published: 2013-10-30T00:00:00Z date_updated: 2023-02-23T10:33:18Z day: '30' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2013-144-v1-1 file: - access_level: open_access checksum: 0f7633081ba8299c543322f0ad08571f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:08Z date_updated: 2020-07-14T12:46:46Z file_id: '5469' file_name: IST-2013-144-v1+1_main.pdf file_size: 336377 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '12' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '144' related_material: record: - id: '2216' relation: later_version status: public status: public title: Edit distance for timed automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '1376' abstract: - lang: eng text: 'We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: 'Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: 13th International Conference on Formal Methods in Computer-Aided Design. IEEE; 2013:18-25. doi:10.1109/FMCAD.2013.6679386' apa: 'Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In 13th International Conference on Formal Methods in Computer-Aided Design (pp. 18–25). Portland, OR, United States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679386' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In 13th International Conference on Formal Methods in Computer-Aided Design, 18–25. IEEE, 2013. https://doi.org/10.1109/FMCAD.2013.6679386. ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in 13th International Conference on Formal Methods in Computer-Aided Design, Portland, OR, United States, 2013, pp. 18–25. ista: 'Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.' mla: Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25, doi:10.1109/FMCAD.2013.6679386. short: K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25. conference: end_date: 2013-10-23 location: Portland, OR, United States name: 'FMCAD: Formal Methods in Computer-Aided Design' start_date: 2013-10-20 date_created: 2018-12-11T11:51:40Z date_published: 2013-12-11T00:00:00Z date_updated: 2023-02-23T12:24:53Z day: '11' department: - _id: KrCh - _id: ToHe doi: 10.1109/FMCAD.2013.6679386 ec_funded: 1 language: - iso: eng month: '12' oa_version: None page: 18 - 25 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 13th International Conference on Formal Methods in Computer-Aided Design publication_status: published publisher: IEEE publist_id: '5835' quality_controlled: '1' related_material: record: - id: '5406' relation: earlier_version status: public status: public title: Distributed synthesis for LTL fragments type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5406' abstract: - lang: eng text: 'We consider the distributed synthesis problem fortemporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTLand our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3)Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed Synthesis for LTL Fragments. IST Austria; 2013. doi:10.15479/AT:IST-2013-130-v1-1 apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013). Distributed synthesis for LTL Fragments. IST Austria. https://doi.org/10.15479/AT:IST-2013-130-v1-1 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. Distributed Synthesis for LTL Fragments. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-130-v1-1. ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, Distributed synthesis for LTL Fragments. IST Austria, 2013. ista: Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL Fragments, IST Austria, 11p. mla: Chatterjee, Krishnendu, et al. Distributed Synthesis for LTL Fragments. IST Austria, 2013, doi:10.15479/AT:IST-2013-130-v1-1. short: K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, Distributed Synthesis for LTL Fragments, IST Austria, 2013. date_created: 2018-12-12T11:39:09Z date_published: 2013-07-08T00:00:00Z date_updated: 2023-02-21T17:01:26Z day: '08' ddc: - '005' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2013-130-v1-1 file: - access_level: open_access checksum: 855513ebaf6f72228800c5fdb522f93c content_type: application/pdf creator: system date_created: 2018-12-12T11:54:18Z date_updated: 2020-07-14T12:46:45Z file_id: '5540' file_name: IST-2013-130-v1+1_Distributed_Synthesis.pdf file_size: 467895 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '11' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '130' related_material: record: - id: '1376' relation: later_version status: public status: public title: Distributed synthesis for LTL Fragments type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5408' abstract: - lang: eng text: "We consider two-player partial-observation stochastic games where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are omega-regular conditions specified as parity objectives. The qualitative analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, they were shown to be decidable in 2EXPTIME under finite-memory strategies. We improve the complexity and show that the qualitative analysis problems for partial-observation stochastic parity games under finite-memory strategies are \r\nEXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Sumit full_name: Nain, Sumit last_name: Nain - first_name: Moshe full_name: Vardi, Moshe last_name: Vardi citation: ama: Chatterjee K, Doyen L, Nain S, Vardi M. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. IST Austria; 2013. doi:10.15479/AT:IST-2013-141-v1-1 apa: Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2013). The complexity of partial-observation stochastic parity games with finite-memory strategies. IST Austria. https://doi.org/10.15479/AT:IST-2013-141-v1-1 chicago: Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-141-v1-1. ieee: K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, The complexity of partial-observation stochastic parity games with finite-memory strategies. IST Austria, 2013. ista: Chatterjee K, Doyen L, Nain S, Vardi M. 2013. The complexity of partial-observation stochastic parity games with finite-memory strategies, IST Austria, 17p. mla: Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. IST Austria, 2013, doi:10.15479/AT:IST-2013-141-v1-1. short: K. Chatterjee, L. Doyen, S. Nain, M. Vardi, The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies, IST Austria, 2013. date_created: 2018-12-12T11:39:10Z date_published: 2013-09-12T00:00:00Z date_updated: 2023-02-23T10:33:11Z day: '12' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-141-v1-1 file: - access_level: open_access checksum: 226bc791124f8d3138379778ce834e86 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:16Z date_updated: 2020-07-14T12:46:46Z file_id: '5477' file_name: IST-2013-141-v1+1_main-tech-rpt.pdf file_size: 300481 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '17' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '141' related_material: record: - id: '2213' relation: later_version status: public status: public title: The complexity of partial-observation stochastic parity games with finite-memory strategies type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5407' abstract: - lang: eng text: This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled to provide an institutional repository as a platform and also a service to the scientists at the institute. It also includes optional features, which would be of strong benefit for the scientists and would increase the usage of the repository, and hence the visibility of research at IST Austria. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Technical Requirements and Features. IST Austria; 2013. apa: Porsche, J. (2013). Technical requirements and features. IST Austria. chicago: Porsche, Jana. Technical Requirements and Features. IST Austria, 2013. ieee: J. Porsche, Technical requirements and features. IST Austria, 2013. ista: Porsche J. 2013. Technical requirements and features, IST Austria,p. mla: Porsche, Jana. Technical Requirements and Features. IST Austria, 2013. short: J. Porsche, Technical Requirements and Features, IST Austria, 2013. date_created: 2018-12-12T11:39:09Z date_published: 2013-07-13T00:00:00Z date_updated: 2020-07-14T23:07:51Z day: '13' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: 9e4f9abf79a56f651f0012a34909880f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:02Z date_updated: 2020-07-14T12:46:46Z file_id: '5463' file_name: IST-2013-135-v1+1_Features.pdf file_size: 90311 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria pubrep_id: '135' status: public title: Technical requirements and features type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5410' abstract: - lang: eng text: "Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. \r\nOur approach generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. " alternative_title: - IST Austria Technical Report author: - first_name: Umair full_name: Ahmed, Umair last_name: Ahmed - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Sumit full_name: Gulwani, Sumit last_name: Gulwani citation: ama: Ahmed U, Chatterjee K, Gulwani S. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-146-v1-1 apa: Ahmed, U., Chatterjee, K., & Gulwani, S. (2013). Automatic generation of alternative starting positions for traditional board games. IST Austria. https://doi.org/10.15479/AT:IST-2013-146-v1-1 chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-146-v1-1. ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative starting positions for traditional board games. IST Austria, 2013. ista: Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p. mla: Ahmed, Umair, et al. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-146-v1-1. short: U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013. date_created: 2018-12-12T11:39:10Z date_published: 2013-12-03T00:00:00Z date_updated: 2023-02-23T10:00:50Z day: '03' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-146-v1-1 file: - access_level: open_access checksum: 409f3aaaf1184e4057b89cbb449dac80 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:06Z date_updated: 2020-07-14T12:46:46Z file_id: '5528' file_name: IST-2013-146-v1+1_main.pdf file_size: 818189 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '13' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '146' related_material: record: - id: '1481' relation: later_version status: public status: public title: Automatic generation of alternative starting positions for traditional board games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2327' abstract: - lang: eng text: 'We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M′ within distance ρ from M satisfy (or violate) φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.' alternative_title: - LNCS author: - 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: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Henzinger TA, Otop J. From model checking to model measuring. 2013;8052:273-287. doi:10.1007/978-3-642-40184-8_20 apa: 'Henzinger, T. A., & Otop, J. (2013). From model checking to model measuring. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-40184-8_20' chicago: Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_20. ieee: T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013. ista: Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052, 273–287. mla: Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring. Vol. 8052, Springer, 2013, pp. 273–87, doi:10.1007/978-3-642-40184-8_20. short: T.A. Henzinger, J. Otop, 8052 (2013) 273–287. conference: end_date: 2013-08-30 location: Buenos Aires, Argentina name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:00Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T12:25:26Z day: '01' ddc: - '005' - '000' department: - _id: ToHe doi: 10.1007/978-3-642-40184-8_20 file: - access_level: open_access checksum: 4c04695c4bfdf2119cd4f5d1babc3e8a content_type: application/pdf creator: system date_created: 2018-12-12T10:17:45Z date_updated: 2020-07-14T12:45:38Z file_id: '5301' file_name: IST-2013-129-v1+1_concur.pdf file_size: 378587 relation: main_file file_date_updated: 2020-07-14T12:45:38Z has_accepted_license: '1' intvolume: ' 8052' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 273 - 287 publication_status: published publisher: Springer publist_id: '4599' pubrep_id: '129' quality_controlled: '1' related_material: record: - id: '5417' relation: earlier_version status: public series_title: Lecture Notes in Computer Science status: public title: From model checking to model measuring type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '590' abstract: - lang: eng text: We present two methods of creating two orthogonally-polarized focal points at customizable relative locations. These schemes may be critical for enhancing entanglement sources and other applications. alternative_title: - Optics InfoBase Conference Papers author: - first_name: David full_name: Schmid, David last_name: Schmid - first_name: Ting full_name: Huang, Ting-Yu last_name: Huang - first_name: Radhika full_name: Dirks, Radhika last_name: Dirks - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing. In: OSA; 2013. doi:10.1364/QIM.2013.W6.23' apa: 'Schmid, D., Huang, T., Dirks, R., Hosten, O., & Kwiat, P. (2013). Polarization dependent focusing. Presented at the QIM: Quantum Information and Measurement, OSA. https://doi.org/10.1364/QIM.2013.W6.23' chicago: Schmid, David, Ting Huang, Radhika Dirks, Onur Hosten, and Paul Kwiat. “Polarization Dependent Focusing.” OSA, 2013. https://doi.org/10.1364/QIM.2013.W6.23. ieee: 'D. Schmid, T. Huang, R. Dirks, O. Hosten, and P. Kwiat, “Polarization dependent focusing,” presented at the QIM: Quantum Information and Measurement, 2013.' ista: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference Papers, .' mla: Schmid, David, et al. Polarization Dependent Focusing. OSA, 2013, doi:10.1364/QIM.2013.W6.23. short: D. Schmid, T. Huang, R. Dirks, O. Hosten, P. Kwiat, in:, OSA, 2013. conference: name: 'QIM: Quantum Information and Measurement' date_created: 2018-12-11T11:47:22Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:05:10Z day: '01' doi: 10.1364/QIM.2013.W6.23 extern: 1 month: '01' publication_status: published publisher: OSA publist_id: '7217' quality_controlled: 0 status: public title: Polarization dependent focusing type: conference year: '2013' ... --- _id: '5920' abstract: - lang: eng text: We study chains of lattice ideals that are invariant under a symmetric group action. In our setting, the ambient rings for these ideals are polynomial rings which are increasing in (Krull) dimension. Thus, these chains will fail to stabilize in the traditional commutative algebra sense. However, we prove a theorem which says that “up to the action of the group”, these chains locally stabilize. We also give an algorithm, which we have implemented in software, for explicitly constructing these stabilization generators for a family of Laurent toric ideals involved in applications to algebraic statistics. We close with several open problems and conjectures arising from our theoretical and computational investigations. article_processing_charge: No article_type: original author: - first_name: Christopher J. full_name: Hillar, Christopher J. last_name: Hillar - first_name: Abraham full_name: Martin del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin del Campo Sanchez citation: ama: Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 2013;50:314-334. doi:10.1016/j.jsc.2012.06.006 apa: Hillar, C. J., & Martin del Campo Sanchez, A. (2013). Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2012.06.006 chicago: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation. Elsevier, 2013. https://doi.org/10.1016/j.jsc.2012.06.006. ieee: C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals,” Journal of Symbolic Computation, vol. 50. Elsevier, pp. 314–334, 2013. ista: Hillar CJ, Martin del Campo Sanchez A. 2013. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 50, 314–334. mla: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation, vol. 50, Elsevier, 2013, pp. 314–34, doi:10.1016/j.jsc.2012.06.006. short: C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation 50 (2013) 314–334. date_created: 2019-02-05T08:48:24Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T08:05:15Z day: '01' doi: 10.1016/j.jsc.2012.06.006 extern: '1' intvolume: ' 50' language: - iso: eng month: '03' oa_version: None page: 314-334 publication: Journal of Symbolic Computation publication_identifier: issn: - 0747-7171 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1016/j.jsc.2015.09.002 status: public title: Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2013' ... --- _id: '591' abstract: - lang: eng text: We present two methods for the precise independent focusing of orthogonal linear polarizations of light at arbitrary relative locations. Our first scheme uses a displaced lens in a polarization Sagnac interferometer to provide adjustable longitudinal and lateral focal displacements via simple geometry; the second uses uniaxial crystals to achieve the same effect in a compact collinear setup. We develop the theoretical applications and limitations of our schemes, and provide experimental confirmation of our calculations. author: - first_name: David full_name: Schmid, David last_name: Schmid - first_name: Ting full_name: Huang, Ting-Yu last_name: Huang - first_name: Shiraz full_name: Hazrat, Shiraz last_name: Hazrat - first_name: Radhika full_name: Dirks, Radhika last_name: Dirks - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Stephan full_name: Quint, Stephan last_name: Quint - first_name: Dickson full_name: Thian, Dickson last_name: Thian - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 2013;21(13):15538-15552. doi:10.1364/OE.21.015538 apa: Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat, P. (2013). Adjustable and robust methods for polarization-dependent focusing. Optics Express. Optical Society of America. https://doi.org/10.1364/OE.21.015538 chicago: Schmid, David, Ting Huang, Shiraz Hazrat, Radhika Dirks, Onur Hosten, Stephan Quint, Dickson Thian, and Paul Kwiat. