--- _id: '8074' abstract: - lang: eng text: Cortical neurons receive balanced excitatory and inhibitory synaptic currents. Such a balance could be established and maintained in an experience-dependent manner by synaptic plasticity at inhibitory synapses. We show that this mechanism provides an explanation for the sparse firing patterns observed in response to natural stimuli and fits well with a recently observed interaction of excitatory and inhibitory receptive field plasticity. The introduction of inhibitory plasticity in suitable recurrent networks provides a homeostatic mechanism that leads to asynchronous irregular network states. Further, it can accommodate synaptic memories with activity patterns that become indiscernible from the background state but can be reactivated by external stimuli. Our results suggest an essential role of inhibitory plasticity in the formation and maintenance of functional cortical circuitry. 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: H. full_name: Sprekeler, H. last_name: Sprekeler - first_name: F. full_name: Zenke, F. last_name: Zenke - first_name: C. full_name: Clopath, C. last_name: Clopath - first_name: W. full_name: Gerstner, W. last_name: Gerstner citation: ama: Vogels TP, Sprekeler H, Zenke F, Clopath C, Gerstner W. Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks. Science. 2011;334(6062):1569-1573. doi:10.1126/science.1211095 apa: Vogels, T. P., Sprekeler, H., Zenke, F., Clopath, C., & Gerstner, W. (2011). Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1211095 chicago: Vogels, Tim P, H. Sprekeler, F. Zenke, C. Clopath, and W. Gerstner. “Inhibitory Plasticity Balances Excitation and Inhibition in Sensory Pathways and Memory Networks.” Science. American Association for the Advancement of Science, 2011. https://doi.org/10.1126/science.1211095. ieee: T. P. Vogels, H. Sprekeler, F. Zenke, C. Clopath, and W. Gerstner, “Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks,” Science, vol. 334, no. 6062. American Association for the Advancement of Science, pp. 1569–1573, 2011. ista: Vogels TP, Sprekeler H, Zenke F, Clopath C, Gerstner W. 2011. Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks. Science. 334(6062), 1569–1573. mla: Vogels, Tim P., et al. “Inhibitory Plasticity Balances Excitation and Inhibition in Sensory Pathways and Memory Networks.” Science, vol. 334, no. 6062, American Association for the Advancement of Science, 2011, pp. 1569–73, doi:10.1126/science.1211095. short: T.P. Vogels, H. Sprekeler, F. Zenke, C. Clopath, W. Gerstner, Science 334 (2011) 1569–1573. date_created: 2020-06-30T13:26:17Z date_published: 2011-12-16T00:00:00Z date_updated: 2021-06-02T14:57:22Z day: '16' doi: 10.1126/science.1211095 extern: '1' external_id: pmid: - '22075724' intvolume: ' 334' issue: '6062' language: - iso: eng month: '12' oa_version: None page: 1569-1573 pmid: 1 publication: Science publication_identifier: issn: - 0036-8075 - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1126/science.336.6083.802-c scopus_import: '1' status: public title: Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 334 year: '2011' ... --- _id: '8469' abstract: - lang: eng text: The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol – based on REDOR – to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP,R18 5/2, and R18 7/1) is provided. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst citation: ama: Schanda P, Meier BH, Ernst M. Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. Journal of Magnetic Resonance. 2011;210(2):246-259. doi:10.1016/j.jmr.2011.03.015 apa: Schanda, P., Meier, B. H., & Ernst, M. (2011). Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.03.015 chicago: Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Accurate Measurement of One-Bond H–X Heteronuclear Dipolar Couplings in MAS Solid-State NMR.” Journal of Magnetic Resonance. Elsevier, 2011. https://doi.org/10.1016/j.jmr.2011.03.015. ieee: P. Schanda, B. H. Meier, and M. Ernst, “Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR,” Journal of Magnetic Resonance, vol. 210, no. 2. Elsevier, pp. 246–259, 2011. ista: Schanda P, Meier BH, Ernst M. 2011. Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. Journal of Magnetic Resonance. 210(2), 246–259. mla: Schanda, Paul, et al. “Accurate Measurement of One-Bond H–X Heteronuclear Dipolar Couplings in MAS Solid-State NMR.” Journal of Magnetic Resonance, vol. 210, no. 2, Elsevier, 2011, pp. 246–59, doi:10.1016/j.jmr.2011.03.015. short: P. Schanda, B.H. Meier, M. Ernst, Journal of Magnetic Resonance 210 (2011) 246–259. date_created: 2020-09-18T10:10:50Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T08:19:29Z day: '01' doi: 10.1016/j.jmr.2011.03.015 extern: '1' intvolume: ' 210' issue: '2' keyword: - Nuclear and High Energy Physics - Biophysics - Biochemistry - Condensed Matter Physics language: - iso: eng month: '06' oa_version: None page: 246-259 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 210 year: '2011' ... --- _id: '8470' abstract: - lang: eng text: 'Adding a new dimension: 4D or 3D proton‐detected spectra of perdeuterated protein samples with 1H labelled amides and methyl groups permit collecting unambiguous distance restraints with high sensitivity and determining protein structure by solid‐state NMR (see picture).' article_processing_charge: No article_type: original author: - first_name: Matthias full_name: Huber, Matthias last_name: Huber - first_name: Sebastian full_name: Hiller, Sebastian last_name: Hiller - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Anja full_name: Böckmann, Anja last_name: Böckmann - first_name: René full_name: Verel, René last_name: Verel - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier citation: ama: Huber M, Hiller S, Schanda P, et al. A proton-detected 4D solid-state NMR experiment for protein structure determination. ChemPhysChem. 2011;12(5):915-918. doi:10.1002/cphc.201100062 apa: Huber, M., Hiller, S., Schanda, P., Ernst, M., Böckmann, A., Verel, R., & Meier, B. H. (2011). A proton-detected 4D solid-state NMR experiment for protein structure determination. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201100062 chicago: Huber, Matthias, Sebastian Hiller, Paul Schanda, Matthias Ernst, Anja Böckmann, René Verel, and Beat H. Meier. “A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.” ChemPhysChem. Wiley, 2011. https://doi.org/10.1002/cphc.201100062. ieee: M. Huber et al., “A proton-detected 4D solid-state NMR experiment for protein structure determination,” ChemPhysChem, vol. 12, no. 5. Wiley, pp. 915–918, 2011. ista: Huber M, Hiller S, Schanda P, Ernst M, Böckmann A, Verel R, Meier BH. 2011. A proton-detected 4D solid-state NMR experiment for protein structure determination. ChemPhysChem. 12(5), 915–918. mla: Huber, Matthias, et al. “A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.” ChemPhysChem, vol. 12, no. 5, Wiley, 2011, pp. 915–18, doi:10.1002/cphc.201100062. short: M. Huber, S. Hiller, P. Schanda, M. Ernst, A. Böckmann, R. Verel, B.H. Meier, ChemPhysChem 12 (2011) 915–918. date_created: 2020-09-18T10:10:56Z date_published: 2011-02-15T00:00:00Z date_updated: 2021-01-12T08:19:30Z day: '15' doi: 10.1002/cphc.201100062 extern: '1' intvolume: ' 12' issue: '5' keyword: - Physical and Theoretical Chemistry - Atomic and Molecular Physics - and Optics language: - iso: eng month: '02' oa_version: None page: 915-918 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: A proton-detected 4D solid-state NMR experiment for protein structure determination type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2011' ... --- _id: '8464' abstract: - lang: eng text: 'Nonsymmetric motion: Solid‐state NMR measurements of dipolar coupling tensors provide insight into protein dynamics. The hitherto ignored asymmetry of the dipolar coupling tensor contains valuable information about motional asymmetry, which was used in the first direct site‐resolved measurement of such tensors. Important motions such as rotamer jumps can now be directly detected in the solid state.' article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Matthias full_name: Huber, Matthias last_name: Huber - first_name: Jérôme full_name: Boisbouvier, Jérôme last_name: Boisbouvier - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst citation: ama: Schanda P, Huber M, Boisbouvier J, Meier BH, Ernst M. Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion. Angewandte Chemie International Edition. 2011;50(46):11005-11009. doi:10.1002/anie.201103944 apa: Schanda, P., Huber, M., Boisbouvier, J., Meier, B. H., & Ernst, M. (2011). Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201103944 chicago: Schanda, Paul, Matthias Huber, Jérôme Boisbouvier, Beat H. Meier, and Matthias Ernst. “Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion.” Angewandte Chemie International Edition. Wiley, 2011. https://doi.org/10.1002/anie.201103944. ieee: P. Schanda, M. Huber, J. Boisbouvier, B. H. Meier, and M. Ernst, “Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion,” Angewandte Chemie International Edition, vol. 50, no. 46. Wiley, pp. 11005–11009, 2011. ista: Schanda P, Huber M, Boisbouvier J, Meier BH, Ernst M. 2011. Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion. Angewandte Chemie International Edition. 50(46), 11005–11009. mla: Schanda, Paul, et al. “Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion.” Angewandte Chemie International Edition, vol. 50, no. 46, Wiley, 2011, pp. 11005–09, doi:10.1002/anie.201103944. short: P. Schanda, M. Huber, J. Boisbouvier, B.H. Meier, M. Ernst, Angewandte Chemie International Edition 50 (2011) 11005–11009. date_created: 2020-09-18T10:09:40Z date_published: 2011-09-14T00:00:00Z date_updated: 2021-01-12T08:19:27Z day: '14' doi: 10.1002/anie.201103944 extern: '1' intvolume: ' 50' issue: '46' language: - iso: eng month: '09' oa_version: None page: 11005-11009 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1002/anie.201206663 status: public title: Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2011' ... --- _id: '8468' article_processing_charge: No article_type: original author: - first_name: Daniela full_name: Lalli, Daniela last_name: Lalli - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Anup full_name: Chowdhury, Anup last_name: Chowdhury - first_name: Joren full_name: Retel, Joren last_name: Retel - first_name: Matthias full_name: Hiller, Matthias last_name: Hiller - first_name: Victoria A. full_name: Higman, Victoria A. last_name: Higman - first_name: Lieselotte full_name: Handel, Lieselotte last_name: Handel - first_name: Vipin full_name: Agarwal, Vipin last_name: Agarwal - first_name: Bernd full_name: Reif, Bernd last_name: Reif - first_name: Barth full_name: van Rossum, Barth last_name: van Rossum - first_name: Ümit full_name: Akbey, Ümit last_name: Akbey - first_name: Hartmut full_name: Oschkinat, Hartmut last_name: Oschkinat citation: ama: Lalli D, Schanda P, Chowdhury A, et al. Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. Journal of Biomolecular NMR. 2011;51(4):477-485. doi:10.1007/s10858-011-9578-1 apa: Lalli, D., Schanda, P., Chowdhury, A., Retel, J., Hiller, M., Higman, V. A., … Oschkinat, H. (2011). Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-011-9578-1 chicago: Lalli, Daniela, Paul Schanda, Anup Chowdhury, Joren Retel, Matthias Hiller, Victoria A. Higman, Lieselotte Handel, et al. “Three-Dimensional Deuterium-Carbon Correlation Experiments for High-Resolution Solid-State MAS NMR Spectroscopy of Large Proteins.” Journal of Biomolecular NMR. Springer Nature, 2011. https://doi.org/10.1007/s10858-011-9578-1. ieee: D. Lalli et al., “Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins,” Journal of Biomolecular NMR, vol. 51, no. 4. Springer Nature, pp. 477–485, 2011. ista: Lalli D, Schanda P, Chowdhury A, Retel J, Hiller M, Higman VA, Handel L, Agarwal V, Reif B, van Rossum B, Akbey Ü, Oschkinat H. 2011. Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. Journal of Biomolecular NMR. 51(4), 477–485. mla: Lalli, Daniela, et al. “Three-Dimensional Deuterium-Carbon Correlation Experiments for High-Resolution Solid-State MAS NMR Spectroscopy of Large Proteins.” Journal of Biomolecular NMR, vol. 51, no. 4, Springer Nature, 2011, pp. 477–85, doi:10.1007/s10858-011-9578-1. short: D. Lalli, P. Schanda, A. Chowdhury, J. Retel, M. Hiller, V.A. Higman, L. Handel, V. Agarwal, B. Reif, B. van Rossum, Ü. Akbey, H. Oschkinat, Journal of Biomolecular NMR 51 (2011) 477–485. date_created: 2020-09-18T10:10:43Z date_published: 2011-10-25T00:00:00Z date_updated: 2021-01-12T08:19:29Z day: '25' doi: 10.1007/s10858-011-9578-1 extern: '1' intvolume: ' 51' issue: '4' language: - iso: eng month: '10' oa_version: None page: 477-485 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2011' ... --- _id: '890' abstract: - lang: eng text: Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered. acknowledgement: | The work was supported by the Plan Nacional grant number BFU2009-09271 from the Spanish Ministry of Science and Innovation. We extend our thanks to A.M. Peklo and I.V. Fadeev for granting us access to ornithological collections, to V.S. Shishkin, M.V. Kalyakin, R.D. Kashkarov, O.V. Belyalov and V.M. Loskot for valuable insights and to L. Svensson for extensive feedback on the manuscript. We thank E.I. Rogaev for access to ancient DNA facility. author: - first_name: Evgeniy full_name: Koblik, Evgeniy A last_name: Koblik - first_name: Yaroslav full_name: Red'Kin, Yaroslav A last_name: Red'Kin - first_name: Margarita full_name: Meer, Margarita S last_name: Meer - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Sofia full_name: Golenkina, Sofia A last_name: Golenkina - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Arkhipov, Vladimir Y last_name: Arkhipov citation: ama: 'Koblik E, Red’Kin Y, Meer M, et al. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 2011;6(4). doi:10.1371/journal.pone.0017716' apa: 'Koblik, E., Red’Kin, Y., Meer, M., Derelle, R., Golenkina, S., Kondrashov, F., & Arkhipov, V. (2011). Acrocephalus orinus: A case of Mistaken identity. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017716' chicago: 'Koblik, Evgeniy, Yaroslav Red’Kin, Margarita Meer, Romain Derelle, Sofia Golenkina, Fyodor Kondrashov, and Vladimir Arkhipov. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017716.' ieee: 'E. Koblik et al., “Acrocephalus orinus: A case of Mistaken identity,” PLoS One, vol. 6, no. 4. Public Library of Science, 2011.' ista: 'Koblik E, Red’Kin Y, Meer M, Derelle R, Golenkina S, Kondrashov F, Arkhipov V. 2011. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 6(4).' mla: 'Koblik, Evgeniy, et al. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One, vol. 6, no. 4, Public Library of Science, 2011, doi:10.1371/journal.pone.0017716.' short: E. Koblik, Y. Red’Kin, M. Meer, R. Derelle, S. Golenkina, F. Kondrashov, V. Arkhipov, PLoS One 6 (2011). date_created: 2018-12-11T11:49:02Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T08:21:18Z day: '01' doi: 10.1371/journal.pone.0017716 extern: 1 intvolume: ' 6' issue: '4' month: '01' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6760' quality_controlled: 0 status: public title: 'Acrocephalus orinus: A case of Mistaken identity' type: journal_article volume: 6 year: '2011' ... --- _id: '90' abstract: - lang: eng text: A popular method for generating micron-sized aerosols is to submerge ultrasonic (ω ∼ MHz) piezoelectric oscillators in a water bath. The submerged oscillator atomizes the fluid, creating droplets with radii proportional to the wavelength of the standing wave at the fluid surface. Classical theory for the Faraday instability predicts a parametric instability driving a capillary wave at the subharmonic (ω / 2) frequency. For many applications it is desirable to reduce the size of the droplets; however, using higher frequency oscillators becomes impractical beyond a few MHz. Observations are presented that demonstrate that smaller droplets may also be created by increasing the driving amplitude of the oscillator, and that this effect becomes more pronounced for large driving frequencies. It is shown that these observations are consistent with a transition from droplets associated with subharmonic (ω/2) capillary waves to harmonic (ω) capillary waves induced by larger driving frequencies and amplitudes, as predicted by a stability analysis of the capillary waves. author: - 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: A full_name: Guillen, A last_name: Guillen - first_name: Nick full_name: Jones, Nick last_name: Jones - first_name: Tom full_name: Donnelly, Tom last_name: Donnelly - first_name: Andrew full_name: Bernoff, Andrew last_name: Bernoff citation: ama: Higginbotham AP, Guillen A, Jones N, Donnelly T, Bernoff A. Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid. Journal of the Acoustical Society of America. 2011;130(5):2694-2699. doi:10.1121/1.3643816 apa: Higginbotham, A. P., Guillen, A., Jones, N., Donnelly, T., & Bernoff, A. (2011). Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid. Journal of the Acoustical Society of America. Acoustical Society of America. https://doi.org/10.1121/1.3643816 chicago: Higginbotham, Andrew P, A Guillen, Nick Jones, Tom Donnelly, and Andrew Bernoff. “Evidence of the Harmonic Faraday Instability in Ultrasonic Atomization Experiments with a Deep, Inviscid Fluid.” Journal of the Acoustical Society of America. Acoustical Society of America, 2011. https://doi.org/10.1121/1.3643816. ieee: A. P. Higginbotham, A. Guillen, N. Jones, T. Donnelly, and A. Bernoff, “Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid,” Journal of the Acoustical Society of America, vol. 130, no. 5. Acoustical Society of America, pp. 2694–2699, 2011. ista: Higginbotham AP, Guillen A, Jones N, Donnelly T, Bernoff A. 2011. Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid. Journal of the Acoustical Society of America. 130(5), 2694–2699. mla: Higginbotham, Andrew P., et al. “Evidence of the Harmonic Faraday Instability in Ultrasonic Atomization Experiments with a Deep, Inviscid Fluid.” Journal of the Acoustical Society of America, vol. 130, no. 5, Acoustical Society of America, 2011, pp. 2694–99, doi:10.1121/1.3643816. short: A.P. Higginbotham, A. Guillen, N. Jones, T. Donnelly, A. Bernoff, Journal of the Acoustical Society of America 130 (2011) 2694–2699. date_created: 2018-12-11T11:44:34Z date_published: 2011-11-16T00:00:00Z date_updated: 2021-01-12T08:21:44Z day: '16' doi: 10.1121/1.3643816 extern: '1' external_id: pmid: - ' 22087897' intvolume: ' 130' issue: '5' language: - iso: eng month: '11' oa_version: None page: 2694 - 2699 pmid: 1 publication: Journal of the Acoustical Society of America publication_status: published publisher: Acoustical Society of America publist_id: '7964' quality_controlled: '1' status: public title: Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2011' ... --- _id: '9144' abstract: - lang: eng text: "A cloud-resolving model is used to investigate the effect of warming on high percentiles of precipitation (precipitation extremes) in the idealized setting of radiative-convective equilibrium. While this idealized setting does not allow for several factors that influence precipitation in the tropics, it does allow for an evaluation of the response of precipitation extremes to warming in simulations with resolved rather than parameterized convection. The methodology developed should also be applicable to less idealized simulations.\r\n\r\nModeled precipitation extremes are found to increase in magnitude in response to an increase in sea surface temperature. A dry static energy budget is used to relate the changes in precipitation extremes to changes in atmospheric temperature, vertical velocity, and precipitation efficiency. To first order, the changes in precipitation extremes are captured by changes in the mean temperature structure of the atmosphere. Changes in vertical velocities play a secondary role and tend to weaken the strength of precipitation extremes, despite an intensification of updraft velocities in the upper troposphere. The influence of changes in condensate transports on precipitation extremes is quantified in terms of a precipitation efficiency; it does not change greatly with warming.\r\n\r\nTropical precipitation extremes have previously been found to increase at a greater fractional rate than the amount of atmospheric water vapor in observations of present-day variability and in some climate model simulations with parameterized convection. But the fractional increases in precipitation extremes in the cloud-resolving simulations are comparable in magnitude to those in surface water vapor concentrations (owing to a partial cancellation between dynamical and thermodynamical changes), and are substantially less than the fractional increases in column water vapor." article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Paul A. full_name: O’Gorman, Paul A. last_name: O’Gorman - first_name: Larissa E. full_name: Back, Larissa E. last_name: Back citation: ama: Muller CJ, O’Gorman PA, Back LE. Intensification of precipitation extremes with warming in a cloud-resolving model. Journal of Climate. 2011;24(11):2784-2800. doi:10.1175/2011jcli3876.1 apa: Muller, C. J., O’Gorman, P. A., & Back, L. E. (2011). Intensification of precipitation extremes with warming in a cloud-resolving model. Journal of Climate. American Meteorological Society. https://doi.org/10.1175/2011jcli3876.1 chicago: Muller, Caroline J, Paul A. O’Gorman, and Larissa E. Back. “Intensification of Precipitation Extremes with Warming in a Cloud-Resolving Model.” Journal of Climate. American Meteorological Society, 2011. https://doi.org/10.1175/2011jcli3876.1. ieee: C. J. Muller, P. A. O’Gorman, and L. E. Back, “Intensification of precipitation extremes with warming in a cloud-resolving model,” Journal of Climate, vol. 24, no. 11. American Meteorological Society, pp. 2784–2800, 2011. ista: Muller CJ, O’Gorman PA, Back LE. 2011. Intensification of precipitation extremes with warming in a cloud-resolving model. Journal of Climate. 24(11), 2784–2800. mla: Muller, Caroline J., et al. “Intensification of Precipitation Extremes with Warming in a Cloud-Resolving Model.” Journal of Climate, vol. 24, no. 11, American Meteorological Society, 2011, pp. 2784–800, doi:10.1175/2011jcli3876.1. short: C.J. Muller, P.A. O’Gorman, L.E. Back, Journal of Climate 24 (2011) 2784–2800. date_created: 2021-02-15T14:39:57Z date_published: 2011-06-01T00:00:00Z date_updated: 2022-01-24T13:52:46Z day: '01' doi: 10.1175/2011jcli3876.1 extern: '1' intvolume: ' 24' issue: '11' keyword: - Atmospheric Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1175/2011JCLI3876.1 month: '06' oa: 1 oa_version: Published Version page: 2784-2800 publication: Journal of Climate publication_identifier: eissn: - 1520-0442 issn: - 0894-8755 publication_status: published publisher: American Meteorological Society quality_controlled: '1' status: public title: Intensification of precipitation extremes with warming in a cloud-resolving model type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 24 year: '2011' ... --- _id: '9143' abstract: - lang: eng text: Understanding and predicting the response of the hydrological cycle to climate change is a major challenge with important societal implications. Much progress has been made in understanding the response of global average precipitation by considering the energy balances of the atmosphere and the surface1,2,3,4,5,6. This energetic perspective reveals that changes in temperature, greenhouse gases, aerosols, solar forcing and cloud feedbacks can all affect the global average rate of precipitation5,7,8,9,10,11. Local precipitation changes have conventionally been analysed using the water vapour budget, but here we show that the energetic approach can be extended to local changes in precipitation by including changes in horizontal energy transport. In simulations of twenty-first century climate change, this energy transport accounts for much of the spatial variability in precipitation change. We show that changes in radiative and surface sensible heat fluxes are a guide to the local precipitation response over land and at large scales, but not at small scales over the ocean, where cloud and water vapour radiative feedbacks dampen the response. The energetic approach described here helps bridge the gap between our understanding of global and regional precipitation changes. It could be applied to better understand the response of regional precipitation to different radiative forcings, including geo-engineering schemes, as well as to understand the differences between the fast and slow responses of regional precipitation to such forcings. article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: P. A. full_name: O’Gorman, P. A. last_name: O’Gorman citation: ama: Muller CJ, O’Gorman PA. An energetic perspective on the regional response of precipitation to climate change. Nature Climate Change. 