[{"department":[{"_id":"Bio"}],"date_published":"2011-06-09T00:00:00Z","oa_version":"Preprint","conference":{"start_date":"2011-03-30","name":"ISBI: International Symposium on Biomedical Imaging","end_date":"2011-04-02","location":"Chicago, Illinois, USA"},"author":[{"last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Straehle","full_name":"Straehle, Christoph","first_name":"Christoph"},{"last_name":"Köthe","full_name":"Köthe, Ullrich","first_name":"Ullrich"},{"last_name":"Hamprecht","first_name":"Fred A.","full_name":"Hamprecht, Fred A."}],"publication":"2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro","publisher":"Institute of Electrical and Electronics Engineers","_id":"9943","doi":"10.1109/isbi.2011.5872394","month":"06","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"conference","language":[{"iso":"eng"}],"publication_status":"published","title":"Ilastik: Interactive learning and segmentation toolkit","oa":1,"article_processing_charge":"No","day":"09","main_file_link":[{"open_access":"1","url":"https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit"}],"citation":{"mla":"Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation Toolkit.” <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>, Institute of Electrical and Electronics Engineers, 2011, doi:<a href=\"https://doi.org/10.1109/isbi.2011.5872394\">10.1109/isbi.2011.5872394</a>.","ieee":"C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive learning and segmentation toolkit,” in <i>2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro</i>, Chicago, Illinois, USA, 2011.","chicago":"Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht. “Ilastik: Interactive Learning and Segmentation Toolkit.” In <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>. Institute of Electrical and Electronics Engineers, 2011. <a href=\"https://doi.org/10.1109/isbi.2011.5872394\">https://doi.org/10.1109/isbi.2011.5872394</a>.","apa":"Sommer, C. M., Straehle, C., Köthe, U., &#38; Hamprecht, F. A. (2011). Ilastik: Interactive learning and segmentation toolkit. In <i>2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro</i>. Chicago, Illinois, USA: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/isbi.2011.5872394\">https://doi.org/10.1109/isbi.2011.5872394</a>","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.","ama":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit. In: <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>. Institute of Electrical and Electronics Engineers; 2011. doi:<a href=\"https://doi.org/10.1109/isbi.2011.5872394\">10.1109/isbi.2011.5872394</a>","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."},"keyword":["image segmentation","biomedical imaging","three dimensional displays","neurons","retina","observers","image color analysis"],"publication_identifier":{"eissn":["1945-8452"],"issn":["1945-7928"],"isbn":["978-1-4244-4127-3"]},"date_updated":"2023-02-23T14:13:38Z","date_created":"2021-08-19T11:49:58Z","year":"2011","quality_controlled":"1","extern":"1","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."}],"status":"public"},{"intvolume":"      6658","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. <i>Graph-Based Representations in Pattern Recognition</i>. Vol 6658. LNIP. Berlin, Heidelberg: Springer; 2011:215-224. doi:<a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">10.1007/978-3-642-20844-7_22</a>","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.","mla":"Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” <i>Graph-Based Representations in Pattern Recognition</i>, edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:<a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">10.1007/978-3-642-20844-7_22</a>.","ieee":"N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of articulated models in a graph pyramid,” in <i>Graph-Based Representations in Pattern Recognition</i>, Münster, Germany, 2011, vol. 6658, pp. 215–224.","chicago":"Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” In <i>Graph-Based Representations in Pattern Recognition</i>, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">https://doi.org/10.1007/978-3-642-20844-7_22</a>.","apa":"Artner, N. M., Ion, A., &#38; Kropatsch, W. G. (2011). Spatio-temporal extraction of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, &#38; A. Torsello (Eds.), <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 6658, pp. 215–224). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">https://doi.org/10.1007/978-3-642-20844-7_22</a>","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."},"day":"01","status":"public","abstract":[{"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.","lang":"eng"}],"editor":[{"last_name":"Jiang","first_name":"Xiaoyi","full_name":"Jiang, Xiaoyi"},{"last_name":"Ferrer","first_name":"Miquel","full_name":"Ferrer, Miquel"},{"last_name":"Torsello","full_name":"Torsello, Andrea","first_name":"Andrea"}],"alternative_title":["LNCS"],"department":[{"_id":"HeEd"}],"acknowledgement":"This work has been partially supported by the Austrian Science Fund under grants S9103-N13 and P18716-N13.","publication_status":"published","title":"Spatio-temporal extraction of articulated models in a graph pyramid","month":"06","_id":"10907","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","place":"Berlin, Heidelberg","publication_identifier":{"isbn":["9783642208430"],"eisbn":["9783642208447"],"issn":["0302-9743"],"eissn":["1611-3349"]},"scopus_import":"1","article_processing_charge":"No","volume":6658,"series_title":"LNIP","year":"2011","date_created":"2022-03-21T08:08:35Z","quality_controlled":"1","page":"215-224","date_updated":"2023-09-05T14:10:15Z","publication":"Graph-Based Representations in Pattern Recognition","author":[{"last_name":"Artner","full_name":"Artner, Nicole M.","first_name":"Nicole M."},{"first_name":"Adrian","full_name":"Ion, Adrian","last_name":"Ion","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kropatsch, Walter G.","first_name":"Walter G.","last_name":"Kropatsch"}],"oa_version":"None","conference":{"name":"GbRPR: Graph-based Representations in Pattern Recognition","start_date":"2011-05-18","location":"Münster, Germany","end_date":"2011-05-20"},"date_published":"2011-06-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","doi":"10.1007/978-3-642-20844-7_22","publisher":"Springer"},{"oa_version":"Published Version","external_id":{"pmid":["21727197"]},"date_published":"2011-07-04T00:00:00Z","publication":"Journal of Cell Biology","issue":"1","author":[{"full_name":"Talamas, Jessica A.","first_name":"Jessica A.","last_name":"Talamas"},{"full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"doi":"10.1083/jcb.201012154","publisher":"Rockefeller University Press","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1083/jcb.201012154"}],"pmid":1,"scopus_import":"1","year":"2011","date_created":"2022-04-07T07:52:18Z","page":"27-37","quality_controlled":"1","date_updated":"2022-07-18T08:53:46Z","volume":194,"month":"07","_id":"11094","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published","oa":1,"title":"POM121 and Sun1 play a role in early steps of interphase NPC assembly","article_type":"original","day":"04","keyword":["Cell Biology"],"intvolume":"       194","citation":{"short":"J.A. Talamas, M. Hetzer, Journal of Cell Biology 194 (2011) 27–37.","ama":"Talamas JA, Hetzer M. POM121 and Sun1 play a role in early steps of interphase NPC assembly. <i>Journal of Cell Biology</i>. 2011;194(1):27-37. doi:<a href=\"https://doi.org/10.1083/jcb.201012154\">10.1083/jcb.201012154</a>","chicago":"Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early Steps of Interphase NPC Assembly.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2011. <a href=\"https://doi.org/10.1083/jcb.201012154\">https://doi.org/10.1083/jcb.201012154</a>.","apa":"Talamas, J. A., &#38; Hetzer, M. (2011). POM121 and Sun1 play a role in early steps of interphase NPC assembly. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201012154\">https://doi.org/10.1083/jcb.201012154</a>","ista":"Talamas JA, Hetzer M. 2011. POM121 and Sun1 play a role in early steps of interphase NPC assembly. Journal of Cell Biology. 194(1), 27–37.","mla":"Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early Steps of Interphase NPC Assembly.” <i>Journal of Cell Biology</i>, vol. 194, no. 1, Rockefeller University Press, 2011, pp. 27–37, doi:<a href=\"https://doi.org/10.1083/jcb.201012154\">10.1083/jcb.201012154</a>.","ieee":"J. A. Talamas and M. Hetzer, “POM121 and Sun1 play a role in early steps of interphase NPC assembly,” <i>Journal of Cell Biology</i>, vol. 194, no. 1. Rockefeller University Press, pp. 27–37, 2011."