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” Optics Express. Optical Society of America, 2013. https://doi.org/10.1364/OE.21.015538. ieee: D. Schmid et al., “Adjustable and robust methods for polarization-dependent focusing,” Optics Express, vol. 21, no. 13. Optical Society of America, pp. 15538–15552, 2013. ista: Schmid D, Huang T, Hazrat S, Dirks R, Hosten O, Quint S, Thian D, Kwiat P. 2013. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 21(13), 15538–15552. mla: Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” Optics Express, vol. 21, no. 13, Optical Society of America, 2013, pp. 15538–52, doi:10.1364/OE.21.015538. short: D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian, P. Kwiat, Optics Express 21 (2013) 15538–15552. date_created: 2018-12-11T11:47:22Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:05:12Z day: '01' doi: 10.1364/OE.21.015538 extern: 1 intvolume: ' 21' issue: '13' month: '07' page: 15538 - 15552 publication: Optics Express publication_status: published publisher: Optical Society of America publist_id: '7218' quality_controlled: 0 status: public title: Adjustable and robust methods for polarization-dependent focusing type: journal_article volume: 21 year: '2013' ... --- _id: '595' article_processing_charge: No author: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Patrick full_name: Cramer, Patrick last_name: Cramer citation: ama: 'Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 2013;32(6):771-772. doi:10.1038/emboj.2013.36' apa: 'Bernecky, C., & Cramer, P. (2013). Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.36' chicago: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.36.' ieee: 'C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs its own extension and destruction,” EMBO Journal, vol. 32, no. 6. Wiley-Blackwell, pp. 771–772, 2013.' ista: 'Bernecky C, Cramer P. 2013. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 32(6), 771–772.' mla: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal, vol. 32, no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:10.1038/emboj.2013.36.' short: C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772. date_created: 2018-12-11T11:47:23Z date_published: 2013-03-20T00:00:00Z date_updated: 2021-01-12T08:05:20Z day: '20' doi: 10.1038/emboj.2013.36 extern: '1' intvolume: ' 32' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/ month: '03' oa: 1 oa_version: None page: 771 - 772 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '7207' status: public title: 'Struggling to let go: A non-coding RNA directs its own extension and destruction' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '6128' abstract: - lang: eng text: Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O2 and CO2. CO2 is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO2 responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing neuron URX inhibits CO2 avoidance. This inhibition can be graded according to O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to modulate CO2 responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans. article_number: e1004011 author: - first_name: Eiji full_name: Kodama-Namba, Eiji last_name: Kodama-Namba - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Andrew J. full_name: Bretscher, Andrew J. last_name: Bretscher - first_name: Einav full_name: Gross, Einav last_name: Gross - first_name: K. Emanuel full_name: Busch, K. Emanuel last_name: Busch - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 2013;9(12). doi:10.1371/journal.pgen.1004011 apa: Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., & de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004011 chicago: Kodama-Namba, Eiji, Lorenz A. Fenk, Andrew J. Bretscher, Einav Gross, K. Emanuel Busch, and Mario de Bono. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics. Public Library of Science (PLoS), 2013. https://doi.org/10.1371/journal.pgen.1004011. ieee: E. Kodama-Namba, L. A. Fenk, A. J. Bretscher, E. Gross, K. E. Busch, and M. de Bono, “Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans,” PLoS Genetics, vol. 9, no. 12. Public Library of Science (PLoS), 2013. ista: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. 2013. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 9(12), e1004011. mla: Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics, vol. 9, no. 12, e1004011, Public Library of Science (PLoS), 2013, doi:10.1371/journal.pgen.1004011. short: E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono, PLoS Genetics 9 (2013). date_created: 2019-03-19T14:58:51Z date_published: 2013-12-19T00:00:00Z date_updated: 2021-01-12T08:06:15Z day: '19' ddc: - '570' doi: 10.1371/journal.pgen.1004011 extern: '1' external_id: pmid: - '24385919' file: - access_level: open_access checksum: 299b6321be79931c7c17c5db6e69c711 content_type: application/pdf creator: kschuh date_created: 2019-03-19T15:14:51Z date_updated: 2020-07-14T12:47:20Z file_id: '6129' file_name: 2013_PLOS_Kodama-Namba.PDF file_size: 4499039 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 9' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science (PLoS) quality_controlled: '1' status: public title: Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '6130' abstract: - lang: eng text: 'Cas9 is an RNA-guided double-stranded DNA nuclease that participates in clustered regularly interspaced short palindromic repeats (CRISPR)-mediated adaptive immunity in prokaryotes. CRISPR–Cas9 has recently been used to generate insertion and deletion mutations in Caenorhabditis elegans, but not to create tailored changes (knock-ins). We show that the CRISPR–CRISPR-associated (Cas) system can be adapted for efficient and precise editing of the C. elegans genome. The targeted double-strand breaks generated by CRISPR are substrates for transgene-instructed gene conversion. This allows customized changes in the C. elegans genome by homologous recombination: sequences contained in the repair template (the transgene) are copied by gene conversion into the genome. The possibility to edit the C. elegans genome at selected locations will facilitate the systematic study of gene function in this widely used model organism.' article_number: e193 author: - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Chen C, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 2013;41(20). doi:10.1093/nar/gkt805 apa: Chen, C., Fenk, L. A., & de Bono, M. (2013). Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkt805 chicago: Chen, Changchun, Lorenz A. Fenk, and Mario de Bono. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research. Oxford University Press, 2013. https://doi.org/10.1093/nar/gkt805. ieee: C. Chen, L. A. Fenk, and M. de Bono, “Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination,” Nucleic Acids Research, vol. 41, no. 20. Oxford University Press, 2013. ista: Chen C, Fenk LA, de Bono M. 2013. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 41(20), e193. mla: Chen, Changchun, et al. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research, vol. 41, no. 20, e193, Oxford University Press, 2013, doi:10.1093/nar/gkt805. short: C. Chen, L.A. Fenk, M. de Bono, Nucleic Acids Research 41 (2013). date_created: 2019-03-19T15:17:40Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '01' ddc: - '570' doi: 10.1093/nar/gkt805 extern: '1' external_id: pmid: - '24013562' file: - access_level: open_access checksum: 0f1f127cefd043cb922b292e1cd16f02 content_type: application/pdf creator: kschuh date_created: 2019-03-19T15:25:42Z date_updated: 2020-07-14T12:47:20Z file_id: '6131' file_name: 2013_OUP_Chen.pdf file_size: 340225 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 41' issue: '20' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nucleic Acids Research publication_identifier: issn: - 1362-4962 - 0305-1048 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2013' ... --- _id: '6133' abstract: - lang: eng text: cGMP signaling is widespread in the nervous system. However, it has proved difficult to visualize and genetically probe endogenously evoked cGMP dynamics in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical O2-binding soluble guanylate cyclase and that is sustained until oxygen levels fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2) and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation following a rise in O2, apparently by keeping in check gating of cGMP channels and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible when the same neuron in an individual animal is stimulated repeatedly, suggesting that cGMP transduction has high intrinsic reliability. However, responses vary substantially across individuals, despite animals being genetically identical and similarly reared. This variability may reflect stochastic differences in expression of cGMP signaling components. Our work provides in vivo insights into the architecture of neuronal cGMP signaling. author: - first_name: A. full_name: Couto, A. last_name: Couto - first_name: S. full_name: Oda, S. last_name: Oda - first_name: V. O. full_name: Nikolaev, V. O. last_name: Nikolaev - first_name: Z. full_name: Soltesz, Z. last_name: Soltesz - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 2013;110(35):E3301-E3310. doi:10.1073/pnas.1217428110 apa: Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., & de Bono, M. (2013). In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1217428110 chicago: Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217428110. ieee: A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,” Proceedings of the National Academy of Sciences, vol. 110, no. 35. Proceedings of the National Academy of Sciences, pp. E3301–E3310, 2013. ista: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 110(35), E3301–E3310. mla: Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of Sciences, vol. 110, no. 35, Proceedings of the National Academy of Sciences, 2013, pp. E3301–10, doi:10.1073/pnas.1217428110. short: A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the National Academy of Sciences 110 (2013) E3301–E3310. date_created: 2019-03-20T14:05:06Z date_published: 2013-08-27T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '27' ddc: - '570' doi: 10.1073/pnas.1217428110 extern: '1' external_id: pmid: - '23940325' file: - access_level: open_access checksum: 3ee28a694f74a49f0d098970ae391a91 content_type: application/pdf creator: kschuh date_created: 2019-03-20T14:07:53Z date_updated: 2020-07-14T12:47:20Z file_id: '6134' file_name: 2013_PNAS_Couto.pdf file_size: 2198763 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 110' issue: '35' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: E3301-E3310 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '6135' abstract: - lang: eng text: Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery. author: - first_name: Miriam full_name: Rodriguez, Miriam last_name: Rodriguez - first_name: L. Basten full_name: Snoek, L. Basten last_name: Snoek - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Jan E. full_name: Kammenga, Jan E. last_name: Kammenga citation: ama: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 2013;29(6):367-374. doi:10.1016/j.tig.2013.01.010' apa: 'Rodriguez, M., Snoek, L. B., de Bono, M., & Kammenga, J. E. (2013). Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2013.01.010' chicago: 'Rodriguez, Miriam, L. Basten Snoek, Mario de Bono, and Jan E. Kammenga. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics. Elsevier, 2013. https://doi.org/10.1016/j.tig.2013.01.010.' ieee: 'M. Rodriguez, L. B. Snoek, M. de Bono, and J. E. Kammenga, “Worms under stress: C. elegans stress response and its relevance to complex human disease and aging,” Trends in Genetics, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.' ista: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. 2013. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 29(6), 367–374.' mla: 'Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics, vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:10.1016/j.tig.2013.01.010.' short: M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29 (2013) 367–374. date_created: 2019-03-20T14:17:42Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T08:06:17Z day: '01' doi: 10.1016/j.tig.2013.01.010 extern: '1' intvolume: ' 29' issue: '6' language: - iso: eng month: '06' oa_version: None page: 367-374 publication: Trends in Genetics publication_identifier: issn: - 0168-9525 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Worms under stress: C. elegans stress response and its relevance to complex human disease and aging' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '6132' author: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: W.R. full_name: Schafer, W.R. last_name: Schafer - first_name: A. full_name: Gottschalk, A. last_name: Gottschalk citation: ama: 'de Bono M, Schafer WR, Gottschalk A. Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Hegemann P, Sigrist S, eds. Optogenetics. Walter de Gruyter; 2013:61-78.' apa: de Bono, M., Schafer, W. R., & Gottschalk, A. (2013). Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In P. Hegemann & S. Sigrist (Eds.), Optogenetics (pp. 61–78). Walter de Gruyter. chicago: Bono, Mario de, W.R. Schafer, and A. Gottschalk. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” In Optogenetics, edited by Peter Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013. ieee: M. de Bono, W. R. Schafer, and A. Gottschalk, “Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans,” in Optogenetics, P. Hegemann and S. Sigrist, Eds. Walter de Gruyter, 2013, pp. 61–78. ista: 'de Bono M, Schafer WR, Gottschalk A. 2013.Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Optogenetics. , 61–78.' mla: de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” Optogenetics, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter, 2013, pp. 61–78. short: M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.), Optogenetics, Walter de Gruyter, 2013, pp. 61–78. date_created: 2019-03-20T13:54:05Z date_published: 2013-08-28T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '28' editor: - first_name: Peter full_name: Hegemann, Peter last_name: Hegemann - first_name: Stephan full_name: Sigrist, Stephan last_name: Sigrist extern: '1' language: - iso: eng month: '08' oa_version: None page: 61-78 publication: Optogenetics publication_identifier: isbn: - 9783110270723; 9783110270716 publication_status: published publisher: Walter de Gruyter quality_controlled: '1' status: public title: Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '6370' abstract: - lang: eng text: 'The molecular and supramolecular origins of the superior nonlinear optical (NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile), are presented. The molecular charge-transfer distribution is topographically mapped, demonstrating that a uniformly delocalized passive electronic medium facilitates the charge-transfer between the phenolic electron donor and the cyano electron acceptors which lie at opposite ends of the molecule. Its ability to act as a “push–pull” π-conjugated molecule is quantified, relative to similar materials, by supporting empirical calculations; these include bond-length alternation and harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with frontier molecular orbital considerations, reveal that OH1 can exist readily in its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals a correlation between the quinoidal resonance contribution to the overall structure of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally locked polyene framework materials. Solid-state tensorial coefficients of the molecular dipole, polarizability, and the first hyperpolarizability for OH1 are derived from the first-, second-, and third-order electronic moments of the experimental charge-density distribution. The overall solid-state molecular dipole moment is compared with those from gas-phase calculations, revealing that crystal field effects are very significant in OH1. The solid-state hyperpolarizability derived from this charge-density study affords good agreement with gas-phase calculations as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced second harmonic (EFISH) generation. This lends support to the further use of