[{"author":[{"first_name":"Michael","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael"},{"last_name":"Wu","first_name":"Selwin","full_name":"Wu, Selwin"},{"last_name":"Gomez","first_name":"Guillermo","full_name":"Gomez, Guillermo"},{"first_name":"Sabine","last_name":"Mangold","full_name":"Mangold, Sabine"},{"first_name":"Alpha","last_name":"Yap","full_name":"Yap, Alpha"},{"full_name":"Hamilton, Nicholas","first_name":"Nicholas","last_name":"Hamilton"}],"date_updated":"2021-01-12T07:42:25Z","date_created":"2018-12-11T12:02:28Z","volume":6,"acknowledgement":"his work was funded by the National Health and Medical Research Council (NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship. A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the Institute for Molecular Bioscience, established with the generous support of the ACRF.","year":"2011","publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"3357","doi":"10.1371/journal.pone.0022458","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"07","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6399","checksum":"57a5eb11dd05241c48c44f492b3ec3ac","date_updated":"2020-07-14T12:46:06Z","date_created":"2019-05-10T10:51:43Z","access_level":"open_access","file_name":"2011_PLOS_Smutny.PDF","file_size":1984567,"content_type":"application/pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3288","status":"public","title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens","ddc":["570"],"intvolume":" 6","abstract":[{"text":"The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA.","lang":"eng"}],"issue":"7","type":"journal_article","date_published":"2011-07-22T00:00:00Z","publication":"PLoS One","citation":{"short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).","mla":"Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458.","chicago":"Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap, and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458.","ama":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458","apa":"Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011). Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0022458","ieee":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.","ista":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 6(7)."},"day":"22","has_accepted_license":"1"},{"day":"01","month":"10","citation":{"ieee":"J. Weghuber et al., “Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells,” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10. Elsevier, pp. 2581–2590, 2011.","apa":"Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger, B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2011.06.007","ista":"Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1808(10), 2581–2590.","ama":"Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590. doi:10.1016/j.bbamem.2011.06.007","chicago":"Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser, Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier, 2011. https://doi.org/10.1016/j.bbamem.2011.06.007.","short":"J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger, J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.","mla":"Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011, pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007."},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication":"Biochimica et Biophysica Acta (BBA) - Biomembranes","page":"2581 - 2590","quality_controlled":0,"doi":"10.1016/j.bbamem.2011.06.007","date_published":"2011-10-01T00:00:00Z","type":"journal_article","issue":"10","publist_id":"3359","abstract":[{"text":"Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes by electrostatic interactions with negatively charged lipids. It turned out that for inhibition of microbial growth a high CAMP membrane concentration is required, which can be realized by the incorporation of hydrophobic groups within the peptide. Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial over eukaryotic host membranes, thereby causing the risk of detrimental side-effects. In this study we addressed how cationic amphipathic peptides—in particular a CAMP with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics of molecules in eukaryotic membranes. We found KLK to selectively inhibit the endocytosis of a subgroup of membrane proteins and lipids by electrostatically interacting with negatively charged sialic acid moieties. Ultrastructural characterization revealed the formation of membrane invaginations representing fission or fusion intermediates, in which the sialylated proteins and lipids were immobilized. Experiments on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively arrest sialylated membrane constituents.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":1,"acknowledgement":"This work was funded by the GEN-AU project of the Austrian Research Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH, Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland), Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota, USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna) for excellent technical assistance in the processing of samples for electron microscopy and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for fruitful discussions. ","_id":"3286","year":"2011","publisher":"Elsevier","intvolume":" 1808","title":"Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells","publication_status":"published","status":"public","author":[{"first_name":"Julian","last_name":"Weghuber","full_name":"Weghuber, Julian"},{"first_name":"Michael","last_name":"Aichinger","full_name":"Aichinger, Michael C."