},"status":"public","extern":"1","abstract":[{"text":"Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear envelope (NE) reformation and into an intact NE as cells progress through interphase. Although recent studies have shown that NPC formation occurs by two different molecular mechanisms at two distinct cell cycle stages, little is known about the molecular players that mediate the fusion of the outer and inner nuclear membranes to form pores. In this paper, we provide evidence that the transmembrane nucleoporin (Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the INM and ONM. Additionally, Sun1, an INM protein that is known to interact with the cytoskeleton, was specifically required for interphase assembly and localized with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact transiently to promote early steps of interphase NPC assembly.","lang":"eng"}]},{"extern":"1","status":"public","day":"01","intvolume":"        23","citation":{"ista":"Hetzer M, Cavalli G. 2011. Editorial overview. Current Opinion in Cell Biology. 23(3), 255–257.","chicago":"Hetzer, Martin, and Giacomo Cavalli. “Editorial Overview.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ceb.2011.04.013\">https://doi.org/10.1016/j.ceb.2011.04.013</a>.","apa":"Hetzer, M., &#38; Cavalli, G. (2011). Editorial overview. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2011.04.013\">https://doi.org/10.1016/j.ceb.2011.04.013</a>","mla":"Hetzer, Martin, and Giacomo Cavalli. “Editorial Overview.” <i>Current Opinion in Cell Biology</i>, vol. 23, no. 3, Elsevier, 2011, pp. 255–57, doi:<a href=\"https://doi.org/10.1016/j.ceb.2011.04.013\">10.1016/j.ceb.2011.04.013</a>.","ieee":"M. Hetzer and G. Cavalli, “Editorial overview,” <i>Current Opinion in Cell Biology</i>, vol. 23, no. 3. Elsevier, pp. 255–257, 2011.","short":"M. Hetzer, G. Cavalli, Current Opinion in Cell Biology 23 (2011) 255–257.","ama":"Hetzer M, Cavalli G. Editorial overview. <i>Current Opinion in Cell Biology</i>. 2011;23(3):255-257. doi:<a href=\"https://doi.org/10.1016/j.ceb.2011.04.013\">10.1016/j.ceb.2011.04.013</a>"},"keyword":["Cell Biology"],"month":"06","_id":"11095","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_type":"letter_note","publication_status":"published","title":"Editorial overview","date_updated":"2022-07-18T08:39:40Z","date_created":"2022-04-07T07:52:27Z","year":"2011","page":"255-257","quality_controlled":"1","volume":23,"article_processing_charge":"No","pmid":1,"scopus_import":"1","publication_identifier":{"issn":["0955-0674"]},"publisher":"Elsevier","doi":"10.1016/j.ceb.2011.04.013","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2011-06-01T00:00:00Z","external_id":{"pmid":["21592757"]},"oa_version":"None","author":[{"last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"first_name":"Giacomo","full_name":"Cavalli, Giacomo","last_name":"Cavalli"}],"issue":"3","publication":"Current Opinion in Cell Biology"},{"type":"journal_article","language":[{"iso":"eng"}],"publisher":"Elsevier","doi":"10.1016/j.ceb.2010.09.008","author":[{"first_name":"Yun","full_name":"Liang, Yun","last_name":"Liang"},{"first_name":"Martin W","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"issue":"1","publication":"Current Opinion in Cell Biology","date_published":"2011-02-01T00:00:00Z","oa_version":"None","external_id":{"pmid":["21030234"]},"volume":23,"date_updated":"2022-07-18T08:53:48Z","quality_controlled":"1","page":"65-70","date_created":"2022-04-07T07:52:37Z","year":"2011","scopus_import":"1","pmid":1,"publication_identifier":{"issn":["0955-0674"]},"article_processing_charge":"No","article_type":"original","title":"Functional interactions between nucleoporins and chromatin","publication_status":"published","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","month":"02","_id":"11096","abstract":[{"text":"As the gatekeepers of the eukaryotic cell nucleus, nuclear pore complexes (NPCs) mediate all molecular trafficking between the nucleoplasm and the cytoplasm. In recent years, transport-independent functions of NPC components, nucleoporins, have been identified including roles in chromatin organization and gene regulation. Here, we summarize our current view of the NPC as a dynamic hub for the integration of chromatin regulation and nuclear trafficking and discuss the functional interplay between nucleoporins and the nuclear genome.","lang":"eng"}],"extern":"1","status":"public","intvolume":"        23","citation":{"ama":"Liang Y, Hetzer M. Functional interactions between nucleoporins and chromatin. <i>Current Opinion in Cell Biology</i>. 2011;23(1):65-70. doi:<a href=\"https://doi.org/10.1016/j.ceb.2010.09.008\">10.1016/j.ceb.2010.09.008</a>","short":"Y. Liang, M. Hetzer, Current Opinion in Cell Biology 23 (2011) 65–70.","mla":"Liang, Yun, and Martin Hetzer. “Functional Interactions between Nucleoporins and Chromatin.” <i>Current Opinion in Cell Biology</i>, vol. 23, no. 1, Elsevier, 2011, pp. 65–70, doi:<a href=\"https://doi.org/10.1016/j.ceb.2010.09.008\">10.1016/j.ceb.2010.09.008</a>.","ieee":"Y. Liang and M. Hetzer, “Functional interactions between nucleoporins and chromatin,” <i>Current Opinion in Cell Biology</i>, vol. 23, no. 1. Elsevier, pp. 65–70, 2011.","chicago":"Liang, Yun, and Martin Hetzer. “Functional Interactions between Nucleoporins and Chromatin.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ceb.2010.09.008\">https://doi.org/10.1016/j.ceb.2010.09.008</a>.","ista":"Liang Y, Hetzer M. 2011. Functional interactions between nucleoporins and chromatin. Current Opinion in Cell Biology. 23(1), 65–70.","apa":"Liang, Y., &#38; Hetzer, M. (2011). Functional interactions between nucleoporins and chromatin. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2010.09.008\">https://doi.org/10.1016/j.ceb.2010.09.008</a>"},"keyword":["Cell Biology"],"day":"01"},{"publication_status":"published","title":"Nuclear pore complexes: Guardians of the nuclear genome","article_type":"original","_id":"11100","month":"04","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","extern":"1","abstract":[{"text":"Eukaryotic cell function depends on the physical separation of nucleoplasmic and cytoplasmic components by the nuclear envelope (NE). Molecular communication between the two compartments involves active, signal-mediated trafficking, a function that is exclusively performed by nuclear pore complexes (NPCs). The individual NPC components and the mechanisms that are involved in nuclear trafficking are well documented and have become textbook knowledge. However, in addition to their roles as nuclear gatekeepers, NPC components-nucleoporins-have been shown to have critical roles in chromatin organization and gene regulation. These findings have sparked new enthusiasm to study the roles of this multiprotein complex in nuclear organization and explore novel functions that in some cases appear to go beyond a role in transport. Here, we discuss our present view of NPC biogenesis, which is tightly linked to proper cell cycle progression and cell differentiation. In addition, we summarize new data suggesting that NPCs represent dynamic hubs for the integration of gene regulation and nuclear transport processes.","lang":"eng"}],"keyword":["Genetics","Molecular Biology","Biochemistry"],"citation":{"mla":"Capelson, M., et al. “Nuclear Pore Complexes: Guardians of the Nuclear Genome.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 75, Cold Spring Harbor Laboratory Press, 2011, pp. 585–97, doi:<a href=\"https://doi.org/10.1101/sqb.2010.75.059\">10.1101/sqb.2010.75.059</a>.","ieee":"M. Capelson, C. Doucet, and M. Hetzer, “Nuclear pore complexes: Guardians of the nuclear genome,” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 75. Cold Spring Harbor Laboratory Press, pp. 585–597, 2011.","chicago":"Capelson, M., C. Doucet, and Martin Hetzer. “Nuclear Pore Complexes: Guardians of the Nuclear Genome.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press, 2011. <a href=\"https://doi.org/10.1101/sqb.2010.75.059\">https://doi.org/10.1101/sqb.2010.75.059</a>.","apa":"Capelson, M., Doucet, C., &#38; Hetzer, M. (2011). Nuclear pore complexes: Guardians of the nuclear genome. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2010.75.059\">https://doi.org/10.1101/sqb.2010.75.059</a>","ista":"Capelson M, Doucet C, Hetzer M. 2011. Nuclear pore complexes: Guardians of the nuclear genome. Cold Spring Harbor Symposia on Quantitative Biology. 75, 585–597.","ama":"Capelson M, Doucet C, Hetzer M. Nuclear pore complexes: Guardians of the nuclear genome. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. 2011;75:585-597. doi:<a href=\"https://doi.org/10.1101/sqb.2010.75.059\">10.1101/sqb.2010.75.059</a>","short":"M. Capelson, C. Doucet, M. Hetzer, Cold Spring Harbor Symposia on Quantitative Biology 75 (2011) 585–597."},"intvolume":"        75","day":"18","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1101/sqb.2010.75.059","publisher":"Cold Spring Harbor Laboratory Press","publication":"Cold Spring Harbor Symposia on Quantitative Biology","author":[{"first_name":"M.","full_name":"Capelson, M.","last_name":"Capelson"},{"last_name":"Doucet","first_name":"C.","full_name":"Doucet, C."},{"first_name":"Martin W","full_name":"HETZER, Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"oa_version":"None","external_id":{"pmid":["21502404"]},"date_published":"2011-04-18T00:00:00Z","volume":75,"year":"2011","date_created":"2022-04-07T07:53:18Z","page":"585-597","quality_controlled":"1","date_updated":"2022-07-18T08:54:23Z","publication_identifier":{"issn":["0091-7451","1943-4456"],"isbn":["9781936113071"]},"pmid":1,"scopus_import":"1","article_processing_charge":"No"},{"article_number":"051302","status":"public","abstract":[{"text":"Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated by recent experiments on streams of grains that exhibit liquid-like breakup into droplets, we use molecular dynamics simulations to investigate the evolution of a dense stream of macroscopic spheres accelerating out of an opening at the bottom of a reservoir. We show how nanoscale details associated with energy dissipation during collisions modify the stream\\'s macroscopic behavior. We find that inelastic collisions collimate the stream, while the presence of short-range attractive interactions drives structure formation. Parameterizing the collision dynamics by the coefficient of restitution (i.e., the ratio of relative velocities before and after impact) and the strength of the cohesive interaction, we map out a spectrum of behaviors that ranges from gaslike jets in which all grains drift apart to liquid-like streams that break into large droplets containing hundreds of grains. We also find a new, intermediate regime in which small aggregates form by capture from the gas phase, similar to what can be observed in molecular beams. Our results show that nearly all aspects of stream behavior are closely related to the velocity gradient associated with vertical free fall. Led by this observation, we propose a simple energy balance model to explain the droplet formation process. The qualitative as well as many quantitative features of the simulations and the model compare well with available experimental data and provide a first quantitative measure of the role of attractions in freely cooling granular streams.","lang":"eng"}],"extern":"1","day":"12","intvolume":"        83","citation":{"ista":"Waitukaitis SR, Grütjen H, Royer J, Jaeger H. 2011. Droplet and cluster formation in freely falling granular streams. Physical Review E. 83(5), 051302.","chicago":"Waitukaitis, Scott R, Helge Grütjen, John Royer, and Heinrich Jaeger. “Droplet and Cluster Formation in Freely Falling Granular Streams.” <i>Physical Review E</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">https://doi.org/10.1103/PhysRevE.83.051302</a>.","apa":"Waitukaitis, S. R., Grütjen, H., Royer, J., &#38; Jaeger, H. (2011). Droplet and cluster formation in freely falling granular streams. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">https://doi.org/10.1103/PhysRevE.83.051302</a>","ieee":"S. R. Waitukaitis, H. Grütjen, J. Royer, and H. Jaeger, “Droplet and cluster formation in freely falling granular streams,” <i>Physical Review E</i>, vol. 83, no. 5. American Physical Society, 2011.","mla":"Waitukaitis, Scott R., et al. “Droplet and Cluster Formation in Freely Falling Granular Streams.” <i>Physical Review E</i>, vol. 83, no. 5, 051302, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">10.1103/PhysRevE.83.051302</a>.","short":"S.R. Waitukaitis, H. Grütjen, J. Royer, H. Jaeger, Physical Review E 83 (2011).","ama":"Waitukaitis SR, Grütjen H, Royer J, Jaeger H. Droplet and cluster formation in freely falling granular streams. <i>Physical Review E</i>. 2011;83(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">10.1103/PhysRevE.83.051302</a>"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"112","month":"05","title":"Droplet and cluster formation in freely falling granular streams","oa":1,"publication_status":"published","acknowledgement":"This work was supported by the NSF through CBET-0933242. We acknowledge use of shared facilities provided by the Keck Facility for Ultrafast Imaging at the University of Chicago and by the Chicago MRSEC through NSF DMR-0820054. Software support by Itasca Consulting Group, Inc., under the Itasca Educational Partnership is gratefully acknowledged. H.G. thanks the German-American Fulbright Commission for fellowship support during his stay at the University of Chicago.","quality_controlled":"1","date_created":"2018-12-11T11:44:41Z","year":"2011","date_updated":"2021-01-12T06:48:25Z","volume":83,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1006.1371"}],"doi":"10.1103/PhysRevE.83.051302","publisher":"American Physical Society","language":[{"iso":"eng"}],"arxiv":1,"type":"journal_article","external_id":{"arxiv":["1006.1371"]},"oa_version":"Preprint","date_published":"2011-05-12T00:00:00Z","issue":"5","publist_id":"7942","publication":"Physical Review E","author":[{"last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grütjen","full_name":"Grütjen, Helge","first_name":"Helge"},{"full_name":"Royer, John","first_name":"John","last_name":"Royer"},{"last_name":"Jaeger","first_name":"Heinrich","full_name":"Jaeger, Heinrich"}]},{"article_type":"original","title":"A comprehensive study of features and algorithms for URL-based topic classification","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11673","month":"07","citation":{"ieee":"E. Baykan, M. H. Henzinger, L. Marian, and I. Weber, “A comprehensive study of features and algorithms for URL-based topic classification,” <i>ACM Transactions on the Web</i>, vol. 5, no. 3. Association for Computing Machinery, 2011.","mla":"Baykan, Eda, et al. “A Comprehensive Study of Features and Algorithms for URL-Based Topic Classification.” <i>ACM Transactions on the Web</i>, vol. 5, no. 3, 15, Association for Computing Machinery, 2011, doi:<a href=\"https://doi.org/10.1145/1993053.1993057\">10.1145/1993053.1993057</a>.","ista":"Baykan E, Henzinger MH, Marian L, Weber I. 2011. A comprehensive study of features and algorithms for URL-based topic classification. ACM Transactions on the Web. 5(3), 15.","chicago":"Baykan, Eda, Monika H Henzinger, Ludmila Marian, and Ingmar Weber. “A Comprehensive Study of Features and Algorithms for URL-Based Topic Classification.” <i>ACM Transactions on the Web</i>. Association for Computing Machinery, 2011. <a href=\"https://doi.org/10.1145/1993053.1993057\">https://doi.org/10.1145/1993053.1993057</a>.","apa":"Baykan, E., Henzinger, M. H., Marian, L., &#38; Weber, I. (2011). A comprehensive study of features and algorithms for URL-based topic classification. <i>ACM Transactions on the Web</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/1993053.1993057\">https://doi.org/10.1145/1993053.1993057</a>","ama":"Baykan E, Henzinger MH, Marian L, Weber I. A comprehensive study of features and algorithms for URL-based topic classification. <i>ACM Transactions on the Web</i>. 2011;5(3). doi:<a href=\"https://doi.org/10.1145/1993053.1993057\">10.1145/1993053.1993057</a>","short":"E. Baykan, M.H. Henzinger, L. Marian, I. Weber, ACM Transactions on the Web 5 (2011)."