2011;1(5):266-271. doi:10.1038/nclimate1169 apa: Muller, C. J., & O’Gorman, P. A. (2011). An energetic perspective on the regional response of precipitation to climate change. Nature Climate Change. Springer Nature. https://doi.org/10.1038/nclimate1169 chicago: Muller, Caroline J, and P. A. O’Gorman. “An Energetic Perspective on the Regional Response of Precipitation to Climate Change.” Nature Climate Change. Springer Nature, 2011. https://doi.org/10.1038/nclimate1169. ieee: C. J. Muller and P. A. O’Gorman, “An energetic perspective on the regional response of precipitation to climate change,” Nature Climate Change, vol. 1, no. 5. Springer Nature, pp. 266–271, 2011. ista: Muller CJ, O’Gorman PA. 2011. An energetic perspective on the regional response of precipitation to climate change. Nature Climate Change. 1(5), 266–271. mla: Muller, Caroline J., and P. A. O’Gorman. “An Energetic Perspective on the Regional Response of Precipitation to Climate Change.” Nature Climate Change, vol. 1, no. 5, Springer Nature, 2011, pp. 266–71, doi:10.1038/nclimate1169. short: C.J. Muller, P.A. O’Gorman, Nature Climate Change 1 (2011) 266–271. date_created: 2021-02-15T14:39:29Z date_published: 2011-07-24T00:00:00Z date_updated: 2022-01-24T13:52:11Z day: '24' doi: 10.1038/nclimate1169 extern: '1' intvolume: ' 1' issue: '5' language: - iso: eng month: '07' oa_version: None page: 266-271 publication: Nature Climate Change publication_identifier: issn: - 1758-678X - 1758-6798 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: An energetic perspective on the regional response of precipitation to climate change type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 1 year: '2011' ... --- _id: '923' abstract: - lang: eng text: The conserved role of Notch signaling in controlling intestinal cell fate specification and homeostasis has been extensively studied. Nevertheless, the precise identity of the cells in which Notch signaling is active and the role of different Notch receptor paralogues in the intestine remain ambiguous, due to the lack of reliable tools to investigate Notch expression and function in vivo. We generated a new series of transgenic mice that allowed us, by lineage analysis, to formally prove that Notch1 and Notch2 are specifically expressed in crypt stem cells. In addition, a novel Notch reporter mouse, Hes1-EmGFP SAT, demonstrated exclusive Notch activity in crypt stem cells and absorptive progenitors. This roster of knock-in and reporter mice represents a valuable resource to functionally explore the Notch pathway in vivo in virtually all tissues. article_number: e25785 author: - first_name: Silvia full_name: Fré, Silvia last_name: Fré - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Sanja full_name: Šale, Sanja last_name: Šale - first_name: Mathilde full_name: Huyghe, Mathilde last_name: Huyghe - first_name: Daniel full_name: Lafkas, Daniel last_name: Lafkas - first_name: Holger full_name: Kissel, Holger last_name: Kissel - first_name: Angeliki full_name: Louvi, Angeliki last_name: Louvi - first_name: Jeffrey full_name: Greve, Jeffrey last_name: Greve - first_name: Daniel full_name: Louvard, Daniel last_name: Louvard - first_name: Spyros full_name: Artavanis Tsakonas, Spyros last_name: Artavanis Tsakonas citation: ama: Fré S, Hannezo EB, Šale S, et al. Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice. PLoS One. 2011;6(10). doi:10.1371/journal.pone.0025785 apa: Fré, S., Hannezo, E. B., Šale, S., Huyghe, M., Lafkas, D., Kissel, H., … Artavanis Tsakonas, S. (2011). Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0025785 chicago: Fré, Silvia, Edouard B Hannezo, Sanja Šale, Mathilde Huyghe, Daniel Lafkas, Holger Kissel, Angeliki Louvi, Jeffrey Greve, Daniel Louvard, and Spyros Artavanis Tsakonas. “Notch Lineages and Activity in Intestinal Stem Cells Determined by a New Set of Knock in Mice.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0025785. ieee: S. Fré et al., “Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice,” PLoS One, vol. 6, no. 10. Public Library of Science, 2011. ista: Fré S, Hannezo EB, Šale S, Huyghe M, Lafkas D, Kissel H, Louvi A, Greve J, Louvard D, Artavanis Tsakonas S. 2011. Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice. PLoS One. 6(10), e25785. mla: Fré, Silvia, et al. “Notch Lineages and Activity in Intestinal Stem Cells Determined by a New Set of Knock in Mice.” PLoS One, vol. 6, no. 10, e25785, Public Library of Science, 2011, doi:10.1371/journal.pone.0025785. short: S. Fré, E.B. Hannezo, S. Šale, M. Huyghe, D. Lafkas, H. Kissel, A. Louvi, J. Greve, D. Louvard, S. Artavanis Tsakonas, PLoS One 6 (2011). date_created: 2018-12-11T11:49:13Z date_published: 2011-10-03T00:00:00Z date_updated: 2021-01-12T08:21:56Z day: '03' ddc: - '570' doi: 10.1371/journal.pone.0025785 extern: '1' file: - access_level: open_access checksum: b4e864125dfcb9fa57a9e01688838081 content_type: application/pdf creator: dernst date_created: 2019-05-10T11:20:26Z date_updated: 2020-07-14T12:48:15Z file_id: '6401' file_name: 2011_PLOS1_Fre.PDF file_size: 2860615 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 6' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6520' quality_controlled: '1' status: public title: Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice 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: 6 year: '2011' ... --- _id: '9483' abstract: - lang: eng text: Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development. article_processing_charge: No article_type: original author: - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Juhyun full_name: Shin, Juhyun last_name: Shin - first_name: Rie full_name: Uzawa, Rie last_name: Uzawa - first_name: Pedro full_name: Silva, Pedro last_name: Silva - first_name: Stephanie full_name: Cohen, Stephanie last_name: Cohen - first_name: Matthew J. full_name: Bauer, Matthew J. last_name: Bauer - first_name: Meryl full_name: Hashimoto, Meryl last_name: Hashimoto - first_name: Ryan C. full_name: Kirkbride, Ryan C. last_name: Kirkbride - first_name: John J. full_name: Harada, John J. last_name: Harada - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 2011;108(5):1755-1762. doi:10.1073/pnas.1019273108 apa: Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1019273108 chicago: Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108. ieee: T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis endosperm,” Proceedings of the National Academy of Sciences, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011. ista: Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762. mla: Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108. short: T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762. date_created: 2021-06-07T07:40:38Z date_published: 2011-02-01T00:00:00Z date_updated: 2021-12-14T08:33:49Z day: '01' department: - _id: DaZi doi: 10.1073/pnas.1019273108 extern: '1' external_id: pmid: - '21257907' intvolume: ' 108' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1019273108 month: '02' oa: 1 oa_version: Published Version page: 1755-1762 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Regulation of imprinted gene expression in Arabidopsis endosperm type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 108 year: '2011' ... --- _id: '967' abstract: - lang: eng text: Motivated by recent experiments on the material Ba3NiSb 2O9, we consider a spin-one quantum antiferromagnet on a triangular lattice with the Heisenberg bilinear and biquadratic exchange interactions and a single-ion anisotropy. Using a fermionic "triplon" representation for spins, we study the phase diagram within mean-field theory. In addition to a fully gapped spin-liquid ground state, we find a state where one gapless triplon mode with a Fermi surface coexists with d+id topological pairing of the other triplons. Despite the existence of a Fermi surface, this ground state has fully gapped bulk spin excitations. Such a state has linear in-temperature specific heat and constant in-plane spin susceptibility, with an unusually high Wilson ratio. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri S last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Senthil T, Lee P. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2011;84(18). doi:10.1103/PhysRevB.84.180403 apa: Serbyn, M., Senthil, T., & Lee, P. (2011). Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.180403 chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.180403. ieee: M. Serbyn, T. Senthil, and P. Lee, “Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18. American Physical Society, 2011. ista: Serbyn M, Senthil T, Lee P. 2011. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 84(18). mla: Serbyn, Maksym, et al. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18, American Physical Society, 2011, doi:10.1103/PhysRevB.84.180403. short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 84 (2011). date_created: 2018-12-11T11:49:27Z date_published: 2011-11-03T00:00:00Z date_updated: 2021-01-12T08:22:18Z day: '03' doi: 10.1103/PhysRevB.84.180403 extern: 1 intvolume: ' 84' issue: '18' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1108.3070 month: '11' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6432' quality_controlled: 0 status: public title: Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice type: journal_article volume: 84 year: '2011' ... --- _id: '969' abstract: - lang: eng text: We investigate the isotope effect on the London penetration depth of a superconductor which measures n S/m*, the ratio of superfluid density to effective mass. We use a simplified model of electrons weakly coupled to a single phonon frequency ω E, but assume that the energy gap Δ does not have any isotope effect. Nevertheless, we find an isotope effect for n S/m* which is significant if Δ is sufficiently large that it becomes comparable to ω E, a regime of interest to high-T c cuprate superconductors and possibly other families of unconventional superconductors with relatively high T c. Our model is too simple to describe the cuprates and it gives the wrong sign of the isotope effect when compared with experiment, but it is a proof of principle that the isotope effect exists for n S/m* in materials where the pairing gap and T c are not of phonon origin and have no isotope effect. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Lee P. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 2011;83(2). doi:10.1103/PhysRevB.83.024506 apa: Serbyn, M., & Lee, P. (2011). Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.83.024506 chicago: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.83.024506. ieee: M. Serbyn and P. Lee, “Isotope effect on the superfluid density in conventional and high-temperature superconductors,” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2. American Physical Society, 2011. ista: Serbyn M, Lee P. 2011. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 83(2). mla: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2, American Physical Society, 2011, doi:10.1103/PhysRevB.83.024506. short: M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics 83 (2011). date_created: 2018-12-11T11:49:28Z date_published: 2011-01-19T00:00:00Z date_updated: 2021-01-12T08:22:19Z day: '19' doi: 10.1103/PhysRevB.83.024506 extern: 1 intvolume: ' 83' issue: '2' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1009.2429 month: '01' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6434' quality_controlled: 0 status: public title: Isotope effect on the superfluid density in conventional and high-temperature superconductors type: journal_article volume: 83 year: '2011' ... --- _id: '8471' abstract: - lang: eng text: Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general. article_processing_charge: No article_type: original author: - first_name: Hélène full_name: Van Melckebeke, Hélène last_name: Van Melckebeke - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Julia full_name: Gath, Julia last_name: Gath - first_name: Christian full_name: Wasmer, Christian last_name: Wasmer - first_name: René full_name: Verel, René last_name: Verel - first_name: Adam full_name: Lange, Adam last_name: Lange - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Anja full_name: Böckmann, Anja last_name: Böckmann citation: ama: Van Melckebeke H, Schanda P, Gath J, et al. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 2011;405(3):765-772. doi:10.1016/j.jmb.2010.11.004 apa: Van Melckebeke, H., Schanda, P., Gath, J., Wasmer, C., Verel, R., Lange, A., … Böckmann, A. (2011). Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2010.11.004 chicago: Van Melckebeke, Hélène, Paul Schanda, Julia Gath, Christian Wasmer, René Verel, Adam Lange, Beat H. Meier, and Anja Böckmann. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology. Elsevier, 2011. https://doi.org/10.1016/j.jmb.2010.11.004. ieee: H. Van Melckebeke et al., “Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR,” Journal of Molecular Biology, vol. 405, no. 3. Elsevier, pp. 765–772, 2011. ista: Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A. 2011. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 405(3), 765–772. mla: Van Melckebeke, Hélène, et al. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology, vol. 405, no. 3, Elsevier, 2011, pp. 765–72, doi:10.1016/j.jmb.2010.11.004. short: H. Van Melckebeke, P. Schanda, J. Gath, C. Wasmer, R. Verel, A. Lange, B.H. Meier, A. Böckmann, Journal of Molecular Biology 405 (2011) 765–772. date_created: 2020-09-18T10:11:03Z date_published: 2011-01-21T00:00:00Z date_updated: 2021-01-12T08:19:30Z day: '21' doi: 10.1016/j.jmb.2010.11.004 extern: '1' intvolume: ' 405' issue: '3' language: - iso: eng month: '01' oa_version: None page: 765-772 publication: Journal of Molecular Biology publication_identifier: issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 405 year: '2011' ... --- _id: '8505' abstract: - lang: eng text: The classical principle of least action says that orbits of mechanical systems extremize action; an important subclass are those orbits that minimize action. In this paper we utilize this principle along with Aubry-Mather theory to construct (Birkhoff) regions of instability for a certain three-body problem, given by a Hamiltonian system of 2 degrees of freedom. We believe that these methods can be applied to construct instability regions for a variety of Hamiltonian systems with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show the existence of instabilities for the orbit of the comet. In particular, we show that a comet which starts close to an orbit in the shape of an ellipse of eccentricity e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper, we extend the result to beyond e=1 and show the existence of ejection orbits. Such orbits are initially well within the range of our solar system. This might give an indication of why most objects rotating around the Sun in our solar system have relatively low eccentricity. article_processing_charge: No article_type: original author: - first_name: Joseph full_name: Galante, Joseph last_name: Galante - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Galante J, Kaloshin V. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 2011;159(2):275-327. doi:10.1215/00127094-1415878 apa: Galante, J., & Kaloshin, V. (2011). Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1415878 chicago: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1415878. ieee: J. Galante and V. Kaloshin, “Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action,” Duke Mathematical Journal, vol. 159, no. 2. Duke University Press, pp. 275–327, 2011. ista: Galante J, Kaloshin V. 2011. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 159(2), 275–327. mla: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal, vol. 159, no. 2, Duke University Press, 2011, pp. 275–327, doi:10.1215/00127094-1415878. short: J. Galante, V. Kaloshin, Duke Mathematical Journal 159 (2011) 275–327. date_created: 2020-09-18T10:47:41Z date_published: 2011-08-04T00:00:00Z date_updated: 2021-01-12T08:19:45Z day: '04' doi: 10.1215/00127094-1415878 extern: '1' intvolume: ' 159' issue: '2' keyword: - General Mathematics language: - iso: eng month: '08' oa_version: None page: 275-327 publication: Duke Mathematical Journal publication_identifier: issn: - 0012-7094 publication_status: published publisher: Duke University Press quality_controlled: '1' status: public title: Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2011' ... --- _id: '881' author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication. Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4' apa: Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene Duplication (pp. 57–76). Wiley-Blackwell. https://doi.org/10.1002/9780470619902.ch4 chicago: Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4. ieee: F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. ista: 'Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene Duplication. , 57–76.' mla: Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4. short: F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. date_created: 2018-12-11T11:49:00Z date_published: 2011-03-14T00:00:00Z date_updated: 2021-01-12T08:21:08Z day: '14' doi: 10.1002/9780470619902.ch4 extern: 1 month: '03' page: 57 - 76 publication: Evolution after Gene Duplication publication_status: published publisher: Wiley-Blackwell publist_id: '6766' quality_controlled: 0 status: public title: Gene Dosage and Duplication type: book_chapter year: '2011' ... --- _id: '919' abstract: - lang: eng text: Collective cell migration in tissues occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion, yet most detailed knowledge of cell migration comes from single-cell studies. As single cells migrate, the shape of the cell body fluctuates dramatically through cyclic processes of extension, adhesion, and retraction, accompanied by erratic changes in migration direction. Within confluent cell layers, such subcellular motions must be coupled between neighbors, yet the influence of these subcellular motions on collective migration is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously measuring collective migration and subcellular motions, covering a broad range of length scales, time scales, and cell densities. At large length scales and time scales collective migration slows as cell density rises, yet the fastest cells move in large, multicell groups whose scale grows with increasing cell density. This behavior has an intriguing analogy to dynamic heterogeneities found in particulate systems as they become more crowded and approach a glass transition. In addition we find a diminishing self-diffusivity of short-wavelength motions within the cell layer, and growing peaks in the vibrational density of states associated with cooperative cell-shape fluctuations. Both of these observations are also intriguingly reminiscent of a glass transition. Thus, these results provide a broad and suggestive analogy between cell motion within a confluent layer and the dynamics of supercooled colloidal and molecular fluids approaching a glass transition. author: - first_name: Thomas full_name: Angelini, Thomas last_name: Angelini - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Xavier full_name: Trepatc, Xavier last_name: Trepatc - first_name: Manuel full_name: Marquez, Manuel last_name: Marquez - first_name: Jeffrey full_name: Fredberg, Jeffrey last_name: Fredberg - first_name: David full_name: Weitz, David last_name: Weitz citation: ama: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(12):4714-4719. doi:10.1073/pnas.1010059108 apa: Angelini, T., Hannezo, E. B., Trepatc, X., Marquez, M., Fredberg, J., & Weitz, D. (2011). Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. PNAS. https://doi.org/10.1073/pnas.1010059108 chicago: Angelini, Thomas, Edouard B Hannezo, Xavier Trepatc, Manuel Marquez, Jeffrey Fredberg, and David Weitz. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America. PNAS, 2011. https://doi.org/10.1073/pnas.1010059108. ieee: T. Angelini, E. B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, and D. Weitz, “Glass-like dynamics of collective cell migration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12. PNAS, pp. 4714–4719, 2011. ista: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. 2011. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 108(12), 4714–4719. mla: Angelini, Thomas, et al. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12, PNAS, 2011, pp. 4714–19, doi:10.1073/pnas.1010059108. short: T. Angelini, E.B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, D. Weitz, Proceedings of the National Academy of Sciences of the United States of America 108 (2011) 4714–4719. date_created: 2018-12-11T11:49:12Z date_published: 2011-03-22T00:00:00Z date_updated: 2021-01-12T08:21:54Z day: '22' doi: 10.1073/pnas.1010059108 extern: '1' intvolume: ' 108' issue: '12' language: - iso: eng month: '03' oa_version: None page: 4714 - 4719 publication: Proceedings of the National Academy of Sciences of the United States of America publication_status: published publisher: PNAS publist_id: '6522' quality_controlled: '1' status: public title: Glass-like dynamics of collective cell migration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2011' ... --- _id: '918' abstract: - lang: eng text: We study theoretically the shapes of a dividing epithelial monolayer of cells lying on top of an elastic stroma. The negative tension created by cell division provokes a buckling instability at a finite wave vector leading to the formation of periodic arrays of villi and crypts. The instability is similar to the buckling of a metallic plate under compression. We use the results to rationalize the various structures of the intestinal lining observed in vivo. Taking into account the coupling between cell division and local curvature, we obtain different patterns of villi and crypts, which could explain the different morphologies of the small intestine and the colon. acknowledgement: We thank S. Fre and M. Huygue for discussion and for showing us in vivo samples and A. Bergès for help with the manuscript. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 2011;107(7). doi:10.1103/PhysRevLett.107.078104 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2011). Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.078104 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.078104. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Instabilities of monolayered epithelia Shape and structure of villi and crypts,” Physical Review Letters, vol. 107, no. 7. American Physical Society, 2011. ista: Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 107(7). mla: Hannezo, Edouard B., et al. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters, vol. 107, no. 7, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.078104. short: E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 107 (2011). date_created: 2018-12-11T11:49:11Z date_published: 2011-08-11T00:00:00Z date_updated: 2021-01-12T08:21:54Z day: '11' doi: 10.1103/PhysRevLett.107.078104 extern: '1' intvolume: ' 107' issue: '7' language: - iso: eng month: '08' oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6521' status: public title: Instabilities of monolayered epithelia Shape and structure of villi and crypts type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2011' ... --- _id: '9522' abstract: - lang: eng text: Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo. article_processing_charge: No author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation. Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018 apa: Zilberman, D. (2011). Balancing parental contributions in plant embryonic gene activation. Developmental Cell (Vol. 20, pp. 735–736). Elsevier. https://doi.org/10.1016/j.devcel.2011.05.018 chicago: Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018. ieee: D. Zilberman, Balancing parental contributions in plant embryonic gene activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736. ista: Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p. mla: Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene Activation.” Developmental Cell, vol. 20, no. 6, Elsevier, 2011, pp. 735–36, doi:10.1016/j.devcel.2011.05.018. short: D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011. date_created: 2021-06-08T06:23:39Z date_published: 2011-06-14T00:00:00Z date_updated: 2021-12-14T08:34:37Z day: '14' department: - _id: DaZi doi: 10.1016/j.devcel.2011.05.018 extern: '1' external_id: pmid: - '21664571' intvolume: ' 20' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2011.05.018 month: '06' oa: 1 oa_version: Published Version page: 735-736 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Balancing parental contributions in plant embryonic gene activation type: other_academic_publication user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 20 year: '2011' ... --- _id: '9648' abstract: - lang: eng text: In this paper, we establish a correspondence between the incremental algorithm for computing AT-models [8,9] and the one for computing persistent homology [6,14,15]. We also present a decremental algorithm for computing AT-models that allows to extend the persistence computation to a wider setting. Finally, we show how to combine incremental and decremental techniques for persistent homology computation. alternative_title: - LNCS article_processing_charge: No author: - first_name: Rocio full_name: Gonzalez-Diaz, Rocio last_name: Gonzalez-Diaz - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Maria Jose full_name: Jimenez, Maria Jose last_name: Jimenez - first_name: Regina full_name: Poyatos, Regina last_name: Poyatos citation: ama: 'Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. Incremental-decremental algorithm for computing AT-models and persistent homology. In: Computer Analysis of Images and Patterns. Vol 6854. Springer Nature; 2011:286-293. doi:10.1007/978-3-642-23672-3_35' apa: 'Gonzalez-Diaz, R., Ion, A., Jimenez, M. J., & Poyatos, R. (2011). Incremental-decremental algorithm for computing AT-models and persistent homology. In Computer Analysis of Images and Patterns (Vol. 6854, pp. 286–293). Seville, Spain: Springer Nature. https://doi.org/10.1007/978-3-642-23672-3_35' chicago: Gonzalez-Diaz, Rocio, Adrian Ion, Maria Jose Jimenez, and Regina Poyatos. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” In Computer Analysis of Images and Patterns, 6854:286–93. Springer Nature, 2011. https://doi.org/10.1007/978-3-642-23672-3_35. ieee: R. Gonzalez-Diaz, A. Ion, M. J. Jimenez, and R. Poyatos, “Incremental-decremental algorithm for computing AT-models and persistent homology,” in Computer Analysis of Images and Patterns, Seville, Spain, 2011, vol. 6854, pp. 286–293. ista: 'Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. 2011. Incremental-decremental algorithm for computing AT-models and persistent homology. Computer Analysis of Images and Patterns. CAIP: International Conference on Computer Analysis of Images and Patterns, LNCS, vol. 6854, 286–293.' mla: Gonzalez-Diaz, Rocio, et al. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” Computer Analysis of Images and Patterns, vol. 6854, Springer Nature, 2011, pp. 286–93, doi:10.1007/978-3-642-23672-3_35. short: R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293. conference: end_date: 2011-08-31 location: Seville, Spain name: 'CAIP: International Conference on Computer Analysis of Images and Patterns' start_date: 2011-08-29 date_created: 2021-07-11T22:01:19Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-08-12T13:53:17Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-642-23672-3_35 intvolume: ' 6854' language: - iso: eng main_file_link: - open_access: '1' url: http://hdl.handle.net/11441/30766 month: '08' oa: 1 oa_version: Published Version page: 286-293 publication: Computer Analysis of Images and Patterns publication_identifier: eissn: - '16113349' isbn: - '9783642236716' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Incremental-decremental algorithm for computing AT-models and persistent homology type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 6854 year: '2011' ... --- _id: '968' abstract: - lang: eng text: A Reply to the Comment by Andrei Sergeev, M. Reizer, and V. Mitin. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Mikhail full_name: Skvortsov, Mikhail A last_name: Skvortsov - first_name: Andrei full_name: Varlamov, Andrei A last_name: Varlamov - first_name: Victor full_name: Galitski, Victor M last_name: Galitski citation: ama: 'Serbyn M, Skvortsov M, Varlamov A, Galitski V. Serbyn et al. Reply: Physical Review Letters. 2011;106(13). doi:10.1103/PhysRevLett.106.139702' apa: 'Serbyn, M., Skvortsov, M., Varlamov, A., & Galitski, V. (2011). Serbyn et al. Reply: Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.139702' chicago: Serbyn, Maksym, Mikhail Skvortsov, Andrei Varlamov, and Victor Galitski. “Serbyn et Al. Reply:” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.139702. ieee: M. Serbyn, M. Skvortsov, A. Varlamov, and V. Galitski, “Serbyn et al. Reply:,” Physical Review Letters, vol. 106, no. 13. American Physical Society, 2011. ista: 'Serbyn M, Skvortsov M, Varlamov A, Galitski V. 2011. Serbyn et al. Reply: Physical Review Letters. 106(13).' mla: Serbyn, Maksym, et al. “Serbyn et Al. Reply:” Physical Review Letters, vol. 106, no. 13, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.139702. short: M. Serbyn, M. Skvortsov, A. Varlamov, V. Galitski, Physical Review Letters 106 (2011). date_created: 2018-12-11T11:49:27Z date_published: 2011-04-01T00:00:00Z date_updated: 2021-01-12T08:22:19Z day: '01' doi: 10.1103/PhysRevLett.106.139702 extern: 1 intvolume: ' 106' issue: '13' month: '04' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6433' quality_controlled: 0 status: public title: 'Serbyn et al. Reply:' type: journal_article volume: 106 year: '2011' ... --- _id: '3395' abstract: - lang: eng text: Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data. acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474). article_processing_charge: No author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Pere full_name: Abello, Pere last_name: Abello - first_name: Enrique full_name: Macpherson, Enrique last_name: Macpherson - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418. doi:10.1111/j.1095-8312.2011.01728.x apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x. ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas,” Biological Journal of the Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011. ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2), 407–418. mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell, 2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x. short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 407–418. date_created: 2018-12-11T12:03:06Z date_published: 2011-09-14T00:00:00Z date_updated: 2023-02-23T14:07:31Z day: '14' department: - _id: NiBa doi: 10.1111/j.1095-8312.2011.01728.x intvolume: ' 104' issue: '2' language: - iso: eng month: '09' oa_version: None page: 407 - 418 publication: Biological Journal of the Linnean Society publication_status: published publisher: Wiley-Blackwell publist_id: '3212' quality_controlled: '1' related_material: record: - id: '9762' relation: research_data status: public scopus_import: '1' status: public title: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 104 year: '2011' ... --- _id: '9762' abstract: - lang: eng text: Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data. article_processing_charge: No author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Pere full_name: Abello, Pere last_name: Abello - first_name: Enrique full_name: Macpherson, Enrique last_name: Macpherson - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8' apa: 'Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. https://doi.org/10.5061/dryad.299h8' chicago: 'Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. https://doi.org/10.5061/dryad.299h8.' ieee: 'F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.' ista: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.' mla: 'Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.' short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011). date_created: 2021-08-02T07:11:19Z date_published: 2011-05-12T00:00:00Z date_updated: 2023-02-23T11:25:25Z day: '12' department: - _id: NiBa doi: 10.5061/dryad.299h8 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.299h8 month: '05' oa: 1 oa_version: Published Version publisher: IST Austria related_material: record: - id: '3395' relation: used_in_publication status: public status: public title: 'Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2011' ... --- _id: '9943' abstract: - lang: eng text: Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org. article_processing_charge: No author: - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Christoph full_name: Straehle, Christoph last_name: Straehle - first_name: Ullrich full_name: Köthe, Ullrich last_name: Köthe - first_name: Fred A. full_name: Hamprecht, Fred A. last_name: Hamprecht citation: ama: 'Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit. In: 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers; 2011. doi:10.1109/isbi.2011.5872394' apa: 'Sommer, C. M., Straehle, C., Köthe, U., & Hamprecht, F. A. (2011). Ilastik: Interactive learning and segmentation toolkit. In 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. Chicago, Illinois, USA: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/isbi.2011.5872394' chicago: 'Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht. “Ilastik: Interactive Learning and Segmentation Toolkit.” In 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers, 2011. https://doi.org/10.1109/isbi.2011.5872394.' ieee: 'C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive learning and segmentation toolkit,” in 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro, Chicago, Illinois, USA, 2011.' ista: 'Sommer CM, Straehle C, Köthe U, Hamprecht FA. 2011. Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. ISBI: International Symposium on Biomedical Imaging.' mla: 'Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation Toolkit.” 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011, doi:10.1109/isbi.2011.5872394.' short: 'C.M. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht, in:, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011.' conference: end_date: 2011-04-02 location: Chicago, Illinois, USA name: 'ISBI: International Symposium on Biomedical Imaging' start_date: 2011-03-30 date_created: 2021-08-19T11:49:58Z date_published: 2011-06-09T00:00:00Z date_updated: 2023-02-23T14:13:38Z day: '09' department: - _id: Bio doi: 10.1109/isbi.2011.5872394 extern: '1' keyword: - image segmentation - biomedical imaging - three dimensional displays - neurons - retina - observers - image color analysis language: - iso: eng main_file_link: - open_access: '1' url: https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit month: '06' oa: 1 oa_version: Preprint publication: '2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro' publication_identifier: eissn: - 1945-8452 isbn: - 978-1-4244-4127-3 issn: - 1945-7928 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' status: public title: 'Ilastik: Interactive learning and segmentation toolkit' type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2011' ... --- _id: '10907' abstract: - lang: eng text: This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts. acknowledgement: This work has been partially supported by the Austrian Science Fund under grants S9103-N13 and P18716-N13. alternative_title: - LNCS article_processing_charge: No author: - first_name: Nicole M. full_name: Artner, Nicole M. last_name: Artner - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Walter G. full_name: Kropatsch, Walter G. last_name: Kropatsch citation: ama: 'Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. Graph-Based Representations in Pattern Recognition. Vol 6658. LNIP. Berlin, Heidelberg: Springer; 2011:215-224. doi:10.1007/978-3-642-20844-7_22' apa: 'Artner, N. M., Ion, A., & Kropatsch, W. G. (2011). Spatio-temporal extraction of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, & A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition (Vol. 6658, pp. 215–224). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-20844-7_22' chicago: 'Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” In Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. https://doi.org/10.1007/978-3-642-20844-7_22.' ieee: N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of articulated models in a graph pyramid,” in Graph-Based Representations in Pattern Recognition, Münster, Germany, 2011, vol. 6658, pp. 215–224. ista: 'Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated models in a graph pyramid. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658, 215–224.' mla: Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:10.1007/978-3-642-20844-7_22. short: N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin, Heidelberg, 2011, pp. 215–224. conference: end_date: 2011-05-20 location: Münster, Germany name: 'GbRPR: Graph-based Representations in Pattern Recognition' start_date: 2011-05-18 date_created: 2022-03-21T08:08:35Z date_published: 2011-06-01T00:00:00Z date_updated: 2023-09-05T14:10:15Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-642-20844-7_22 editor: - first_name: Xiaoyi full_name: Jiang, Xiaoyi last_name: Jiang - first_name: Miquel full_name: Ferrer, Miquel last_name: Ferrer - first_name: Andrea full_name: Torsello, Andrea last_name: Torsello intvolume: ' 6658' language: - iso: eng month: '06' oa_version: None page: 215-224 place: Berlin, Heidelberg publication: Graph-Based Representations in Pattern Recognition publication_identifier: eisbn: - '9783642208447' eissn: - 1611-3349 isbn: - '9783642208430' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' series_title: LNIP status: public title: Spatio-temporal extraction of articulated models in a graph pyramid type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6658 year: '2011' ... --- _id: '3275' abstract: - lang: eng text: 'Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. ' acknowledgement: "I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kathrin full_name: Schumann, Kathrin id: F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F last_name: Schumann citation: ama: Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011. apa: Schumann, K. (2011). The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria. chicago: Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011. ieee: K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011. ista: Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria. mla: Schumann, Kathrin. The Role of Chemotactic Gradients in Dendritic Cell Migration. Institute of Science and Technology Austria, 2011. short: K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011. date_created: 2018-12-11T12:02:24Z date_published: 2011-03-01T00:00:00Z date_updated: 2023-09-07T11:31:48Z day: '01' ddc: - '570' - '579' degree_awarded: PhD department: - _id: MiSi file: - access_level: closed checksum: e69eee6252660f0b694a2ea8923ddc72 content_type: application/pdf creator: dernst date_created: 2019-03-26T08:12:21Z date_updated: 2020-07-14T12:46:06Z file_id: '6177' file_name: 2011_Thesis_Kathrin_Schumann.pdf file_size: 4487708 relation: main_file - access_level: open_access checksum: 71727d63f424b5b446f68f4b87ecadc0 content_type: application/pdf creator: dernst date_created: 2021-02-22T11:24:30Z date_updated: 2021-02-22T11:24:30Z file_id: '9175' file_name: 2011_Thesis_Schumann_noS.pdf file_size: 4313127 relation: main_file success: 1 file_date_updated: 2021-02-22T11:24:30Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '141' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '3371' pubrep_id: '11' status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: The role of chemotactic gradients in dendritic cell migration type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2011' ... --- _id: '3273' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 citation: ama: Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011. apa: Maître, J.-L. (2011). Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria. chicago: Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011. ieee: J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011. ista: Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria. mla: Maître, Jean-Léon. Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors. Institute of Science and Technology Austria, 2011. short: J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors, Institute of Science and Technology Austria, 2011. date_created: 2018-12-11T12:02:23Z date_published: 2011-12-12T00:00:00Z date_updated: 2023-09-07T11:30:16Z day: '12' degree_awarded: PhD department: - _id: CaHe language: - iso: eng month: '12' oa_version: None publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '3373' status: public supervisor: - 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 title: Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2011' ... --- _id: '3238' abstract: - lang: eng text: We construct efficient authentication protocols and message-authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work - starting with the HB protocol of Hopper and Blum in 2001 - until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle (MIM) attacks. A MAC implies such a (two-round) protocol. © 2011 International Association for Cryptologic Research acknowledgement: The European Regional Development Fund (ERDF),Guardtime,Qualcomm,Swedbank alternative_title: - LNCS author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - 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: David full_name: Cash, David last_name: Cash - first_name: Abhishek full_name: Jain, Abhishek last_name: Jain - first_name: Daniele full_name: Venturi, Daniele last_name: Venturi citation: ama: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. Efficient authentication from hard learning problems. In: Vol 6632. Springer; 2011:7-26. doi:10.1007/978-3-642-20465-4_3' apa: 'Kiltz, E., Pietrzak, K. Z., Cash, D., Jain, A., & Venturi, D. (2011). Efficient authentication from hard learning problems (Vol. 6632, pp. 7–26). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia: Springer. https://doi.org/10.1007/978-3-642-20465-4_3' chicago: Kiltz, Eike, Krzysztof Z Pietrzak, David Cash, Abhishek Jain, and Daniele Venturi. “Efficient Authentication from Hard Learning Problems,” 6632:7–26. Springer, 2011. https://doi.org/10.1007/978-3-642-20465-4_3. ieee: 'E. Kiltz, K. Z. Pietrzak, D. Cash, A. Jain, and D. Venturi, “Efficient authentication from hard learning problems,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia, 2011, vol. 6632, pp. 7–26.' ista: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. 2011. Efficient authentication from hard learning problems. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 6632, 7–26.' mla: Kiltz, Eike, et al. Efficient Authentication from Hard Learning Problems. Vol. 6632, Springer, 2011, pp. 7–26, doi:10.1007/978-3-642-20465-4_3. short: E. Kiltz, K.Z. Pietrzak, D. Cash, A. Jain, D. Venturi, in:, Springer, 2011, pp. 7–26. conference: end_date: 2011-05-19 location: Tallinn, Estonia name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2011-05-15 date_created: 2018-12-11T12:02:11Z date_published: 2011-05-01T00:00:00Z date_updated: 2023-09-20T11:20:57Z day: '01' doi: 10.1007/978-3-642-20465-4_3 extern: '1' intvolume: ' 6632' language: - iso: eng month: '05' oa_version: None page: 7 - 26 publication_status: published publisher: Springer publist_id: '3442' quality_controlled: '1' related_material: record: - id: '1187' relation: later_version status: public status: public title: Efficient authentication from hard learning problems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6632 year: '2011' ... --- _id: '3392' abstract: - lang: eng text: Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing edge, or uropod. Although in vitro experiments in cell lines or activated primary cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional surfaces and nuclear propulsion through narrow pores in three-dimensional matrices, less is known about the role of these two events during the recirculation of primary, nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin II, we report that inhibition of uropod contractility blocked integrin-independent mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling on chemokine-coated endothelial cells under shear was severely impaired by ROCK inhibition, whereas transendothelial migration was only reduced through endothelial cells with high, but not low, barrier properties. Using three-dimensional thick-tissue imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue, we demonstrated a significant role for uropod contractility in intraluminal crawling and transendothelial migration through lymph node, but not bone marrow, endothelial cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or integrin-independent interactions, reduced parenchymal motility of inhibitor-treated T cells within the dense lymphoid microenvironment, thus assigning context-dependent roles for uropod contraction during lymphocyte recirculation. article_processing_charge: No article_type: original author: - first_name: Silvia full_name: Soriano, Silvia last_name: Soriano - first_name: Miroslav full_name: Hons, Miroslav last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Kathrin full_name: Schumann, Kathrin last_name: Schumann - first_name: Varsha full_name: Kumar, Varsha last_name: Kumar - first_name: Timo full_name: Dennier, Timo last_name: Dennier - first_name: Ruth full_name: Lyck, Ruth last_name: Lyck - 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: Jens full_name: Stein, Jens last_name: Stein citation: ama: Soriano S, Hons M, Schumann K, et al. In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. 2011;187(5):2356-2364. doi:10.4049/jimmunol.1100935 apa: Soriano, S., Hons, M., Schumann, K., Kumar, V., Dennier, T., Lyck, R., … Stein, J. (2011). In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. American Association of Immunologists. https://doi.org/10.4049/jimmunol.1100935 chicago: Soriano, Silvia, Miroslav Hons, Kathrin Schumann, Varsha Kumar, Timo Dennier, Ruth Lyck, Michael K Sixt, and Jens Stein. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” Journal of Immunology. American Association of Immunologists, 2011. https://doi.org/10.4049/jimmunol.1100935. ieee: S. Soriano et al., “In vivo analysis of uropod function during physiological T cell trafficking,” Journal of Immunology, vol. 187, no. 5. American Association of Immunologists, pp. 2356–2364, 2011. ista: Soriano S, Hons M, Schumann K, Kumar V, Dennier T, Lyck R, Sixt MK, Stein J. 2011. In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. 187(5), 2356–2364. mla: Soriano, Silvia, et al. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” Journal of Immunology, vol. 187, no. 5, American Association of Immunologists, 2011, pp. 2356–64, doi:10.4049/jimmunol.1100935. short: S. Soriano, M. Hons, K. Schumann, V. Kumar, T. Dennier, R. Lyck, M.K. Sixt, J. Stein, Journal of Immunology 187 (2011) 2356–2364. date_created: 2018-12-11T12:03:04Z date_published: 2011-09-01T00:00:00Z date_updated: 2023-10-10T13:14:59Z day: '01' department: - _id: MiSi doi: 10.4049/jimmunol.1100935 intvolume: ' 187' issue: '5' language: - iso: eng month: '09' oa_version: None page: 2356 - 2364 publication: Journal of Immunology publication_identifier: eissn: - 1550-6606 issn: - 0022-1767 publication_status: published publisher: American Association of Immunologists publist_id: '3215' quality_controlled: '1' scopus_import: '1' status: public title: In vivo analysis of uropod function during physiological T cell trafficking type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 187 year: '2011' ... --- _id: '3163' abstract: - lang: eng text: We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds. author: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Lampert C. Maximum margin multi-label structured prediction. In: Neural Information Processing Systems; 2011.' apa: 'Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information Processing Systems.' chicago: Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.” Neural Information Processing Systems, 2011. ieee: 'C. Lampert, “Maximum margin multi-label structured prediction,” presented at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.' ista: 'Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS: Neural Information Processing Systems.' mla: Lampert, Christoph. Maximum Margin Multi-Label Structured Prediction. Neural Information Processing Systems, 2011. short: C. Lampert, in:, Neural Information Processing Systems, 2011. conference: end_date: 2011-12-14 location: Granada, Spain name: 'NIPS: Neural Information Processing Systems' start_date: 2011-12-12 date_created: 2018-12-11T12:01:45Z date_published: 2011-12-01T00:00:00Z date_updated: 2023-10-17T11:47:35Z day: '01' department: - _id: ChLa language: - iso: eng