--- OA_place: publisher _id: '22258' 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." acknowledged_ssus: - _id: ScienComp 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Al full_name: Depope, Al id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830 last_name: Depope citation: ama: 'Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:10.15479/AT-ISTA-22258' apa: '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. https://doi.org/10.15479/AT-ISTA-22258' 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. https://doi.org/10.15479/AT-ISTA-22258.' 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.' 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.' mla: '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, doi:10.15479/AT-ISTA-22258.' 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.' corr_author: '1' das_tickbox: '1' date_created: 2026-07-10T13:27:20Z date_published: 2026-07-11T00:00:00Z date_updated: 2026-10-20T09:03:21Z day: '11' ddc: - '576' - '610' - '006' degree_awarded: PhD department: - _id: GradSch - _id: MaRo - _id: MaMo doi: 10.15479/AT-ISTA-22258 doi_confirm: '1' file: - access_level: open_access checksum: 9ab386790515628d957a194f30a7ccb4 content_type: application/pdf creator: adepope date_created: 2026-07-13T14:52:19Z date_updated: 2026-07-13T14:52:19Z file_id: '22316' file_name: 2026_Depope_Al_Thesis.pdf file_size: 25109878 relation: main_file - access_level: closed checksum: 8ed8fb63f76a695d5b6fec35343f4b90 content_type: application/zip creator: adepope date_created: 2026-07-13T14:56:41Z date_updated: 2026-07-13T14:56:41Z file_id: '22317' file_name: 2026_Depope_Al_Thesis.zip file_size: 1203199939 relation: source_file file_date_updated: 2026-07-13T14:56:41Z fulldoi: https://doi.org/10.15479/AT-ISTA-22258 has_accepted_license: '1' keyword: - Approximate Message Passing - GWAS - Genomics - Proteomics - Survival modeling language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '169' project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf grant_number: '101161364' name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits' - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21488' relation: part_of_dissertation status: public status: public supervisor: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 title: 'From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '22667' acknowledged_ssus: - _id: Bio - _id: LifeSc 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. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic orcid: 0000-0002-5494-0941 citation: ama: Vijatovic D. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. 2026. doi:10.15479/AT-ISTA-22667 apa: Vijatovic, D. (2026). Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22667 chicago: Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22667. ieee: D. Vijatovic, “Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis,” Institute of Science and Technology Austria, 2026. ista: Vijatovic D. 2026. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria. mla: Vijatovic, David. Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22667. short: D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-08-10T13:44:30Z date_published: 2026-08-10T00:00:00Z date_updated: 2026-10-20T09:04:22Z day: '10' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: LoSw doi: 10.15479/AT-ISTA-22667 doi_confirm: '1' file: - access_level: closed checksum: e3acfea4b1a3abf99e74224656740a15 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dvijatov date_created: 2026-08-10T13:35:39Z date_updated: 2026-08-10T13:35:39Z file_id: '22669' file_name: 2026_Vijatovic_David_Thesis.docx file_size: 14322760 relation: source_file - access_level: closed checksum: dc8c78ae14f69e54faa41e65db5c6402 content_type: application/pdf creator: dvijatov date_created: 2026-08-12T13:44:36Z date_updated: 2026-08-12T13:44:36Z embargo: 2027-08-10 embargo_to: open_access file_id: '22695' file_name: 2026_Vijatovic_David_Thesis.pdf file_size: 116926375 relation: main_file file_date_updated: 2026-08-12T13:44:36Z fulldoi: https://doi.org/10.15479/AT-ISTA-22667 has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '172' project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis - _id: 34a02c70-11ca-11ed-8bc3-fbfd2c86c88f grant_number: 3(GG016346-01) name: Development of Viral Vectors for Amphibian Gene Delivery and Manipulation publication_identifier: isbn: - 978-3-99078-082-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15016' relation: part_of_dissertation status: public - id: '21746' relation: part_of_dissertation status: public status: public supervisor: - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 title: Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '22399' alternative_title: - ISTA Master’s Thesis article_processing_charge: No author: - first_name: Aleksa full_name: Spasić, Aleksa id: ecee9d38-4040-11ef-8843-b941efb445d6 last_name: Spasić citation: ama: Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:10.15479/AT-ISTA-22399 apa: Spasić, A. (2026). Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22399 chicago: Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22399. ieee: A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026. ista: Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria. mla: Spasić, Aleksa. Studying the Evolutionary Systems Biology of the Lac Operon. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22399. short: A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026. corr_author: '1' das_tickbox: '0' date_created: 2026-07-25T13:08:32Z date_published: 2026-07-27T00:00:00Z date_updated: 2026-10-21T07:47:08Z day: '27' ddc: - '576' degree_awarded: MS department: - _id: GradSch - _id: GaTk - _id: CaGu doi: 10.15479/AT-ISTA-22399 doi_confirm: '1' file: - access_level: closed checksum: c29880dd71fcc37f23ac6e2843066ede content_type: application/pdf creator: aspasic date_created: 2026-07-27T13:00:07Z date_updated: 2026-10-20T08:47:40Z embargo: 2027-07-30 embargo_to: open_access file_id: '22588' file_name: Aleksa_Spasic_Thesis_final.pdf file_size: 1986078 relation: main_file - access_level: closed checksum: 4ebe3bd2d833d913c0756343cca5e5f0 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: aspasic date_created: 2026-07-27T13:00:22Z date_updated: 2026-07-27T13:07:23Z file_id: '22589' file_name: Thesis_final.docx file_size: 1868853 relation: source_file file_date_updated: 2026-10-20T08:47:40Z fulldoi: https://doi.org/10.15479/AT-ISTA-22399 has_accepted_license: '1' language: - iso: eng month: '07' oa_version: Published Version page: '32' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Studying the evolutionary systems biology of the lac operon type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '22281' abstract: - lang: eng 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." 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Antoine full_name: El-Hayek, Antoine id: 888a098e-fcac-11ee-aff7-d347be57b725 last_name: El-Hayek orcid: 0000-0003-4268-7368 citation: ama: 'El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. 2026. doi:10.15479/AT-ISTA-22281' apa: 'El-Hayek, A. (2026). Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22281' chicago: 'El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22281.' ieee: 'A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks,” Institute of Science and Technology Austria, 2026.' ista: 'El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria.' mla: 'El-Hayek, Antoine. Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22281.' short: 'A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-07-13T09:39:59Z date_published: 2026-07-13T00:00:00Z date_updated: 2026-10-21T08:05:35Z day: '13' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: MoHe doi: 10.15479/AT-ISTA-22281 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 923e4ca769c9ef2f6b0b005444faf462 content_type: application/pdf creator: aelhayek date_created: 2026-07-17T11:39:47Z date_updated: 2026-07-17T11:39:47Z file_id: '22356' file_name: 2026_El-Hayek_Antoine_Thesis.pdf file_size: 5465973 relation: main_file success: 1 - access_level: closed checksum: 262689f9df27dd6c2c7c7861f1de7329 content_type: application/x-zip-compressed creator: aelhayek date_created: 2026-07-17T11:40:34Z date_updated: 2026-07-20T11:29:38Z file_id: '22357' file_name: 2026_El-Hayek_Antoine_Thesis.zip file_size: 9116107 relation: source_file file_date_updated: 2026-07-20T11:29:38Z fulldoi: https://doi.org/10.15479/AT-ISTA-22281 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '244' project: - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures - _id: bda196b2-d553-11ed-ba76-8e8ee6c21103 grant_number: I05982 name: Static and Dynamic Hierarchical Graph Decompositions - _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe grant_number: P33775 name: Fast Algorithms for a Reactive Network Layer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publisher_comment: Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are All Rights Reserved. related_material: record: - id: '20051' relation: part_of_dissertation status: public - id: '19982' relation: part_of_dissertation status: public - id: '21720' relation: part_of_dissertation status: public - id: '22374' relation: part_of_dissertation status: public - id: '22373' relation: part_of_dissertation status: public - id: '18557' relation: part_of_dissertation status: public status: public supervisor: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 title: 'Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '20991' abstract: - lang: eng 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." 