[{"page":"187","title":"Towards efficient secure group messaging","fulldoi":"https://doi.org/10.15479/AT-ISTA-22664","file":[{"access_level":"open_access","checksum":"d61beeb9a250a04396c2c61bbd0783aa","content_type":"application/pdf","creator":"mcuetono","relation":"main_file","file_id":"22702","date_updated":"2026-08-19T11:36:46Z","date_created":"2026-08-13T09:39:00Z","file_name":"2026_CuetoNoval_Miguel_Thesis.pdf","file_size":1390255},{"access_level":"closed","content_type":"application/zip","file_id":"22703","creator":"mcuetono","date_updated":"2026-08-14T10:26:06Z","relation":"source_file","checksum":"4d6def422cc93a108faf5e5defc0f807","file_name":"2026_CuetoNoval_Miguel_Thesis.zip","date_created":"2026-08-13T09:39:01Z","file_size":9923509}],"author":[{"last_name":"Cueto Noval","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel","first_name":"Miguel","orcid":"0000-0002-2505-4246"}],"file_date_updated":"2026-08-19T11:36:46Z","ddc":["000"],"publication_identifier":{"isbn":[" 978-3-99078-087-9"],"issn":["2663-337X"]},"related_material":{"record":[{"id":"21262","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14691"},{"status":"public","id":"18702","relation":"part_of_dissertation"}]},"date_updated":"2026-10-16T10:14:40Z","doi":"10.15479/AT-ISTA-22664","OA_place":"publisher","year":"2026","citation":{"mla":"Cueto Noval, Miguel. <i>Towards Efficient Secure Group Messaging</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22664\">10.15479/AT-ISTA-22664</a>.","short":"M. Cueto Noval, Towards Efficient Secure Group Messaging, Institute of Science and Technology Austria, 2026.","apa":"Cueto Noval, M. (2026). <i>Towards efficient secure group messaging</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22664\">https://doi.org/10.15479/AT-ISTA-22664</a>","chicago":"Cueto Noval, Miguel. “Towards Efficient Secure Group Messaging.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22664\">https://doi.org/10.15479/AT-ISTA-22664</a>.","ama":"Cueto Noval M. Towards efficient secure group messaging. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22664\">10.15479/AT-ISTA-22664</a>","ista":"Cueto Noval M. 2026. Towards efficient secure group messaging. Institute of Science and Technology Austria.","ieee":"M. Cueto Noval, “Towards efficient secure group messaging,” Institute of Science and Technology Austria, 2026."},"department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","doi_confirm":"1","degree_awarded":"PhD","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"day":"10","_id":"22664","type":"dissertation","corr_author":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"month":"08","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2026-08-10T10:18:35Z","oa_version":"Published Version","article_processing_charge":"No","date_published":"2026-08-10T00:00:00Z","abstract":[{"lang":"eng","text":"The widespread adoption of apps like Whatsapp and Signal has translated into billions of people all around the world communicating on a regular basis by making use of services that offer end-to-end encryption and even provide security guarantees when a user's device is compromised.\r\n\r\nThis was made possible by the introduction of the Double Ratchet Algorithm~\\cite{double_ratchet}, which was designed for a setting where communication takes place between two parties.\r\nHowever, in practice, many apps offer the possibility of creating groups.\r\nThe protocols they use to secure communication are inefficient for large group which has the undesireable consequence that the aforementioned apps have established limits on the group size of roughly 1000 users.\r\nThis has motivated the introduction of the Messaging Layer Security (MLS) standard~\\cite{rfc9420} by the IETF which is based on a primitive called Continuous Group Key Agreement (CGKA)~\\cite{C:ACDT20}.\r\n\r\nThis primitive allows a group of users to maintain a shared secret key that is frequently rotated by the group members in order to change group membership, achieve forward secrecy (FS) and post compromise security (PCS).\r\nMost protocols are based on binary trees where the nodes are associated to a pair formed by public key and a secret key.\r\nEach leaf corresponds to one of the group members and a user knows the secret keys associated to nodes along the path from their leaf to the root.\r\nWhen a user wants to update their key material they have to change $ \\log(N) $ many keys.\r\nThis requires uploading $ \\log(N) $ many ciphertexts to communicate the new keys to the rest of the group members in a way that respects the tree structure.\r\n\r\nIn this thesis we study how much communication between group members is required in order to add and remove users from a group as well as in order to provide PCS when we consider CGKAs built using standard cryptographic primitives like pseudo-random functions and public-key encryption. Furthermore, we also consider the case of MLS and provide the first lower bound showing that its communication complexity is much worse than previously believed, i.e., it is very far from $ \\log(N) $.\r\nFinally, we also propose a variant of MLS which provably achieves the same security properties with a much lower communication cost."}],"has_accepted_license":"1","publication_status":"published","status":"public","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"]},{"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","has_accepted_license":"1","supplementarymaterial":"no","status":"public","publication_status":"published","abstract":[{"text":"Artificial intelligence and machine learning have undergone an unprecedented evolution in the past decade, motivating a research effort toward a theory able to capture the qualitative behavior of large-scale neural systems. A central puzzle has been the clear benefit of scaling architecture size and overfitting the training set in supervised learning tasks. This evidence, in apparent contradiction with classical statistical learning theory, pushed researchers to develop a new theory capturing the interplay between the algorithmic and architectural bias of training and the specific target function, differently from previous methods rooted in uniform stability.\r\nThis approach has enabled a grounded understanding of novel learning regimes, typically through formal limits where the number of training samples $n$, data dimensions $d$, and model parameters $p$ grow to infinity at different rates. \\\\\r\nIn this thesis, we follow this approach, focusing on the trustworthiness of high-dimensional models: properties that are difficult to control during training or deployment and often emerge under unpredictable or adversarial conditions. In such settings, it is crucial to formally ensure a priori the reliability of machine learning systems.\r\nFirst, we study data memorization, both as label fitting and as the storage of private information about training samples in trained parameters. We prove that $p = \\Omega(n)$ parameters are sufficient for a deep neural network to memorize a generic set of labels, and for a model to memorize spurious features across training data. We then give evidence that $p = \\Omega(dn)$ parameters are instead necessary for an adversary to reconstruct the full training set from the trained parameters.\r\nSecond, we study robustness, both to adversarial perturbations and to distribution shift. We first prove that $p = \\Omega(dn)$ parameters can be sufficient for a class of neural networks to overfit the training data while guaranteeing robustness to adversarial perturbations. Then, we focus on spurious correlations learning in high-dimensional regression, studying the effect of the ridge regularization parameter in the proportional regime $n = \\Theta(d)$, and connecting it via an equivalence argument to the role of over-parameterization $p = \\Omega(n)$ in neural networks. We also investigate the architectural bias of attention-based networks, showing that they are sensitive to the replacement of individual words in an embedded sentence, allowing them to generalize on sentences where the contextual meaning depends on one or few words.\r\nFinally, we study differentially private optimization in high-dimensional regimes. We prove that standard private gradient methods do not suffer in the over-parameterized regime $p = \\Omega(n)$, challenging the current wisdom based on stability-derived generalization bounds. We then consider linear regression in the proportional regime $n = \\Theta(d)$, showing that standard private gradient descent can achieve optimal rates under appropriate hyper-parameter scaling, such as sufficiently small gradient clipping constants, whose role is still debated in practice.","lang":"eng"}],"date_published":"2026-09-08T00:00:00Z","article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","researchdata_availability":"no","date_created":"2026-09-08T13:40:08Z","keyword":["machine learning","high-dimensional statistics","deep learning theory","privacy","memorization","robustness"],"month":"09","corr_author":"1","_id":"22857","day":"08","type":"dissertation","supervisor":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"oa":1,"OA_place":"publisher","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"year":"2026","citation":{"ieee":"S. Bombari, “Trustworthy machine learning in high dimensions,” Institute of Science and Technology Austria, 2026.","ista":"Bombari S. 2026. Trustworthy machine learning in high dimensions. Institute of Science and Technology Austria.","ama":"Bombari S. Trustworthy machine learning in high dimensions. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22857\">10.15479/AT-ISTA-22857</a>","chicago":"Bombari, Simone. “Trustworthy Machine Learning in High Dimensions.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22857\">https://doi.org/10.15479/AT-ISTA-22857</a>.","apa":"Bombari, S. (2026). <i>Trustworthy machine learning in high dimensions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22857\">https://doi.org/10.15479/AT-ISTA-22857</a>","short":"S. Bombari, Trustworthy Machine Learning in High Dimensions, Institute of Science and Technology Austria, 2026.","mla":"Bombari, Simone. <i>Trustworthy Machine Learning in High Dimensions</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22857\">10.15479/AT-ISTA-22857</a>."},"date_updated":"2026-10-16T10:42:36Z","doi":"10.15479/AT-ISTA-22857","ddc":["519"],"acknowledgement":"This project was partially supported by the 2019 Lopez-Loreta prize,\r\nthe European Union (ERC, INF2\r\n, project number 101161364), the Austrian Science Fund\r\n(FWF) 10.55776/COE12, and a Google PhD fellowship in machine intelligence. Furthermore,\r\nthe candidate acknowledges the support from the Scientific Service Units of the Institute of\r\nScience and Technology Austria through resources provided by Scientific Computing.","file_date_updated":"2026-09-10T10:03:48Z","related_material":{"record":[{"id":"12537","status":"public","relation":"part_of_dissertation"},{"id":"21324","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"22894"},{"id":"19627","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12859","status":"public"},{"relation":"part_of_dissertation","id":"18973","status":"public"},{"relation":"part_of_dissertation","id":"18972","status":"public"}]},"das_tickbox":"0","publication_identifier":{"isbn":["978-3-99078-091-6"],"issn":["2663-337X"]},"title":"Trustworthy machine learning in high dimensions","page":"446","author":[{"last_name":"Bombari","id":"ca726dda-de17-11ea-bc14-f9da834f63aa","full_name":"Bombari, Simone","first_name":"Simone"}],"file":[{"date_created":"2026-09-08T13:28:38Z","file_name":"Thesis copy.zip","file_size":99154325,"access_level":"closed","checksum":"8eab99d6dc6e4476826bdfc7c00fdebb","creator":"sbombari","relation":"source_file","date_updated":"2026-09-08T13:28:38Z","file_id":"22859","content_type":"application/zip"},{"file_size":12856211,"date_created":"2026-09-10T10:03:48Z","file_name":"2026_Bombari_Simone_Thesis.pdf","success":1,"checksum":"007033bafe4622ff4c2e758301354df1","relation":"main_file","date_updated":"2026-09-10T10:03:48Z","file_id":"22898","creator":"sbombari","content_type":"application/pdf","access_level":"open_access"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22857","project":[{"name":"Trustworthy Deep Learning Theory: Private Over-Parameterized Models and Robust LLMs","_id":"92099302-16d5-11f0-9cad-f9a785f54fbd"},{"_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","grant_number":"101161364"},{"grant_number":"COE12","name":"Bilateral Artificial Intelligence (Mondelli)","_id":"74caaef7-b034-11f1-8f2d-e0e993bb422e"}]},{"das_tickbox":"1","publication_identifier":{"eissn":["2331-7019"]},"acknowledgement":"The authors thank Afonso Oliveira, Stefano Calcaterra, Daniel Chrastina, and Giovanni Isella for providing the Ge/SiGe heterostructure. This work was supported by the Research Council of Norway through its Centers of Excellence funding scheme, Project No. 262633, “QuSpin,” the FWF Project with DOI:10.55776/PAT7682124, OeAD “ISTA Austria: ISTernship Summer Programme, Non-EU countries” (Ref. No.: MPC-2025-00945), the Spanish Comunidad de Madrid (CM) “Talento Program” (Project No. 2022-T1/IND-24070), and the Spanish Ministry of Science, Innovation, and Universities through Grants No. CEX2024-001445-S (Severo Ochoa Centres of Excellence program) and No. PID2022-140552NA-I00, funded by MCIN/AEI/10.13039/501100011033.","issue":"4","author":[{"last_name":"Tjøtta","first_name":"Maxim","full_name":"Tjøtta, Maxim"},{"id":"de191434-4e7e-11ef-bf4b-9a056fc19fc3","last_name":"Shah","full_name":"Shah, Devashish C","orcid":"0009-0007-5829-7707","first_name":"Devashish C"},{"last_name":"Modi","id":"f05345fd-900f-11f1-bfd8-8c0b6eadcc7f","full_name":"Modi, Kanishk","first_name":"Kanishk"},{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","first_name":"Marco","full_name":"Valentini, Marco"},{"first_name":"Rubén","full_name":"Seoane Souto, Rubén","last_name":"Seoane Souto"},{"first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jeroen","full_name":"Danon, Jeroen","last_name":"Danon"}],"publication":"Physical Review Applied","fulldoi":"https://doi.org/10.1103/d3gl-qntm","project":[{"name":"Superconducting spin qubits in planar Ge","grant_number":"PAT 7682124","_id":"5b9e579c-ab3d-11f0-914f-88754c5b5a3f"}],"title":"Fast-driving spectroscopy of current-phase relationships of individual Josephson elements","volume":26,"publisher":"American Physical Society","citation":{"ama":"Tjøtta M, Shah DC, Modi K, et al. Fast-driving spectroscopy of current-phase relationships of individual Josephson elements. <i>Physical Review Applied</i>. 