month: '12' oa_version: None publication_status: published publisher: Neural Information Processing Systems publist_id: '3522' quality_controlled: '1' related_material: record: - id: '3322' relation: later_version status: public scopus_import: 1 status: public title: Maximum margin multi-label structured prediction type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3322' abstract: - lang: eng text: We study multi-label prediction for structured output spaces, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multi-label classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label space, which is infeasible in case of structured outputs. Relying on techniques originally designed for single- label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular a formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds. article_processing_charge: No author: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Lampert C. Maximum Margin Multi Label Structured Prediction. Neural Information Processing Systems Foundation; 2011. apa: 'Lampert, C. (2011). Maximum margin multi label structured prediction. NIPS: Neural Information Processing Systems. Neural Information Processing Systems Foundation.' chicago: 'Lampert, Christoph. Maximum Margin Multi Label Structured Prediction. NIPS: Neural Information Processing Systems. Neural Information Processing Systems Foundation, 2011.' ieee: C. Lampert, Maximum margin multi label structured prediction. Neural Information Processing Systems Foundation, 2011. ista: Lampert C. 2011. Maximum margin multi label structured prediction, Neural Information Processing Systems Foundation,p. mla: 'Lampert, Christoph. “Maximum Margin Multi Label Structured Prediction.” NIPS: Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2011.' short: C. Lampert, Maximum Margin Multi Label Structured Prediction, Neural Information Processing Systems Foundation, 2011. date_created: 2018-12-11T12:02:40Z date_published: 2011-12-13T00:00:00Z date_updated: 2023-10-17T11:47:36Z day: '13' department: - _id: ChLa language: - iso: eng month: '12' oa_version: None publication: 'NIPS: Neural Information Processing Systems' publication_status: published publisher: Neural Information Processing Systems Foundation publist_id: '3313' related_material: record: - id: '3163' relation: earlier_version status: public status: public title: Maximum margin multi label structured prediction type: conference_poster user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3320' abstract: - lang: eng text: Powerful statistical models that can be learned efficiently from large amounts of data are currently revolutionizing computer vision. These models possess a rich internal structure reflecting task-specific relations and constraints. This monograph introduces the reader to the most popular classes of structured models in computer vision. Our focus is discrete undirected graphical models which we cover in detail together with a description of algorithms for both probabilistic inference and maximum a posteriori inference. We discuss separately recently successful techniques for prediction in general structured models. In the second part of this monograph we describe methods for parameter learning where we distinguish the classic maximum likelihood based methods from the more recent prediction-based parameter learning methods. We highlight developments to enhance current models and discuss kernelized models and latent variable models. To make the monograph more practical and to provide links to further study we provide examples of successful application of many methods in the computer vision literature. article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Nowozin, Sebastian last_name: Nowozin - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Nowozin S, Lampert C. Structured learning and prediction in computer vision. Foundations and Trends in Computer Graphics and Vision. 2011;6(3-4):185-365. doi:10.1561/0600000033 apa: Nowozin, S., & Lampert, C. (2011). Structured learning and prediction in computer vision. Foundations and Trends in Computer Graphics and Vision. Now Publishers. https://doi.org/10.1561/0600000033 chicago: Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction in Computer Vision.” Foundations and Trends in Computer Graphics and Vision. Now Publishers, 2011. https://doi.org/10.1561/0600000033. ieee: S. Nowozin and C. Lampert, “Structured learning and prediction in computer vision,” Foundations and Trends in Computer Graphics and Vision, vol. 6, no. 3–4. Now Publishers, pp. 185–365, 2011. ista: Nowozin S, Lampert C. 2011. Structured learning and prediction in computer vision. Foundations and Trends in Computer Graphics and Vision. 6(3–4), 185–365. mla: Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction in Computer Vision.” Foundations and Trends in Computer Graphics and Vision, vol. 6, no. 3–4, Now Publishers, 2011, pp. 185–365, doi:10.1561/0600000033. short: S. Nowozin, C. Lampert, Foundations and Trends in Computer Graphics and Vision 6 (2011) 185–365. date_created: 2018-12-11T12:02:39Z date_published: 2011-05-23T00:00:00Z date_updated: 2023-10-17T11:52:46Z day: '23' ddc: - '000' department: - _id: ChLa doi: 10.1561/0600000033 file: - access_level: open_access checksum: f1043ef389f1558e2a226bb51568511f content_type: application/pdf creator: dernst date_created: 2020-05-14T14:34:47Z date_updated: 2020-07-14T12:46:07Z file_id: '7837' file_name: 2011_CompGraphicsVision_Nowozin.pdf file_size: 3745064 relation: main_file file_date_updated: 2020-07-14T12:46:07Z has_accepted_license: '1' intvolume: ' 6' issue: 3-4 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 185 - 365 publication: Foundations and Trends in Computer Graphics and Vision publication_status: published publisher: Now Publishers publist_id: '3315' quality_controlled: '1' scopus_import: '1' status: public title: Structured learning and prediction in computer vision type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2011' ... --- _id: '3319' abstract: - lang: eng text: We address the problem of metric learning for multi-view data, namely the construction of embedding projections from data in different representations into a shared feature space, such that the Euclidean distance in this space provides a meaningful within-view as well as between-view similarity. Our motivation stems from the problem of cross-media retrieval tasks, where the availability of a joint Euclidean distance function is a pre-requisite to allow fast, in particular hashing-based, nearest neighbor queries. We formulate an objective function that expresses the intuitive concept that matching samples are mapped closely together in the output space, whereas non-matching samples are pushed apart, no matter in which view they are available. The resulting optimization problem is not convex, but it can be decomposed explicitly into a convex and a concave part, thereby allowing efficient optimization using the convex-concave procedure. Experiments on an image retrieval task show that nearest-neighbor based cross-view retrieval is indeed possible, and the proposed technique improves the retrieval accuracy over baseline techniques. article_processing_charge: No 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. Learning multi-view neighborhood preserving projections. In: ML Research Press; 2011:425-432.' apa: 'Quadrianto, N., & Lampert, C. (2011). Learning multi-view neighborhood preserving projections (pp. 425–432). Presented at the ICML: International Conference on Machine Learning, Bellevue, United States: ML Research Press.' chicago: Quadrianto, Novi, and Christoph Lampert. “Learning Multi-View Neighborhood Preserving Projections,” 425–32. ML Research Press, 2011. ieee: 'N. Quadrianto and C. Lampert, “Learning multi-view neighborhood preserving projections,” presented at the ICML: International Conference on Machine Learning, Bellevue, United States, 2011, pp. 425–432.' ista: 'Quadrianto N, Lampert C. 2011. Learning multi-view neighborhood preserving projections. ICML: International Conference on Machine Learning, 425–432.' mla: Quadrianto, Novi, and Christoph Lampert. Learning Multi-View Neighborhood Preserving Projections. ML Research Press, 2011, pp. 425–32. short: N. Quadrianto, C. Lampert, in:, ML Research Press, 2011, pp. 425–432. conference: end_date: 2011-07-02 location: Bellevue, United States name: 'ICML: International Conference on Machine Learning' start_date: 2011-06-28 date_created: 2018-12-11T12:02:39Z date_published: 2011-01-01T00:00:00Z date_updated: 2023-10-17T11:59:50Z day: '01' department: - _id: ChLa language: - iso: eng month: '01' oa_version: None page: 425 - 432 publication_status: published publisher: ML Research Press publist_id: '3316' scopus_import: '1' status: public title: Learning multi-view neighborhood preserving projections type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3373' abstract: - lang: eng text: The use of optical traps to measure or apply forces on the molecular level requires a precise knowledge of the trapping force field. Close to the trap center, this field is typically approximated as linear in the displacement of the trapped microsphere. However, applications demanding high forces at low laser intensities can probe the light-microsphere interaction beyond the linear regime. Here, we measured the full nonlinear force and displacement response of an optical trap in two dimensions using a dual-beam optical trap setup with back-focal-plane photodetection. We observed a substantial stiffening of the trap beyond the linear regime that depends on microsphere size, in agreement with Mie theory calculations. Surprisingly, we found that the linear detection range for forces exceeds the one for displacement by far. Our approach allows for a complete calibration of an optical trap. article_processing_charge: No author: - first_name: Marcus full_name: Jahnel, Marcus last_name: Jahnel - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Anita full_name: Jannasch, Anita last_name: Jannasch - first_name: Erik full_name: Schaeffer, Erik last_name: Schaeffer - first_name: Stephan full_name: Grill, Stephan last_name: Grill citation: ama: Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. Measuring the complete force field of an optical trap. Optics Letters. 2011;36(7):1260-1262. doi:10.1364/OL.36.001260 apa: Jahnel, M., Behrndt, M., Jannasch, A., Schaeffer, E., & Grill, S. (2011). Measuring the complete force field of an optical trap. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.36.001260 chicago: Jahnel, Marcus, Martin Behrndt, Anita Jannasch, Erik Schaeffer, and Stephan Grill. “Measuring the Complete Force Field of an Optical Trap.” Optics Letters. Optica Publishing Group, 2011. https://doi.org/10.1364/OL.36.001260. ieee: M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, and S. Grill, “Measuring the complete force field of an optical trap,” Optics Letters, vol. 36, no. 7. Optica Publishing Group, pp. 1260–1262, 2011. ista: Jahnel M, Behrndt M, Jannasch A, Schaeffer E, Grill S. 2011. Measuring the complete force field of an optical trap. Optics Letters. 