[{"_id":"8386","article_processing_charge":"No","ec_funded":1,"author":[{"first_name":"Ran","last_name":"Zhang","orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Ran"}],"file":[{"access_level":"closed","date_created":"2020-09-14T01:02:59Z","file_name":"Thesis_Ran.zip","relation":"source_file","creator":"rzhang","content_type":"application/x-zip-compressed","file_id":"8388","date_updated":"2020-09-14T12:18:43Z","file_size":1245800191,"checksum":"edcf578b6e1c9b0dd81ff72d319b66ba"},{"file_name":"PhD_thesis_Ran Zhang_20200915.pdf","success":1,"relation":"main_file","date_created":"2020-09-15T12:51:53Z","access_level":"open_access","checksum":"817e20c33be9247f906925517c56a40d","date_updated":"2020-09-15T12:51:53Z","file_size":161385316,"content_type":"application/pdf","file_id":"8396","creator":"rzhang"}],"date_created":"2020-09-14T01:04:53Z","type":"dissertation","degree_awarded":"PhD","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting."}],"page":"148","year":"2020","doi":"10.15479/AT:ISTA:8386","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","alternative_title":["ISTA Thesis"],"citation":{"ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8386\">https://doi.org/10.15479/AT:ISTA:8386</a>.","apa":"Zhang, R. (2020). <i>Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8386\">https://doi.org/10.15479/AT:ISTA:8386</a>","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8386\">10.15479/AT:ISTA:8386</a>","mla":"Zhang, Ran. <i>Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8386\">10.15479/AT:ISTA:8386</a>.","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria."},"acknowledged_ssus":[{"_id":"SSU"}],"date_updated":"2023-09-22T09:49:31Z","language":[{"iso":"eng"}],"file_date_updated":"2020-09-15T12:51:53Z","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2020-09-14T00:00:00Z","supervisor":[{"first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"has_accepted_license":"1","oa":1,"month":"09","ddc":["003"],"related_material":{"record":[{"status":"public","id":"486","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1002"}]},"publication_status":"published","day":"14"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","department":[{"_id":"ChLa"}],"has_accepted_license":"1","date_published":"2020-09-14T00:00:00Z","status":"public","supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"ddc":["000"],"oa":1,"month":"09","day":"14","publication_status":"published","related_material":{"record":[{"status":"public","id":"7936","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7937"},{"status":"public","relation":"part_of_dissertation","id":"8193"},{"id":"8092","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"911"}]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"doi":"10.15479/AT:ISTA:8390","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"citation":{"chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>.","apa":"Royer, A. (2020). <i>Leveraging structure in Computer Vision tasks for flexible Deep Learning models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>","mla":"Royer, Amélie. <i>Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020."},"alternative_title":["ISTA Thesis"],"date_updated":"2023-10-16T10:04:02Z","language":[{"iso":"eng"}],"file_date_updated":"2020-09-14T13:39:17Z","date_created":"2020-09-14T13:42:09Z","type":"dissertation","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-007-7"],"issn":["2663-337X"]},"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"197","abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"year":"2020","_id":"8390","article_processing_charge":"No","author":[{"first_name":"Amélie","last_name":"Royer","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","full_name":"Royer, Amélie"}],"file":[{"creator":"dernst","file_id":"8391","content_type":"application/pdf","file_size":30224591,"date_updated":"2020-09-14T13:39:14Z","checksum":"c914d2f88846032f3d8507734861b6ee","access_level":"open_access","date_created":"2020-09-14T13:39:14Z","relation":"main_file","file_name":"2020_Thesis_Royer.pdf","success":1},{"checksum":"ae98fb35d912cff84a89035ae5794d3c","date_updated":"2020-09-14T13:39:17Z","file_size":74227627,"creator":"dernst","content_type":"application/x-zip-compressed","file_id":"8392","file_name":"thesis_sources.zip","relation":"main_file","date_created":"2020-09-14T13:39:17Z","access_level":"closed"}]},{"intvolume":"        18","_id":"8402","article_processing_charge":"No","extern":"1","author":[{"first_name":"Heike","last_name":"Rampelt","full_name":"Rampelt, Heike"},{"first_name":"Iva","last_name":"Sucec","full_name":"Sucec, Iva"},{"last_name":"Bersch","first_name":"Beate","full_name":"Bersch, Beate"},{"full_name":"Horten, Patrick","last_name":"Horten","first_name":"Patrick"},{"full_name":"Perschil, Inge","last_name":"Perschil","first_name":"Inge"},{"last_name":"Martinou","first_name":"Jean-Claude","full_name":"Martinou, Jean-Claude"},{"first_name":"Martin","last_name":"van der Laan","full_name":"van der Laan, Martin"},{"last_name":"Wiedemann","first_name":"Nils","full_name":"Wiedemann, Nils"},{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"Nikolaus","last_name":"Pfanner","full_name":"Pfanner, Nikolaus"}],"article_type":"original","publication_identifier":{"issn":["1741-7007"]},"oa_version":"Published Version","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"],"type":"journal_article","date_created":"2020-09-17T10:26:53Z","volume":18,"external_id":{"pmid":["31907035"]},"year":"2020","abstract":[{"text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.","lang":"eng"}],"article_number":"2","citation":{"apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>.","ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. 2020;18. doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2.","mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>, vol. 18, 2, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>.","short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","ieee":"H. Rampelt <i>et al.</i>, “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” <i>BMC Biology</i>, vol. 18. Springer Nature, 2020."