2026;26(4). doi:<a href=\"https://doi.org/10.1103/d3gl-qntm\">10.1103/d3gl-qntm</a>","ista":"Tjøtta M, Shah DC, Modi K, Valentini M, Seoane Souto R, Katsaros G, Danon J. 2026. Fast-driving spectroscopy of current-phase relationships of individual Josephson elements. Physical Review Applied. 26(4), 044017.","chicago":"Tjøtta, Maxim, Devashish C Shah, Kanishk Modi, Marco Valentini, Rubén Seoane Souto, Georgios Katsaros, and Jeroen Danon. “Fast-Driving Spectroscopy of Current-Phase Relationships of Individual Josephson Elements.” <i>Physical Review Applied</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/d3gl-qntm\">https://doi.org/10.1103/d3gl-qntm</a>.","ieee":"M. Tjøtta <i>et al.</i>, “Fast-driving spectroscopy of current-phase relationships of individual Josephson elements,” <i>Physical Review Applied</i>, vol. 26, no. 4. American Physical Society, 2026.","short":"M. Tjøtta, D.C. Shah, K. Modi, M. Valentini, R. Seoane Souto, G. Katsaros, J. Danon, Physical Review Applied 26 (2026).","apa":"Tjøtta, M., Shah, D. C., Modi, K., Valentini, M., Seoane Souto, R., Katsaros, G., &#38; Danon, J. (2026). Fast-driving spectroscopy of current-phase relationships of individual Josephson elements. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/d3gl-qntm\">https://doi.org/10.1103/d3gl-qntm</a>","mla":"Tjøtta, Maxim, et al. “Fast-Driving Spectroscopy of Current-Phase Relationships of Individual Josephson Elements.” <i>Physical Review Applied</i>, vol. 26, no. 4, 044017, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/d3gl-qntm\">10.1103/d3gl-qntm</a>."},"year":"2026","department":[{"_id":"GeKa"},{"_id":"GradSch"}],"OA_place":"repository","scopus_import":"1","external_id":{"arxiv":["2511.14313"]},"date_updated":"2026-10-19T07:25:01Z","doi":"10.1103/d3gl-qntm","researchdata_availability":"yes","date_created":"2026-10-18T22:01:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        26","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2511.14313"}],"month":"10","arxiv":1,"dataavailabilitystatement":"The data that support the findings of this article are openly available at [10.5281/zenodo.22646275].","OA_type":"green","oa":1,"quality_controlled":"1","type":"journal_article","_id":"23156","day":"01","article_number":"044017","article_type":"original","language":[{"iso":"eng"}],"date_published":"2026-10-01T00:00:00Z","abstract":[{"text":"Extracting the current-phase relationship (CPR) of a single superconducting junction is challenging in practice and traditionally involves embedding the junction in a larger superconducting circuit containing SQUIDs and/or resonators. Applying ac driving to the junction has proven to be a viable and less invasive way to extract information about the few lowest harmonics of the CPR, by locating the integer and fractional Shapiro steps in the 𝐼⁢𝑉-curve of the driven junction. Here, we present an alternative driving-based method that allows to extract the full harmonic content of a CPR in a relatively noninvasive way, by fitting the measured critical currents of the driven junction as a function of driving power. We test our method, both using numerical simulations and in experiments, and we show that it works accurately.","lang":"eng"}],"publication_status":"published","supplementarymaterial":"yes","status":"public","article_processing_charge":"No","oa_version":"Preprint"},{"title":"Self-lensing flares from black hole binaries. V. Systematic searches in LSST","fulldoi":"https://doi.org/10.1103/p328-62sl","file":[{"access_level":"open_access","creator":"dernst","date_updated":"2026-10-19T08:06:17Z","file_id":"23167","relation":"main_file","content_type":"application/pdf","success":1,"checksum":"764bd6512975216dd63655da64ceeb95","file_name":"2026_PhysicalReviewD_Park.pdf","date_created":"2026-10-19T08:06:17Z","file_size":3535182}],"publication":"Physical Review D","author":[{"id":"c0a7603b-66e5-11f0-aaf9-b02edf8b2969","last_name":"Park","first_name":"Kevin S","full_name":"Park, Kevin S"},{"last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán","orcid":"0000-0003-3633-5403","full_name":"Haiman, Zoltán"},{"first_name":"Chengcheng","full_name":"Xin, Chengcheng","last_name":"Xin"},{"last_name":"Shen","full_name":"Shen, Tzuken","first_name":"Tzuken"},{"last_name":"Villar","full_name":"Villar, Ashley","first_name":"Ashley"},{"first_name":"Jordy","full_name":"Davelaar, Jordy","last_name":"Davelaar"}],"file_date_updated":"2026-10-19T08:06:17Z","issue":"4","ddc":["520"],"acknowledgement":"We acknowledge support by NASA Grants No. 80NSSC22K0822 and No. 80NSSC24K0440 (Z. H). V. A. V. acknowledges support through the David and Lucile Packard Foundation, National Science Foundation under No. PHY-2019786 (The NSF AI Institute for Artificial Intelligence and Fundamental Interactions, [63]), No. AST-2433718, No. AST-2407922 and No. AST-2406110, as well as an Aramont Fellowship for Emerging Science Research. J. D. acknowledges support by a joint Columbia/Flatiron Postdoctoral Fellowship. Research at the Flatiron Institute is supported by the Simons Foundation. This research was supported in part by the National Science Foundation under Grant No. NSF PHY-1748958 to the Kavli Institute for Theoretical Physics (KITP). This research has made use of NASA’s Astrophysics Data System. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computational resources. V. A. V. acknowledges support through the David and Lucile Packard Foundation, National Science Foundation under No. AST-2433718, No. AST-2407922 and No. AST-2406110, as well as an Aramont Fellowship for Emerging Science Research. This work is supported by the National Science Foundation under Cooperative Agreement No. PHY-2019786 (The NSF AI Institute for Artificial Intelligence and Fundamental Interactions, [63]).","publication_identifier":{"eissn":["2470-0029"],"issn":["2470-0010"]},"das_tickbox":"1","external_id":{"arxiv":["2512.08427"]},"doi":"10.1103/p328-62sl","date_updated":"2026-10-19T08:08:21Z","scopus_import":"1","OA_place":"publisher","year":"2026","citation":{"ieee":"K. S. Park, Z. Haiman, C. Xin, T. Shen, A. Villar, and J. Davelaar, “Self-lensing flares from black hole binaries. V. Systematic searches in LSST,” <i>Physical Review D</i>, vol. 113, no. 4. American Physical Society, 2026.","chicago":"Park, Kevin S, Zoltán Haiman, Chengcheng Xin, Tzuken Shen, Ashley Villar, and Jordy Davelaar. “Self-Lensing Flares from Black Hole Binaries. V. Systematic Searches in LSST.” <i>Physical Review D</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/p328-62sl\">https://doi.org/10.1103/p328-62sl</a>.","ista":"Park KS, Haiman Z, Xin C, Shen T, Villar A, Davelaar J. 2026. Self-lensing flares from black hole binaries. V. Systematic searches in LSST. Physical Review D. 113(4), 043055.","ama":"Park KS, Haiman Z, Xin C, Shen T, Villar A, Davelaar J. Self-lensing flares from black hole binaries. V. Systematic searches in LSST. <i>Physical Review D</i>. 2026;113(4). doi:<a href=\"https://doi.org/10.1103/p328-62sl\">10.1103/p328-62sl</a>","mla":"Park, Kevin S., et al. “Self-Lensing Flares from Black Hole Binaries. V. Systematic Searches in LSST.” <i>Physical Review D</i>, vol. 113, no. 4, 043055, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/p328-62sl\">10.1103/p328-62sl</a>.","short":"K.S. Park, Z. Haiman, C. Xin, T. Shen, A. Villar, J. Davelaar, Physical Review D 113 (2026).","apa":"Park, K. S., Haiman, Z., Xin, C., Shen, T., Villar, A., &#38; Davelaar, J. (2026). Self-lensing flares from black hole binaries. V. Systematic searches in LSST. <i>Physical Review D</i>. American Physical Society. <a href=\"https://doi.org/10.1103/p328-62sl\">https://doi.org/10.1103/p328-62sl</a>"},"department":[{"_id":"GradSch"},{"_id":"ZoHa"}],"volume":113,"publisher":"American Physical Society","_id":"23159","day":"25","type":"journal_article","quality_controlled":"1","PlanS_conform":"1","oa":1,"OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"dataavailabilitystatement":"The data are not publicly available. The data are available from the authors upon reasonable request.","arxiv":1,"intvolume":"       113","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-10-18T22:01:53Z","researchdata_availability":"no","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","date_published":"2026-02-25T00:00:00Z","supplementarymaterial":"yes","publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"The Vera C. Rubin Observatory has now seen first light, and over a 10 year duration, Legacy Survey of Space and Time (LSST) is projected to catalog tens of millions of quasars, many of which are expected to be associated with subparsec supermassive black hole binaries (SMBHBs). Out of these SMBHBs, up to thousands of relatively massive binary-quasars are expected to exhibit gravitational self-lensing flares (SLFs) that last for at least 20–30 days. We assess the effectiveness of the Lomb-Scargle (LS) periodogram and matched filters (MFs) as methods for systematic searches for these binaries, using toy-models of hydrodynamical, Doppler, and self-lensing variability from equal-mass, eccentric SMBHBs. We inject SLFs into random realizations of damped random walk (DRW) lightcurves, representing stochastic quasar variability, and compute the LS periodogram with and without the SLF. We find that periodograms of SLF+DRW light-curves do not have maximum peak heights that could not arise from DRW-only periodograms. On the other hand, the matched filter signal-to-noise ratio (SNR) can distinguish SLFs from noise even with LSST-like cadences and DRW noise. Furthermore, we develop a three-step procedure with matched filters, which can also recover injected binary parameters from these light-curves. We expect this method to be computationally efficient enough to be applicable to millions of quasar light-curves in LSST."}],"has_accepted_license":"1","language":[{"iso":"eng"}],"article_type":"original","article_number":"043055"},{"scopus_import":"1","external_id":{"arxiv":["2505.22875"]},"date_updated":"2026-10-19T07:39:17Z","doi":"10.1214/26-AAP2345","OA_place":"publisher","publisher":"Institute of Mathematical Statistics","volume":36,"year":"2026","citation":{"mla":"Hollom, Lawrence, et al. “Monotonicity and Decompositions of Random Regular Graphs.” <i>Annals of Applied Probability</i>, vol. 36, no. 5, Institute of Mathematical Statistics, 2026, pp. 4716–38, doi:<a href=\"https://doi.org/10.1214/26-AAP2345\">10.1214/26-AAP2345</a>.","short":"L. Hollom, L. Lichev, A. Mond, J. Portier, Y. Wang, Annals of Applied Probability 36 (2026) 4716–4738.","apa":"Hollom, L., Lichev, L., Mond, A., Portier, J., &#38; Wang, Y. (2026). Monotonicity and decompositions of random regular graphs. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/26-AAP2345\">https://doi.org/10.1214/26-AAP2345</a>","chicago":"Hollom, Lawrence, Lyuben Lichev, Adva Mond, Julien Portier, and Yiting Wang. “Monotonicity and Decompositions of Random Regular Graphs.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2026. <a href=\"https://doi.org/10.1214/26-AAP2345\">https://doi.org/10.1214/26-AAP2345</a>.","ista":"Hollom L, Lichev L, Mond A, Portier J, Wang Y. 2026. Monotonicity and decompositions of random regular graphs. Annals of Applied Probability. 