charge-density studies to calculate solid-state hyperpolarizability coefficients in other organic NLO materials. Finally, this charge-density study is also employed to provide an advanced classification of hydrogen bonds in OH1, which requires more stringent criteria than those from conventional structure analysis. As a result, only the strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed, it is this electrostatic interaction that influences the molecular charge transfer: the other four, weaker, nonbonded contacts nonetheless affect the crystal packing. Overall, the establishment of these structure–property relationships lays a blueprint for designing further, more NLO efficient, materials in this industrially leading organic family of compounds.' author: - first_name: Tze-Chia full_name: Lin, Tze-Chia last_name: Lin - first_name: Jacqueline M. full_name: Cole, Jacqueline M. last_name: Cole - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Alison J. full_name: Edwards, Alison J. last_name: Edwards - first_name: Ross O. full_name: Piltz, Ross O. last_name: Piltz - first_name: Javier full_name: Pérez-Moreno, Javier last_name: Pérez-Moreno - first_name: Ji-Youn full_name: Seo, Ji-Youn last_name: Seo - first_name: Seung-Chul full_name: Lee, Seung-Chul last_name: Lee - first_name: Koen full_name: Clays, Koen last_name: Clays - first_name: O-Pil full_name: Kwon, O-Pil last_name: Kwon citation: ama: 'Lin T-C, Cole JM, Higginbotham AP, et al. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 2013;117(18):9416-9430. doi:10.1021/jp400648q' apa: 'Lin, T.-C., Cole, J. M., Higginbotham, A. P., Edwards, A. J., Piltz, R. O., Pérez-Moreno, J., … Kwon, O.-P. (2013). Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. American Chemical Society (ACS). https://doi.org/10.1021/jp400648q' chicago: 'Lin, Tze-Chia, Jacqueline M. Cole, Andrew P Higginbotham, Alison J. Edwards, Ross O. Piltz, Javier Pérez-Moreno, Ji-Youn Seo, Seung-Chul Lee, Koen Clays, and O-Pil Kwon. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry C. American Chemical Society (ACS), 2013. https://doi.org/10.1021/jp400648q.' ieee: 'T.-C. Lin et al., “Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations,” The Journal of Physical Chemistry C, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.' ista: 'Lin T-C, Cole JM, Higginbotham AP, Edwards AJ, Piltz RO, Pérez-Moreno J, Seo J-Y, Lee S-C, Clays K, Kwon O-P. 2013. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 117(18), 9416–9430.' mla: 'Lin, Tze-Chia, et al. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry C, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:10.1021/jp400648q.' short: T.-C. Lin, J.M. Cole, A.P. Higginbotham, A.J. Edwards, R.O. Piltz, J. Pérez-Moreno, J.-Y. Seo, S.-C. Lee, K. Clays, O.-P. Kwon, The Journal of Physical Chemistry C 117 (2013) 9416–9430. date_created: 2019-05-03T09:40:31Z date_published: 2013-05-09T00:00:00Z date_updated: 2021-01-12T08:07:17Z day: '09' doi: 10.1021/jp400648q extern: '1' intvolume: ' 117' issue: '18' language: - iso: eng month: '05' oa_version: None page: 9416-9430 publication: The Journal of Physical Chemistry C publication_identifier: issn: - 1932-7447 - 1932-7455 publication_status: published publisher: American Chemical Society (ACS) quality_controlled: '1' status: public title: 'Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2013' ... --- _id: '6440' abstract: - lang: eng text: In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations. We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance. In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations. alternative_title: - IST Austria Technical Report author: - 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: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: Henzinger TA, Payer H, Sezgin A. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria; 2013. doi:10.15479/AT:IST-2013-124-v1-1 apa: Henzinger, T. A., Payer, H., & Sezgin, A. (2013). Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria. https://doi.org/10.15479/AT:IST-2013-124-v1-1 chicago: Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-124-v1-1. ieee: T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria, 2013. ista: Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p. mla: Henzinger, Thomas A., et al. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013, doi:10.15479/AT:IST-2013-124-v1-1. short: T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013. date_created: 2019-05-13T14:13:27Z date_published: 2013-06-13T00:00:00Z date_updated: 2020-07-14T23:06:19Z day: '13' ddc: - '000' - '005' department: - _id: ToHe doi: 10.15479/AT:IST-2013-124-v1-1 file: - access_level: open_access checksum: a219ba4eada6cd62befed52262ee15d4 content_type: application/pdf creator: dernst date_created: 2019-05-13T14:11:39Z date_updated: 2020-07-14T12:47:30Z file_id: '6441' file_name: 2013_TechRep_Henzinger.pdf file_size: 549684 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '23' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '124' status: public title: 'Replacing competition with cooperation to achieve scalable lock-free FIFO queues ' type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '6768' abstract: - lang: eng text: The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme. article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: Mondelli M. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 2013;3:68-111. doi:10.5201/ipol.2013.53 apa: Mondelli, M. (2013). A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. Image Processing On Line. https://doi.org/10.5201/ipol.2013.53 chicago: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line. Image Processing On Line, 2013. https://doi.org/10.5201/ipol.2013.53. ieee: M. Mondelli, “A finite difference scheme for the stack filter simulating the MCM,” Image Processing On Line, vol. 3. Image Processing On Line, pp. 68–111, 2013. ista: Mondelli M. 2013. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 3, 68–111. mla: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line, vol. 3, Image Processing On Line, 2013, pp. 68–111, doi:10.5201/ipol.2013.53. short: M. Mondelli, Image Processing On Line 3 (2013) 68–111. date_created: 2019-08-05T12:30:38Z date_published: 2013-07-11T00:00:00Z date_updated: 2021-01-12T08:08:56Z day: '11' ddc: - '510' doi: 10.5201/ipol.2013.53 extern: '1' file: - access_level: open_access checksum: 83b7d429bc248c6c461229d3504fb139 content_type: application/pdf creator: dernst date_created: 2019-08-05T12:33:40Z date_updated: 2020-07-14T12:47:40Z file_id: '6769' file_name: 2013_IPOL_Mondelli.pdf file_size: 4306158 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 68-111 publication: Image Processing On Line publication_identifier: issn: - 2105-1232 publication_status: published publisher: Image Processing On Line quality_controlled: '1' status: public title: A finite difference scheme for the stack filter simulating the MCM tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2329' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. 2013;8052:500-515. doi:10.1007/978-3-642-40184-8_35 apa: 'Chatterjee, K., & Velner, Y. (2013). Hyperplane separation technique for multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentinia: Springer. https://doi.org/10.1007/978-3-642-40184-8_35' chicago: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_35. ieee: K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013. ista: Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515. mla: Chatterjee, Krishnendu, and Yaron Velner. Hyperplane Separation Technique for Multidimensional Mean-Payoff Games. Vol. 8052, Springer, 2013, pp. 500–15, doi:10.1007/978-3-642-40184-8_35. short: K. Chatterjee, Y. Velner, 8052 (2013) 500–515. conference: end_date: 2013-08-30 location: Buenos Aires, Argentinia name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:01Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T13:00:42Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-40184-8_35 ec_funded: 1 external_id: arxiv: - '1210.3141' intvolume: ' 8052' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1210.3141 month: '08' oa: 1 oa_version: Preprint page: 500 - 515 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4597' quality_controlled: '1' related_material: record: - id: '717' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Hyperplane separation technique for multidimensional mean-payoff games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '7306' abstract: - lang: eng text: Rechargeable lithium–air (O2) batteries are receiving intense