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12915-019-0733-6"}],"title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","doi":"10.1186/s12915-019-0733-6","quality_controlled":"1","date_updated":"2021-01-12T08:19:02Z","language":[{"iso":"eng"}],"status":"public","date_published":"2020-01-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","publication_status":"published","day":"06","pmid":1,"publication":"BMC Biology","month":"01","oa":1},{"status":"public","oa_version":"Preprint","date_published":"2020-09-17T00:00:00Z","publisher":"Cold Spring Harbor Laboratory","type":"preprint","date_created":"2020-09-17T10:27:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","day":"17","publication_status":"submitted","abstract":[{"text":"Chaperones are essential for assisting protein folding, and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding of how additional interactions enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1, and Tim23 which has an additional disordered hydrophilic domain. Combining NMR, SAXS and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity <jats:italic>vs.</jats:italic> specificity.","lang":"eng"}],"month":"09","oa":1,"publication":"bioRxiv","citation":{"ieee":"I. Sučec <i>et al.</i>, “Structural basis of client specificity in mitochondrial membrane-protein chaperones,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Sučec I, Wang Y, Dakhlaoui O, Weinhäupl K, Jores T, Costa D, Hessel A, Brennich M, Rapaport D, Lindorff-Larsen K, Bersch B, Schanda P. Structural basis of client specificity in mitochondrial membrane-protein chaperones. bioRxiv, <a href=\"https://doi.org/10.1101/2020.06.08.140772\">10.1101/2020.06.08.140772</a>.","ama":"Sučec I, Wang Y, Dakhlaoui O, et al. Structural basis of client specificity in mitochondrial membrane-protein chaperones. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.06.08.140772\">10.1101/2020.06.08.140772</a>","mla":"Sučec, Iva, et al. “Structural Basis of Client Specificity in Mitochondrial Membrane-Protein Chaperones.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.06.08.140772\">10.1101/2020.06.08.140772</a>.","short":"I. Sučec, Y. Wang, O. Dakhlaoui, K. Weinhäupl, T. Jores, D. Costa, A. Hessel, M. Brennich, D. Rapaport, K. Lindorff-Larsen, B. Bersch, P. Schanda, BioRxiv (n.d.).","apa":"Sučec, I., Wang, Y., Dakhlaoui, O., Weinhäupl, K., Jores, T., Costa, D., … Schanda, P. (n.d.). Structural basis of client specificity in mitochondrial membrane-protein chaperones. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.06.08.140772\">https://doi.org/10.1101/2020.06.08.140772</a>","chicago":"Sučec, Iva, Yong Wang, Ons Dakhlaoui, Katharina Weinhäupl, Tobias Jores, Doriane Costa, Audrey Hessel, et al. “Structural Basis of Client Specificity in Mitochondrial Membrane-Protein Chaperones.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.06.08.140772\">https://doi.org/10.1101/2020.06.08.140772</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.06.08.140772"}],"title":"Structural basis of client specificity in mitochondrial membrane-protein chaperones","doi":"10.1101/2020.06.08.140772","_id":"8403","article_processing_charge":"No","extern":"1","date_updated":"2021-01-12T08:19:02Z","language":[{"iso":"eng"}],"author":[{"full_name":"Sučec, Iva","first_name":"Iva","last_name":"Sučec"},{"last_name":"Wang","first_name":"Yong","full_name":"Wang, Yong"},{"full_name":"Dakhlaoui, Ons","last_name":"Dakhlaoui","first_name":"Ons"},{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"last_name":"Jores","first_name":"Tobias","full_name":"Jores, Tobias"},{"full_name":"Costa, Doriane","last_name":"Costa","first_name":"Doriane"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"full_name":"Brennich, Martha","last_name":"Brennich","first_name":"Martha"},{"first_name":"Doron","last_name":"Rapaport","full_name":"Rapaport, Doron"},{"full_name":"Lindorff-Larsen, Kresten","first_name":"Kresten","last_name":"Lindorff-Larsen"},{"last_name":"Bersch","first_name":"Beate","full_name":"Bersch, Beate"},{"last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-17T10:27:59Z","publisher":"Cold Spring Harbor Laboratory","type":"preprint","date_published":"2020-03-14T00:00:00Z","status":"public","oa_version":"Preprint","publication":"bioRxiv","oa":1,"abstract":[{"lang":"eng","text":"<jats:p>The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9·10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9·10·12 complex is the anchor point at the inner-membrane insertase complex TIM22. The mechanism of client transport by TIM9·10 has been resolved recently, but the structure and subunit composition of the TIM9·10·12 complex remains largely unresolved. Furthermore, the assembly process of the hexameric TIM chaperones from its subunits remained elusive. We investigate the structural and dynamical properties of the Tim subunits, and show that they are highly dynamic. In their non-assembled form, the subunits behave as intrinsically disordered proteins; when the conserved cysteines of the CX<jats:sub>3</jats:sub>C-X<jats:sub><jats:italic>n</jats:italic></jats:sub>-CX<jats:sub>3</jats:sub>C motifs are formed, short marginally stable <jats:italic>α</jats:italic>-helices are formed, which are only fully stabilized upon hexamer formation to the mature chaperone. Subunits are in equilibrium between their hexamer-embedded and a free form, with exchange kinetics on a minutes time scale. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9·10·12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12) with a conserved hydrophobic client-binding groove and flexible N- and C-terminal tentacles.</jats:p>"}],"month":"03","day":"14","publication_status":"submitted","year":"2020","article_processing_charge":"No","_id":"8404","doi":"10.1101/2020.03.13.990150","title":"Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone","main_file_link":[{"url":"https://doi.org/10.1101/2020.03.13.990150","open_access":"1"}],"citation":{"ieee":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, and P. Schanda, “Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Weinhäupl, K., Wang, Y., Hessel, A., Brennich, M., Lindorff-Larsen, K., &#38; Schanda, P. (n.d.). Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.03.13.990150\">https://doi.org/10.1101/2020.03.13.990150</a>","chicago":"Weinhäupl, Katharina, Yong Wang, Audrey Hessel, Martha Brennich, Kresten Lindorff-Larsen, and Paul Schanda. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.03.13.990150\">https://doi.org/10.1101/2020.03.13.990150</a>.","ista":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. bioRxiv, <a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>.","ama":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>","mla":"Weinhäupl, Katharina, et al. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>.","short":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, P. Schanda, BioRxiv (n.d.)."