36(5), 4716–4738.","ama":"Hollom L, Lichev L, Mond A, Portier J, Wang Y. Monotonicity and decompositions of random regular graphs. <i>Annals of Applied Probability</i>. 2026;36(5):4716-4738. doi:<a href=\"https://doi.org/10.1214/26-AAP2345\">10.1214/26-AAP2345</a>","ieee":"L. Hollom, L. Lichev, A. Mond, J. Portier, and Y. Wang, “Monotonicity and decompositions of random regular graphs,” <i>Annals of Applied Probability</i>, vol. 36, no. 5. Institute of Mathematical Statistics, pp. 4716–4738, 2026."},"department":[{"_id":"MaKw"},{"_id":"GradSch"}],"page":"4716-4738","title":"Monotonicity and decompositions of random regular graphs","author":[{"last_name":"Hollom","full_name":"Hollom, Lawrence","first_name":"Lawrence"},{"last_name":"Lichev","id":"9aa8388e-d003-11ee-8458-c4c1d7447977","first_name":"Lyuben","full_name":"Lichev, Lyuben"},{"last_name":"Mond","first_name":"Adva","full_name":"Mond, Adva"},{"last_name":"Portier","full_name":"Portier, Julien","first_name":"Julien"},{"first_name":"Yiting","full_name":"Wang, Yiting","last_name":"Wang","id":"1917d194-076e-11ed-97cd-837255f88785"}],"publication":"Annals of Applied Probability","project":[{"name":"Randomness and structure in combinatorics","grant_number":"101076777","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"},{"_id":"e19fef4c-1f3d-11f0-ac04-b8b1af6886d8","grant_number":"E624","name":"THRESHOLDS IN SEMI-RANDOM PROCESSES AND GRAPH EMBEDDINGS"}],"fulldoi":"https://doi.org/10.1214/26-AAP2345","file":[{"file_size":320593,"file_name":"2026_AnnalsAppliedProbability_Hollom.pdf","date_created":"2026-10-19T07:33:58Z","creator":"dernst","relation":"main_file","date_updated":"2026-10-19T07:33:58Z","file_id":"23165","content_type":"application/pdf","success":1,"checksum":"46101e61d29cf40f0a204801d15a848f","access_level":"open_access"}],"ddc":["500"],"acknowledgement":"We are grateful to Béla Bollobás, to Matthew Kwan and to Fabio\r\nToninelli for their helpful comments and suggestions, and to Nicholas Wormald for useful\r\nremarks on a preliminary version of this work and pointing us towards the reference [29].\r\nThe authors would also like to thank several anonymous referees for many useful suggestions,\r\nincluding pointing out that Lemma 2.10 already appeared in [11].\r\nPart of this research was done during a visit of the fourth author to IST Austria. We thank\r\nIST Austria for its hospitality.\r\nFor open access purposes, the authors have applied a CC BY public copyright license to\r\nany author accepted manuscript version arising from this submission. L. Hollom was supported by the Internal Graduate Studentship of Trinity College, Cambridge.\r\nL. Lichev was supported by the Austrian Science Fund (FWF) grant No. 10.55776/ESP624.\r\nA. Mond was supported by UK Research and Innovation grant MR/W007320/2. Wang was\r\nsupported by the ERC Starting Grant “RANDSTRUCT” No. 101076777.","file_date_updated":"2026-10-19T07:33:58Z","issue":"5","das_tickbox":"0","publication_identifier":{"issn":["1050-5164"],"eissn":["2168-8737"]},"oa_version":"Published Version","date_published":"2026-10-01T00:00:00Z","publication_status":"published","status":"public","supplementarymaterial":"no","has_accepted_license":"1","abstract":[{"lang":"eng","text":"In this work we establish several monotonicity and decomposition results in the framework of random regular graphs. Among other results, we\r\nshow that, for a wide range of parameters d1 ≤ d2, there exists a coupling of\r\nG(n,d1) and G(n,d2) satisfying that G(n,d1) ⊆ G(n,d2) with high probability, confirming a conjecture of Gao, Isaev and McKay in a new regime.\r\nOur contributions include new tools for analysing contiguity and total variation distance between random regular graph models, a novel procedure for\r\ngenerating unions of random edge-disjoint perfect matchings, and refined estimates of Gao’s bounds on the number of perfect matchings in random regular graphs. In addition, we make progress towards another conjecture of Isaev,\r\nMcKay, Southwell and Zhukovskii."}],"article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"article_type":"original","PlanS_conform":"1","quality_controlled":"1","type":"journal_article","_id":"23155","day":"01","oa":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"arxiv":1,"OA_type":"hybrid","keyword":["Random regular graphs","coupling","contiguity","total variation distance","decomposition"],"mathsc":["05C80"],"date_created":"2026-10-18T22:01:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"no","intvolume":"        36","month":"10"},{"OA_place":"publisher","department":[{"_id":"PaSc"},{"_id":"GradSch"}],"year":"2026","citation":{"ieee":"D. Rohden, F. Napoli, R. J. Lichtenecker, and P. Schanda, “Chemoenzymatic proline isotope labeling for solution and magic-angle spinning protein nuclear magnetic resonance,” <i>ACS Chemical Biology</i>. American Chemical Society, 2026.","chicago":"Rohden, Darja, Federico Napoli, Roman J. Lichtenecker, and Paul Schanda. “Chemoenzymatic Proline Isotope Labeling for Solution and Magic-Angle Spinning Protein Nuclear Magnetic Resonance.” <i>ACS Chemical Biology</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acschembio.6c00587\">https://doi.org/10.1021/acschembio.6c00587</a>.","ama":"Rohden D, Napoli F, Lichtenecker RJ, Schanda P. Chemoenzymatic proline isotope labeling for solution and magic-angle spinning protein nuclear magnetic resonance. <i>ACS Chemical Biology</i>. 2026. doi:<a href=\"https://doi.org/10.1021/acschembio.6c00587\">10.1021/acschembio.6c00587</a>","ista":"Rohden D, Napoli F, Lichtenecker RJ, Schanda P. 2026. Chemoenzymatic proline isotope labeling for solution and magic-angle spinning protein nuclear magnetic resonance. ACS Chemical Biology.","mla":"Rohden, Darja, et al. “Chemoenzymatic Proline Isotope Labeling for Solution and Magic-Angle Spinning Protein Nuclear Magnetic Resonance.” <i>ACS Chemical Biology</i>, American Chemical Society, 2026, doi:<a href=\"https://doi.org/10.1021/acschembio.6c00587\">10.1021/acschembio.6c00587</a>.","apa":"Rohden, D., Napoli, F., Lichtenecker, R. J., &#38; Schanda, P. (2026). Chemoenzymatic proline isotope labeling for solution and magic-angle spinning protein nuclear magnetic resonance. <i>ACS Chemical Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acschembio.6c00587\">https://doi.org/10.1021/acschembio.6c00587</a>","short":"D. Rohden, F. Napoli, R.J. Lichtenecker, P. Schanda, ACS Chemical Biology (2026)."},"publisher":"American Chemical Society","date_updated":"2026-10-19T11:20:33Z","doi":"10.1021/acschembio.6c00587","external_id":{"pmid":["42863127"]},"pmid":1,"scopus_import":"1","acknowledgement":"We thank Undina Guillerm, Rajkumar Singh and Anna Kapitonova for help with protein production. We are grateful to Dominique Madern for discussions and for providing the plasmid of IiMDH. We acknowledge the Scientific Service Units (SSU) of the Institute of Science and Technology Austria (ISTA) through resources provided by the NMR Facility and the Lab Support Facility, as well as the NMR centre and MS centre of the University of Vienna. This work was supported by the Austrian Science Fund (FWF; project number I5812-B) through a French-Austrian binational research project, as well as by the L’Oréal-UNESCO For Women in Science Fellowship, awarded in cooperation with the Austrian Academy of Sciences (ÖAW) and the Austrian Commission for UNESCO.","ddc":["540"],"publication_identifier":{"eissn":["1554-8937"],"issn":["1554-8929"]},"das_tickbox":"1","title":"Chemoenzymatic proline isotope labeling for solution and magic-angle spinning protein nuclear magnetic resonance","project":[{"_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery","grant_number":"I05812"}],"fulldoi":"https://doi.org/10.1021/acschembio.6c00587","publication":"ACS Chemical Biology","author":[{"id":"81dc668a-19fa-11f0-bf31-d56534059ef3","last_name":"Rohden","full_name":"Rohden, Darja","first_name":"Darja"},{"id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","last_name":"Napoli","full_name":"Napoli, Federico","orcid":"0000-0002-9043-136X","first_name":"Federico"},{"last_name":"Lichtenecker","first_name":"Roman J.","full_name":"Lichtenecker, Roman J."},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_type":"original","language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"publication_status":"epub_ahead","has_accepted_license":"1","status":"public","abstract":[{"text":"The prevalence of proline residues in intrinsically disordered proteins, functional hinges of enzymes, and protein interaction sites highlights the importance of studying their local dynamics and interactions at atomic resolution. While nuclear magnetic resonance (NMR) spectroscopy is, in principle, ideally suited for such investigations, the absence of an amide proton precludes the use of conventional 1H–15N amide-detected experiments. 1H–13C-based approaches, though possible, remain challenging in large proteins. In this work, we present a selective labeling strategy that introduces an isolated 1H2δ–13Cδ–15N spin system in proline residues in otherwise deuterated proteins. Our method leverages the enzymatic conversion of ornithine, synthesized from cost-effective isotopic precursors. We demonstrate the utility of this approach by applying it to a 134 kDa enzyme using magic-angle spinning NMR, highlighting its potential to efficiently probe functionally relevant sites in proteins.","lang":"eng"}],"date_published":"2026-10-13T00:00:00Z","OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"dataavailabilitystatement":"Supporting Information is available free of charge at https://pubs.acs.org/10.1021/acschembio.6c00587.\r\n\r\nDetailed description of experimental methods; spectra supporting the residue assignment for IiMDH; relaxation analysis of IiMDH proline-Cδ sites; NMR spectra of isolated [13Cδ,15N,2Hβγ4]-Pro (PDF)","month":"10","main_file_link":[{"url":"https://doi.org/10.1021/acschembio.6c00587","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-10-19T11:12:28Z","_id":"23173","day":"13","type":"journal_article","corr_author":"1","quality_controlled":"1","oa":1},{"fulldoi":"https://doi.org/10.1126/sciadv.aea6020","file":[{"file_size":11101140,"file_name":"2026_ScienceAdv_Markovitsch.pdf","date_created":"2026-05-04T09:16:36Z","checksum":"3eed470fe73e53d2a8d55d6fba6934e3","success":1,"content_type":"application/pdf","file_id":"21786","relation":"main_file","creator":"dernst","date_updated":"2026-05-04T09:16:36Z","access_level":"open_access"}],"publication":"Science Advances","author":[{"full_name":"Markovitsch, Johann W.","first_name":"Johann W.","last_name":"Markovitsch"},{"first_name":"Daniel","full_name":"Mitić, Daniel","last_name":"Mitić"},{"full_name":"Del Pilar Jiménez García, Alisa","first_name":"Alisa","last_name":"Del Pilar Jiménez García"},{"id":"60f7509a-f652-11ea-9d86-b963d6490d7c","last_name":"Zane","first_name":"Alsberga","orcid":"0009-0003-0415-7603","full_name":"Zane, Alsberga"},{"last_name":"Kainz","first_name":"Sarah","full_name":"Kainz, Sarah"},{"full_name":"Kaur, Rashmit","first_name":"Rashmit","last_name":"Kaur"},{"last_name":"Hummel","full_name":"Hummel, Thomas","first_name":"Thomas"}],"title":"Sequential formation of Drosophila circuit asymmetry via prolonged structural plasticity","publication_identifier":{"eissn":["2375-2548"]},"issue":"13","file_date_updated":"2026-05-04T09:16:36Z","ddc":["570"],"acknowledgement":"We thank I. Salecker (Flybow), B. Altenhein (Fas2-Gal4Mz507), A. Nose (UAS-intra- and extra-Fas2::YFP), and C. S. Goodman (UAS-Fas2PEST+/−), as well as the Bloomington Stock Center for providing materials and fly stocks. We thank S. Waddell and the lab, especially B. Senapati, for providing the opportunity to conduct memory experiments at the CNCB, University of Oxford, and for supervision and discussions during this period. We also thank W. Kallina, S. Ilgerl, D. Bartel, A. Grimm, and A. Litin for technical support and the Hummel Lab for stimulating discussions and critical comments on the manuscript. We acknowledge the early exploratory work of A. Mattia, S. Trkulja, C. Schönherr, S. Bogner, B. Simpson, L. Tomasek, H. Roth, H. Vokač, R. Gredler, F. Kapelari, T. Kolarova, C. Ignitsch, Á. Bautista-Soldevila, and M. Kassem.\r\nThis research was funded by the University of Vienna, the Vienna Doctoral School Cognition, Behaviour and Neuroscience (uni:docs fellowship) (to J.W.M.) and by the Austrian Science Fund (FWF) (Cluster of Excellence Neuronal Circuits in Health and Disease, grant DOI 10.55776/COE16; https://www.fwf.ac.at/en/research-radar/10.55776/COE16) (to T.H.). For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","doi":"10.1126/sciadv.aea6020","date_updated":"2026-10-20T08:11:29Z","scopus_import":"1","citation":{"ieee":"J. W. Markovitsch <i>et al.