},"intvolume":"         5","keyword":["Topic classification","URL","ODP"],"day":"01","abstract":[{"text":"Given only the URL of a Web page, can we identify its topic? We study this problem in detail by exploring a large number of different feature sets and algorithms on several datasets. We also show that the inherent overlap between topics and the sparsity of the information in URLs makes this a very challenging problem. Web page classification without a page’s content is desirable when the content is not available at all, when a classification is needed before obtaining the content, or when classification speed is of utmost importance. For our experiments we used five different corpora comprising a total of about 3 million (URL, classification) pairs. We evaluated several techniques for feature generation and classification algorithms. The individual binary classifiers were then combined via boosting into metabinary classifiers. We achieve typical F-measure values between 80 and 85, and a typical precision of around 86. The precision can be pushed further over 90 while maintaining a typical level of recall between 30 and 40.","lang":"eng"}],"extern":"1","article_number":"15","status":"public","author":[{"last_name":"Baykan","first_name":"Eda","full_name":"Baykan, Eda"},{"first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Ludmila","full_name":"Marian, Ludmila","last_name":"Marian"},{"full_name":"Weber, Ingmar","first_name":"Ingmar","last_name":"Weber"}],"issue":"3","publication":"ACM Transactions on the Web","date_published":"2011-07-01T00:00:00Z","oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","doi":"10.1145/1993053.1993057","scopus_import":"1","publication_identifier":{"issn":["1559-1131"],"eissn":["1559-114X"]},"article_processing_charge":"No","volume":5,"date_updated":"2022-09-12T08:46:56Z","quality_controlled":"1","date_created":"2022-07-27T13:48:11Z","year":"2011"},{"oa_version":"None","date_published":"2011-01-15T00:00:00Z","issue":"4","publication":"Information Processing Letters","author":[{"last_name":"Dütting","full_name":"Dütting, Paul","first_name":"Paul"},{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Ingmar","full_name":"Weber, Ingmar","last_name":"Weber"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11760","month":"01","doi":"10.1016/j.ipl.2010.11.022","publisher":"Elsevier","title":"Offline file assignments for online load balancing","language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","type":"journal_article","day":"15","article_processing_charge":"No","publication_identifier":{"issn":["0020-0190"]},"scopus_import":"1","intvolume":"       111","citation":{"mla":"Dütting, Paul, et al. “Offline File Assignments for Online Load Balancing.” <i>Information Processing Letters</i>, vol. 111, no. 4, Elsevier, 2011, pp. 178–83, doi:<a href=\"https://doi.org/10.1016/j.ipl.2010.11.022\">10.1016/j.ipl.2010.11.022</a>.","ieee":"P. Dütting, M. H. Henzinger, and I. Weber, “Offline file assignments for online load balancing,” <i>Information Processing Letters</i>, vol. 111, no. 4. Elsevier, pp. 178–183, 2011.","apa":"Dütting, P., Henzinger, M. H., &#38; Weber, I. (2011). Offline file assignments for online load balancing. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2010.11.022\">https://doi.org/10.1016/j.ipl.2010.11.022</a>","ista":"Dütting P, Henzinger MH, Weber I. 2011. Offline file assignments for online load balancing. Information Processing Letters. 111(4), 178–183.","chicago":"Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Offline File Assignments for Online Load Balancing.” <i>Information Processing Letters</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ipl.2010.11.022\">https://doi.org/10.1016/j.ipl.2010.11.022</a>.","ama":"Dütting P, Henzinger MH, Weber I. Offline file assignments for online load balancing. <i>Information Processing Letters</i>. 2011;111(4):178-183. doi:<a href=\"https://doi.org/10.1016/j.ipl.2010.11.022\">10.1016/j.ipl.2010.11.022</a>","short":"P. Dütting, M.H. Henzinger, I. Weber, Information Processing Letters 111 (2011) 178–183."},"quality_controlled":"1","page":"178-183","year":"2011","date_created":"2022-08-08T11:33:03Z","date_updated":"2022-09-12T09:38:05Z","status":"public","abstract":[{"text":"We study a novel load balancing problem that arises in web search engines. The problem is a combination of an offline assignment problem, where files need to be (copied and) assigned to machines, and an online load balancing problem, where requests ask for specific files and need to be assigned to a corresponding machine, whose load is increased\r\nby this. We present simple deterministic algorithms for this problem and exhibit an interesting trade-off between the available space to make file copies and the obtainable makespan. We also give non-trivial lower bounds for a large class of deterministic algorithms and present a randomized algorithm that beats these bounds with high probability.","lang":"eng"}],"volume":111,"extern":"1"},{"date_published":"2011-09-01T00:00:00Z","oa_version":"None","conference":{"name":"ESA: European Symposium on Algorithms","start_date":"2011-09-05","location":"Saarbrücken, Germany","end_date":"2011-09-09"},"author":[{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Vidali, Angelina","first_name":"Angelina","last_name":"Vidali"}],"publication":"19th Annual European Symposium on Algorithms","alternative_title":["LNCS"],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","_id":"11796","doi":"10.1007/978-3-642-23719-5_17","type":"conference","title":"Multi-parameter mechanism design under budget and matroid constraints","publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"01","scopus_import":"1","intvolume":"      6942","citation":{"ama":"Henzinger MH, Vidali A. Multi-parameter mechanism design under budget and matroid constraints. In: <i>19th Annual European Symposium on Algorithms</i>. Vol 6942. Springer Nature; 2011:192–202. doi:<a href=\"https://doi.org/10.1007/978-3-642-23719-5_17\">10.1007/978-3-642-23719-5_17</a>","short":"M.H. Henzinger, A. Vidali, in:, 19th Annual European Symposium on Algorithms, Springer Nature, 2011, pp. 192–202.","ieee":"M. H. Henzinger and A. Vidali, “Multi-parameter mechanism design under budget and matroid constraints,” in <i>19th Annual European Symposium on Algorithms</i>, Saarbrücken, Germany, 2011, vol. 6942, pp. 192–202.","mla":"Henzinger, Monika H., and Angelina Vidali. “Multi-Parameter Mechanism Design under Budget and Matroid Constraints.” <i>19th Annual European Symposium on Algorithms</i>, vol. 6942, Springer Nature, 2011, pp. 192–202, doi:<a href=\"https://doi.org/10.1007/978-3-642-23719-5_17\">10.1007/978-3-642-23719-5_17</a>.","apa":"Henzinger, M. H., &#38; Vidali, A. (2011). Multi-parameter mechanism design under budget and matroid constraints. In <i>19th Annual European Symposium on Algorithms</i> (Vol. 6942, pp. 192–202). Saarbrücken, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-23719-5_17\">https://doi.org/10.1007/978-3-642-23719-5_17</a>","ista":"Henzinger MH, Vidali A. 2011. Multi-parameter mechanism design under budget and matroid constraints. 19th Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LNCS, vol. 6942, 192–202.","chicago":"Henzinger, Monika H, and Angelina Vidali. “Multi-Parameter Mechanism Design under Budget and Matroid Constraints.” In <i>19th Annual European Symposium on Algorithms</i>, 6942:192–202. Springer Nature, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23719-5_17\">https://doi.org/10.1007/978-3-642-23719-5_17</a>."},"publication_identifier":{"isbn":["9783642237188"],"issn":["1611-3349"]},"date_updated":"2023-02-13T11:32:41Z","page":"192–202","quality_controlled":"1","year":"2011","date_created":"2022-08-11T11:51:39Z","volume":6942,"abstract":[{"text":"The design of truthful auctions that approximate the optimal expected revenue is a central problem in algorithmic mechanism design. 30 years after Myerson’s characterization of Bayesian optimal auctions in single-parameter domains [8], characterizing but also providing efficient mechanisms for multi-parameter domains still remains a very important unsolved problem. Our work improves upon recent results in this area, introducing new techniques for tackling the problem, while also combining and extending recently introduced tools.