interest because their high theoretical specific energy exceeds that of lithium-ion batteries. If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does seem to demonstrate better stability. However, nanoporous gold is not a suitable cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific energy), it is too expensive and too difficult to fabricate. Identifying a suitable cathode material for the Li–O2 cell is one of the greatest challenges at present. Here we show that a TiC-based cathode reduces greatly side reactions (arising from the electrolyte and electrode degradation) compared with carbon and exhibits better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98% capacity retention after 100 cycles, compared with 95% for nanoporous gold); it is also four times lighter, of lower cost and easier to fabricate. The stability may originate from the presence of TiO2 (along with some TiOC) on the surface of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more viable, stable, cathode for aprotic Li–O2 cells. article_processing_charge: No article_type: original author: - first_name: Muhammed M. full_name: Ottakam Thotiyl, Muhammed M. last_name: Ottakam Thotiyl - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Zheng full_name: Liu, Zheng last_name: Liu - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056. doi:10.1038/nmat3737 apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., & Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat3737 chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737. ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P. G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” Nature Materials, vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013. ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056. mla: Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56, doi:10.1038/nmat3737. short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce, Nature Materials 12 (2013) 1050–1056. date_created: 2020-01-15T12:18:29Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:12:55Z day: '01' doi: 10.1038/nmat3737 extern: '1' intvolume: ' 12' issue: '11' language: - iso: eng month: '09' oa_version: None page: 1050-1056 publication: Nature Materials publication_identifier: issn: - 1476-1122 - 1476-4660 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: A stable cathode for the aprotic Li–O2 battery type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2013' ... --- _id: '7307' abstract: - lang: eng text: The non-aqueous Li–air (O2) battery is receiving intense interest because its theoretical specific energy exceeds that of Li-ion batteries. Recharging the Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed on discharge within the porous cathode. However, transporting charge between Li2O2 particles and the solid electrode surface is at best very difficult and leads to voltage polarization on charging, even at modest rates. This is a significant problem facing the non-aqueous Li–O2 battery. Here we show that incorporation of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that are impossible for the cell in the absence of the mediator. On charging, TTF is oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2, which results in the regeneration of TTF. The mediator acts as an electron–hole transfer agent that permits efficient oxidation of solid Li2O2. The cell with the mediator demonstrated 100 charge/discharge cycles. article_processing_charge: No article_type: original author: - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646 apa: Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013). Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.1646 chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine, and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646. ieee: Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no. 6. Springer Nature, pp. 489–494, 2013. ista: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 5(6), 489–494. mla: Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646. short: Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry 5 (2013) 489–494. date_created: 2020-01-15T12:18:43Z date_published: 2013-05-12T00:00:00Z date_updated: 2021-01-12T08:12:56Z day: '12' doi: 10.1038/nchem.1646 extern: '1' intvolume: ' 5' issue: '6' language: - iso: eng month: '05' oa_version: None page: 489-494 publication: Nature Chemistry publication_identifier: issn: - 1755-4330 - 1755-4349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Charging a Li–O2 battery using a redox mediator type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2013' ... --- _id: '7596' abstract: - lang: eng text: Casein kinase1 (CK1) plays crucial roles in regulating growth and development via phosphorylating various substrates throughout the eukaryote kingdom. Blue light is crucial for normal growth of both plants and animals, and blue light receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and degradation in planta. To study the function of plant CK1s, systematic genetic analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3 and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive response to blue light by CRY2 overexpression. Biochemical studies showed that CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and negatively regulate CRY2 stability in planta, which are stimulated by blue light, further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is stimulated by blue light and feedback regulated by CRY2-mediated signaling. These results provide direct evidence for CRY2 phosphorylation and informative clues on the mechanisms of CRY2-mediated light responses. article_processing_charge: No article_type: original author: - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: C. full_name: Dai, C. last_name: Dai - first_name: H.-T. full_name: Liu, H.-T. last_name: Liu - first_name: H.-W. full_name: Xue, H.-W. last_name: Xue citation: ama: Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322 apa: Tan, S., Dai, C., Liu, H.-T., & Xue, H.-W. (2013). Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322 chicago: Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322. ieee: S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,” The Plant Cell, vol. 25, no. 7. American Society of Plant Biologists, pp. 2618–2632, 2013. ista: Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 25(7), 2618–2632. mla: Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322. short: S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632. date_created: 2020-03-21T16:06:55Z date_published: 2013-08-26T00:00:00Z date_updated: 2021-01-12T08:14:24Z day: '26' doi: 10.1105/tpc.113.114322 extern: '1' external_id: pmid: - '23897926' intvolume: ' 25' issue: '7' language: - iso: eng month: '08' oa_version: None page: 2618-2632 pmid: 1 publication: The Plant Cell publication_identifier: issn: - 1040-4651 - 1532-298X publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' status: public title: Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '7595' abstract: - lang: eng text: Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate which can be finally transferred to inositol hexaphosphate (IP6) and play important roles during plant growth and development. There are 4 putative ITPK members in Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning electron microscopy (SEM) analysis showed that the epidermis structure of seed coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed a dramatic decrease in composition of suberin and cutin, which relate to the permeability of seed coat and the formation of which is accompanied with seed coat development. These results indicate that ITPK2 plays an essential role in seed coat development and lipid polyester barrier formation. article_processing_charge: No article_type: original author: - first_name: Yong full_name: Tang, Yong last_name: Tang - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Hongwei full_name: Xue, Hongwei last_name: Xue citation: ama: Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 2013;45(7):549-560. doi:10.1093/abbs/gmt039 apa: Tang, Y., Tan, S., & Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. Oxford University Press. https://doi.org/10.1093/abbs/gmt039 chicago: Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039. ieee: Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013. ista: Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 45(7), 549–560. mla: Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039. short: Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560. date_created: 