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)" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Diego Fernando full_name: Garcia Castillo, Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo citation: ama: Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:10.15479/AT-ISTA-20991 apa: Garcia Castillo, D. F. (2026). The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20991 chicago: Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20991. ieee: D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026. ista: Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. mla: Garcia Castillo, Diego Fernando. The Genomic Architecture of Local Adaptation in Introduced Populations. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20991. short: D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-01-16T09:47:59Z date_published: 2026-01-16T00:00:00Z date_updated: 2026-10-21T08:18:21Z day: '16' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20991 file: - access_level: closed checksum: 841f1bc073d667125729b2a017f8c37a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20996' file_name: 2026_Garcia_Diego_Thesis.docx file_size: 22456421 relation: source_file - access_level: open_access checksum: a1f33d4f183ce7072eee42a6ccf5340b content_type: application/pdf creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20997' file_name: 2026_Garcia_Diego_Thesis.pdf file_size: 9556719 relation: main_file success: 1 - access_level: closed checksum: 98a80691067174c30fe53f38ce7344e6 content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z 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. file_id: '20998' file_name: 2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar file_size: 54491433 relation: supplementary_material - access_level: open_access checksum: 99a3cab2fa36666b9a92eefc27d586da content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z file_id: '20999' file_name: 2026_DiegoGarcia_Thesis-Supplementary_Material.rar file_size: 7982811 relation: supplementary_material - access_level: open_access checksum: 255fdf56b2932c46bf27c63aa6106a4f content_type: text/plain creator: dgarciac date_created: 2026-01-16T13:08:59Z date_updated: 2026-01-16T13:08:59Z file_id: '21000' file_name: README.txt file_size: 732 relation: supplementary_material file_date_updated: 2026-01-16T13:08:59Z fulldoi: https://doi.org/10.15479/AT-ISTA-20991 has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '199' publication_identifier: isbn: - 978-3-99078-077-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18498' relation: research_data status: public - id: '18491' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 title: The genomic architecture of local adaptation in introduced populations tmp: image: /images/cc_by_nc_sa.png 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) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_place: publisher _id: '22684' abstract: - lang: eng 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." acknowledged_ssus: - _id: NanoFab - _id: ScienComp - _id: LifeSc - _id: M-Shop - _id: EM-Fac 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Felix full_name: Pertl, Felix id: 6313aec0-15b2-11ec-abd3-ed67d16139af last_name: Pertl orcid: 0000-0003-0463-5794 citation: ama: Pertl F. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. 2026. doi:10.15479/AT-ISTA-22684 apa: Pertl, F. (2026). Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22684 chicago: Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22684. ieee: F. Pertl, “Experimental probing of nanoscale charge features and surface morphology changes during tribocharging,” Institute of Science and Technology Austria, 2026. ista: Pertl F. 2026. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria. mla: Pertl, Felix. Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22684. short: F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-08-12T09:44:40Z date_published: 2026-08-12T00:00:00Z date_updated: 2026-10-21T08:39:24Z day: '12' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: ScWa doi: 10.15479/AT-ISTA-22684 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 0a4f5a941c40b921447e72291d72bc6f content_type: application/x-zip-compressed creator: fpertl date_created: 2026-08-12T13:04:21Z date_updated: 2026-08-12T13:04:21Z file_id: '22690' file_name: 2026_Pertl_Felix_Thesis.zip file_size: 31192621 relation: source_file - access_level: open_access checksum: ae60dcdb363222138886b2857643d4e3 content_type: application/pdf creator: fpertl date_created: 2026-08-12T13:04:21Z date_updated: 2026-08-12T13:04:21Z file_id: '22691' file_name: 2026_Pertl_Felix_Thesis.pdf file_size: 27882509 relation: main_file file_date_updated: 2026-08-12T13:04:21Z fulldoi: https://doi.org/10.15479/AT-ISTA-22684 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '107' project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication_identifier: isbn: - 978-3-99078-083-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20481' relation: part_of_dissertation status: public - id: '12109' relation: part_of_dissertation status: public - id: '19278' relation: part_of_dissertation status: public - id: '17373' relation: part_of_dissertation status: public status: public supervisor: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 title: Experimental probing of nanoscale charge features and surface morphology changes during tribocharging tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: green _id: '21763' abstract: - lang: eng 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. acknowledged_ssus: - _id: LifeSc - _id: Bio 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." article_processing_charge: No article_type: original author: - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Shiqiang full_name: Gao, Shiqiang last_name: Gao - first_name: Matteo full_name: Citterico, Matteo last_name: Citterico - first_name: Kai R. full_name: Konrad, Kai R. last_name: Konrad - first_name: Georg full_name: Nagel, Georg last_name: Nagel - first_name: Michael full_name: Wrzaczek, Michael last_name: Wrzaczek - first_name: Léa full_name: Cascaro, Léa last_name: Cascaro - first_name: Pauline full_name: Vinet, Pauline last_name: Vinet - first_name: Pauline full_name: Durand, Pauline last_name: Durand - first_name: Atef full_name: Asnacios, Atef last_name: Asnacios - first_name: Lokesh full_name: Verma, Lokesh last_name: Verma - first_name: Malcolm J. full_name: Bennett, Malcolm J. last_name: Bennett - first_name: Bipin K. full_name: Pandey, Bipin K. last_name: Pandey - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kulich I, Vladimirtsev D, Randuch M, et al. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. Science. 2026;392(6795):296-300. doi:10.1126/science.adu8197 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. Science. AAAS. https://doi.org/10.1126/science.adu8197 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.” Science. AAAS, 2026. https://doi.org/10.1126/science.adu8197. ieee: I. Kulich et al., “Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation,” Science, vol. 392, no. 6795. AAAS, pp. 296–300, 2026. 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.” Science, vol. 392, no. 6795, AAAS, 2026, pp. 296–300, doi:10.1126/science.adu8197. 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. corr_author: '1' date_created: 2026-04-26T22:01:47Z date_published: 2026-04-16T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '16' ddc: - '580' department: - _id: JiFr - _id: GradSch doi: 10.1126/science.adu8197 external_id: pmid: - '41990180' file: - access_level: open_access checksum: eb5b29247832ecdc53c8146da0509bbe content_type: application/pdf creator: dernst date_created: 2026-05-07T05:54:43Z date_updated: 2026-05-07T05:54:43Z file_id: '21832' file_name: 2026_Science_Kulich_accepted.pdf file_size: 6150733 relation: main_file success: 1 file_date_updated: 2026-05-07T05:54:43Z fulldoi: https://doi.org/10.1126/science.adu8197 has_accepted_license: '1' intvolume: ' 392' issue: '6795' language: - iso: eng month: '04' oa: 1 oa_version: Accepted Version page: 296-300 pmid: 1 project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' related_material: record: - id: '23145' relation: dissertation_contains status: public scopus_import: '1' status: public title: Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 392 year: '2026' ... --- OA_place: publisher _id: '23145' acknowledged_ssus: - _id: LifeSc - _id: M-Shop - _id: CampIT - _id: Bio 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 " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch citation: ama: 'Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic . 2026. doi:10.15479/AT-ISTA-23145' apa: 'Randuch, M. (2026). Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-23145' chicago: 'Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-23145.' ieee: 'M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic ,” Institute of Science and Technology Austria, 2026.' ista: 'Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria.' mla: 'Randuch, Marek. Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-23145.' short: 'M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic , Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-10-16T17:14:40Z date_published: 2026-10-18T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '18' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-23145 doi_confirm: '1' file: - access_level: closed checksum: 4ace20ba4f1bb0f8dcc3f8eb45eb68fa content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mranduch date_created: 2026-10-20T09:17:28Z date_updated: 2026-10-20T11:48:37Z file_id: '23176' file_name: 2026_Marek_Randuch_Thesis.docx file_size: 89544771 relation: source_file - access_level: closed checksum: fc630c7e8d795e7f13000cbb428424b3 content_type: application/pdf creator: mranduch date_created: 2026-10-20T09:17:20Z date_updated: 2026-10-20T11:48:37Z embargo: 2027-10-20 embargo_to: open_access file_id: '23177' file_name: 2026_Marek_Randuch_Thesis.pdf file_size: 28321059 relation: main_file file_date_updated: 2026-10-20T11:48:37Z fulldoi: https://doi.org/10.15479/AT-ISTA-23145 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '10' oa_version: Published Version page: '289' project: - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '21763' relation: part_of_dissertation status: public - id: '23175' relation: part_of_dissertation status: public - id: '23174' relation: part_of_dissertation status: public - id: '20656' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Fast growth responses in plants: Growth regulation and phospho-proteomic ' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21983' abstract: - lang: eng text: 'Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology.' acknowledgement: "We thank Nick Barton and Noa Ottilie Borst for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA).\r\nThis study was supported by the European Molecular Biology Laboratory (J.C.); the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under the Marie Skłodowska-Curie Actions cofund (S.H.A.)." article_number: '102483' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Elia full_name: Mascolo, Elia id: 776a6ed0-a053-11f0-8635-80b95e0e0d53 last_name: Mascolo orcid: 0000-0003-2977-7844 - first_name: Reka E full_name: Körei, Reka E id: 50FDE43E-AA30-11E9-A72B-8A12E6697425 last_name: Körei - first_name: Santiago full_name: Herrera-Álvarez, Santiago last_name: Herrera-Álvarez - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Justin full_name: Crocker, Justin last_name: Crocker - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: 'Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics & Development. 2026;99. doi:10.1016/j.gde.2026.102483' apa: 'Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., Crocker, J., & Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2026.102483' chicago: 'Mascolo, Elia, Reka E Körei, Santiago Herrera-Álvarez, Calin C Guet, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” Current Opinion in Genetics & Development. Elsevier, 2026. https://doi.org/10.1016/j.gde.2026.102483.' ieee: 'E. Mascolo, R. E. Körei, S. Herrera-Álvarez, C. C. Guet, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps,” Current Opinion in Genetics & Development, vol. 99. Elsevier, 2026.' ista: 'Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics & Development. 99, 102483.' mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” Current Opinion in Genetics & Development, vol. 99, 102483, Elsevier, 2026, doi:10.1016/j.gde.2026.102483.' short: E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik, Current Opinion in Genetics & Development 99 (2026). corr_author: '1' date_created: 2026-06-10T07:37:12Z date_published: 2026-05-09T00:00:00Z date_updated: 2026-10-27T13:12:27Z day: '09' ddc: - '570' department: - _id: GradSch - _id: CaGu - _id: GaTk doi: 10.1016/j.gde.2026.102483 external_id: arxiv: - '2601.19681' fulldoi: https://doi.org/10.1016/j.gde.2026.102483 has_accepted_license: '1' intvolume: ' 99' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.gde.2026.102483 month: '05' oa: 1 oa_version: Published Version publication: Current Opinion in Genetics & Development publication_identifier: eissn: - 1879-0380 issn: - 0959-437X publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '18706' 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." 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. article_processing_charge: Yes article_type: original author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. 2026;37(3):614-642. doi:10.1017/s0956792524000810 apa: Portinale, L., & Quattrocchi, F. (2026). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. Cambridge University Press. https://doi.org/10.1017/s0956792524000810 chicago: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics. Cambridge University Press, 2026. https://doi.org/10.1017/s0956792524000810. ieee: L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” European Journal of Applied Mathematics, vol. 37, no. 3. Cambridge University Press, pp. 614–642, 2026. 