\r\n\r\nIn particular we give the first approximation algorithms for Bayesian auctions with multiple heterogeneous items when bidders have additive valuations, budget constraints and general matroid feasibility constraints.","lang":"eng"}],"extern":"1","status":"public"},{"date_updated":"2023-02-17T10:21:18Z","year":"2011","date_created":"2022-08-16T09:05:34Z","quality_controlled":"1","page":"127 - 136","extern":"1","abstract":[{"lang":"eng","text":"Auctions are widely used on the Web. Applications range from internet advertising to platforms such as eBay. In most of these applications the auctions in use are single/multi-item auctions with unit demand. The main drawback of standard mechanisms for this type of auctions, such as VCG and GSP, is the limited expressiveness that they offer to the bidders. The General Auction Mechanism (GAM) of [1] is taking a first step towards addressing the problem of limited expressiveness by computing a bidder optimal, envy free outcome for linear utility functions with identical slopes and a single discontinuity per bidder-item pair. We show that in many practical situations this does not suffice to adequately model the preferences of the bidders, and we overcome this problem by presenting the first mechanism for piece-wise linear utility functions with non-identical slopes and multiple discontinuities. Our mechanism runs in polynomial time. Like GAM it is incentive compatible for inputs that fulfill a certain non-degeneracy requirement, but our requirement is more general than the requirement of GAM. For discontinuous utility functions that are non-degenerate as well as for continuous utility functions the outcome of our mechanism is a competitive equilibrium. We also show how our mechanism can be used to compute approximately bidder optimal, envy free outcomes for a general class of continuous utility functions via piece-wise linear approximation. Finally, we prove hardness results for even more expressive settings."}],"status":"public","article_processing_charge":"No","day":"01","citation":{"short":"P. Dütting, M.H. Henzinger, I. Weber, in:, Proceedings of the 20th International Conference on World Wide Web, Association for Computing Machinery, 2011, pp. 127–136.","ama":"Dütting P, Henzinger MH, Weber I. An expressive mechanism for auctions on the web. In: <i>Proceedings of the 20th International Conference on World Wide Web</i>. Association for Computing Machinery; 2011:127-136. doi:<a href=\"https://doi.org/10.1145/1963405.1963427\">10.1145/1963405.1963427</a>","apa":"Dütting, P., Henzinger, M. H., &#38; Weber, I. (2011). An expressive mechanism for auctions on the web. In <i>Proceedings of the 20th international conference on World wide web</i> (pp. 127–136). Hyderabad, India: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/1963405.1963427\">https://doi.org/10.1145/1963405.1963427</a>","chicago":"Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “An Expressive Mechanism for Auctions on the Web.” In <i>Proceedings of the 20th International Conference on World Wide Web</i>, 127–36. Association for Computing Machinery, 2011. <a href=\"https://doi.org/10.1145/1963405.1963427\">https://doi.org/10.1145/1963405.1963427</a>.","ista":"Dütting P, Henzinger MH, Weber I. 2011. An expressive mechanism for auctions on the web. Proceedings of the 20th international conference on World wide web. WWW: International Conference on World Wide Web, 127–136.","mla":"Dütting, Paul, et al. “An Expressive Mechanism for Auctions on the Web.” <i>Proceedings of the 20th International Conference on World Wide Web</i>, Association for Computing Machinery, 2011, pp. 127–36, doi:<a href=\"https://doi.org/10.1145/1963405.1963427\">10.1145/1963405.1963427</a>.","ieee":"P. Dütting, M. H. Henzinger, and I. Weber, “An expressive mechanism for auctions on the web,” in <i>Proceedings of the 20th international conference on World wide web</i>, Hyderabad, India, 2011, pp. 127–136."},"scopus_import":"1","publication_identifier":{"isbn":["978-145030632-4"]},"publisher":"Association for Computing Machinery","_id":"11864","month":"04","doi":"10.1145/1963405.1963427","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","language":[{"iso":"eng"}],"publication_status":"published","title":"An expressive mechanism for auctions on the web","date_published":"2011-04-01T00:00:00Z","conference":{"name":"WWW: International Conference on World Wide Web","start_date":"2011-03-28","location":"Hyderabad, India","end_date":"2011-04-01"},"oa_version":"None","author":[{"last_name":"Dütting","full_name":"Dütting, Paul","first_name":"Paul"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Weber, Ingmar","first_name":"Ingmar","last_name":"Weber"}],"publication":"Proceedings of the 20th international conference on World wide web"},{"day":"11","has_accepted_license":"1","intvolume":"         3","citation":{"short":"B. Vicoso, D. Bachtrog, Genome Biology and Evolution 3 (2011) 230–235.","ama":"Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. <i>Genome Biology and Evolution</i>. 2011;3(1):230-235. doi:<a href=\"https://doi.org/10.1093/gbe/evr010\">10.1093/gbe/evr010</a>","apa":"Vicoso, B., &#38; Bachtrog, D. (2011). Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evr010\">https://doi.org/10.1093/gbe/evr010</a>","ista":"Vicoso B, Bachtrog D. 2011. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 3(1), 230–235.","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1093/gbe/evr010\">https://doi.org/10.1093/gbe/evr010</a>.","ieee":"B. Vicoso and D. Bachtrog, “Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite,” <i>Genome Biology and Evolution</i>, vol. 3, no. 1. Oxford University Press, pp. 230–235, 2011.","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and Evolution</i>, vol. 3, no. 1, Oxford University Press, 2011, pp. 230–35, doi:<a href=\"https://doi.org/10.1093/gbe/evr010\">10.1093/gbe/evr010</a>."},"status":"public","abstract":[{"lang":"eng","text":"Many species have morphologically and genetically differentiated sex chromosomes, such as the XY pair of mammals. Y chromosomes are often highly degenerated and carry few functional genes, so that XY males have only one copy of most Xlinked genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage compensation, such as the mammalian X-inactivation, often evolve to reestablish expression balance. A similar phenomenon is expected in femaleheterogametic species, where ZW females should suffer from imbalances due to W-chromosome degeneration. However, no global dosage compensation mechanisms have been detected in the two independent ZW systems that have been studied systematically (birds and silkworm), leading to the suggestion that lack of global dosage compensation may be a general feature of female-heterogametic species. However, analyses of other independently evolved ZW systems are required to test if this is the case. In this study, we use published genomic and expression data to test for the presence of global dosage compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis in humans. We find that Z-linked expression is reduced relative to autosomal expression in females but not males, consistent with incomplete or localized dosage compensation. This gives further support to the theory that female-heterogametic species may not require global mechanisms of dosage compensation."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2072","month":"02","title":"Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite","oa":1,"publication_status":"published","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"page":"230 - 235","quality_controlled":"1","date_created":"2018-12-11T11:55:33Z","year":"2011","date_updated":"2021-01-12T06:55:08Z","volume":3,"file":[{"file_name":"2011_GBE_Vicoso.pdf","content_type":"application/pdf","date_created":"2019-05-10T07:41:28Z","file_id":"6395","access_level":"open_access","date_updated":"2020-07-14T12:45:27Z","relation":"main_file","checksum":"7855c134436e4f6a13d63b6606d7e8dd","file_size":212547,"creator":"dernst"}],"oa_version":"Published Version","date_published":"2011-02-11T00:00:00Z","issue":"1","publist_id":"4966","publication":"Genome Biology and Evolution","ddc":["570"],"author":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"},{"first_name":"Doris","full_name":"Bachtrog, Doris","last_name":"Bachtrog"}],"doi":"10.1093/gbe/evr010","publisher":"Oxford University Press","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:27Z","type":"journal_article"},{"date_updated":"2021-01-12T06:55:17Z","date_created":"2018-12-11T11:55:42Z","year":"2011","page":"413 - 426","quality_controlled":0,"extern":1,"abstract":[{"text":"This chapter presents a method for real-time animation of highly detailed facial expressions based on sparse motion captures data and a limited set of static example poses. The method for real-time animation of highly detailed facial expressions decomposes geometry into large-scale motion and fine-scale details, such as expression wrinkles. Both large- and fine-scale deformation algorithms run entirely on the GPU, and our implementation based on