</i>, “Sequential formation of Drosophila circuit asymmetry via prolonged structural plasticity,” <i>Science Advances</i>, vol. 12, no. 13. AAAS, 2026.","ista":"Markovitsch JW, Mitić D, Del Pilar Jiménez García A, Zane A, Kainz S, Kaur R, Hummel T. 2026. Sequential formation of Drosophila circuit asymmetry via prolonged structural plasticity. Science Advances. 12(13), eaea6020.","ama":"Markovitsch JW, Mitić D, Del Pilar Jiménez García A, et al. Sequential formation of Drosophila circuit asymmetry via prolonged structural plasticity. <i>Science Advances</i>. 2026;12(13). doi:<a href=\"https://doi.org/10.1126/sciadv.aea6020\">10.1126/sciadv.aea6020</a>","chicago":"Markovitsch, Johann W., Daniel Mitić, Alisa Del Pilar Jiménez García, Alsberga Zane, Sarah Kainz, Rashmit Kaur, and Thomas Hummel. “Sequential Formation of Drosophila Circuit Asymmetry via Prolonged Structural Plasticity.” <i>Science Advances</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/sciadv.aea6020\">https://doi.org/10.1126/sciadv.aea6020</a>.","apa":"Markovitsch, J. W., Mitić, D., Del Pilar Jiménez García, A., Zane, A., Kainz, S., Kaur, R., &#38; Hummel, T. (2026). Sequential formation of Drosophila circuit asymmetry via prolonged structural plasticity. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.aea6020\">https://doi.org/10.1126/sciadv.aea6020</a>","short":"J.W. Markovitsch, D. Mitić, A. Del Pilar Jiménez García, A. Zane, S. Kainz, R. Kaur, T. Hummel, Science Advances 12 (2026).","mla":"Markovitsch, Johann W., et al. “Sequential Formation of Drosophila Circuit Asymmetry via Prolonged Structural Plasticity.” <i>Science Advances</i>, vol. 12, no. 13, eaea6020, AAAS, 2026, doi:<a href=\"https://doi.org/10.1126/sciadv.aea6020\">10.1126/sciadv.aea6020</a>."},"year":"2026","department":[{"_id":"MiSi"},{"_id":"GradSch"}],"publisher":"AAAS","volume":12,"OA_place":"publisher","oa":1,"DOAJ_listed":"1","day":"27","_id":"21707","type":"journal_article","quality_controlled":"1","intvolume":"        12","month":"03","date_created":"2026-04-12T22:01:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_processing_charge":"Yes","date_published":"2026-03-27T00:00:00Z","status":"public","abstract":[{"text":"Structural and functional differences between brain hemispheres are a common feature of animal nervous systems with reduced bilateral asymmetry often linked to impaired cognitive performance. How neuronal left-right asymmetry is initiated and integrated into a bilaterally symmetrical ground pattern is poorly understood. Here, we show that the directional asymmetry of a Drosophila central brain circuit originates from axonal interactions of two types of bilateral pioneer neurons. Subsequent recruitment of neighboring neurons into the asymmetric neuropil primordium results in hemisphere-specific microcircuits. Circuit lateralization requires dynamic expression of the cell adhesion molecule Fasciclin 2 to maintain structural plasticity in axonal remodeling. Reduced circuit asymmetry following cell type–specific Fasciclin 2 manipulation affects adult brain function. These results reveal an unexpected degree of developmental plasticity of late-born Drosophila neurons in the formation of a circuit node via the lateralized recruitment of symmetric circuit components.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","oa_version":"Published Version","language":[{"iso":"eng"}],"article_type":"original","article_number":"eaea6020"},{"date_updated":"2026-10-20T08:55:33Z","doi":"10.15479/AT-ISTA-22744","department":[{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"MiSi"}],"citation":{"mla":"Javoor, Manjunath. <i>Large-Scale Imaging of Cellular Actin Networks at Single Filament Resolution Using Montage Cryo-Electron Tomography</i>. Institute of Science and Technology Austria , 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22744\">10.15479/AT-ISTA-22744</a>.","short":"M. Javoor, Large-Scale Imaging of Cellular Actin Networks at Single Filament Resolution Using Montage Cryo-Electron Tomography, Institute of Science and Technology Austria , 2026.","apa":"Javoor, M. (2026). <i>Large-scale imaging of cellular actin networks at single filament resolution using montage cryo-electron tomography</i>. Institute of Science and Technology Austria . <a href=\"https://doi.org/10.15479/AT-ISTA-22744\">https://doi.org/10.15479/AT-ISTA-22744</a>","chicago":"Javoor, Manjunath. “Large-Scale Imaging of Cellular Actin Networks at Single Filament Resolution Using Montage Cryo-Electron Tomography.” Institute of Science and Technology Austria , 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22744\">https://doi.org/10.15479/AT-ISTA-22744</a>.","ama":"Javoor M. Large-scale imaging of cellular actin networks at single filament resolution using montage cryo-electron tomography. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22744\">10.15479/AT-ISTA-22744</a>","ista":"Javoor M. 2026. Large-scale imaging of cellular actin networks at single filament resolution using montage cryo-electron tomography. Institute of Science and Technology Austria .","ieee":"M. Javoor, “Large-scale imaging of cellular actin networks at single filament resolution using montage cryo-electron tomography,” Institute of Science and Technology Austria , 2026."},"year":"2026","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria ","doi_confirm":"1","OA_place":"publisher","file":[{"date_updated":"2026-08-27T12:48:42Z","creator":"mjavoor","relation":"source_file","file_id":"22767","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"f9c2847df9f1ac5a3d60c06b3b81a450","access_level":"closed","file_size":27430796,"date_created":"2026-08-26T12:02:47Z","file_name":"2026_Javoor_Manjunath_Thesis.docx"},{"file_name":"2026_Javoor_Manjunath_Thesis.pdf","date_created":"2026-08-26T12:02:46Z","file_size":19489230,"embargo":"2027-08-21","access_level":"closed","content_type":"application/pdf","embargo_to":"open_access","file_id":"22768","date_updated":"2026-08-26T12:02:46Z","relation":"main_file","creator":"mjavoor","checksum":"8e9b4c0fcafbccf5c3796eacc9134a08"}],"project":[{"_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","name":"A molecular atlas of Actin filament IDentities in the cell motility machinery","grant_number":"101076260"},{"grant_number":"101071793","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22744","author":[{"full_name":"Javoor, Manjunath","orcid":"0000-0003-2311-2112","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor"}],"title":"Large-scale imaging of cellular actin networks at single filament resolution using montage cryo-electron tomography","page":"121","publication_identifier":{"isbn":["978-3-99078-090-9 "],"issn":["2663-337X"]},"related_material":{"record":[{"id":"12334","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"21762"},{"status":"public","id":"12421","relation":"part_of_dissertation"},{"id":"19795","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2026-08-27T12:48:42Z","acknowledgement":"This work was supported by the ERC StG grant ActinID (PRA01221F1049A) awarded to Florian\r\nSchur, the ERC-SyG grant Pushing from within (P01071793) awarded to Michael Sixt, and by ISTA.\r\nI would like to thank the Scientific Service Units at ISTA for their essential support throughout\r\nthis work. In particular, I am grateful to the Electron Microscopy Facility, Imaging and Optics\r\nFacility, Zebrafish Facility, Scientific Computing Facility, and Lab Support Facility for their services,\r\nand technical support, all of which were important for the successful completion of this project.","ddc":["570"],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"publication_status":"published","status":"public","has_accepted_license":"1","date_published":"2026-08-21T00:00:00Z","oa_version":"None","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"day":"21","_id":"22744","type":"dissertation","OA_embargo":"12","supervisor":[{"full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"}],"corr_author":"1","month":"08","date_created":"2026-08-21T09:11:04Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Actin cytoskeleton","Cell migration","cryo-electron tomography"],"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"}},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (in subscription journal)","date_published":"2026-02-02T00:00:00Z","abstract":[{"lang":"eng","text":"During complex vocal interactions, different features of acoustic stimuli are integrated to produce appropriate vocal responses,1 such as copying sounds during vocal matching behavior in some animals.2,3,4,5,6,7,8,9,10,11,12 However, little is known about the interplay and possible trade-offs between the different temporal and spectral acoustic features during these vocal exchanges.2,13,14 Nightingales can flexibly match the pitch of their tonal “whistle songs” in real time during counter-singing duels.15,16 Here, we show that the syllable duration of whistle playbacks could alter the song responses of wild nightingales, causing their whistle duration distribution to shift toward the presented stimulus duration. When exposed to whistle playbacks featuring unnatural combinations of pitch and duration, nightingales demonstrate a flexible trade-off between pitch matching and temporal imitation, yet they are constrained by their vocal repertoire. They selectively adapted their vocal responses to approximate these novel stimuli, aligning them with their natural whistle repertoire. We developed a computational model of nightingale whistle-matching behavior that revealed a hierarchical organization of acoustic feature production. During whistle matching, the feature integration process is constrained by the duration of syllables, and pitch matching follows within this temporal framework, forcing a trade-off between the two features. Our findings reveal a complex interplay between the spectral and temporal domains that shapes song-matching behavior."}],"has_accepted_license":"1","status":"public","publication_status":"published","supplementarymaterial":"yes","oa_version":"Published Version","intvolume":"        36","month":"02","researchdata_availability":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-01-14T12:00:29Z","OA_type":"hybrid","dataavailabilitystatement":"All data have been deposited at https://github.com/vallentinlab/NG-whistle-durations and are publicly available as of the date of publication.\r\nAll original code has been deposited at https://github.com/vallentinlab/NG-whistle-durations and is publicly available as of the date of publication.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa":1,"_id":"20986","day":"02","type":"journal_article","quality_controlled":"1","PlanS_conform":"1","year":"2026","citation":{"apa":"Calderon Garcia, J. S., Costalunga, G., Vogels, T. P., &#38; Vallentin, D. (2026). Interplay between syllable duration and pitch during whistle matching in wild nightingales. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2025.12.025\">https://doi.org/10.1016/j.cub.2025.12.025</a>","short":"J.S. Calderon Garcia, G. Costalunga, T.P. Vogels, D. Vallentin, Current Biology 36 (2026) 791–798.e6.","mla":"Calderon Garcia, Juan Sebastian, et al. “Interplay between Syllable Duration and Pitch during Whistle Matching in Wild Nightingales.” <i>Current Biology</i>, vol. 36, no. 3, Cell Press, 2026, p. 791–798.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2025.12.025\">10.1016/j.cub.2025.12.025</a>.","ieee":"J. S. Calderon Garcia, G. Costalunga, T. P. Vogels, and D. Vallentin, “Interplay between syllable duration and pitch during whistle matching in wild nightingales,” <i>Current Biology</i>, vol. 36, no. 3. Cell Press, p. 791–798.e6, 2026.","ista":"Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. 2026. Interplay between syllable duration and pitch during whistle matching in wild nightingales. Current Biology. 36(3), 791–798.e6.","ama":"Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. Interplay between syllable duration and pitch during whistle matching in wild nightingales. <i>Current Biology</i>. 2026;36(3):791-798.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2025.12.025\">10.1016/j.cub.2025.12.025</a>","chicago":"Calderon Garcia, Juan Sebastian, Giacomo Costalunga, Tim P Vogels, and Daniela Vallentin. “Interplay between Syllable Duration and Pitch during Whistle Matching in Wild Nightingales.” <i>Current Biology</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cub.2025.12.025\">https://doi.org/10.1016/j.cub.2025.12.025</a>."