},{"first_name":"Mario","last_name":"Brameshuber","full_name":"Brameshuber, Mario"},{"first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","full_name":"Stefan Wieser"},{"full_name":"Verena Ruprecht","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena"},{"last_name":"Plochberger","first_name":"Birgit","full_name":"Plochberger, Birgit"},{"first_name":"Josef","last_name":"Madl","full_name":"Madl, Josef"},{"first_name":"Andreas","last_name":"Horner","full_name":"Horner, Andreas"},{"full_name":"Reipert, Siegfried","last_name":"Reipert","first_name":"Siegfried"},{"last_name":"Lohner","first_name":"Karl","full_name":"Lohner, Karl"},{"first_name":"Tamas","last_name":"Henics","full_name":"Henics, Tamas"},{"first_name":"Gerhard","last_name":"Schuetz","full_name":"Schuetz, Gerhard J"}],"volume":1808,"date_created":"2018-12-11T12:02:28Z","date_updated":"2021-01-12T07:42:24Z"},{"scopus_import":1,"day":"01","month":"12","citation":{"ista":"Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724.","apa":"Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we learn from single molecule trajectories? Current Protein & Peptide Science. Bentham Science Publishers. https://doi.org/10.2174/138920311798841753","ieee":"V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” Current Protein & Peptide Science, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.","ama":"Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule trajectories? Current Protein & Peptide Science. 2011;12(8):714-724. doi:10.2174/138920311798841753","chicago":"Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753.","mla":"Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753.","short":"V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide Science 12 (2011) 714–724."},"publication":"Current Protein & Peptide Science","page":"714 - 724","quality_controlled":"1","doi":"10.2174/138920311798841753","date_published":"2011-12-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"8","publist_id":"3358","abstract":[{"text":"Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion.","lang":"eng"}],"_id":"3287","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","publisher":"Bentham Science Publishers","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"intvolume":" 12","status":"public","publication_status":"published","title":"What can we learn from single molecule trajectories?","author":[{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena"},{"full_name":"Axmann, Markus","first_name":"Markus","last_name":"Axmann"},{"full_name":"Wieser, Stefan","first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217"},{"last_name":"Schuetz","first_name":"Gerhard","full_name":"Schuetz, Gerhard"}],"volume":12,"oa_version":"None","date_created":"2018-12-11T12:02:28Z","date_updated":"2021-01-12T07:42:24Z"},{"publist_id":"3360","issue":"11","abstract":[{"lang":"eng","text":"Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents."}],"extern":"1","type":"journal_article","author":[{"orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan"},{"full_name":"Marguet, Didier","last_name":"Marguet","first_name":"Didier"},{"full_name":"Schuetz, Gerhard","last_name":"Schuetz","first_name":"Gerhard"}],"oa_version":"None","volume":100,"date_created":"2018-12-11T12:02:27Z","date_updated":"2021-01-12T07:42:23Z","_id":"3285","acknowledgement":"Y 250-B03/Austrian Science Fund FWF/Austria","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2011","publisher":"Biophysical Society","intvolume":" 100","status":"public","publication_status":"published","title":"Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes","day":"08","month":"06","doi":"10.1016/j.bpj.2011.04.035","date_published":"2011-06-08T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 2011;100(11):2839-2845. doi:10.1016/j.bpj.2011.04.035","apa":"Ruprecht, V., Wieser, S., Marguet, D., & Schuetz, G. (2011). Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2011.04.035","ieee":"V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes,” Biophysical Journal, vol. 100, no. 11. Biophysical Society, pp. 2839–2845, 2011.","ista":"Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 100(11), 2839–2845.","short":"V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011) 2839–2845.","mla":"Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035.","chicago":"Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical Journal. Biophysical Society, 2011. https://doi.org/10.1016/j.bpj.2011.04.035."