},"author":[{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"full_name":"Wang, Yong","first_name":"Yong","last_name":"Wang"},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"first_name":"Martha","last_name":"Brennich","full_name":"Brennich, Martha"},{"last_name":"Lindorff-Larsen","first_name":"Kresten","full_name":"Lindorff-Larsen, Kresten"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"}],"language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:03Z","extern":"1"},{"extern":"1","series_title":"AMS","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2021-12-21T10:50:49Z","author":[{"last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"},{"full_name":"Zhang, Ke","last_name":"Zhang","first_name":"Ke"}],"intvolume":"       208","citation":{"ieee":"V. Kaloshin and K. Zhang, <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>, 1st ed., vol. 208. Princeton University Press, 2020.","ama":"Kaloshin V, Zhang K. <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>. Vol 208. 1st ed. Princeton University Press; 2020. doi:<a href=\"https://doi.org/10.1515/9780691204932\">10.1515/9780691204932</a>","ista":"Kaloshin V, Zhang K. 2020. Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom 1st ed., Princeton University Press, 224p.","mla":"Kaloshin, Vadim, and Ke Zhang. <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>. 1st ed., vol. 208, Princeton University Press, 2020, doi:<a href=\"https://doi.org/10.1515/9780691204932\">10.1515/9780691204932</a>.","short":"V. Kaloshin, K. Zhang, Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom, 1st ed., Princeton University Press, 2020.","apa":"Kaloshin, V., &#38; Zhang, K. (2020). <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i> (1st ed., Vol. 208). Princeton University Press. <a href=\"https://doi.org/10.1515/9780691204932\">https://doi.org/10.1515/9780691204932</a>","chicago":"Kaloshin, Vadim, and Ke Zhang. <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>. 1st ed. Vol. 208. AMS. Princeton University Press, 2020. <a href=\"https://doi.org/10.1515/9780691204932\">https://doi.org/10.1515/9780691204932</a>."},"alternative_title":["Annals of Mathematics Studies"],"_id":"8414","article_processing_charge":"No","doi":"10.1515/9780691204932","title":"Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom","edition":"1","day":"01","publication_status":"published","year":"2020","scopus_import":"1","page":"224","abstract":[{"lang":"eng","text":"Arnold diffusion, which concerns the appearance of chaos in classical mechanics, is one of the most important problems in the fields of dynamical systems and mathematical physics. Since it was discovered by Vladimir Arnold in 1963, it has attracted the efforts of some of the most prominent researchers in mathematics. The question is whether a typical perturbation of a particular system will result in chaotic or unstable dynamical phenomena. In this groundbreaking book, Vadim Kaloshin and Ke Zhang provide the first complete proof of Arnold diffusion, demonstrating that that there is topological instability for typical perturbations of five-dimensional integrable systems (two and a half degrees of freedom).\r\nThis proof realizes a plan John Mather announced in 2003 but was unable to complete before his death. Kaloshin and Zhang follow Mather’s strategy but emphasize a more Hamiltonian approach, tying together normal forms theory, hyperbolic theory, Mather theory, and weak KAM theory. Offering a complete, clean, and modern explanation of the steps involved in the proof, and a clear account of background material, this book is designed to be accessible to students as well as researchers. The result is a critical contribution to mathematical physics and dynamical systems, especially Hamiltonian systems."}],"month":"03","publication_identifier":{"isbn":["9-780-6912-0253-2"]},"date_published":"2020-03-01T00:00:00Z","oa_version":"None","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":208,"date_created":"2020-09-17T10:41:05Z","type":"book","publisher":"Princeton University Press"},{"file":[{"access_level":"open_access","date_created":"2020-09-17T14:07:51Z","file_name":"2020_JournalCellScience_Dimchev.pdf","relation":"main_file","embargo":"2020-10-10","content_type":"application/pdf","file_id":"8435","creator":"dernst","date_updated":"2020-10-11T22:30:02Z","file_size":13493302,"checksum":"ba917e551acc4ece2884b751434df9ae"}],"article_type":"original","author":[{"first_name":"Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"last_name":"Amiri","first_name":"Behnam","full_name":"Amiri, Behnam"},{"full_name":"Humphries, Ashley C.","last_name":"Humphries","first_name":"Ashley C."},{"full_name":"Schaks, Matthias","first_name":"Matthias","last_name":"Schaks"},{"last_name":"Dimchev","first_name":"Vanessa","full_name":"Dimchev, Vanessa"},{"last_name":"Stradal","first_name":"Theresia E. B.","full_name":"Stradal, Theresia E. B."},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"full_name":"Krause, Matthias","first_name":"Matthias","last_name":"Krause"},{"last_name":"Way","first_name":"Michael","full_name":"Way, Michael"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"}],"intvolume":"       133","article_processing_charge":"No","_id":"8434","year":"2020","external_id":{"isi":["000534387800005"],"pmid":[" 32094266"]},"abstract":[{"text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ","lang":"eng"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"date_created":"2020-09-17T14:00:33Z","volume":133,"type":"journal_article","project":[{"_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF"}],"keyword":["Cell Biology"],"quality_controlled":"1","file_date_updated":"2020-10-11T22:30:02Z","language":[{"iso":"eng"}],"date_updated":"2023-09-05T15:41:48Z","article_number":"jcs239020","citation":{"chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. 2020;133(7). doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>","ieee":"G. A. Dimchev <i>et al.</i>, “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” <i>Journal of Cell Science</i>, vol. 133, no. 7. The Company of Biologists, 2020."