},"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"volume":36,"publisher":"Cell Press","OA_place":"publisher","ec_funded":1,"pmid":1,"external_id":{"pmid":["41529680"]},"date_updated":"2026-10-20T09:02:18Z","doi":"10.1016/j.cub.2025.12.025","scopus_import":"1","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"das_tickbox":"1","issue":"3","file_date_updated":"2026-07-27T10:47:55Z","ddc":["570","577"],"acknowledgement":"We would like to thank J. Benichov and N. Hein for their help with fieldwork; M. Ramadas for helping with the segmentation analysis; T. Eliav, C. Chintaluri, G. Tkacik, and A. Navas for providing helpful comments to the project and manuscript; and A. Costalunga for the drawings of nightingales. Funding sources: The Joachim Herz Stiftung Add-on Fellowships for Interdisciplinary Life Science, awarded to G.C.; the ERC Consolidator Grant 819603 SYNAPSEEK, awarded to T.P.V.; and DFG Research Unit 5768–532521431, DFG Research Grant-547921981, DFG SFB 1315–327654276, and the ERC Starting Grant 757459 MIDNIGHT, awarded to D.V.","project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"}],"fulldoi":"https://doi.org/10.1016/j.cub.2025.12.025","file":[{"file_name":"2026_CurrentBiology_CalderonGarcia.pdf","date_created":"2026-07-27T10:47:55Z","file_size":7120959,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_updated":"2026-07-27T10:47:55Z","file_id":"22416","relation":"main_file","checksum":"e17c3537193d5ab4886596d1a04f9b0e","success":1}],"publication":"Current Biology","author":[{"first_name":"Juan Sebastian","full_name":"Calderon Garcia, Juan Sebastian","last_name":"Calderon Garcia","id":"1271b54b-dbcd-11ea-9d1d-d92da838fe2c"},{"full_name":"Costalunga, Giacomo","first_name":"Giacomo","last_name":"Costalunga"},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P"},{"last_name":"Vallentin","first_name":"Daniela","full_name":"Vallentin, Daniela"}],"page":"791-798.e6","title":"Interplay between syllable duration and pitch during whistle matching in wild nightingales"},{"corr_author":"1","quality_controlled":"1","day":"06","_id":"22286","type":"journal_article","OA_type":"closed access","date_created":"2026-07-13T09:39:40Z","researchdata_availability":"no","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","intvolume":"        36","oa_version":"None","abstract":[{"lang":"eng","text":"Plants are remarkable organisms. Unlike animals, they cannot flee and, rooted in one place, they must cope with whatever challenges arise — nutrient scarcity, drought, shade, wind or obstacles in the soil. Their extraordinary ability to survive in such unstable environmental conditions lies in their capacity to adapt. In response to environmental signals, plants can rapidly adjust the rate of organ growth, change the direction of growth, bend toward resources, or remodel their body architecture by promoting or suppressing the formation of new organs such as lateral roots, branches, leaves, or flowers. This unique developmental plasticity depends on chemical signals, plant hormones that serve as regulators and coordinators of endogenous molecular and cellular processes. Chief among these signals is auxin, a plant hormone central to nearly every aspect of plant life."}],"publication_status":"published","status":"public","supplementarymaterial":"no","date_published":"2026-07-06T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","title":"Auxin and the control of plant growth and development","page":"R739-R744","author":[{"full_name":"Leitner, Valentin","first_name":"Valentin","last_name":"Leitner","id":"4c665ce3-0016-11ec-bea0-e44de7a4fa3d"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"publication":"Current Biology","fulldoi":"https://doi.org/10.1016/j.cub.2026.04.047","issue":"13","das_tickbox":"0","publication_identifier":{"issn":["0960-9822"]},"scopus_import":"1","date_updated":"2026-10-20T09:00:35Z","doi":"10.1016/j.cub.2026.04.047","external_id":{"pmid":["42407441"]},"pmid":1,"publisher":"Cell Press","volume":36,"department":[{"_id":"EvBe"},{"_id":"GradSch"}],"year":"2026","citation":{"short":"V. Leitner, E. Benková, Current Biology 36 (2026) R739–R744.","apa":"Leitner, V., &#38; Benková, E. (2026). Auxin and the control of plant growth and development. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">https://doi.org/10.1016/j.cub.2026.04.047</a>","mla":"Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” <i>Current Biology</i>, vol. 36, no. 13, Cell Press, 2026, pp. R739–44, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">10.1016/j.cub.2026.04.047</a>.","ieee":"V. Leitner and E. Benková, “Auxin and the control of plant growth and development,” <i>Current Biology</i>, vol. 36, no. 13. Cell Press, pp. R739–R744, 2026.","ama":"Leitner V, Benková E. Auxin and the control of plant growth and development. <i>Current Biology</i>. 2026;36(13):R739-R744. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">10.1016/j.cub.2026.04.047</a>","ista":"Leitner V, Benková E. 2026. Auxin and the control of plant growth and development. Current Biology. 36(13), R739–R744.","chicago":"Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” <i>Current Biology</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">https://doi.org/10.1016/j.cub.2026.04.047</a>."}},{"OA_place":"publisher","publisher":"Cell Press","volume":45,"year":"2026","citation":{"apa":"Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M., Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>","short":"D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild, M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026).","mla":"Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>, vol. 45, no. 4, 117227, Cell Press, 2026, doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>.","ista":"Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 45(4), 117227.","ama":"Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. 2026;45(4). doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>","chicago":"Vijatovic, David, Florina Alexandra  Toma, Y Ignatyev, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>.","ieee":"D. Vijatovic <i>et al.</i>, “Multifold increase in spinal inhibitory cell types with emergence of limb movement,” <i>Cell Reports</i>, vol. 45, no. 4. Cell Press, 2026."},"department":[{"_id":"LoSw"},{"_id":"GradSch"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"scopus_import":"1","pmid":1,"external_id":{"pmid":["41964955 "]},"doi":"10.1016/j.celrep.2026.117227","date_updated":"2026-10-20T09:04:23Z","ddc":["570"],"acknowledgement":"We would like to thank the members of the Sweeney Lab, Mario de Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript. We are also grateful to Tom Jessell and Chris Kintner for their scientific insight and mentorship during the conception of this project. It would also have not been possible without the technical support of the Aquatics and Imaging and Optics Facility support teams (ISTA). We thank Martin Estermann for preparing the initial draft of the graphical abstract and Niki Barolini for the final version. In addition, we thank our funding sources for providing the resources to do these experiments: GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.), Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858 (to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC) (to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472 (to Z.H.), and Project A.L.S. (to S.B.-M.).","file_date_updated":"2026-05-04T12:20:10Z","issue":"4","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"22667"}]},"publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"title":"Multifold increase in spinal inhibitory cell types with emergence of limb movement","author":[{"last_name":"Vijatovic","id":"cf391e77-ec3c-11ea-a124-d69323410b58","full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941","first_name":"David"},{"first_name":"Florina Alexandra ","full_name":"Toma, Florina Alexandra ","last_name":"Toma","id":"2f73f876-f128-11eb-9611-b96b5a30cb0e"},{"last_name":"Ignatyev","first_name":"Y","full_name":"Ignatyev, Y"},{"full_name":"Harrington, Zoe P","orcid":"0009-0008-0158-4032","first_name":"Zoe P","last_name":"Harrington","id":"a8144562-32c9-11ee-b5ce-d9800628bda2"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"id":"7a231d52-e216-11ee-a0bb-8acd55f8f1f0","last_name":"Smits","full_name":"Smits, Matthijs Geert","first_name":"Matthijs Geert"},{"id":"02a7a869-ff06-11ed-a87f-86649d6077e5","last_name":"Dalla Vecchia","full_name":"Dalla Vecchia, Marco","first_name":"Marco"},{"last_name":"Trevisan","first_name":"Alexandra J.","full_name":"Trevisan, Alexandra J."},{"last_name":"Chapman","first_name":"Phillip","full_name":"Chapman, Phillip"},{"full_name":"Julseth, Mara","first_name":"Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","last_name":"Julseth"},{"last_name":"Brenner-Morton","first_name":"Susan","full_name":"Brenner-Morton, Susan"},{"last_name":"Gabitto","first_name":"Mariano I.","full_name":"Gabitto, Mariano I."},{"last_name":"Dasen","first_name":"Jeremy S.","full_name":"Dasen, Jeremy S."},{"last_name":"Bikoff","first_name":"Jay B.","full_name":"Bikoff, Jay B."},{"orcid":"0000-0001-9242-5601","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney"}],"publication":"Cell Reports","fulldoi":"https://doi.org/10.1016/j.celrep.2026.117227","project":[{"grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"},{"grant_number":"F7814","name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e"},{"name":"Tools for automation and feedback microscopy","grant_number":"CZI01","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473"},{"name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","grant_number":"FTI21-D-046","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"_id":"cf428362-b037-11f1-b015-8277a8a2f63d","grant_number":"COE16","name":"Neuronal circuits in health and disease (Sweeney)"}],"file":[{"date_created":"2026-05-04T12:20:10Z","file_name":"2026_CellReports_Vijatovic.pdf","file_size":14925958,"access_level":"open_access","checksum":"0d26cdb5b8d8dec3a911d8261a65cdef","success":1,"content_type":"application/pdf","file_id":"21795","creator":"dernst","date_updated":"2026-05-04T12:20:10Z","relation":"main_file"}],"article_number":"117227","language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","date_published":"2026-04-28T00:00:00Z","abstract":[{"text":"As vertebrates transitioned from water to land, locomotion shifted from undulatory swimming to limb-based movement. How spinal circuits and their cell types evolved to support this transition remains unclear. We leverage frog metamorphosis, which recapitulates this transition within a single organism, to define how spinal circuits generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons. As limbs develop and their movement complexifies, spinal circuits expand in neuron number and subtype diversity. This expansion is most pronounced for V1 inhibitory neurons, which increase ∼70-fold and diversify into transcriptionally distinct subtypes. Disrupting transcription factors defining emerging motor and V1 populations reveals molecular segregation between swim and limb circuits, highlighting the role of subtype diversity in motor coordination. A multifold increase in inhibitory neuron diversity thus underlies the tail-to-limb locomotor transition, providing a framework for spinal circuit adaptation during vertebrate evolution.","lang":"eng"}],"status":"public","publication_status":"published","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"gold","date_created":"2026-04-19T22:07:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        45","month":"04","PlanS_conform":"1","corr_author":"1","quality_controlled":"1","type":"journal_article","_id":"21746","day":"28","DOAJ_listed":"1","oa":1},{"date_published":"2026-07-11T00:00:00Z","abstract":[{"lang":"eng","text":"Uncovering the genetic architecture of complex traits and pinpointing causal molecular drivers require the ability to distinguish true signals from noise within massive, high-dimensional omics datasets. To extract meaningful biological insights from these datasets, such as identifying causal genetic variants and proteins, scalable and accurate inference methods are essential. To this end, this thesis develops novel Bayesian inference frameworks based on Vector Approximate Message Passing and demonstrates their effectiveness in the modeling of disease onset times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that enables the joint modeling of quantitative complex traits across millions of genetic variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample polygenic risk prediction compared to state-of-the-art approaches. We model human height using 17 million whole-genome sequence variants from the UK Biobank, incorporating a vast number of rare variants and revealing novel associations. gVAMP achieves a prediction accuracy of approximately 46% for human height, representing the highest reported performance for this trait to date. \r\n\r\nSecond, we present vampW, a Bayesian framework for survival analysis applied to proteomic data. By effectively handling right-censoring and complex protein dependencies within the UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations across 24 disease outcomes, the majority of which are not among the top marginal discoveries. We further adjust protein levels for exponential age effects, yielding 1,308 associations and highlighting the sensitivity of the analysis to the chosen age-correction methodology. Finally, vampW improves upon the variable selection capabilities of the commonly used (penalized) variants of the Cox proportional hazards model and delivers state-of-the-art out-of-sample prediction of disease onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting the genetic architecture of complex traits and the proteomic drivers of disease onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions of onset times, this work advances the capabilities of personalized medicine and clinical risk stratification."