36(7), 1260–1262. mla: Jahnel, Marcus, et al. “Measuring the Complete Force Field of an Optical Trap.” Optics Letters, vol. 36, no. 7, Optica Publishing Group, 2011, pp. 1260–62, doi:10.1364/OL.36.001260. short: M. Jahnel, M. Behrndt, A. Jannasch, E. Schaeffer, S. Grill, Optics Letters 36 (2011) 1260–1262. date_created: 2018-12-11T12:02:58Z date_published: 2011-03-30T00:00:00Z date_updated: 2023-10-17T12:16:58Z day: '30' department: - _id: CaHe doi: 10.1364/OL.36.001260 intvolume: ' 36' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.osapublishing.org/ol/abstract.cfm?uri=ol-36-7-1260 month: '03' oa: 1 oa_version: Published Version page: 1260 - 1262 publication: Optics Letters publication_status: published publisher: Optica Publishing Group publist_id: '3234' quality_controlled: '1' related_material: record: - id: '1403' relation: dissertation_contains status: public scopus_import: '1' status: public title: Measuring the complete force field of an optical trap type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2011' ... --- _id: '3375' abstract: - lang: eng text: 'By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states.' article_processing_charge: No article_type: original author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - 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: de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438 apa: de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2010.0438 chicago: Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface. The Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438. ieee: H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” Journal of the Royal Society Interface, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011. ista: de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 8(58), 720–739. mla: de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:10.1098/rsif.2010.0438. short: H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739. date_created: 2018-12-11T12:02:58Z date_published: 2011-05-01T00:00:00Z date_updated: 2023-10-18T06:39:05Z day: '01' department: - _id: NiBa doi: 10.1098/rsif.2010.0438 ec_funded: 1 external_id: pmid: - '21084341' intvolume: ' 8' issue: '58' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/ month: '05' oa: 1 oa_version: Submitted Version page: 720 - 739 pmid: 1 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 the Royal Society Interface publication_status: published publisher: The Royal Society publist_id: '3232' quality_controlled: '1' scopus_import: '1' status: public title: The statistical mechanics of a polygenic character under stabilizing selection mutation and drift type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2011' ... --- _id: '3393' abstract: - lang: eng text: 'Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.' article_processing_charge: No article_type: original 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: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: 'Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75. doi:10.1086/661246' apa: 'Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. The University of Chicago Press. https://doi.org/10.1086/661246' chicago: 'Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist. The University of Chicago Press, 2011. https://doi.org/10.1086/661246.' ieee: 'N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects,” American Naturalist, vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.' ista: 'Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3), E48–E75.' mla: 'Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist, vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.' short: N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75. date_created: 2018-12-11T12:03:05Z date_published: 2011-09-01T00:00:00Z date_updated: 2023-10-18T08:01:43Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1086/661246 file: - access_level: open_access checksum: 7fd22a2ef3321a6fca6a439b3be5d8f4 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:31Z date_updated: 2020-07-14T12:46:11Z file_id: '4692' file_name: IST-2016-554-v1+1_BartonTurelli2011_copy.pdf file_size: 629130 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 178' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: E48 - E75 publication: American Naturalist publication_identifier: eissn: - 1537-5323 issn: - 0003-0147 publication_status: published publisher: The University of Chicago Press publist_id: '3214' pubrep_id: '554' quality_controlled: '1' scopus_import: '1' status: public title: 'Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 178 year: '2011' ... --- _id: '14305' abstract: - lang: eng text: Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association. article_processing_charge: No article_type: original author: - first_name: Annett full_name: Bachmann, Annett last_name: Bachmann - first_name: Dirk full_name: Wildemann, Dirk last_name: Wildemann - first_name: Florian M full_name: Praetorius, Florian M id: dfec9381-4341-11ee-8fd8-faa02bba7d62 last_name: Praetorius - first_name: Gunter full_name: Fischer, Gunter last_name: Fischer - first_name: Thomas full_name: Kiefhaber, Thomas last_name: Kiefhaber citation: ama: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. 2011;108(10):3952-3957. doi:10.1073/pnas.1012668108 apa: Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., & Kiefhaber, T. (2011). Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1012668108 chicago: Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer, and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS. Proceedings of the National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1012668108. ieee: A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber, “Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction,” PNAS, vol. 108, no. 10. Proceedings of the National Academy of Sciences, pp. 3952–3957, 2011. ista: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. 108(10), 3952–3957. mla: Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS, vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57, doi:10.1073/pnas.1012668108. short: A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS 108 (2011) 3952–3957. date_created: 2023-09-06T12:54:36Z date_published: 2011-01-12T00:00:00Z date_updated: 2023-11-07T11:50:29Z day: '12' doi: 10.1073/pnas.1012668108 extern: '1' external_id: pmid: - '21325613' intvolume: ' 108' issue: '10' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1012668108 month: '01' oa: 1 oa_version: Published Version page: 3952-3957 pmid: 1 publication: PNAS publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2011' ... --- _id: '7701' abstract: - lang: eng text: During assembly of the Drosophila olfactory circuit, projection neuron (PN) dendrites prepattern the developing antennal lobe before the arrival of axons from their presynaptic partners, the adult olfactory receptor neurons (ORNs). We previously found that levels of transmembrane Semaphorin-1a, which acts as a receptor, instruct PN dendrite targeting along the dorsolateral-ventromedial axis. Here we show that two secreted semaphorins, Sema-2a and Sema-2b, provide spatial cues for PN dendrite targeting. Sema-2a and Sema-2b proteins are distributed in gradients opposing the Sema-1a protein gradient, and Sema-1a binds to Sema-2a-expressing cells. In Sema-2a and Sema-2b double mutants, PN dendrites that normally target dorsolaterally in the antennal lobe mistarget ventromedially, phenocopying cell-autonomous Sema-1a removal from these PNs. Cell ablation, cell-specific knockdown, and rescue experiments indicate that secreted semaphorins from degenerating larval ORN axons direct dendrite targeting. Thus, a degenerating brain structure instructs the wiring of a developing circuit through the repulsive action of secreted semaphorins. article_processing_charge: No article_type: original author: - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 - first_name: Ya-Hui full_name: Chou, Ya-Hui last_name: Chou - first_name: Zhuhao full_name: Wu, Zhuhao last_name: Wu - first_name: William full_name: Joo, William last_name: Joo - first_name: Takaki full_name: Komiyama, Takaki last_name: Komiyama - first_name: Christopher J. full_name: Potter, Christopher J. last_name: Potter - first_name: Alex L. full_name: Kolodkin, Alex L. last_name: Kolodkin - first_name: K. Christopher full_name: Garcia, K. Christopher last_name: Garcia - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: ama: Sweeney LB, Chou Y-H, Wu Z, et al. Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting. Neuron. 2011;72(5):734-747. doi:10.1016/j.neuron.2011.09.026 apa: Sweeney, L. B., Chou, Y.-H., Wu, Z., Joo, W., Komiyama, T., Potter, C. J., … Luo, L. (2011). Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2011.09.026 chicago: Sweeney, Lora B., Ya-Hui Chou, Zhuhao Wu, William Joo, Takaki Komiyama, Christopher J. Potter, Alex L. Kolodkin, K. Christopher Garcia, and Liqun Luo. “Secreted Semaphorins from Degenerating Larval ORN Axons Direct Adult Projection Neuron Dendrite Targeting.” Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.09.026. ieee: L. B. Sweeney et al., “Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting,” Neuron, vol. 72, no. 5. Elsevier, pp. 734–747, 2011. ista: Sweeney LB, Chou Y-H, Wu Z, Joo W, Komiyama T, Potter CJ, Kolodkin AL, Garcia KC, Luo L. 2011. Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting. Neuron. 72(5), 734–747. mla: Sweeney, Lora B., et al. “Secreted Semaphorins from Degenerating Larval ORN Axons Direct Adult Projection Neuron Dendrite Targeting.” Neuron, vol. 72, no. 5, Elsevier, 2011, pp. 734–47, doi:10.1016/j.neuron.2011.09.026. short: L.B. Sweeney, Y.-H. Chou, Z. Wu, W. Joo, T. Komiyama, C.J. Potter, A.L. Kolodkin, K.C. Garcia, L. Luo, Neuron 72 (2011) 734–747. date_created: 2020-04-30T10:36:12Z date_published: 2011-12-08T00:00:00Z date_updated: 2024-01-31T10:13:39Z day: '08' doi: 10.1016/j.neuron.2011.09.026 extern: '1' intvolume: ' 72' issue: '5' language: - iso: eng month: '12' oa_version: None page: 734-747 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 72 year: '2011' ... --- _id: '7702' abstract: - lang: eng text: Longitudinal axon fascicles within the Drosophila embryonic CNS provide connections between body segments and are required for coordinated neural signaling along the anterior-posterior axis. We show here that establishment of select CNS longitudinal tracts and formation of precise mechanosensory afferent innervation to the same CNS region are coordinately regulated by the secreted semaphorins Sema-2a and Sema-2b. Both Sema-2a and Sema-2b utilize the same neuronal receptor, plexin B (PlexB), but serve distinct guidance functions. Localized Sema-2b attraction promotes the initial assembly of a subset of CNS longitudinal projections and subsequent targeting of chordotonal sensory afferent axons to these same longitudinal connectives, whereas broader Sema-2a repulsion serves to prevent aberrant innervation. In the absence of Sema-2b or PlexB, chordotonal afferent connectivity within the CNS is severely disrupted, resulting in specific larval behavioral deficits. These results reveal that distinct semaphorin-mediated guidance functions converge at PlexB and are critical for functional neural circuit assembly. article_processing_charge: No article_type: original author: - first_name: Zhuhao full_name: Wu, Zhuhao last_name: Wu - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 - first_name: Joseph C. full_name: Ayoob, Joseph C. last_name: Ayoob - first_name: Kayam full_name: Chak, Kayam last_name: Chak - first_name: Benjamin J. full_name: Andreone, Benjamin J. last_name: Andreone - first_name: Tomoko full_name: Ohyama, Tomoko last_name: Ohyama - first_name: Rex full_name: Kerr, Rex last_name: Kerr - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Marta full_name: Zlatic, Marta last_name: Zlatic - first_name: Alex L. full_name: Kolodkin, Alex L. last_name: Kolodkin citation: ama: Wu Z, Sweeney LB, Ayoob JC, et al. A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron. 2011;70(2):281-298. doi:10.1016/j.neuron.2011.02.050 apa: Wu, Z., Sweeney, L. B., Ayoob, J. C., Chak, K., Andreone, B. J., Ohyama, T., … Kolodkin, A. L. (2011). A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2011.02.050 chicago: Wu, Zhuhao, Lora B. Sweeney, Joseph C. Ayoob, Kayam Chak, Benjamin J. Andreone, Tomoko Ohyama, Rex Kerr, Liqun Luo, Marta Zlatic, and Alex L. Kolodkin. “A Combinatorial Semaphorin Code Instructs the Initial Steps of Sensory Circuit Assembly in the Drosophila CNS.” Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.02.050. ieee: Z. Wu et al., “A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS,” Neuron, vol. 70, no. 2. Elsevier, pp. 281–298, 2011. ista: Wu Z, Sweeney LB, Ayoob JC, Chak K, Andreone BJ, Ohyama T, Kerr R, Luo L, Zlatic M, Kolodkin AL. 2011. A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron. 70(2), 281–298. mla: Wu, Zhuhao, et al. “A Combinatorial Semaphorin Code Instructs the Initial Steps of Sensory Circuit Assembly in the Drosophila CNS.” Neuron, vol. 70, no. 2, Elsevier, 2011, pp. 281–98, doi:10.1016/j.neuron.2011.02.050. short: Z. Wu, L.B. Sweeney, J.C. Ayoob, K. Chak, B.J. Andreone, T. Ohyama, R. Kerr, L. Luo, M. Zlatic, A.L. Kolodkin, Neuron 70 (2011) 281–298. date_created: 2020-04-30T10:36:30Z date_published: 2011-04-28T00:00:00Z date_updated: 2024-01-31T10:14:29Z day: '28' doi: 10.1016/j.neuron.2011.02.050 extern: '1' intvolume: ' 70' issue: '2' language: - iso: eng month: '04' oa_version: None page: 281-298 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2011' ...