},"publication":"Biophysical Journal","page":"2839 - 2845"},{"type":"conference","publist_id":"3338","file_date_updated":"2020-07-14T12:46:06Z","abstract":[{"text":"Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We present a new job execution environment Flextic that exploits scal- able static scheduling techniques to provide the user with a flexible pricing model, such as a tradeoff between dif- ferent degrees of execution speed and execution price, and at the same time, reduce scheduling overhead for the cloud provider. We have evaluated a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various data parallel jobs from machine learning, im- age processing, and gene sequencing that we considered, Flextic has low scheduling overhead and reduces job du- ration by up to 15% compared to Hadoop, a dynamic cloud scheduler.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3302","year":"2011","department":[{"_id":"ToHe"}],"publisher":"USENIX","title":"Static scheduling in clouds","ddc":["000","005"],"status":"public","publication_status":"published","pubrep_id":"90","author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"last_name":"Singh","first_name":"Anmol","id":"72A86902-E99F-11E9-9F62-915534D1B916","full_name":"Singh, Anmol"},{"full_name":"Singh, Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu","last_name":"Singh"},{"full_name":"Wies, Thomas","first_name":"Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","first_name":"Damien","last_name":"Zufferey","full_name":"Zufferey, Damien"}],"oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf","creator":"system","file_size":232770,"content_type":"application/pdf","file_id":"5333","relation":"main_file","checksum":"21a461ac004bb535c83320fe79b30375","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:18:14Z"}],"date_updated":"2021-01-12T07:42:31Z","date_created":"2018-12-11T12:02:33Z","has_accepted_license":"1","day":"14","month":"06","citation":{"ista":"Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. 2011. Static scheduling in clouds. HotCloud: Workshop on Hot Topics in Cloud Computing, 1–6.","apa":"Henzinger, T. A., Singh, A., Singh, V., Wies, T., & Zufferey, D. (2011). Static scheduling in clouds (pp. 1–6). Presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, USENIX.","ieee":"T. A. Henzinger, A. Singh, V. Singh, T. Wies, and D. Zufferey, “Static scheduling in clouds,” presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, 2011, pp. 1–6.","ama":"Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds. In: USENIX; 2011:1-6.","chicago":"Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey. “Static Scheduling in Clouds,” 1–6. USENIX, 2011.","mla":"Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 2011, pp. 1–6.","short":"T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6."},"oa":1,"page":"1 - 6","quality_controlled":"1","date_published":"2011-06-14T00:00:00Z","conference":{"name":"HotCloud: Workshop on Hot Topics in Cloud Computing","end_date":"2011-06-15","start_date":"2011-06-14"},"language":[{"iso":"eng"}]},{"_id":"3301","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","publication_status":"published","status":"public","ddc":["005","570"],"title":"Tail approximation for the chemical master equation","publisher":"Tampere International Center for Signal Processing","department":[{"_id":"ToHe"}],"author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Mateescu","first_name":"Maria","full_name":"Mateescu, Maria"}],"pubrep_id":"91","date_created":"2018-12-11T12:02:33Z","date_updated":"2021-01-12T07:42:30Z","file":[{"content_type":"application/pdf","file_size":240820,"creator":"system","access_level":"open_access","file_name":"IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf","checksum":"aa4d7a832a5419e6c0090650ebff2b9a","date_created":"2018-12-12T10:18:12Z","date_updated":"2020-07-14T12:46:06Z","relation":"main_file","file_id":"5331"}],"oa_version":"Submitted Version","type":"conference","file_date_updated":"2020-07-14T12:46:06Z","abstract":[{"lang":"eng","text":"The chemical master equation is a differential equation describing the time evolution of the probability distribution over the possible “states” of a biochemical system. The solution of this equation is of interest within the systems biology field ever since the importance of the molec- ular noise has been acknowledged. Unfortunately, most of the systems do not have analytical solutions, and numerical solutions suffer from the course of dimensionality and therefore need to be approximated. Here, we introduce the concept of tail approximation, which retrieves an approximation of the probabilities in the tail of a distribution from the total probability of the tail and its conditional expectation. This approximation method can then be used to numerically compute the solution of the chemical master equation on a subset of the state space, thus fighting the explosion of the state space, for which this problem is renowned."}],"publist_id":"3339","oa":1,"citation":{"short":"T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal Processing, 2011.","mla":"Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical Master Equation. Tampere International Center for Signal Processing, 2011.