},"doi":"10.1242/jcs.239020","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","issue":"7","pmid":1,"publication_status":"published","day":"09","oa":1,"month":"04","isi":1,"publication":"Journal of Cell Science","ddc":["570"],"date_published":"2020-04-09T00:00:00Z","status":"public","has_accepted_license":"1","publisher":"The Company of Biologists","department":[{"_id":"FlSc"}],"acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_status":"published","day":"08","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-18912-9","relation":"erratum"},{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release"}],"record":[{"status":"public","id":"13056","relation":"research_data"}]},"ddc":["530"],"publication":"Nature Communications","isi":1,"month":"09","oa":1,"has_accepted_license":"1","date_published":"2020-09-08T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","department":[{"_id":"JoFi"}],"quality_controlled":"1","file_date_updated":"2020-09-18T13:02:37Z","date_updated":"2024-08-07T07:11:51Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"article_number":"4460","citation":{"ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>"},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","doi":"10.1038/s41467-020-18269-z","external_id":{"isi":["000577280200001"]},"year":"2020","abstract":[{"lang":"eng","text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform."}],"publication_identifier":{"issn":["2041-1723"]},"oa_version":"Published Version","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","grant_number":"732894"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"type":"journal_article","date_created":"2020-09-18T10:56:20Z","volume":11,"file":[{"relation":"main_file","file_name":"2020_NatureComm_Arnold.pdf","success":1,"date_created":"2020-09-18T13:02:37Z","access_level":"open_access","checksum":"88f92544889eb18bb38e25629a422a86","file_size":1002818,"date_updated":"2020-09-18T13:02:37Z","file_id":"8530","content_type":"application/pdf","creator":"dernst"}],"ec_funded":1,"author":[{"last_name":"Arnold","first_name":"Georg M","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876"},{"first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias"},{"last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","first_name":"William J","last_name":"Hease"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","last_name":"Hassani","first_name":"Farid"},{"last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"article_type":"original","intvolume":"        11","_id":"8529","article_processing_charge":"No"},{"oa":1,"month":"09","publication":"International Journal of Molecular Sciences","isi":1,"ddc":["570"],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9562"}]},"issue":"18","day":"14","publication_status":"published","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","department":[{"_id":"RySh"}],"publisher":"MDPI","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-09-14T00:00:00Z","status":"public","has_accepted_license":"1","date_updated":"2024-03-25T23:30:16Z","language":[{"iso":"eng"}],"file_date_updated":"2020-09-21T14:08:58Z","quality_controlled":"1","doi":"10.3390/ijms21186737","title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"6737","citation":{"apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., &#38; Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. 2020;21(18). doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>","mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18, 6737, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>.","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18. MDPI, 2020."},"abstract":[{"text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography.","lang":"eng"}],"scopus_import":"1","year":"2020","external_id":{"isi":["000579945300001"]},"volume":21,"date_created":"2020-09-20T22:01:35Z","type":"journal_article","project":[{"grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"25D32BC0-B435-11E9-9278-68D0E5697425","name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus"},{"grant_number":"785907","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","_id":"26436750-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"article_type":"original","author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst"},{"last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","first_name":"Pradeep","last_name":"Bhandari"},{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case","first_name":"Matthew J"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"file":[{"creator":"dernst","file_id":"8551","content_type":"application/pdf","checksum":"2e4f62f3cfe945b7391fc3070e5a289f","file_size":5748456,"date_updated":"2020-09-21T14:08:58Z","access_level":"open_access","relation":"main_file","file_name":"2020_JournMolecSciences_Kleindienst.pdf","success":1,"date_created":"2020-09-21T14:08:58Z"}],"_id":"8532","article_processing_charge":"No","intvolume":"        21"},{"arxiv":1,"publication_identifier":{"isbn":["9783959771597"],"issn":["18688969"]},"conference":{"end_date":"2020-08-28","start_date":"2020-08-24","location":"Prague, Czech Republic","name":"MFCS: Symposium on Mathematical Foundations of Computer Science"},"oa_version":"Published Version","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"type":"conference","volume":170,"date_created":"2020-09-20T22:01:36Z","external_id":{"arxiv":["2007.02894"]},"year":"2020","scopus_import":"1","license":"https://creativecommons.org/licenses/by/3.0/","abstract":[{"text":"Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete.","lang":"eng"}],"intvolume":"       170","_id":"8533","article_processing_charge":"No","file":[{"creator":"dernst","file_id":"8550","content_type":"application/pdf","checksum":"bbd7c4f55d45f2ff2a0a4ef0e10a77b1","date_updated":"2020-09-21T13:57:34Z","file_size":491374,"access_level":"open_access","success":1,"file_name":"2020_LIPIcs_Chatterjee.pdf","relation":"main_file","date_created":"2020-09-21T13:57:34Z"}],"ec_funded":1,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jecker, Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","last_name":"Jecker","first_name":"Ismael R"},{"full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub"}],"has_accepted_license":"1","date_published":"2020-08-18T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Krishnendu Chatterjee: The research was partially supported by the Vienna Science and\r\nTechnology Fund (WWTF) Project ICT15-003.\r\nIsmaël Jecker: This project has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","publication_status":"published","day":"18","ddc":["000"],"publication":"45th International Symposium on Mathematical Foundations of Computer Science","month":"08","oa":1,"article_number":"22:1-22:13","citation":{"ieee":"K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Simplified game of life: Algorithms and complexity,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170.","ista":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2020. Simplified game of life: Algorithms and complexity. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 22:1-22:13.","ama":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Simplified game of life: Algorithms and complexity. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>","mla":"Chatterjee, Krishnendu, et al. “Simplified Game of Life: Algorithms and Complexity.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 22:1-22:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","apa":"Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., &#38; Svoboda, J. (2020). Simplified game of life: Algorithms and complexity. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub Svoboda. “Simplified Game of Life: Algorithms and Complexity.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>."},"alternative_title":["LIPIcs"],"tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"title":"Simplified game of life: Algorithms and complexity","doi":"10.4230/LIPIcs.MFCS.2020.22","file_date_updated":"2020-09-21T13:57:34Z","quality_controlled":"1","date_updated":"2025-06-02T08:53:42Z","language":[{"iso":"eng"}]},{"author":[{"id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R","first_name":"Ismael R","last_name":"Jecker"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"},{"last_name":"Mazzocchi","first_name":"Nicolas","full_name":"Mazzocchi, Nicolas"}],"ec_funded":1,"file":[{"content_type":"application/pdf","file_id":"8552","creator":"dernst","checksum":"2dc9e2fad6becd4563aef3e27a473f70","date_updated":"2020-09-21T14:17:08Z","file_size":597977,"access_level":"open_access","file_name":"2020_LIPIcsMFCS_Jecker.pdf","success":1,"relation":"main_file","date_created":"2020-09-21T14:17:08Z"}],"_id":"8534","article_processing_charge":"No","intvolume":"       170","scopus_import":"1","abstract":[{"text":"A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs.","lang":"eng"}],"year":"2020","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"type":"conference","date_created":"2020-09-20T22:01:36Z","volume":170,"publication_identifier":{"issn":["18688969"],"isbn":["9783959771597"]},"conference":{"start_date":"2020-08-24","end_date":"2020-08-28","name":"MFCS: Symposium on Mathematical Foundations of Computer Science","location":"Prague, Czech Republic"},"oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:56Z","quality_controlled":"1","file_date_updated":"2020-09-21T14:17:08Z","tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"title":"Unary prime languages","doi":"10.4230/LIPIcs.MFCS.2020.51","article_number":"51:1-51:12","citation":{"apa":"Jecker, I. R., Kupferman, O., &#38; Mazzocchi, N. (2020). Unary prime languages. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>","chicago":"Jecker, Ismael R, Orna Kupferman, and Nicolas Mazzocchi. “Unary Prime Languages.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>.","mla":"Jecker, Ismael R., et al. “Unary Prime Languages.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 51:1-51:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>.","ista":"Jecker IR, Kupferman O, Mazzocchi N. 2020. Unary prime languages. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 51:1-51:12.","ama":"Jecker IR, Kupferman O, Mazzocchi N. Unary prime languages. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>","short":"I.R. Jecker, O. Kupferman, N. Mazzocchi, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"I. R. Jecker, O. Kupferman, and N. Mazzocchi, “Unary prime languages,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170."},"alternative_title":["LIPIcs"],"ddc":["000"],"publication":"45th International Symposium on Mathematical Foundations of Computer Science","month":"08","oa":1,"publication_status":"published","day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Ismaël Jecker: This project has received funding from the European Union’s Horizon\r\n2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.\r\n754411. Nicolas Mazzocchi: PhD fellowship FRIA from the F.R.S.-FNRS.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"has_accepted_license":"1","status":"public","date_published":"2020-08-18T00:00:00Z"},{"article_processing_charge":"No","_id":"8535","intvolume":"        39","ec_funded":1,"author":[{"last_name":"Skrivan","first_name":"Tomas","full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Soderstrom","first_name":"Andreas","full_name":"Soderstrom, Andreas"},{"full_name":"Johansson, John","last_name":"Johansson","first_name":"John"},{"last_name":"Sprenger","first_name":"Christoph","full_name":"Sprenger, Christoph"},{"first_name":"Ken","last_name":"Museth","full_name":"Museth, Ken"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J"}],"article_type":"original","file":[{"date_updated":"2020-09-21T07:51:44Z","file_size":20223953,"checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","content_type":"application/pdf","creator":"dernst","file_id":"8541","date_created":"2020-09-21T07:51:44Z","file_name":"2020_ACM_Skrivan.pdf","success":1,"relation":"main_file","access_level":"open_access"}],"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"type":"journal_article","volume":39,"date_created":"2020-09-20T22:01:37Z","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"oa_version":"Published Version","scopus_import":"1","abstract":[{"lang":"eng","text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation."}],"external_id":{"isi":["000583700300038"]},"year":"2020","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","doi":"10.1145/3386569.3392466","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.","mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>.","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &#38; Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>."},"article_number":"65","language":[{"iso":"eng"}],"date_updated":"2023-08-22T09:28:27Z","quality_controlled":"1","file_date_updated":"2020-09-21T07:51:44Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"has_accepted_license":"1","status":"public","date_published":"2020-07-08T00:00:00Z","ddc":["000"],"publication":"ACM Transactions on Graphics","isi":1,"month":"07","oa":1,"publication_status":"published","day":"08","issue":"4"},{"citation":{"ieee":"M. Mondelli, S. A. Hashemi, J. Cioffi, and A. Goldsmith, “Simplified successive cancellation decoding of polar codes has sublinear latency,” in <i>IEEE International Symposium on Information Theory - Proceedings</i>, Los Angeles, CA, United States, 2020, vol. 2020–June.","ama":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. Simplified successive cancellation decoding of polar codes has sublinear latency. In: <i>IEEE International Symposium on Information Theory - Proceedings</i>. Vol 2020-June. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>","ista":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. 2020. Simplified successive cancellation decoding of polar codes has sublinear latency. IEEE International Symposium on Information Theory - Proceedings. ISIT: Internation Symposium on Information Theory vol. 2020–June, 401–406.","mla":"Mondelli, Marco, et al. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” <i>IEEE International Symposium on Information Theory - Proceedings</i>, vol. 2020–June, 401–406, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>.","short":"M. Mondelli, S.A. Hashemi, J. Cioffi, A. Goldsmith, in:, IEEE International Symposium on Information Theory - Proceedings, IEEE, 2020.","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J., &#38; Goldsmith, A. (2020). Simplified successive cancellation decoding of polar codes has sublinear latency. In <i>IEEE International Symposium on Information Theory - Proceedings</i> (Vol. 2020–June). Los Angeles, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John Cioffi, and Andrea Goldsmith. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” In <i>IEEE International Symposium on Information Theory - Proceedings</i>, Vol. 2020–June. IEEE, 2020. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>."},"article_number":"401-406","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"doi":"10.1109/ISIT44484.2020.9174141","title":"Simplified successive cancellation decoding of polar codes has sublinear latency","quality_controlled":"1","date_updated":"2023-08-07T13:36:24Z","language":[{"iso":"eng"}],"status":"public","date_published":"2020-06-01T00:00:00Z","acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162 and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei.","publisher":"IEEE","department":[{"_id":"MaMo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"later_version","id":"9047"}]},"publication_status":"published","day":"01","oa":1,"month":"06","publication":"IEEE International Symposium on Information Theory - Proceedings","article_processing_charge":"No","_id":"8536","author":[{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"last_name":"Goldsmith","first_name":"Andrea","full_name":"Goldsmith, Andrea"}],"oa_version":"Preprint","conference":{"end_date":"2020-06-26","start_date":"2020-06-21","location":"Los Angeles, CA, United States","name":"ISIT: Internation Symposium on Information Theory"},"publication_identifier":{"isbn":["9781728164328"],"issn":["21578095"]},"arxiv":1,"volume":"2020-June","date_created":"2020-09-20T22:01:37Z","type":"conference","year":"2020","external_id":{"arxiv":["1909.04892"]},"abstract":[{"lang":"eng","text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1."}],"scopus_import":"1"},{"abstract":[{"lang":"eng","text":"We prove some recent experimental observations of Dan Reznik concerning periodic billiard orbits in ellipses. For example, the sum of cosines of the angles of a periodic billiard polygon remains constant in the 1-parameter family of such polygons (that exist due to the Poncelet porism). In our proofs, we use geometric and complex analytic methods."}],"scopus_import":"1","year":"2020","external_id":{"arxiv":["2001.02934"]},"date_created":"2020-09-20T22:01:38Z","type":"journal_article","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","arxiv":1,"publication_identifier":{"issn":["2199-675X"],"eissn":["2199-6768"]},"article_type":"original","ec_funded":1,"author":[{"last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"last_name":"Schwartz","first_name":"Richard","full_name":"Schwartz, Richard"},{"full_name":"Tabachnikov, Serge","last_name":"Tabachnikov","first_name":"Serge"}],"_id":"8538","article_processing_charge":"No","oa":1,"month":"09","publication":"European Journal of Mathematics","day":"09","publication_status":"published","acknowledgement":" This paper would not be written if not for Dan Reznik’s curiosity and persistence; we are very grateful to him. We also thank R. Garcia and J. Koiller for interesting discussions. It is a pleasure to thank the Mathematical Institute of the University of Heidelberg for its stimulating atmosphere. ST thanks M. Bialy for interesting discussions and the Tel Aviv\r\nUniversity for its invariable hospitality. AA was supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). RS is supported by NSF Grant DMS-1807320. ST was supported by NSF grant DMS-1510055 and SFB/TRR 191.","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","date_published":"2020-09-09T00:00:00Z","date_updated":"2021-12-02T15:10:17Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1007/s40879-020-00426-9","title":"Billiards in ellipses revisited","main_file_link":[{"url":"https://arxiv.org/abs/2001.02934","open_access":"1"}],"citation":{"ieee":"A. Akopyan, R. Schwartz, and S. Tabachnikov, “Billiards in ellipses revisited,” <i>European Journal of Mathematics</i>. Springer Nature, 2020.","chicago":"Akopyan, Arseniy, Richard Schwartz, and Serge Tabachnikov. “Billiards in Ellipses Revisited.” <i>European Journal of Mathematics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s40879-020-00426-9\">https://doi.org/10.1007/s40879-020-00426-9</a>.","apa":"Akopyan, A., Schwartz, R., &#38; Tabachnikov, S. (2020). Billiards in ellipses revisited. <i>European Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40879-020-00426-9\">https://doi.org/10.1007/s40879-020-00426-9</a>","short":"A. Akopyan, R. Schwartz, S. Tabachnikov, European Journal of Mathematics (2020).","ama":"Akopyan A, Schwartz R, Tabachnikov S. Billiards in ellipses revisited. <i>European Journal of Mathematics</i>. 2020. doi:<a href=\"https://doi.org/10.1007/s40879-020-00426-9\">10.1007/s40879-020-00426-9</a>","mla":"Akopyan, Arseniy, et al. “Billiards in Ellipses Revisited.” <i>European Journal of Mathematics</i>, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1007/s40879-020-00426-9\">10.1007/s40879-020-00426-9</a>.","ista":"Akopyan A, Schwartz R, Tabachnikov S. 2020. Billiards in ellipses revisited. European Journal of Mathematics."}},{"article_type":"original","author":[{"full_name":"Su, C.","last_name":"Su","first_name":"C."