2020-03-21T16:06:36Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:14:23Z day: '01' doi: 10.1093/abbs/gmt039 extern: '1' external_id: pmid: - '23595027' intvolume: ' 45' issue: '7' language: - iso: eng month: '07' oa_version: None page: 549-560 pmid: 1 publication: Acta Biochimica et Biophysica Sinica publication_identifier: issn: - 1745-7270 - 1672-9145 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2013' ... --- _id: '765' abstract: - lang: eng text: Renaming is a classic distributed coordination task in which a set of processes must pick distinct identifiers from a small namespace. In this paper, we consider the time complexity of this problem when the namespace is linear in the number of participants, a variant known as loose renaming. We give a non-adaptive algorithm with O(log log n) (individual) step complexity, where n is a known upper bound on contention, and an adaptive algorithm with step complexity O((log log k)2), where k is the actual contention in the execution. We also present a variant of the adaptive algorithm which requires O(k log log k) total process steps. All upper bounds hold with high probability against a strong adaptive adversary. We complement the algorithms with an ω(log log n) expected time lower bound on the complexity of randomized renaming using test-and-set operations and linear space. The result is based on a new coupling technique, and is the first to apply to non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects, our results provide matching bounds on the cost of loose renaming in this setting. acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923, \ and by grants from the Oracle\r\nand Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE 204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: George full_name: Giakkoupis, George last_name: Giakkoupis - first_name: Philipp full_name: Woelfel, Philipp last_name: Woelfel citation: ama: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240' apa: 'Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240' chicago: Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240. ieee: 'D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed Computing, 2013, pp. 200–209.' ista: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.' mla: Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time. ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240. short: D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:23Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-23T13:13:14Z day: '01' doi: 10.1145/2484239.2484240 extern: '1' language: - iso: eng month: '01' oa_version: None page: 200 - 209 publication_status: published publisher: ACM publist_id: '6889' status: public title: Randomized loose renaming in O(loglogn) time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '7745' abstract: - lang: eng text: The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems. article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Isabelle full_name: DeCauwer, Isabelle last_name: DeCauwer - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375 apa: Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate, J. (2013). Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375 chicago: Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon, and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375. ieee: M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning of genetic variation across the genome using multimarker methods in a wild bird population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980, 2013. ista: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 22(15), 3963–3980. mla: Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375. short: M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3963–3980. date_created: 2020-04-30T11:00:15Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:15:14Z day: '01' doi: 10.1111/mec.12375 extern: '1' intvolume: ' 22' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3963-3980 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '7746' abstract: - lang: eng text: Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait. article_processing_charge: No article_type: original author: - first_name: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Isabelle full_name: De Cauwer, Isabelle last_name: De Cauwer - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Jocelyn full_name: Poissant, Jocelyn last_name: Poissant - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376 apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C., & Slate, J. (2013). Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12376 chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376. ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3949–3962, 2013. ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 22(15), 3949–3962. mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376. short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3949–3962. date_created: 2020-04-30T11:00:32Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:15:14Z day: '01' doi: 10.1111/mec.12376 extern: '1' intvolume: ' 22' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3949-3962 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '7747' abstract: - lang: eng text: Acquisition and allocation of resources are central to life‐history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to partition the genetic basis of multivariate plasticity into independent axes of genetic variation, and quantify for the first time, the extent to which specific traits drive multitrait genotype–environment interactions. Our framework generalises to analyses of plasticity, growth and ageing. We apply this approach to a unique, large‐scale, multivariate study of acquisition, allocation and plasticity in the life history of the cricket, Gryllus firmus. We demonstrate that resource acquisition and allocation are genetically correlated, and that plasticity in trade‐offs between allocation to components of fitness is 90% dependent on genetic variance for total resource acquisition. These results suggest that genotype–environment effects for resource acquisition can maintain variation in life‐history components that are typically observed in the wild. article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Andrew P. full_name: Beckerman, Andrew P. last_name: Beckerman citation: ama: 'Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047' apa: 'Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047' chicago: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters. Wiley, 2013. https://doi.org/10.1111/ele.12047.' ieee: 'M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley, pp. 281–290, 2013.' ista: 'Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 16(3), 281–290.' mla: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters, vol. 16, no. 3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.' short: M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290. date_created: 2020-04-30T11:00:49Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T08:15:15Z day: '01' doi: 10.1111/ele.12047 extern: '1' intvolume: ' 16' issue: '3' language: - iso: eng month: '03' oa_version: None page: 281-290 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2013' ... --- _id: '7775' abstract: - lang: eng text: As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition. article_number: '11000' article_processing_charge: No article_type: original author: - first_name: Samuel S. full_name: Schoenholz, Samuel S. last_name: Schoenholz - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Oleg full_name: Kogan, Oleg last_name: Kogan - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d' apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d' chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.' ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.' mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51096d.' short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:58Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51096d extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings II: The transverse length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '7774' abstract: - lang: eng text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*. article_number: '10993' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Wouter G. full_name: Ellenbroek, Wouter G. last_name: Ellenbroek - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu citation: ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f' apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51095f' chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.' ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.' mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51095f.' short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:42Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51095f extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings I: The rigidity length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '8030' abstract: - lang: eng text: While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012. article_number: '119' article_processing_charge: No article_type: original author: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: R. C. full_name: Froemke, R. C. last_name: Froemke - first_name: N. full_name: Doyon, N. last_name: Doyon - first_name: M. full_name: Gilson, M. last_name: Gilson - first_name: J. S. full_name: Haas, J. S. last_name: Haas - first_name: R. full_name: Liu, R. last_name: Liu - first_name: A. full_name: Maffei, A. last_name: Maffei - first_name: P. full_name: Miller, P. last_name: Miller - first_name: C. J. full_name: Wierenga, C. J. last_name: Wierenga - first_name: M. A. full_name: Woodin, M. A. last_name: Woodin - first_name: F. full_name: Zenke, F. last_name: Zenke - first_name: H. full_name: Sprekeler, H. last_name: Sprekeler citation: ama: 'Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 2013;7. doi:10.3389/fncir.2013.00119' apa: 'Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R., … Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. Frontiers Media. https://doi.org/10.3389/fncir.2013.00119' chicago: 'Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu, A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media, 2013. https://doi.org/10.3389/fncir.2013.00119.' ieee: 'T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers Media, 2013.' ista: 'Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 7, 119.' mla: 'Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119, Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.' short: T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural Circuits 7 (2013). date_created: 2020-06-25T13:23:50Z date_published: 2013-07-18T00:00:00Z date_updated: 2021-01-12T08:16:38Z day: '18' ddc: - '570' doi: 10.3389/fncir.2013.00119 extern: '1' external_id: pmid: - '23882186' file: - access_level: open_access checksum: 9c321cb12977d84048712eefa7f0c497 content_type: application/pdf creator: cziletti date_created: 2020-07-16T11:23:40Z date_updated: 2020-07-16T11:23:40Z file_id: '8123' file_name: 2013_FrontNeurCirc_Vogels.pdf file_size: 1530469 relation: main_file success: 1 file_date_updated: 2020-07-16T11:23:40Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Neural Circuits publication_identifier: eissn: - 1662-5110 publication_status: published publisher: Frontiers Media quality_controlled: '1' status: public title: 'Inhibitory synaptic plasticity: Spike timing-dependence and putative network function' 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: 7 year: '2013' ... --- _id: '811' abstract: - lang: eng text: Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration. acknowledgement: |- This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release. We thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis. author: - first_name: Anika full_name: Steffen, Anika last_name: Steffen - first_name: Markus full_name: Ladwein, Markus last_name: Ladwein - first_name: Georgi A full_name: Georgi Dimchev id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev - first_name: Anke full_name: Hein, Anke last_name: Hein - first_name: Lisa full_name: Schwenkmezger, Lisa last_name: Schwenkmezger - first_name: Stefan full_name: Arens, Stefan last_name: Arens - first_name: Kathrin full_name: Ladwein, Kathrin I last_name: Ladwein - first_name: J. full_name: Holleboom, J. Margit last_name: Holleboom - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: John full_name: Small, John V last_name: Small - first_name: Janett full_name: Schwarz, Janett last_name: Schwarz - first_name: Ralf full_name: Gerhard, Ralf last_name: Gerhard - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Theresia full_name: Stradal, Theresia E last_name: Stradal - first_name: Cord full_name: Brakebusch, Cord H last_name: Brakebusch - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232 apa: Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens, S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.118232 chicago: Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger, Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232. ieee: A. Steffen et al., “Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation,” Journal of Cell Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013. ista: Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch C, Rottner K. 2013. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 126(20), 4572–4588. mla: Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science, vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232. short: A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens, K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix, T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588. date_created: 2018-12-11T11:48:38Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:16:57Z day: '01' doi: 10.1242/jcs.118232 extern: 1 intvolume: ' 126' issue: '20' month: '01' page: 4572 - 4588 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6840' quality_controlled: 0 status: public title: Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation 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 volume: 126 year: '2013' ... --- _id: '812' abstract: - lang: eng text: Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes. acknowledgement: "This work was supported in part by Deutsche Forschungsgemeinschaft Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology \ Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and \ Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR. Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner \ for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg for technical assistance." author: - first_name: Stefan full_name: Koestler, Stefan A last_name: Koestler - first_name: Anika full_name: Steffen, Anika last_name: Steffen - first_name: Maria full_name: Maria Nemethova id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Moritz full_name: Winterhoff, Moritz last_name: Winterhoff - first_name: Ningning full_name: Luo, Ningning last_name: Luo - first_name: J. full_name: Holleboom, J. Margit last_name: Holleboom - first_name: Jessica full_name: Krupp, Jessica last_name: Krupp - first_name: Sonja full_name: Jacob, Sonja last_name: Jacob - first_name: Marlene full_name: Vinzenz, Marlene last_name: Vinzenz - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Kai full_name: Schlüter, Kai last_name: Schlüter - first_name: Peter full_name: Gunning, Peter W last_name: Gunning - first_name: Christoph full_name: Winkler, Christoph last_name: Winkler - first_name: Christian full_name: Schmeiser, Christian last_name: Schmeiser - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Theresia full_name: Stradal, Theresia E last_name: Stradal - first_name: John full_name: Small, John V last_name: Small - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857 apa: Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857 chicago: Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857. ieee: S. Koestler et al., “Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin,” Molecular Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875, 2013. ista: Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C, Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 24(18), 2861–2875. mla: Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75, doi:10.1091/mbc.E12-12-0857. short: S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom, J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler, C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of the Cell 24 (2013) 2861–2875. date_created: 2018-12-11T11:48:38Z date_published: 2013-09-15T00:00:00Z date_updated: 2021-01-12T08:17:00Z day: '15' doi: 10.1091/mbc.E12-12-0857 extern: 1 intvolume: ' 24' issue: '18' month: '09' page: 2861 - 2875 publication: Molecular Biology of the Cell publication_status: published publisher: American Society for Biology publist_id: '6841' quality_controlled: 0 status: public title: Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin type: journal_article volume: 24 year: '2013' ...