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011.","ama":"Henzinger TA, Mateescu M. Tail approximation for the chemical master equation. In: Tampere International Center for Signal Processing; 2011.","ieee":"T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP), 2011.","apa":"Henzinger, T. A., & Mateescu, M. (2011). Tail approximation for the chemical master equation. Presented at the WCSB: Workshop on Computational Systems Biology (TICSP), Tampere International Center for Signal Processing.","ista":"Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP)."},"quality_controlled":"1","conference":{"name":"WCSB: Workshop on Computational Systems Biology (TICSP)"},"date_published":"2011-01-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","month":"01","has_accepted_license":"1"},{"citation":{"chicago":"Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing Biochemical Reaction Networks,” 1–3. Springer, 2011. https://doi.org/10.1145/2037509.2037510.","short":"T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.","mla":"Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510.","apa":"Henzinger, T. A., & Mateescu, M. (2011). Propagation models for computing biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational Methods in Systems Biology, Paris, France: Springer. https://doi.org/10.1145/2037509.2037510","ieee":"T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical reaction networks,” presented at the CMSB: Computational Methods in Systems Biology, Paris, France, 2011, pp. 1–3.","ista":"Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.","ama":"Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction networks. In: Springer; 2011:1-3. doi:10.1145/2037509.2037510"},"page":"1 - 3","date_published":"2011-09-21T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"21","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3299","title":"Propagation models for computing biochemical reaction networks","status":"public","ddc":["000","004"],"pubrep_id":"92","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":255780,"access_level":"open_access","file_name":"IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf","checksum":"7f5c65509db1a9fb049abedd9663ed06","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:07:50Z","file_id":"4649","relation":"main_file"}],"type":"conference","abstract":[{"lang":"eng","text":"We introduce propagation models, a formalism designed to support general and efficient data structures for the transient analysis of biochemical reaction networks. We give two use cases for propagation abstract data types: the uniformization method and numerical integration. We also sketch an implementation of a propagation abstract data type, which uses abstraction to approximate states."}],"oa":1,"quality_controlled":"1","doi":"10.1145/2037509.2037510","conference":{"end_date":"2011-09-23","start_date":"2011-09-21","location":"Paris, France","name":"CMSB: Computational Methods in Systems Biology"},"language":[{"iso":"eng"}],"month":"09","year":"2011","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Maria","last_name":"Mateescu","full_name":"Mateescu, Maria"}],"date_updated":"2021-01-12T07:42:29Z","date_created":"2018-12-11T12:02:32Z","publist_id":"3341","file_date_updated":"2020-07-14T12:46:06Z"},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1109/SIES.2011.5953660","conference":{"name":" SIES: International Symposium on Industrial Embedded Systems","end_date":"2011-06-17","location":"Vasteras, Sweden","start_date":"2011-06-15"},"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse"}],"oa":1,"ec_funded":1,"publist_id":"3323","date_created":"2018-12-11T12:02:38Z","date_updated":"2021-01-12T07:42:36Z","author":[{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Greimel, Karin","last_name":"Greimel","first_name":"Karin"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","year":"2011","article_processing_charge":"No","day":"14","scopus_import":1,"date_published":"2011-07-14T00:00:00Z","page":"176 - 185","citation":{"ama":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered robustness. In: 6th IEEE International Symposium on Industrial and Embedded Systems. IEEE; 2011:176-185. doi:10.1109/SIES.2011.5953660","ieee":"R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered robustness,” in 6th IEEE International Symposium on Industrial and Embedded Systems, Vasteras, Sweden, 2011, pp. 176–185.","apa":"Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann, B. (2011). Specification-centered robustness. In 6th IEEE International Symposium on Industrial and Embedded Systems (pp. 176–185). Vasteras, Sweden: IEEE. https://doi.org/10.1109/SIES.2011.5953660","ista":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered robustness. 6th IEEE International Symposium on Industrial and Embedded Systems. SIES: International Symposium on Industrial Embedded Systems, 176–185.","short":"R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–185.","mla":"Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Specification-Centered Robustness.” In 6th IEEE International Symposium on Industrial and Embedded Systems, 176–85. IEEE, 2011. https://doi.org/10.1109/SIES.2011.5953660."