CUDA achieves an overall performance of about 30 fps. The face conveys the most relevant visual characteristics of human identity and expression. Hence, realistic facial animations or interactions with virtual avatars are important for storytelling and gameplay. However, current approaches are either computationally expensive, require very specialized capture hardware, or are extremely labor intensive. At runtime, given an arbitrary facial expression, the algorithm computes the skin strain from the relative distance between marker points and derives fine-scale corrections for the largescale deformation. During gameplay only the sparse set of marker-point positions is transmitted to the GPU. The face animation is entirely computed on the GPU where the resulting mesh can directly be used as input for the rendering stages. This data can be easily obtained by traditional capture hardware. The proposed in-game algorithm is fast. It also is easy to implement and maps well onto programmable GPUs.","lang":"eng"}],"status":"public","day":"01","citation":{"ieee":"B. Bickel and M. Lang, “From sparse mocap to highly detailed facial animation,” in <i>GPU Computing Gems Emerald Edition</i>, Science Direct, 2011, pp. 413–426.","mla":"Bickel, Bernd, and Manuel Lang. “From Sparse Mocap to Highly Detailed Facial Animation.” <i>GPU Computing Gems Emerald Edition</i>, Science Direct, 2011, pp. 413–26, doi:<a href=\"https://doi.org/10.1016/B978-0-12-384988-5.00027-9\">10.1016/B978-0-12-384988-5.00027-9</a>.","chicago":"Bickel, Bernd, and Manuel Lang. “From Sparse Mocap to Highly Detailed Facial Animation.” In <i>GPU Computing Gems Emerald Edition</i>, 413–26. Science Direct, 2011. <a href=\"https://doi.org/10.1016/B978-0-12-384988-5.00027-9\">https://doi.org/10.1016/B978-0-12-384988-5.00027-9</a>.","apa":"Bickel, B., &#38; Lang, M. (2011). From sparse mocap to highly detailed facial animation. In <i>GPU Computing Gems Emerald Edition</i> (pp. 413–426). Science Direct. <a href=\"https://doi.org/10.1016/B978-0-12-384988-5.00027-9\">https://doi.org/10.1016/B978-0-12-384988-5.00027-9</a>","ista":"Bickel B, Lang M. 2011.From sparse mocap to highly detailed facial animation. In: GPU Computing Gems Emerald Edition. , 413–426.","ama":"Bickel B, Lang M. From sparse mocap to highly detailed facial animation. In: <i>GPU Computing Gems Emerald Edition</i>. Science Direct; 2011:413-426. doi:<a href=\"https://doi.org/10.1016/B978-0-12-384988-5.00027-9\">10.1016/B978-0-12-384988-5.00027-9</a>","short":"B. Bickel, M. Lang, in:, GPU Computing Gems Emerald Edition, Science Direct, 2011, pp. 413–426."},"publisher":"Science Direct","_id":"2098","doi":"10.1016/B978-0-12-384988-5.00027-9","month":"01","type":"book_chapter","publication_status":"published","title":"From sparse mocap to highly detailed facial animation","date_published":"2011-01-01T00:00:00Z","author":[{"last_name":"Bickel","first_name":"Bernd","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lang","first_name":"Manuel","full_name":"Lang, Manuel"}],"publist_id":"4935","publication":"GPU Computing Gems Emerald Edition"},{"author":[{"last_name":"Beeler","first_name":"Thabo","full_name":"Beeler, Thabo"},{"first_name":"Fabian","full_name":"Hahn, Fabian","last_name":"Hahn"},{"first_name":"Derek","full_name":"Bradley, Derek J","last_name":"Bradley"},{"last_name":"Bickel","first_name":"Bernd","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Beardsley","first_name":"Paul","full_name":"Beardsley, Paul A"},{"first_name":"Craig","full_name":"Gotsman, Craig","last_name":"Gotsman"},{"last_name":"Sumner","first_name":"Robert","full_name":"Sumner, Robert W"},{"last_name":"Groß","full_name":"Groß, Markus S","first_name":"Markus"}],"publication":"ACM Transactions on Graphics","publist_id":"4936","issue":"4","date_published":"2011-07-01T00:00:00Z","type":"journal_article","publication_status":"published","title":"High-quality passive facial performance capture using anchor frames","publisher":"ACM","_id":"2099","month":"07","doi":"10.1145/2010324.1964970","citation":{"short":"T. Beeler, F. Hahn, D. Bradley, B. Bickel, P. Beardsley, C. Gotsman, R. Sumner, M. Groß, ACM Transactions on Graphics 30 (2011).","ama":"Beeler T, Hahn F, Bradley D, et al. High-quality passive facial performance capture using anchor frames. <i>ACM Transactions on Graphics</i>. 2011;30(4). doi:<a href=\"https://doi.org/10.1145/2010324.1964970\">10.1145/2010324.1964970</a>","apa":"Beeler, T., Hahn, F., Bradley, D., Bickel, B., Beardsley, P., Gotsman, C., … Groß, M. (2011). High-quality passive facial performance capture using anchor frames. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2010324.1964970\">https://doi.org/10.1145/2010324.1964970</a>","chicago":"Beeler, Thabo, Fabian Hahn, Derek Bradley, Bernd Bickel, Paul Beardsley, Craig Gotsman, Robert Sumner, and Markus Groß. “High-Quality Passive Facial Performance Capture Using Anchor Frames.” <i>ACM Transactions on Graphics</i>. ACM, 2011. <a href=\"https://doi.org/10.1145/2010324.1964970\">https://doi.org/10.1145/2010324.1964970</a>.","ista":"Beeler T, Hahn F, Bradley D, Bickel B, Beardsley P, Gotsman C, Sumner R, Groß M. 2011. High-quality passive facial performance capture using anchor frames. ACM Transactions on Graphics. 30(4).","ieee":"T. Beeler <i>et al.</i>, “High-quality passive facial performance capture using anchor frames,” <i>ACM Transactions on Graphics</i>, vol. 30, no. 4. ACM, 2011.","mla":"Beeler, Thabo, et al. “High-Quality Passive Facial Performance Capture Using Anchor Frames.” <i>ACM Transactions on Graphics</i>, vol. 30, no. 4, ACM, 2011, doi:<a href=\"https://doi.org/10.1145/2010324.1964970\">10.1145/2010324.1964970</a>."},"intvolume":"        30","day":"01","extern":1,"volume":30,"abstract":[{"text":"We present a new technique for passive and markerless facial performance capture based on anchor frames. Our method starts with high resolution per-frame geometry acquisition using state-of-theart stereo reconstruction, and proceeds to establish a single triangle mesh that is propagated through the entire performance. Leveraging the fact that facial performances often contain repetitive subsequences, we identify anchor frames as those which contain similar facial expressions to a manually chosen reference expression. Anchor frames are automatically computed over one or even multiple performances. We introduce a robust image-space tracking method that computes pixel matches directly from the reference frame to all anchor frames, and thereby to the remaining frames in the sequence via sequential matching. This allows us to propagate one reconstructed frame to an entire sequence in parallel, in contrast to previous sequential methods. Our anchored reconstruction approach also limits tracker drift and robustly handles occlusions and motion blur. The parallel tracking and mesh propagation offer low computation times. Our technique will even automatically match anchor frames across different sequences captured on different occasions, propagating a single mesh to all performances.","lang":"eng"}],"status":"public","date_updated":"2021-01-12T06:55:17Z","date_created":"2018-12-11T11:55:42Z","year":"2011","quality_controlled":0},{"publist_id":"4934","author":[{"full_name":"Pfeil, Jonas","first_name":"Jonas","last_name":"Pfeil"},{"first_name":"Kristian","full_name":"Hildebrand, Kristian","last_name":"Hildebrand"},{"last_name":"Gremzow","full_name":"Gremzow, Carsten","first_name":"Carsten"},{"first_name":"Bernd","full_name":"Bernd Bickel","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Marc","full_name":"Alexa, Marc","last_name":"Alexa"}],"conference":{"name":"SIGGRAPH Asia"},"date_published":"2011-12-01T00:00:00Z","title":"Throwable panoramic ball camera","publication_status":"published","type":"conference","_id":"2100","month":"12","doi":"10.1145/2073370.2073373","publisher":"ACM","citation":{"short":"J. Pfeil, K. Hildebrand, C. Gremzow, B. Bickel, M. Alexa, in:, ACM, 2011.","ama":"Pfeil J, Hildebrand K, Gremzow C, Bickel B, Alexa M. Throwable panoramic ball camera. In: ACM; 2011. doi:<a href=\"https://doi.org/10.1145/2073370.2073373\">10.1145/2073370.2073373</a>","apa":"Pfeil, J., Hildebrand, K., Gremzow, C., Bickel, B., &#38; Alexa, M. (2011). Throwable panoramic ball camera. Presented at the SIGGRAPH Asia, ACM. <a href=\"https://doi.org/10.1145/2073370.2073373\">https://doi.org/10.1145/2073370.2073373</a>","chicago":"Pfeil, Jonas, Kristian Hildebrand, Carsten Gremzow, Bernd Bickel, and Marc Alexa. “Throwable Panoramic Ball Camera.” ACM, 2011. <a href=\"https://doi.org/10.1145/2073370.2073373\">https://doi.org/10.1145/2073370.2073373</a>.","ista":"Pfeil J, Hildebrand K, Gremzow C, Bickel B, Alexa M. 2011. Throwable panoramic ball camera. SIGGRAPH Asia.","mla":"Pfeil, Jonas, et al. <i>Throwable Panoramic Ball Camera</i>. ACM, 2011, doi:<a href=\"https://doi.org/10.1145/2073370.2073373\">10.1145/2073370.2073373</a>.","ieee":"J. Pfeil, K. Hildebrand, C. Gremzow, B. Bickel, and M. Alexa, “Throwable panoramic ball camera,” presented at the SIGGRAPH Asia, 2011."