},{"last_name":"Zhao","first_name":"Gufang","full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhong, C.","first_name":"C.","last_name":"Zhong"}],"article_processing_charge":"No","_id":"8539","intvolume":"        53","abstract":[{"text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions.","lang":"eng"},{"text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. ","lang":"fre"}],"scopus_import":"1","page":"663-671","year":"2020","external_id":{"arxiv":["1708.08013"],"isi":["000592182600004"]},"volume":53,"date_created":"2020-09-20T22:01:38Z","type":"journal_article","oa_version":"Preprint","arxiv":1,"publication_identifier":{"issn":["0012-9593"]},"date_updated":"2023-08-22T09:27:57Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.24033/asens.2431","title":"On the K-theory stable bases of the springer resolution","main_file_link":[{"url":"https://arxiv.org/abs/1708.08013","open_access":"1"}],"citation":{"ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020.","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Société Mathématique de France, 2020. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>.","apa":"Su, C., Zhao, G., &#38; Zhong, C. (2020). On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Société Mathématique de France. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.","mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. 2020;53(3):663-671. doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>"},"oa":1,"month":"06","isi":1,"publication":"Annales Scientifiques de l'Ecole Normale Superieure","issue":"3","day":"01","publication_status":"published","publisher":"Société Mathématique de France","department":[{"_id":"TaHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2020-06-01T00:00:00Z"},{"title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","doi":"10.1101/2020.09.18.301481","article_processing_charge":"No","_id":"8557","citation":{"ieee":"V. Belyaeva <i>et al.</i>, “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” <i>bioRxiv</i>. .","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, <a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>.","ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.09.18.301481\">10.1101/2020.09.18.301481</a>","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>.","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.09.18.301481\">https://doi.org/10.1101/2020.09.18.301481</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.18.301481"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"author":[{"full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","first_name":"Vera"},{"last_name":"Wachner","first_name":"Stephanie","full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","full_name":"Gridchyn, Igor","first_name":"Igor","last_name":"Gridchyn"},{"first_name":"Markus","last_name":"Linder","full_name":"Linder, Markus"},{"full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","last_name":"Emtenani","first_name":"Shamsi"},{"last_name":"György","first_name":"Attila","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X"},{"last_name":"Sibilia","first_name":"Maria","full_name":"Sibilia, Maria"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E"}],"date_updated":"2024-03-25T23:30:12Z","ec_funded":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"type":"preprint","date_created":"2020-09-23T09:36:47Z","project":[{"call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"},{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800","name":"Tissue barrier penetration is crucial for immunity and metastasis"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","status":"public","date_published":"2020-09-18T00:00:00Z","month":"09","abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues."}],"oa":1,"publication":"bioRxiv","year":"2020","related_material":{"record":[{"status":"public","id":"10614","relation":"later_version"},{"id":"8983","relation":"dissertation_contains","status":"public"}]},"day":"18","publication_status":"submitted"},{"file_date_updated":"2023-05-23T20:54:43Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2024-02-21T12:43:21Z","article_number":"208","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. 2020;39(6). doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>","chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>.","ieee":"K. Gavriil <i>et al.</i>, “Computational design of cold bent glass façades,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6. Association for Computing Machinery, 2020."},"title":"Computational design of cold bent glass façades","doi":"10.1145/3414685.3417843","issue":"6","related_material":{"record":[{"id":"8366","relation":"dissertation_contains","status":"public"},{"id":"8761","relation":"research_data","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/bend-dont-break/","relation":"press_release","description":"News on IST Homepage"}]},"day":"26","publication_status":"published","month":"11","oa":1,"ddc":["000"],"publication":"ACM Transactions on Graphics","isi":1,"status":"public","date_published":"2020-11-26T00:00:00Z","has_accepted_license":"1","publisher":"Association for Computing Machinery","acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","department":[{"_id":"BeBi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","creator":"bbickel","file_id":"13084","file_size":28964641,"date_updated":"2023-05-23T20:54:43Z","checksum":"c7f67717ad74e670b7daeae732abe151","access_level":"open_access","date_created":"2023-05-23T20:54:43Z","relation":"main_file","file_name":"coldglass.pdf","success":1}],"ec_funded":1,"author":[{"full_name":"Gavriil, Konstantinos","first_name":"Konstantinos","last_name":"Gavriil"},{"full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","first_name":"Ruslan"},{"full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus"},{"full_name":"Pellis, Davide","first_name":"Davide","last_name":"Pellis"},{"first_name":"Paul M","last_name":"Henderson","orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M"},{"full_name":"Rist, Florian","last_name":"Rist","first_name":"Florian"},{"last_name":"Pottmann","first_name":"Helmut","full_name":"Pottmann, Helmut"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"}],"article_type":"original","intvolume":"        39","_id":"8562","article_processing_charge":"No","external_id":{"isi":["000595589100048"],"arxiv":["2009.03667"]},"year":"2020","abstract":[{"lang":"eng","text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface."}],"scopus_import":"1","oa_version":"Submitted Version","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"arxiv":1,"type":"journal_article","date_created":"2020-09-23T11:30:02Z","volume":39,"project":[{"grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}]},{"file":[{"success":1,"file_name":"upload.tgz","relation":"main_file","date_created":"2020-09-23T14:36:17Z","access_level":"open_access","checksum":"a16098a6d172f9c42ab5af5f6991668c","date_updated":"2020-09-23T14:36:17Z","file_size":145243906,"content_type":"application/x-compressed","creator":"jozsef","file_id":"8564"},{"file_size":11648,"date_updated":"2020-10-19T10:12:29Z","checksum":"0bfc54b7e14c0694cd081617318ba606","file_id":"8675","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jozsef","date_created":"2020-10-19T10:12:29Z","relation":"main_file","success":1,"file_name":"redme.docx","access_level":"open_access"}],"file_date_updated":"2020-10-19T10:12:29Z","date_updated":"2024-02-21T12:43:41Z","author":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L"},{"full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","last_name":"Gridchyn","first_name":"Igor"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp","first_name":"Philipp","last_name":"Schönenberger"}],"contributor":[{"contributor_type":"project_leader","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"citation":{"chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>.","apa":"Csicsvari, J. L., Gridchyn, I., &#38; Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>","mla":"Csicsvari, Jozsef L., et al. <i>Optogenetic Alteration of Hippocampal Network Activity</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>.","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>.","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020."},"doi":"10.15479/AT:ISTA:8563","title":"Optogenetic alteration of hippocampal network activity","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"No","_id":"8563","related_material":{"record":[{"id":"8740","relation":"used_in_publication","status":"public"}]},"year":"2020","day":"19","oa":1,"abstract":[{"text":"Supplementary data  provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife.","lang":"eng"}],"month":"10","ddc":["570"],"status":"public","oa_version":"Published Version","date_published":"2020-10-19T00:00:00Z","has_accepted_license":"1","date_created":"2020-09-23T14:39:54Z","department":[{"_id":"JoCs"}],"type":"research_data","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","department":[{"_id":"StFr"}],"has_accepted_license":"1","status":"public","date_published":"2020-09-24T00:00:00Z","publication":"Nature Communications","isi":1,"ddc":["530"],"oa":1,"month":"09","publication_status":"published","day":"24","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-020-18610-6","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","citation":{"chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., &#38; Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>, vol. 11, 4838, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>.","ieee":"C. Prehal <i>et al.</i>, “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020."},"article_number":"4838","date_updated":"2023-08-22T09:37:24Z","language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-09-28T13:16:15Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_created":"2020-09-25T07:23:13Z","volume":11,"type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"oa_version":"Published Version","abstract":[{"text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.","lang":"eng"}],"year":"2020","external_id":{"isi":["000573756600004"]},"article_processing_charge":"No","_id":"8568","intvolume":"        11","article_type":"original","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"first_name":"Harald","last_name":"Fitzek","full_name":"Fitzek, Harald"},{"last_name":"Kothleitner","first_name":"Gerald","full_name":"Kothleitner, Gerald"},{"last_name":"Presser","first_name":"Volker","full_name":"Presser, Volker"},{"full_name":"Gollas, Bernhard","first_name":"Bernhard","last_name":"Gollas"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"},{"first_name":"Qamar","last_name":"Abbas","full_name":"Abbas, Qamar"}],"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"8585","checksum":"eada7bc8dd16a49390137cff882ef328","file_size":1822469,"date_updated":"2020-09-28T13:16:15Z","access_level":"open_access","relation":"main_file","success":1,"file_name":"2020_NatureComm_Prehal.pdf","date_created":"2020-09-28T13:16:15Z"}]},{"intvolume":"         8","_id":"8569","article_processing_charge":"Yes (via OA deal)","file":[{"date_updated":"2020-09-28T13:11:17Z","file_size":5527139,"checksum":"01f731824194c94c81a5da360d997073","file_id":"8584","content_type":"application/pdf","creator":"dernst","date_created":"2020-09-28T13:11:17Z","file_name":"2020_Frontiers_Hansen.pdf","success":1,"relation":"main_file","access_level":"open_access"}],"author":[{"first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}],"ec_funded":1,"article_type":"original","publication_identifier":{"issn":["2296-634X"]},"oa_version":"Published Version","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"},{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","volume":8,"date_created":"2020-09-26T06:11:07Z","external_id":{"isi":["000577915900001"],"pmid":["33102480"]},"year":"2020","scopus_import":"1","abstract":[{"text":"Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future.","lang":"eng"}],"citation":{"short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020).","ista":"Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382.","ama":"Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. <i>Frontiers in Cell and Developmental Biology</i>. 2020;8(9). doi:<a href=\"https://doi.org/10.3389/fcell.2020.574382\">10.3389/fcell.2020.574382</a>","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 8, no. 9, 574382, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fcell.2020.574382\">10.3389/fcell.2020.574382</a>.","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fcell.2020.574382\">https://doi.org/10.3389/fcell.2020.574382</a>.","apa":"Hansen, A. H., &#38; Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fcell.2020.574382\">https://doi.org/10.3389/fcell.2020.574382</a>","ieee":"A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 8, no. 9. Frontiers, 2020."},"article_number":"574382","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","doi":"10.3389/fcell.2020.574382","file_date_updated":"2020-09-28T13:11:17Z","quality_controlled":"1","date_updated":"2024-03-25T23:30:23Z","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","date_published":"2020-09-25T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.","publisher":"Frontiers","department":[{"_id":"SiHi"}],"day":"25","publication_status":"published","pmid":1,"issue":"9","related_material":{"record":[{"status":"public","id":"9962","relation":"dissertation_contains"}]},"ddc":["570"],"publication":"Frontiers in Cell and Developmental Biology","isi":1,"month":"09","oa":1}]