},"publication":"6th IEEE International Symposium on Industrial and Embedded Systems","abstract":[{"lang":"eng","text":"In addition to being correct, a system should be robust, that is, it should behave reasonably even after receiving unexpected inputs. In this paper, we summarize two formal notions of robustness that we have introduced previously for reactive systems. One of the notions is based on assigning costs for failures on a user-provided notion of incorrect transitions in a specification. Here, we define a system to be robust if a finite number of incorrect inputs does not lead to an infinite number of incorrect outputs. We also give a more refined notion of robustness that aims to minimize the ratio of output failures to input failures. The second notion is aimed at liveness. In contrast to the previous notion, it has no concept of recovery from an error. Instead, it compares the ratio of the number of liveness constraints that the system violates to the number of liveness constraints that the environment violates."}],"type":"conference","oa_version":"Published Version","status":"public","title":"Specification-centered robustness","_id":"3316","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","publist_id":"3321","abstract":[{"lang":"eng","text":"Parvalbumin is thought to act in a manner similar to EGTA, but how a slow Ca2+ buffer affects nanodomain-coupling regimes at GABAergic synapses is unclear. Direct measurements of parvalbumin concentration and paired recordings in rodent hippocampus and cerebellum revealed that parvalbumin affects synaptic dynamics only when expressed at high levels. Modeling suggests that, in high concentrations, parvalbumin may exert BAPTA-like effects, modulating nanodomain coupling via competition with local saturation of endogenous fixed buffers."}],"publisher":"Nature Publishing Group","intvolume":" 15","department":[{"_id":"PeJo"}],"title":"How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses","publication_status":"published","status":"public","_id":"3318","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","volume":15,"oa_version":"Submitted Version","date_created":"2018-12-11T12:02:38Z","date_updated":"2021-01-12T07:42:37Z","author":[{"first_name":"Emmanuel","last_name":"Eggermann","full_name":"Eggermann, Emmanuel"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"scopus_import":1,"month":"12","day":"04","page":"20 - 22","quality_controlled":"1","citation":{"short":"E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22.","mla":"Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” Nature Neuroscience, vol. 15, Nature Publishing Group, 2011, pp. 20–22, doi:10.1038/nn.3002.","chicago":"Eggermann, Emmanuel, and Peter M Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.3002.","ama":"Eggermann E, Jonas PM. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. 2011;15:20-22. doi:10.1038/nn.3002","apa":"Eggermann, E., & Jonas, P. M. (2011). How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3002","ieee":"E. Eggermann and P. M. Jonas, “How the ‘slow’ Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses,” Nature Neuroscience, vol. 15. Nature Publishing Group, pp. 20–22, 2011.","ista":"Eggermann E, Jonas PM. 2011. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. 15, 20–22."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/"}],"publication":"Nature Neuroscience","language":[{"iso":"eng"}],"doi":"10.1038/nn.3002","date_published":"2011-12-04T00:00:00Z"},{"abstract":[{"text":"We study the topology of the Megaparsec Cosmic Web in terms of the scale-dependent Betti numbers, which formalize the topological information content of the cosmic mass distribution. While the Betti numbers do not fully quantify topology, they extend the information beyond conventional cosmological studies of topology in terms of genus and Euler characteristic. The richer information content of Betti numbers goes along the availability of fast algorithms to compute them. For continuous density fields, we determine the scale-dependence of Betti numbers by invoking the cosmologically familiar filtration of sublevel or superlevel sets defined by density thresholds. For the discrete galaxy distribution, however, the analysis is based on the alpha shapes of the particles. These simplicial complexes constitute an ordered sequence of nested subsets of the Delaunay tessellation, a filtration defined by the scale parameter, α. As they are homotopy equivalent to the sublevel sets of the distance field, they are an excellent tool for assessing the topological structure of a discrete point distribution. In order to develop an intuitive understanding for the behavior of Betti numbers as a function of α, and their relation to the morphological patterns in the Cosmic Web, we first study them within the context of simple heuristic Voronoi clustering models. These can be tuned to consist of specific morphological elements of the Cosmic Web, i.e. clusters, filaments, or sheets. To elucidate the relative prominence of the various Betti numbers in different stages of morphological evolution, we introduce the concept of alpha tracks. Subsequently, we address the topology of structures emerging in the standard LCDM scenario and in cosmological scenarios