},"day":"01","status":"public","abstract":[{"lang":"eng","text":"Acquiring panoramic images using stitching takes a lot of time and moving objects may cause ghosting. It is also difficult to obtain a full spherical panorama, because the downward picture cannot be captured while the camera is mounted on the tripod."}],"extern":1,"quality_controlled":0,"date_created":"2018-12-11T11:55:43Z","year":"2011","date_updated":"2021-01-12T06:55:19Z"},{"status":"public","extern":1,"abstract":[{"lang":"eng","text":"Let P be the Ornstein-Uhlenbeck semigroup associated with the stochastic Cauchy problem  dU(t)=AU(t)dt+dWH(t), where A is the generator of a C 0-semigroup S on a Banach space E, H is a Hilbert subspace of E, and W H is an H-cylindrical Brownian motion. Assuming that S restricts to a C 0-semigroup on H, we obtain L p -bounds for D H P(t). We show that if P is analytic, then the invariance assumption is fulfilled. As an application we determine the L p -domain of the generator of P explicitly in the case where S restricts to a C 0-semigroup on H which is similar to an analytic contraction semigroup. The results are applied to the 1D stochastic heat equation driven by additive space-time white noise."}],"volume":80,"date_created":"2018-12-11T11:55:48Z","year":"2011","page":"463 - 477","quality_controlled":0,"date_updated":"2021-01-12T06:55:24Z","intvolume":"        80","citation":{"ama":"Maas J, Van Neerven J. Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators. In: <i>Parabolic Problems</i>. Vol 80. Birkhäuser; 2011:463-477. doi:<a href=\"https://doi.org/10.1007/978-3-0348-0075-4_24\">10.1007/978-3-0348-0075-4_24</a>","short":"J. Maas, J. Van Neerven, in:, Parabolic Problems, Birkhäuser, 2011, pp. 463–477.","mla":"Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification for Analytic Ornstein-Uhlenbeck Operators.” <i>Parabolic Problems</i>, vol. 80, Birkhäuser, 2011, pp. 463–77, doi:<a href=\"https://doi.org/10.1007/978-3-0348-0075-4_24\">10.1007/978-3-0348-0075-4_24</a>.","ieee":"J. Maas and J. Van Neerven, “Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators,” in <i>Parabolic Problems</i>, vol. 80, Birkhäuser, 2011, pp. 463–477.","chicago":"Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification for Analytic Ornstein-Uhlenbeck Operators.” In <i>Parabolic Problems</i>, 80:463–77. Birkhäuser, 2011. <a href=\"https://doi.org/10.1007/978-3-0348-0075-4_24\">https://doi.org/10.1007/978-3-0348-0075-4_24</a>.","ista":"Maas J, Van Neerven J. 2011.Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators. In: Parabolic Problems. vol. 80, 463–477.","apa":"Maas, J., &#38; Van Neerven, J. (2011). Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators. In <i>Parabolic Problems</i> (Vol. 80, pp. 463–477). Birkhäuser. <a href=\"https://doi.org/10.1007/978-3-0348-0075-4_24\">https://doi.org/10.1007/978-3-0348-0075-4_24</a>"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0911.4336 "}],"day":"10","publication_status":"published","oa":1,"title":"Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators","type":"book_chapter","_id":"2116","doi":"10.1007/978-3-0348-0075-4_24","month":"06","publisher":"Birkhäuser","publication":"Parabolic Problems","publist_id":"4918","author":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas","full_name":"Jan Maas","first_name":"Jan"},{"last_name":"Van Neerven","first_name":"Jan","full_name":"Van Neerven, Jan"}],"acknowledgement":"The authors are supported by VIDI subsidy 639.032.201 (JM) and VICI subsidy 639.033.604 (JvN) of the Netherlands Organisation for Scientific Research (NWO). ","date_published":"2011-06-10T00:00:00Z"},{"publisher":"Universitat Autònoma de Barcelona, Departament de Matemàtique","_id":"2122","doi":"10.5565/PUBLMAT_55211_03\t ","month":"07","type":"journal_article","publication_status":"published","title":"Conical square functions and non-tangential maximal functions with respect to the Gaussian measure","oa":1,"acknowledgement":"The first named author is supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). The second named author is supported by VICI subsidy 639.033.604 of the Netherlands Organisation for Scientific Research (NWO","date_published":"2011-07-01T00:00:00Z","author":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Jan Maas","first_name":"Jan","last_name":"Maas"},{"first_name":"Jan","full_name":"van Neerven, Jan M","last_name":"Van Neerven"},{"last_name":"Portal","full_name":"Portal, Pierre","first_name":"Pierre"}],"issue":"2","publist_id":"4910","publication":"Publicacions Matemàtiques","date_updated":"2021-01-12T06:55:26Z","date_created":"2018-12-11T11:55:50Z","year":"2011","quality_controlled":0,"page":"313 - 341","extern":1,"volume":55,"abstract":[{"text":"We study, in L1(R̃n; γ) with respect to the gaussian measure, non- tangential maximal functions and conical square functions associ- ated with the Ornstein-Uhlenbeck operator by developing a set of techniques which allow us, to some extent, to compensate for the non-doubling character of the gaussian measure. The main result asserts that conical square functions can be controlled in L1-norm by non-tangential maximal functions. Along the way we prove a change of aperture result for the latter. This complements recent results on gaussian Hardy spaces due to Mauceri and Meda.","lang":"eng"}],"status":"public","day":"01","citation":{"ista":"Maas J, Van Neerven J, Portal P. 2011. Conical square functions and non-tangential maximal functions with respect to the Gaussian measure. Publicacions Matemàtiques. 55(2), 313–341.","apa":"Maas, J., Van Neerven, J., &#38; Portal, P. (2011). Conical square functions and non-tangential maximal functions with respect to the Gaussian measure. <i>Publicacions Matemàtiques</i>. Universitat Autònoma de Barcelona, Departament de Matemàtique. <a href=\"https://doi.org/10.5565/PUBLMAT_55211_03  \">https://doi.org/10.5565/PUBLMAT_55211_03  </a>","chicago":"Maas, Jan, Jan Van Neerven, and Pierre Portal. “Conical Square Functions and Non-Tangential Maximal Functions with Respect to the Gaussian Measure.” <i>Publicacions Matemàtiques</i>. Universitat Autònoma de Barcelona, Departament de Matemàtique, 2011. <a href=\"https://doi.org/10.5565/PUBLMAT_55211_03  \">https://doi.org/10.5565/PUBLMAT_55211_03  </a>.","ieee":"J. Maas, J. Van Neerven, and P. Portal, “Conical square functions and non-tangential maximal functions with respect to the Gaussian measure,” <i>Publicacions Matemàtiques</i>, vol. 55, no. 2. Universitat Autònoma de Barcelona, Departament de Matemàtique, pp. 313–341, 2011.","mla":"Maas, Jan, et al. “Conical Square Functions and Non-Tangential Maximal Functions with Respect to the Gaussian Measure.” <i>Publicacions Matemàtiques</i>, vol. 55, no. 2, Universitat Autònoma de Barcelona, Departament de Matemàtique, 2011, pp. 313–41, doi:<a href=\"https://doi.org/10.5565/PUBLMAT_55211_03  \">10.5565/PUBLMAT_55211_03  </a>.","short":"J. Maas, J. Van Neerven, P. Portal, Publicacions Matemàtiques 55 (2011) 313–341.","ama":"Maas J, Van Neerven J, Portal P. Conical square functions and non-tangential maximal functions with respect to the Gaussian measure. <i>Publicacions Matemàtiques</i>. 2011;55(2):313-341. doi:<a href=\"https://doi.org/10.5565/PUBLMAT_55211_03  \">10.5565/PUBLMAT_55211_03  </a>"},"intvolume":"        55","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1003.4092"}]},{"_id":"2123","month":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","oa":1,"title":"A Trotter product formula for gradient flows in metric spaces","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s00028-012-0173-z"}]},"acknowledgement":"The second named author is supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO).","status":"public","extern":"1","abstract":[{"text":"We prove a Trotter product formula for gradient flows in metric spaces. This result is applied to establish convergence in the L 2-Wasserstein metric of the splitting method for some Fokker-Planck equations and porous medium type equations perturbed by a potential.","lang":"eng"}],"day":"21","intvolume":"        11","citation":{"short":"P. Clément, J. Maas, Journal of Evolution Equations 11 (2011) 405–427.","ama":"Clément P, Maas J. A Trotter product formula for gradient flows in metric spaces. <i>Journal of Evolution Equations</i>. 