}],"status":"public","publication_status":"published","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"oa":1,"corr_author":"1","supervisor":[{"last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"}],"type":"dissertation","_id":"22258","day":"11","keyword":["Approximate Message Passing","GWAS","Genomics","Proteomics","Survival modeling"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2026-07-10T13:27:20Z","month":"07","date_updated":"2026-10-20T09:03:21Z","doi":"10.15479/AT-ISTA-22258","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","year":"2026","citation":{"mla":"Depope, Al. <i>From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>.","short":"A. Depope, From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science and Technology Austria, 2026.","apa":"Depope, A. (2026). <i>From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>","ieee":"A. Depope, “From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics,” Institute of Science and Technology Austria, 2026.","chicago":"Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>.","ista":"Depope A. 2026. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria.","ama":"Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>"},"department":[{"_id":"GradSch"},{"_id":"MaRo"},{"_id":"MaMo"}],"OA_place":"publisher","author":[{"full_name":"Depope, Al","first_name":"Al","last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","grant_number":"101161364"},{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22258","file":[{"access_level":"open_access","file_id":"22316","creator":"adepope","date_updated":"2026-07-13T14:52:19Z","relation":"main_file","content_type":"application/pdf","checksum":"9ab386790515628d957a194f30a7ccb4","file_name":"2026_Depope_Al_Thesis.pdf","date_created":"2026-07-13T14:52:19Z","file_size":25109878},{"file_size":1203199939,"file_name":"2026_Depope_Al_Thesis.zip","date_created":"2026-07-13T14:56:41Z","checksum":"8ed8fb63f76a695d5b6fec35343f4b90","relation":"source_file","date_updated":"2026-07-13T14:56:41Z","file_id":"22317","creator":"adepope","content_type":"application/zip","access_level":"closed"}],"page":"169","title":"From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics","das_tickbox":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"21488"}]},"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"This work was supported in part by the Swiss National Science Foundation through the\r\nEccellenza Grant \"Improving estimation and prediction of common complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n","ddc":["576","610","006"],"file_date_updated":"2026-07-13T14:56:41Z"},{"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"No","date_published":"2026-08-10T00:00:00Z","has_accepted_license":"1","status":"public","publication_status":"published","month":"08","date_created":"2026-08-10T13:44:30Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"full_name":"Sweeney, Lora Beatrice Jaeger","first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney"}],"_id":"22667","type":"dissertation","day":"10","corr_author":"1","OA_place":"publisher","year":"2026","citation":{"mla":"Vijatovic, David. <i>Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22667\">10.15479/AT-ISTA-22667</a>.","apa":"Vijatovic, D. (2026). <i>Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22667\">https://doi.org/10.15479/AT-ISTA-22667</a>","short":"D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026.","ieee":"D. Vijatovic, “Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis,” Institute of Science and Technology Austria, 2026.","chicago":"Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22667\">https://doi.org/10.15479/AT-ISTA-22667</a>.","ista":"Vijatovic D. 2026. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria.","ama":"Vijatovic D. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22667\">10.15479/AT-ISTA-22667</a>"},"department":[{"_id":"GradSch"},{"_id":"LoSw"}],"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-22667","date_updated":"2026-10-20T09:04:22Z","file_date_updated":"2026-08-12T13:44:36Z","ddc":["573"],"acknowledgement":"I am also grateful for the financial support that made this work possible, including the\r\nEuropean Research Council (ERC Starting Grant 101041551), the Austrian Science\r\nFund (FWF, Cluster of Excellence 10.55776/COE16), the GFF Lower Austria FTI\r\nStrategy Dissertation Fellowship (FTI21-D-046), and the FENS/IBRO-PERC\r\nExchange Fellowship. ","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-082-4"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"15016","status":"public"},{"relation":"part_of_dissertation","id":"21746","status":"public"}]},"page":"172","title":"Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis","fulldoi":"https://doi.org/10.15479/AT-ISTA-22667","project":[{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551"},{"name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","grant_number":"FTI21-D-046","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"name":"Development of Viral Vectors for Amphibian Gene Delivery and Manipulation","grant_number":"3(GG016346-01)","_id":"34a02c70-11ca-11ed-8bc3-fbfd2c86c88f"}],"file":[{"creator":"dvijatov","file_id":"22669","date_updated":"2026-08-10T13:35:39Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"e3acfea4b1a3abf99e74224656740a15","access_level":"closed","file_size":14322760,"file_name":"2026_Vijatovic_David_Thesis.docx","date_created":"2026-08-10T13:35:39Z"},{"content_type":"application/pdf","date_updated":"2026-08-12T13:44:36Z","creator":"dvijatov","file_id":"22695","relation":"main_file","embargo_to":"open_access","checksum":"dc8c78ae14f69e54faa41e65db5c6402","access_level":"closed","file_size":116926375,"embargo":"2027-08-10","file_name":"2026_Vijatovic_David_Thesis.pdf","date_created":"2026-08-12T13:44:36Z"}],"author":[{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941","first_name":"David"}]},{"doi":"10.15479/AT-ISTA-22399","date_updated":"2026-10-21T07:47:08Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"GaTk"},{"_id":"CaGu"}],"year":"2026","citation":{"apa":"Spasić, A. (2026). <i>Studying the evolutionary systems biology of the lac operon</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>","short":"A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026.","mla":"Spasić, Aleksa. <i>Studying the Evolutionary Systems Biology of the Lac Operon</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>.","ieee":"A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026.","ama":"Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>","ista":"Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria.","chicago":"Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>."},"degree_awarded":"MS","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","title":"Studying the evolutionary systems biology of the lac operon","page":"32","file":[{"file_name":"Aleksa_Spasic_Thesis_final.pdf","date_created":"2026-07-27T13:00:07Z","file_size":1986078,"embargo":"2027-07-30","access_level":"closed","checksum":"c29880dd71fcc37f23ac6e2843066ede","content_type":"application/pdf","relation":"main_file","embargo_to":"open_access","date_updated":"2026-10-20T08:47:40Z","creator":"aspasic","file_id":"22588"},{"access_level":"closed","checksum":"4ebe3bd2d833d913c0756343cca5e5f0","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"22589","relation":"source_file","creator":"aspasic","date_updated":"2026-07-27T13:07:23Z","date_created":"2026-07-27T13:00:22Z","file_name":"Thesis_final.docx","file_size":1868853}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22399","author":[{"first_name":"Aleksa","full_name":"Spasić, Aleksa","last_name":"Spasić","id":"ecee9d38-4040-11ef-8843-b941efb445d6"}],"file_date_updated":"2026-10-20T08:47:40Z","ddc":["576"],"publication_identifier":{"issn":["2791-4585"]},"das_tickbox":"0","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","has_accepted_license":"1","status":"public","date_published":"2026-07-27T00:00:00Z","language":[{"iso":"eng"}],"alternative_title":["ISTA Master’s Thesis"],"day":"27","_id":"22399","type":"dissertation","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"corr_author":"1","month":"07","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2026-07-25T13:08:32Z"},{"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"In this thesis, we took a look at networks, and more specifically, at networks that change over time, whether those are networks in the distributed algorithms sense of the word, or the graph algorithm sense. \r\n\r\nIn distributed algorithms, we looked at two main problems. First, the broadcast problem: given n agents, each agent is tasked to forward a (unique) message to every other agent. Agents collaborate and can copy and forward all messages they have received up until that point. Broadcast is achieved when one agent has successfully broadcast its message to everyone else. We studied the case where the communication network is controlled by an adversary, under the condition that the graph is rooted in every round of communication. We show that the adversary can delay broadcast for at most  l\r\n(1 + √\r\n2)n\r\nm\r\n rounds, improving on the $O(n\\log\\log n)$ previous upper bound~\\cite{fugger2020radius}, and asymptotically matching the $\\sim 1.5n$ lower bound~\\cite{schwarz2017linear}.\r\n\r\nWe then looked at the stochastic version of the problem: here, the adversary -- parametrized by $k$ where $k=0$ signifies that the adversary has no control,  and $k=n$ that the adversary has full control -- can choose parts of the graph, and the graph is then completed stochastically. Here, we are able to look at a stronger version of broadcast: instead of having $n$ messages trying to be broadcast in parallel, we can assume that only one message needs to be broadcasted. We show the bound $\\Theta(k+\\log n)$.\r\n\r\nThen, we looked at undecided states dynamics in population protocols: given a population of $n$ agents, where each initially holds an opinion among $k$ different ones. In each round, two agents are chosen uniformly at random, and can interact. If they have different opinions, they forget their opinions and become undecided. If one of them is undecided while the other has an opinion, they undecided agent copies they opinion of the decided one. The question is then, how many interactions does it take for the whole population to share the same opinion? We show a $\\Omega(kn\\log \\frac {\\sqrt n} {k \\log n})$ lower bound  for any $k = o\\left(\\frac {\\sqrt n}{\\log n}\\right)$.\r\nThis is tight for any $ k \\le n^{\\frac 1 2 - \\epsilon}$, where $\\epsilon >0$ can be any small constant, matching the known $O(kn\\log n)$ upper bound for $k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right)$~\\cite{DBLP:conf/podc/AmirABBHKL23}.\r\n\r\nFinally, in dynamic algorithms, we study the minimum cut problem: we are given a graph, whose vertex set we want to partition into two subsets such that the number of edges crossing from one subset to the other is minimized. Then, the graph can be updated via edge insertions or deletions, and we must update the solution without recomputing everything from scratch. We present an exact fully-dynamic minimum cut algorithm that runs in $n^{o(1)}$ deterministic update time when the minimum cut size is at most $2^{\\Theta(\\log^{3/4-c}n)}$ for any $c>0$, improving on the previous algorithm~\\cite{DBLP:conf/soda/JinST24} whose minimum cut size limit is $(\\log n)^{o(1)}$. Using sparsification and randomization techniques, we are able to extend this to all values of the minimum cut in weighted graphs, at the cost of a $(1+o(1))$-approximation ratio.","lang":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","date_published":"2026-07-13T00:00:00Z","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_created":"2026-07-13T09:39:59Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"07","corr_author":"1","type":"dissertation","_id":"22281","day":"13","supervisor":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"}],"oa":1,"OA_place":"publisher","degree_awarded":"PhD","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MoHe"}],"year":"2026","citation":{"mla":"El-Hayek, Antoine. <i>Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>.","short":"A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks, Institute of Science and Technology Austria, 2026.","apa":"El-Hayek, A. (2026). <i>Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>","ieee":"A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks,” Institute of Science and Technology Austria, 2026.","chicago":"El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>.","ista":"El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria.","ama":"El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>"},"publisher_comment":"Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are All Rights Reserved.","doi":"10.15479/AT-ISTA-22281","date_updated":"2026-10-21T08:05:35Z","ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564)\r\n\"The Design and Evaluation of Modern Fully Dynamic Data Structures\" , from the\r\nAustrian Science Fund (FWF) grant DOI 10.55776/I5982 \"Static and Dynamic Hierarchical\r\nGraph Decompositions\", and from the Austrian Science Fund (FWF) and netIDEE SCIENCE\r\nproject P 33775-N, \"Fast Algorithms for a Reactive Network Layer\".