with alternative dark energy content. The evolution of the Betti numbers is shown to reflect the hierarchical evolution of the Cosmic Web. We also demonstrate that the scale-dependence of the Betti numbers yields a promising measure of cosmological parameters, with a potential to help in determining the nature of dark energy and to probe primordial non-Gaussianities. We also discuss the expected Betti numbers as a function of the density threshold for superlevel sets of a Gaussian random field. Finally, we introduce the concept of persistent homology. It measures scale levels of the mass distribution and allows us to separate small from large scale features. Within the context of the hierarchical cosmic structure formation, persistence provides a natural formalism for a multiscale topology study of the Cosmic Web.","lang":"eng"}],"type":"book_chapter","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3335","status":"public","title":"Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web","intvolume":" 6970","day":"09","scopus_import":1,"series_title":"Special Issue on Voronoi Diagrams and Delaunay Triangulation","date_published":"2011-11-09T00:00:00Z","publication":"Transactions on Computational Science XIV","citation":{"chicago":"Van De Weygaert, Rien, Gert Vegter, Herbert Edelsbrunner, Bernard Jones, Pratyush Pranav, Changbom Park, Wojciech Hellwing, et al. “Alpha, Betti and the Megaparsec Universe: On the Topology of the Cosmic Web.” In Transactions on Computational Science XIV, edited by Marina Gavrilova, Kenneth Tan, and Mir Mostafavi, 6970:60–101. Special Issue on Voronoi Diagrams and Delaunay Triangulation. Springer, 2011. https://doi.org/10.1007/978-3-642-25249-5_3.","short":"R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park, W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi (Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101.","mla":"Van De Weygaert, Rien, et al. “Alpha, Betti and the Megaparsec Universe: On the Topology of the Cosmic Web.” Transactions on Computational Science XIV, edited by Marina Gavrilova et al., vol. 6970, Springer, 2011, pp. 60–101, doi:10.1007/978-3-642-25249-5_3.","apa":"Van De Weygaert, R., Vegter, G., Edelsbrunner, H., Jones, B., Pranav, P., Park, C., … Teillaud, M. (2011). Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In M. Gavrilova, K. Tan, & M. Mostafavi (Eds.), Transactions on Computational Science XIV (Vol. 6970, pp. 60–101). Springer. https://doi.org/10.1007/978-3-642-25249-5_3","ieee":"R. Van De Weygaert et al., “Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web,” in Transactions on Computational Science XIV, vol. 6970, M. Gavrilova, K. Tan, and M. Mostafavi, Eds. Springer, 2011, pp. 60–101.","ista":"Van De Weygaert R, Vegter G, Edelsbrunner H, Jones B, Pranav P, Park C, Hellwing W, Eldering B, Kruithof N, Bos P, Hidding J, Feldbrugge J, Ten Have E, Van Engelen M, Caroli M, Teillaud M. 2011.Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In: Transactions on Computational Science XIV. LNCS, vol. 6970, 60–101.","ama":"Van De Weygaert R, Vegter G, Edelsbrunner H, et al. Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In: Gavrilova M, Tan K, Mostafavi M, eds. Transactions on Computational Science XIV. Vol 6970. Special Issue on Voronoi Diagrams and Delaunay Triangulation. Springer; 2011:60-101. doi:10.1007/978-3-642-25249-5_3"},"page":"60 - 101","publist_id":"3295","author":[{"full_name":"Van De Weygaert, Rien","first_name":"Rien","last_name":"Van De Weygaert"},{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Jones, Bernard","last_name":"Jones","first_name":"Bernard"},{"first_name":"Pratyush","last_name":"Pranav","full_name":"Pranav, Pratyush"},{"first_name":"Changbom","last_name":"Park","full_name":"Park, Changbom"},{"full_name":"Hellwing, Wojciech","last_name":"Hellwing","first_name":"Wojciech"},{"last_name":"Eldering","first_name":"Bob","full_name":"Eldering, Bob"},{"last_name":"Kruithof","first_name":"Nico","full_name":"Kruithof, Nico"},{"last_name":"Bos","first_name":"Patrick","full_name":"Bos, Patrick"},{"full_name":"Hidding, Johan","last_name":"Hidding","first_name":"Johan"},{"full_name":"Feldbrugge, Job","last_name":"Feldbrugge","first_name":"Job"},{"full_name":"Ten Have, Eline","first_name":"Eline","last_name":"Ten Have"},{"full_name":"Van Engelen, Matti","last_name":"Van Engelen","first_name":"Matti"},{"full_name":"Caroli, Manuel","first_name":"Manuel","last_name":"Caroli"},{"first_name":"Monique","last_name":"Teillaud","full_name":"Teillaud, Monique"}],"date_updated":"2021-01-12T07:42:44Z","date_created":"2018-12-11T12:02:44Z","volume":6970,"year":"2011","publication_status":"published","department":[{"_id":"HeEd"}],"editor":[{"full_name":"Gavrilova, Marina","last_name":"Gavrilova","first_name":"Marina"},{"last_name":"Tan","first_name":"Kenneth","full_name":"Tan, Kenneth"},{"full_name":"Mostafavi, Mir","last_name":"Mostafavi","first_name":"Mir"}],"publisher":"Springer","month":"11","doi":"10.1007/978-3-642-25249-5_3","language":[{"iso":"eng"}],"external_id":{"arxiv":["1306.3640"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.3640"}],"quality_controlled":"1"}]