2011;11(2):405-427. doi:<a href=\"https://doi.org/10.1007/s00028-010-0096-5\">10.1007/s00028-010-0096-5</a>","ista":"Clément P, Maas J. 2011. A Trotter product formula for gradient flows in metric spaces. Journal of Evolution Equations. 11(2), 405–427.","apa":"Clément, P., &#38; Maas, J. (2011). A Trotter product formula for gradient flows in metric spaces. <i>Journal of Evolution Equations</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00028-010-0096-5\">https://doi.org/10.1007/s00028-010-0096-5</a>","chicago":"Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient Flows in Metric Spaces.” <i>Journal of Evolution Equations</i>. Birkhäuser, 2011. <a href=\"https://doi.org/10.1007/s00028-010-0096-5\">https://doi.org/10.1007/s00028-010-0096-5</a>.","ieee":"P. Clément and J. Maas, “A Trotter product formula for gradient flows in metric spaces,” <i>Journal of Evolution Equations</i>, vol. 11, no. 2. Birkhäuser, pp. 405–427, 2011.","mla":"Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient Flows in Metric Spaces.” <i>Journal of Evolution Equations</i>, vol. 11, no. 2, Birkhäuser, 2011, pp. 405–27, doi:<a href=\"https://doi.org/10.1007/s00028-010-0096-5\">10.1007/s00028-010-0096-5</a>."},"doi":"10.1007/s00028-010-0096-5","publisher":"Birkhäuser","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","date_published":"2011-01-21T00:00:00Z","publication":"Journal of Evolution Equations","publist_id":"4911","issue":"2","author":[{"last_name":"Clément","full_name":"Clément, Philippe","first_name":"Philippe"},{"first_name":"Jan","full_name":"Maas, Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"year":"2011","date_created":"2018-12-11T11:55:51Z","page":"405 - 427","date_updated":"2021-11-16T08:05:46Z","volume":11,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1005.0998"}]},{"publication":"Journal of Functional Analysis","issue":"8","publist_id":"4909","author":[{"full_name":"Jan Maas","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"}],"acknowledgement":"Supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO)","date_published":"2011-03-04T00:00:00Z","publication_status":"published","oa":1,"title":"Gradient flows of the entropy for finite Markov chains","type":"journal_article","_id":"2126","doi":"10.1016/j.jfa.2011.06.009 ","month":"03","publisher":"Academic Press","main_file_link":[{"url":"http://arxiv.org/abs/1102.5238","open_access":"1"}],"citation":{"mla":"Maas, Jan. “Gradient Flows of the Entropy for Finite Markov Chains.” <i>Journal of Functional Analysis</i>, vol. 261, no. 8, Academic Press, 2011, pp. 2250–92, doi:<a href=\"https://doi.org/10.1016/j.jfa.2011.06.009 \">10.1016/j.jfa.2011.06.009 </a>.","ieee":"J. Maas, “Gradient flows of the entropy for finite Markov chains,” <i>Journal of Functional Analysis</i>, vol. 261, no. 8. Academic Press, pp. 2250–2292, 2011.","ista":"Maas J. 2011. Gradient flows of the entropy for finite Markov chains. Journal of Functional Analysis. 261(8), 2250–2292.","apa":"Maas, J. (2011). Gradient flows of the entropy for finite Markov chains. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2011.06.009 \">https://doi.org/10.1016/j.jfa.2011.06.009 </a>","chicago":"Maas, Jan. “Gradient Flows of the Entropy for Finite Markov Chains.” <i>Journal of Functional Analysis</i>. Academic Press, 2011. <a href=\"https://doi.org/10.1016/j.jfa.2011.06.009 \">https://doi.org/10.1016/j.jfa.2011.06.009 </a>.","ama":"Maas J. Gradient flows of the entropy for finite Markov chains. <i>Journal of Functional Analysis</i>. 2011;261(8):2250-2292. doi:<a href=\"https://doi.org/10.1016/j.jfa.2011.06.009 \">10.1016/j.jfa.2011.06.009 </a>","short":"J. Maas, Journal of Functional Analysis 261 (2011) 2250–2292."},"intvolume":"       261","day":"04","status":"public","extern":1,"abstract":[{"lang":"eng","text":"Let K be an irreducible and reversible Markov kernel on a finite set X. We construct a metric W on the set of probability measures on X and show that with respect to this metric, the law of the continuous time Markov chain evolves as the gradient flow of the entropy. This result is a discrete counterpart of the Wasserstein gradient flow interpretation of the heat flow in Rn by Jordan, Kinderlehrer and Otto (1998). The metric W is similar to, but different from, the L2-Wasserstein metric, and is defined via a discrete variant of the Benamou–Brenier formula.\n"}],"volume":261,"year":"2011","date_created":"2018-12-11T11:55:51Z","page":"2250 - 2292","quality_controlled":0,"date_updated":"2021-01-12T06:55:28Z"},{"author":[{"last_name":"Ağanoğlu","full_name":"Ağanoğlu, Ruzin","first_name":"Ruzin"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Mikhail Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Břetislav","full_name":"Friedrich, Břetislav","last_name":"Friedrich"},{"last_name":"González Férez","full_name":"González-Férez, Rosario","first_name":"Rosario"},{"last_name":"Koch","first_name":"Christiane","full_name":"Koch, Christiane P"}],"publist_id":"4886","publication":"Unknown","acknowledgement":"Financial support from the Deutsche Forschungsgemeinschaft (Grant No. KO 2301/2), by the Spanish project FIS2008-02380 (MICINN) as well as the Grants FQM-2445 and FQM-4643 (Junta de Andaluc´ıa), Campus de Excelencia Internacional Proyecto GENIL CEB09-0010","date_published":"2011-05-04T00:00:00Z","type":"preprint","publication_status":"published","oa":1,"title":"Controlling a diatomic shape resonance with non-resonant light","publisher":"ArXiv","_id":"2138","month":"05","citation":{"ama":"Ağanoğlu R, Lemeshko M, Friedrich B, González Férez R, Koch C. Controlling a diatomic shape resonance with non-resonant light. <i>Unknown</i>. 2011.","short":"R. Ağanoğlu, M. Lemeshko, B. Friedrich, R. González Férez, C. Koch, Unknown (2011).","mla":"Ağanoğlu, Ruzin, et al. “Controlling a Diatomic Shape Resonance with Non-Resonant Light.” <i>Unknown</i>, ArXiv, 2011.","ieee":"R. Ağanoğlu, M. Lemeshko, B. Friedrich, R. González Férez, and C. Koch, “Controlling a diatomic shape resonance with non-resonant light,” <i>Unknown</i>. ArXiv, 2011.","apa":"Ağanoğlu, R., Lemeshko, M., Friedrich, B., González Férez, R., &#38; Koch, C. (2011). Controlling a diatomic shape resonance with non-resonant light. <i>Unknown</i>. ArXiv.","ista":"Ağanoğlu R, Lemeshko M, Friedrich B, González Férez R, Koch C. 2011. Controlling a diatomic shape resonance with non-resonant light. Unknown, .","chicago":"Ağanoğlu, Ruzin, Mikhail Lemeshko, Břetislav Friedrich, Rosario González Férez, and Christiane Koch. “Controlling a Diatomic Shape Resonance with Non-Resonant Light.” <i>Unknown</i>. ArXiv, 2011."},"main_file_link":[{"url":"http://arxiv.org/abs/1105.0761","open_access":"1"}],"day":"04","extern":1,"abstract":[{"text":"A (diatomic) shape resonance is a metastable state of a pair of colliding atoms quasi-bound by the centrifugal barrier imposed by the angular momentum involved in the collision. The temporary trapping of the atoms' scattering wavefunction corresponds to an enhanced atom pair density at low interatomic separations. This leads to larger overlap of the wavefunctions involved in a molecule formation process such as photoassociation, rendering the process more efficient. However, for an ensemble of atoms, the atom pair density will only be enhanced if the energy of the resonance comes close to the temperature of the atomic ensemble. Herein we explore the possibility of controlling the energy of a shape resonance by shifting it toward the temperature of atoms confined in a trap. The shifts are imparted by the interaction of non-resonant light with the anisotropic polarizability of the atom pair, which affects both the centrifugal barrier and the pair's rotational and vibrational levels. We find that at laser intensities of up to 5×109 W/cm2 the pair density is increased by one order of magnitude for 87Rb atoms at 100μK and by two orders of magnitude for 88Sr atoms at 20μK.","lang":"eng"}],"status":"public","date_updated":"2021-01-12T06:55:32Z","date_created":"2018-12-11T11:55:55Z","year":"2011","quality_controlled":0}]