\r\n","ddc":["000"],"file_date_updated":"2026-07-20T11:29:38Z","related_material":{"record":[{"id":"20051","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"19982"},{"relation":"part_of_dissertation","status":"public","id":"21720"},{"status":"public","id":"22374","relation":"part_of_dissertation"},{"id":"22373","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18557"}]},"publication_identifier":{"issn":["2663-337X"]},"title":"Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks","page":"244","author":[{"orcid":"0000-0003-4268-7368","first_name":"Antoine","full_name":"El-Hayek, Antoine","last_name":"El-Hayek","id":"888a098e-fcac-11ee-aff7-d347be57b725"}],"file":[{"access_level":"open_access","content_type":"application/pdf","creator":"aelhayek","relation":"main_file","file_id":"22356","date_updated":"2026-07-17T11:39:47Z","checksum":"923e4ca769c9ef2f6b0b005444faf462","success":1,"file_name":"2026_El-Hayek_Antoine_Thesis.pdf","date_created":"2026-07-17T11:39:47Z","file_size":5465973},{"file_size":9116107,"date_created":"2026-07-17T11:40:34Z","file_name":"2026_El-Hayek_Antoine_Thesis.zip","checksum":"262689f9df27dd6c2c7c7861f1de7329","content_type":"application/x-zip-compressed","file_id":"22357","date_updated":"2026-07-20T11:29:38Z","relation":"source_file","creator":"aelhayek","access_level":"closed"}],"project":[{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22281"},{"oa_version":"Published Version","date_published":"2026-01-16T00:00:00Z","publication_status":"published","abstract":[{"text":"Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms.","lang":"eng"}],"has_accepted_license":"1","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M"}],"day":"16","_id":"20991","type":"dissertation","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_created":"2026-01-16T09:47:59Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","doi":"10.15479/AT-ISTA-20991","date_updated":"2026-10-21T08:18:21Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","citation":{"ieee":"D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026.","chicago":"Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>.","ista":"Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria.","ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>","mla":"Garcia Castillo, Diego Fernando. <i>The Genomic Architecture of Local Adaptation in Introduced Populations</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>.","apa":"Garcia Castillo, D. F. (2026). <i>The genomic architecture of local adaptation in introduced populations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>","short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026."},"year":"2026","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"page":"199","title":"The genomic architecture of local adaptation in introduced populations","author":[{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20991","file":[{"date_created":"2026-01-16T12:25:13Z","file_name":"2026_Garcia_Diego_Thesis.docx","file_size":22456421,"access_level":"closed","checksum":"841f1bc073d667125729b2a017f8c37a","file_id":"20996","relation":"source_file","creator":"dgarciac","date_updated":"2026-01-16T12:25:13Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_size":9556719,"date_created":"2026-01-16T12:25:13Z","file_name":"2026_Garcia_Diego_Thesis.pdf","checksum":"a1f33d4f183ce7072eee42a6ccf5340b","success":1,"content_type":"application/pdf","relation":"main_file","creator":"dgarciac","file_id":"20997","date_updated":"2026-01-16T12:25:13Z","access_level":"open_access"},{"file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar","date_created":"2026-01-16T13:08:14Z","file_size":54491433,"description":"Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis.","access_level":"closed","checksum":"98a80691067174c30fe53f38ce7344e6","relation":"supplementary_material","file_id":"20998","date_updated":"2026-01-16T13:08:14Z","creator":"dgarciac","content_type":"application/x-compressed"},{"file_size":7982811,"date_created":"2026-01-16T13:08:14Z","file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar","checksum":"99a3cab2fa36666b9a92eefc27d586da","content_type":"application/x-compressed","creator":"dgarciac","date_updated":"2026-01-16T13:08:14Z","relation":"supplementary_material","file_id":"20999","access_level":"open_access"},{"access_level":"open_access","content_type":"text/plain","date_updated":"2026-01-16T13:08:59Z","creator":"dgarciac","relation":"supplementary_material","file_id":"21000","checksum":"255fdf56b2932c46bf27c63aa6106a4f","date_created":"2026-01-16T13:08:59Z","file_name":"README.txt","file_size":732}],"acknowledgement":"I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)","ddc":["576"],"file_date_updated":"2026-01-16T13:08:59Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"18498"},{"relation":"part_of_dissertation","status":"public","id":"18491"}]},"publication_identifier":{"isbn":["978-3-99078-077-0"],"issn":["2663-337X"]}},{"oa":1,"corr_author":"1","type":"dissertation","_id":"22684","day":"12","supervisor":[{"first_name":"Scott R","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis"}],"date_created":"2026-08-12T09:44:40Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"08","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"abstract":[{"text":"Contact electrification (CE) is a simple yet elusive phenomenon that occurs when two materials come into contact and separate, leaving behind net electrical charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In this thesis, we investigate CE from three complementary perspectives: developing a quantitative method to measure charge at the nanoscale, exploring the dynamic behavior of charge on insulating surfaces, and uncovering the role of mechanical history in forming a triboelectric series.\r\n\r\nIn the first part, we establish a rigorous framework for converting qualitative Kelvin probe force microscopy (KPFM) voltage maps into quantitative charge density distributions. Using finite element method (FEM) simulations, we determine the point-spread function of the KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed by numerical deconvolution. This procedure enables the recovery of both the magnitude and sign of charge density with high fidelity, resolving nanoscale features that are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces, we show that existing analytical approximations, such as parallel plate or spherical models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM approach therefore provides a fast and general method to convert qualitative KPFM signals into quantitative charge data, enabling nanoscale charge mapping under realistic experimental conditions.\r\n\r\nIn the second part, we study the temporal stability of CE-induced charges and identify the key material factors that determine whether KPFM can capture meaningful charge patterns. Through time-resolved experiments combining a custom-built transfer system with both microscopic and macroscopic measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve CE charge long enough for stationary imaging. For less conductive polymers, such as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction. Using a simple capacitor-based model, we reproduce the observed decay dynamics and confirm that the transferred charge decays characteristic to the sample's bulk conductivity. Further, we always observe homogeneous charge transfer.\r\n\r\nIn the third part, we address the question: can we form a triboelectric series with identical materials? Using controlled repetitive contact experiments, we show that nominally identical materials can progressively order themselves into a triboelectric series, where surfaces with more contact history charge negatively relative to fresher ones. By constructing a minimal model based on this ``contact bias'', we replicate the evolution from random to ordered charging observed in experiments. Supporting surface analyses, including atomic force microscopy, reveal that repeated contact induces nanoscale morphological changes, suggesting a mechanism tightly coupled to mechanical strain. These results highlight the crucial role of surface history and nanoscale mechanics in dictating charge transfer, motivating further exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric polarization.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","date_published":"2026-08-12T00:00:00Z","article_processing_charge":"No","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"author":[{"first_name":"Felix","orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af"}],"file":[{"file_name":"2026_Pertl_Felix_Thesis.zip","date_created":"2026-08-12T13:04:21Z","file_size":31192621,"access_level":"closed","content_type":"application/x-zip-compressed","date_updated":"2026-08-12T13:04:21Z","creator":"fpertl","file_id":"22690","relation":"source_file","checksum":"0a4f5a941c40b921447e72291d72bc6f"},{"access_level":"open_access","checksum":"ae60dcdb363222138886b2857643d4e3","content_type":"application/pdf","date_updated":"2026-08-12T13:04:21Z","relation":"main_file","file_id":"22691","creator":"fpertl","file_name":"2026_Pertl_Felix_Thesis.pdf","date_created":"2026-08-12T13:04:21Z","file_size":27882509}],"project":[{"grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22684","title":"Experimental probing of nanoscale charge features and surface morphology changes during tribocharging","page":"107","related_material":{"record":[{"id":"20481","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"12109","relation":"part_of_dissertation"},{"id":"19278","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17373","status":"public"}]},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-083-1"]},"ddc":["530"],"acknowledgement":"This project has received financing from the European Research Council grant agreement\r\nno. 949120 under the European Union’s Horizon 2020 research and innovation programme.\r\nThis research was supported by the Scientific Service Units of The Institute of Science\r\nand Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the\r\nNanofabrication Facility, the Lab Support Facility, the Scientific Computing Facility and the\r\nElectron Microscopy Facility. We thank Florian Stumpf from Park Systems for useful discussions\r\nand support with scanning probe microscopy. We thank Joaquin Garcia-Suarez and Guillaume\r\nAnciaux for the suggestion to look into the roughness power spectral density. We thank\r\nIrina-Malina Strugaru for help with testing the device for Young’s modulus measurements.\r\n","file_date_updated":"2026-08-12T13:04:21Z","ec_funded":1,"doi":"10.15479/AT-ISTA-22684","date_updated":"2026-10-21T08:39:24Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","department":[{"_id":"GradSch"},{"_id":"ScWa"}],"year":"2026","citation":{"apa":"Pertl, F. (2026). <i>Experimental probing of nanoscale charge features and surface morphology changes during tribocharging</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>","short":"F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging, Institute of Science and Technology Austria, 2026.","mla":"Pertl, Felix. <i>Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>.","ista":"Pertl F. 2026. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria.","ama":"Pertl F. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>","chicago":"Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>.","ieee":"F. Pertl, “Experimental probing of nanoscale charge features and surface morphology changes during tribocharging,” Institute of Science and Technology Austria, 2026."},"OA_place":"publisher"},{"OA_place":"repository","publisher":"AAAS","volume":392,"department":[{"_id":"JiFr"},{"_id":"GradSch"}],"year":"2026","citation":{"ieee":"I. Kulich <i>et al.</i>, “Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation,” <i>Science</i>, vol. 392, no. 6795. AAAS, pp. 296–300, 2026.","chicago":"Kulich, Ivan, Dmitrii Vladimirtsev, Marek Randuch, Shiqiang Gao, Matteo Citterico, Kai R. Konrad, Georg Nagel, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.adu8197\">https://doi.org/10.1126/science.adu8197</a>.","ama":"Kulich I, Vladimirtsev D, Randuch M, et al. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. <i>Science</i>. 2026;392(6795):296-300. doi:<a href=\"https://doi.org/10.1126/science.adu8197\">10.1126/science.adu8197</a>","ista":"Kulich I, Vladimirtsev D, Randuch M, Gao S, Citterico M, Konrad KR, Nagel G, Wrzaczek M, Cascaro L, Vinet P, Durand P, Asnacios A, Verma L, Bennett MJ, Pandey BK, Friml J. 2026. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. Science. 392(6795), 296–300.","mla":"Kulich, Ivan, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” <i>Science</i>, vol. 392, no. 6795, AAAS, 2026, pp. 296–300, doi:<a href=\"https://doi.org/10.1126/science.adu8197\">10.1126/science.adu8197</a>.","apa":"Kulich, I., Vladimirtsev, D., Randuch, M., Gao, S., Citterico, M., Konrad, K. R., … Friml, J. (2026). Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adu8197\">https://doi.org/10.1126/science.adu8197</a>","short":"I. Kulich, D. Vladimirtsev, M. Randuch, S. Gao, M. Citterico, K.R. Konrad, G. Nagel, M. Wrzaczek, L. Cascaro, P. Vinet, P. Durand, A. Asnacios, L. Verma, M.J. Bennett, B.K. Pandey, J. Friml, Science 392 (2026) 296–300."},"scopus_import":"1","date_updated":"2026-10-22T09:15:44Z","doi":"10.1126/science.adu8197","external_id":{"pmid":["41990180"]},"pmid":1,"acknowledgement":"We gratefully acknowledge the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) (both of ISTA) and the Hounsfield CT Facility (University of Nottingham) for support with imaging and the Growth Facility (IPMB) for plant cultivation. We thank M. Fendrych and his team for help with the microfluidics upgrades and J. Atkinson at the University of Nottingham MakerSpace for 3D printing of Arabidopsis mini-soil columns.\r\nThis project received funding from the European Research Council (ERC; 101142681 CYNIPS) and the Austrian Science Fund (FWF; P 37051-B). I.K. was cofunded by the European Union, Horizon Europe, project MOLIPEC, ID 101087030 and CSF project 25-16449S. L.V. and B.K.P. acknowledge funding from UK Research and Innovation (UKRI) Frontiers Research (EP/Y036697/1). M.J.B. acknowledges funding from ERC SYNERGY (grant 101118769 HYDROSENSING). The study was partially supported by the Université Paris Cité, Idex ANR-18-IDEX-0001, funded by the French Government through its “Investments for the Future” program and also by the projects “Mecha-Nuc” ANR-20-CE13-0025-03 and “scEm-bryoMech” ANR-21-CE13-0046. P.D. acknowledges support by Human Frontier Science Program Organization grant 2022-RG107. P.V. acknowledges support provided by “Programme blanc” of the Graduate School BIOSPHERA, Université Paris-Saclay. Phytohormonal analysis was performed using the service laboratory funded by Toward Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the European Regional Development Fund (ERDF) program Johannes Amos Comenius. This research was funded in whole or in part by the Austrian Science Fund (P 37051-B) and UK Research and Innovation (EP/Y036697/1), cOAlition S organizations, and by the European Research Council (101142681 CYNIPS, 101118769 HYDROSENSING); as required, the author will make the Author Accepted Manuscript (AAM) version available under a CC BY public copyright license.","ddc":["580"],"file_date_updated":"2026-05-07T05:54:43Z","issue":"6795","related_material":{"record":[{"relation":"dissertation_contains","id":"23145","status":"public"}]},"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"title":"Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation","page":"296-300","publication":"Science","author":[{"full_name":"Kulich, Ivan","first_name":"Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","last_name":"Kulich"},{"first_name":"Dmitrii","full_name":"Vladimirtsev, Dmitrii","last_name":"Vladimirtsev","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","full_name":"Randuch, Marek","first_name":"Marek"},{"full_name":"Gao, Shiqiang","first_name":"Shiqiang","last_name":"Gao"},{"last_name":"Citterico","full_name":"Citterico, Matteo","first_name":"Matteo"},{"last_name":"Konrad","full_name":"Konrad, Kai R.","first_name":"Kai R."},{"first_name":"Georg","full_name":"Nagel, Georg","last_name":"Nagel"},{"last_name":"Wrzaczek","first_name":"Michael","full_name":"Wrzaczek, Michael"},{"last_name":"Cascaro","full_name":"Cascaro, Léa","first_name":"Léa"},{"first_name":"Pauline","full_name":"Vinet, Pauline","last_name":"Vinet"},{"last_name":"Durand","first_name":"Pauline","full_name":"Durand, Pauline"},{"full_name":"Asnacios, Atef","first_name":"Atef","last_name":"Asnacios"},{"full_name":"Verma, Lokesh","first_name":"Lokesh","last_name":"Verma"},{"full_name":"Bennett, Malcolm J.","first_name":"Malcolm J.","last_name":"Bennett"},{"last_name":"Pandey","first_name":"Bipin K.","full_name":"Pandey, Bipin K."},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"file":[{"date_created":"2026-05-07T05:54:43Z","file_name":"2026_Science_Kulich_accepted.pdf","file_size":6150733,"access_level":"open_access","checksum":"eb5b29247832ecdc53c8146da0509bbe","success":1,"content_type":"application/pdf","creator":"dernst","date_updated":"2026-05-07T05:54:43Z","relation":"main_file","file_id":"21832"}],"fulldoi":"https://doi.org/10.1126/science.adu8197","project":[{"_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"}],"article_type":"original","language":[{"iso":"eng"}],"oa_version":"Accepted Version","status":"public","abstract":[{"text":"Reactive oxygen species (ROS) have been implicated in multiple signaling processes in plants, but the underlying mechanisms and roles remain enigmatic. In this study, we developed a method of live imaging of apoplastic ROS at the root surface. Distinct signals, including auxin, extracellular adenosine triphosphate, and rapid alkalinization factor 1 peptide, induce cytosolic calcium transients and apoplastic ROS bursts. Genetic and optogenetic manipulations of Arabidopsis identified calcium transients as necessary and sufficient for ROS bursts through activation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases RBOHC and RBOHF. Apoplastic ROS bursts are not required, but they do limit gravity-induced root bending. Root bending is sensed by the stretch-activated calcium channel MCA1, leading to NADPH oxidase activation. The resulting ROS production stiffens cell walls to facilitate soil penetration. Apoplastic ROS thus provides a means to balance tissue flexibility and stiffness to navigate soil.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","date_published":"2026-04-16T00:00:00Z","article_processing_charge":"No","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-04-26T22:01:47Z","month":"04","intvolume":"       392","quality_controlled":"1","corr_author":"1","day":"16","_id":"21763","type":"journal_article","oa":1},{"supervisor":[{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"_id":"23145","day":"18","type":"dissertation","corr_author":"1","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"month":"10","date_created":"2026-10-16T17:14:40Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"},{"_id":"Bio"}],"article_processing_charge":"No","date_published":"2026-10-18T00:00:00Z","publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"page":"289","title":"Fast growth responses in plants: Growth regulation and phospho-proteomic ","project":[{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"},{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-23145","file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-10-20T11:48:37Z","file_id":"23176","creator":"mranduch","relation":"source_file","checksum":"4ace20ba4f1bb0f8dcc3f8eb45eb68fa","date_created":"2026-10-20T09:17:28Z","file_name":"2026_Marek_Randuch_Thesis.docx","file_size":89544771},{"date_created":"2026-10-20T09:17:20Z","file_name":"2026_Marek_Randuch_Thesis.pdf","embargo":"2027-10-20","file_size":28321059,"access_level":"closed","checksum":"fc630c7e8d795e7f13000cbb428424b3","creator":"mranduch","embargo_to":"open_access","relation":"main_file","date_updated":"2026-10-20T11:48:37Z","file_id":"23177","content_type":"application/pdf"}],"author":[{"full_name":"Randuch, Marek","first_name":"Marek","last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"}],"file_date_updated":"2026-10-20T11:48:37Z","acknowledgement":"European Research Council (101142681 CYNIPS), Cyclic nucleotides as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors, \r\nDOI: https://doi.org/10.55776/P37051 ","ddc":["580"],"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12291"},{"id":"21763","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"23175","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"23174","status":"public"},{"relation":"part_of_dissertation","id":"20656","status":"public"}]},"doi":"10.15479/AT-ISTA-23145","date_updated":"2026-10-22T09:15:44Z","OA_place":"publisher","citation":{"ieee":"M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic ,” Institute of Science and Technology Austria, 2026.","ama":"Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>","ista":"Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria.","chicago":"Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>.","apa":"Randuch, M. (2026). <i>Fast growth responses in plants: Growth regulation and phospho-proteomic </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>","short":"M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic , Institute of Science and Technology Austria, 2026.","mla":"Randuch, Marek. <i>Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>."},"year":"2026","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD"},{"language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","publication_status":"published","status":"public","supplementarymaterial":"no","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We prove discrete-to-continuum convergence for dynamical optimal transport on  Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of  1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations."}],"date_published":"2026-06-01T00:00:00Z","article_processing_charge":"Yes","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"gold","researchdata_availability":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-12-23T11:03:59Z","keyword":["optimal transport","discrete-to-continuum","homogenisation","linear growth","gamma-convergence"],"month":"06","intvolume":"        37","PlanS_conform":"1","quality_controlled":"1","_id":"18706","type":"journal_article","day":"01","DOAJ_listed":"1","oa":1,"OA_place":"publisher","volume":37,"publisher":"Cambridge University Press","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"citation":{"ieee":"L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” <i>European Journal of Applied Mathematics</i>, vol. 37, no. 3. Cambridge University Press, pp. 614–642, 2026.","ama":"Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. 2026;37(3):614-642. doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>","ista":"Portinale L, Quattrocchi F. 2026. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. 37(3), 614–642.","chicago":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>. Cambridge University Press, 2026. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>.","apa":"Portinale, L., &#38; Quattrocchi, F. (2026). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>","short":"L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics 37 (2026) 614–642.","mla":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>, vol. 37, no. 3, Cambridge University Press, 2026, pp. 614–42, doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>."},"year":"2026","scopus_import":"1","date_updated":"2026-10-25T23:31:21Z","doi":"10.1017/s0956792524000810","external_id":{"isi":["001381435800001"]},"ddc":["500"],"acknowledgement":"L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","file_date_updated":"2026-07-23T05:55:03Z","issue":"3","related_material":{"record":[{"relation":"dissertation_contains","id":"20563","status":"public"}]},"das_tickbox":"0","publication_identifier":{"issn":["0956-7925"],"eissn":["1469-4425"]},"title":"Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs","page":"614-642","author":[{"last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"},{"first_name":"Filippo","orcid":"0009-0000-9773-1931","full_name":"Quattrocchi, Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi"}],"publication":"European Journal of Applied Mathematics","file":[{"date_created":"2026-07-23T05:55:03Z","file_name":"2026_EuropJourAppliedMath_Portinale.pdf","file_size":612317,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"22386","date_updated":"2026-07-23T05:55:03Z","checksum":"d038f4d00cbfbde2672c17138eab21c9","success":1}],"fulldoi":"https://doi.org/10.1017/s0956792524000810","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}]}]