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. mla: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics, vol. 37, no. 3, Cambridge University Press, 2026, pp. 614–42, doi:10.1017/s0956792524000810. short: L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics 37 (2026) 614–642. das_tickbox: '0' date_created: 2024-12-23T11:03:59Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-11-06T23:31:06Z day: '01' ddc: - '500' department: - _id: GradSch - _id: JaMa doi: 10.1017/s0956792524000810 external_id: isi: - '001381435800001' file: - access_level: open_access checksum: d038f4d00cbfbde2672c17138eab21c9 content_type: application/pdf creator: dernst date_created: 2026-07-23T05:55:03Z date_updated: 2026-07-23T05:55:03Z file_id: '22386' file_name: 2026_EuropJourAppliedMath_Portinale.pdf file_size: 612317 relation: main_file success: 1 file_date_updated: 2026-07-23T05:55:03Z fulldoi: https://doi.org/10.1017/s0956792524000810 has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '3' keyword: - optimal transport - discrete-to-continuum - homogenisation - linear growth - gamma-convergence language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 614-642 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: European Journal of Applied Mathematics publication_identifier: eissn: - 1469-4425 issn: - 0956-7925 publication_status: published publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '20563' relation: dissertation_contains status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 37 year: '2026' ... --- OA_place: repository _id: '21423' abstract: - lang: eng text: "Biological systems, such as cytoskeletal filaments and multicellular collectives, exhibit rich \r\nself-organization driven by their intrinsic activity and physical constraints. Across scales, \r\ngeometry plays a central role: the shape of active units and the structure of their environment \r\nstrongly influence how order emerges in these far-from-equilibrium systems. In this thesis, \r\nwe combine minimal active-matter models with bottom-up in vitro experiments to identify \r\nthe principles by which geometry and activity shape collective behavior in biological matter. \r\nAt the subcellular scale, we investigate how the physical properties of chiral FtsZ filaments \r\ngovern their large-scale organization. Using a mesoscopic model validated by reconstituted \r\nfilament assays, we show that filament shape, intrinsic curvature, and flexibility, together with \r\nactivity-driven straightening, determine whether filaments form chiral rings, polar bands, or \r\nnematic-like states. Our model shows that small changes in filament mechanics produce large \r\nshifts in collective structures, revealing how the geometry of individual filaments amplifies \r\nthrough activity to control patterns relevant for bacterial cytokinesis. \r\nAt the cellular scale, we examine how geometry of the external environment influences \r\ncollective cancer cell migration. Experiments in controlled microfabricated obstacle \r\nenvironments demonstrate that geometric disorder alone can induce a transition from \r\ncollective to single-cell invasion. A minimal model of active particles in disordered geometries \r\nreproduces these effects, demonstrating that cell dissemination results both from local \r\ngeometrical constraints and a global integration of spatial disorder over time. Surprisingly, \r\nthis transition is accompanied by a change in the universality class of interface dynamics, \r\nrevealing that cell-environment interactions can shift the collective behavior of an invasive \r\nfront purely through mechanics. \r\nIn the last system, we study how cell-intrinsic geometry and chirality affect collective motion \r\nin confined and unconfined settings. Using a minimal model inspired by in vitro experiments, \r\nwe analyze motile cells that exhibit persistent rotation due to intrinsic left-right asymmetry. \r\nIn circular confinement, this simplified chiral model reproduces several experimentally \r\nobserved features within specific parameter regimes. At high densities in unconfined \r\nenvironments, however, intrinsic chirality becomes masked even before the onset of the \r\njamming transition. These results show that single-cell geometric asymmetry does not \r\nnecessarily translate into large-scale chiral flows, offering new insight into how forces and \r\nsymmetries shape collective motion in dense cellular systems. \r\nOverall, this work uncovers how geometric constraints – embedded in the intrinsic \r\narchitecture of an active filament or encoded in the complexity of a microenvironment \r\ncouple to active forces to generate different classes of complex behaviors. " acknowledged_ssus: - _id: ScienComp acknowledgement: "Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova citation: ama: Dunajova Z. Geometry-driven self-organization of migrating cells and chiral filaments. 2026. doi:10.15479/AT-ISTA-21423 apa: Dunajova, Z. (2026). Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21423 chicago: Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423. ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026. ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria. mla: Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423. short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-03-11T08:30:49Z date_published: 2026-03-11T00:00:00Z date_updated: 2026-10-16T08:12:11Z day: '11' ddc: - '539' - '570' degree_awarded: PhD department: - _id: GradSch - _id: EdHa doi: 10.15479/AT-ISTA-21423 doi_confirm: '1' file: - access_level: open_access checksum: 47ce6a48a0c63f28eca6e64c9ffd2c84 content_type: application/pdf creator: zdunajov date_created: 2026-03-12T20:38:52Z date_updated: 2026-09-11T22:30:02Z embargo: 2026-09-11 file_id: '21446' file_name: 2026_Dunajova_Zuzana_Thesis_pdfA.pdf file_size: 14662770 relation: main_file - access_level: closed checksum: 5dec5afdffd47c2b0b162d0fe1bed925 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: zdunajov date_created: 2026-03-12T20:40:18Z date_updated: 2026-09-11T22:30:02Z embargo_to: open_access file_id: '21447' file_name: Thesis-Dunajova_source_file.docx file_size: 32961408 relation: source_file file_date_updated: 2026-09-11T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-21423 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '110' project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication_identifier: isbn: - 978-3-99078-076-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: part_of_dissertation status: public - id: '13116' relation: research_data status: public - id: '21439' relation: research_data status: public - id: '21427' relation: part_of_dissertation status: public status: public supervisor: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Geometry-driven self-organization of migrating cells and chiral filaments tmp: image: /images/cc_by_nc_sa.png 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) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: free access _id: '21439' abstract: - lang: eng text: These files contain supplementary movies accompanying the PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” by Zuzana Dunajova (2026). The videos provide additional visual material supporting the experiments and results described in the thesis. acknowledged_ssus: - _id: Bio - _id: ScienComp article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova citation: ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:10.15479/AT-ISTA-21439 apa: Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21439 chicago: Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21439. ieee: Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization of migrating cells and chiral filaments.’” Institute of Science and Technology Austria, 2026. ista: Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21439. mla: Dunajova, Zuzana. Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21439. short: Z. Dunajova, (2026). contributor: - contributor_type: researcher first_name: Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - contributor_type: researcher first_name: Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' corr_author: '1' date_created: 2026-03-11T21:05:20Z date_published: 2026-03-12T00:00:00Z date_updated: 2026-11-06T23:31:10Z day: '12' ddc: - '570' department: - _id: GradSch - _id: EdHa doi: 10.15479/AT-ISTA-21439 file: - access_level: open_access checksum: 47809a9a31b748b16e21e92d11ddc87f content_type: application/zip creator: zdunajov date_created: 2026-03-11T20:41:28Z date_updated: 2026-03-11T20:41:28Z file_id: '21440' file_name: Supplementary_movies_Thesis_Dunajova.zip file_size: 154465214 relation: main_file success: 1 - access_level: open_access checksum: a64a174bc6abf0a5e77631e4fd121f1f content_type: text/plain creator: zdunajov date_created: 2026-03-11T20:52:39Z date_updated: 2026-03-11T20:52:39Z file_id: '21441' file_name: readme.txt file_size: 2289 relation: main_file success: 1 file_date_updated: 2026-03-11T20:52:39Z fulldoi: https://doi.org/10.15479/AT-ISTA-21439 has_accepted_license: '1' month: '03' oa: 1 oa_version: Published Version project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: used_in_publication status: public - id: '21427' relation: used_in_publication status: public - id: '21423' relation: used_in_publication status: public status: public title: Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” tmp: image: /images/cc_by_nc_sa.png 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) short: CC BY-NC-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- _id: '20842' abstract: - lang: eng text: Probing the possibility of entanglement generation through gravity offers a path to tackle the question of whether gravitational fields possess a quantum mechanical nature. A potential realization necessitates systems with low-frequency dynamics at an optimal mass scale, for which the microgram-to-milligram range is a strong contender. Here, after refining a figure-of-merit for the problem, we present a 1-milligram torsional pendulum operating at 18 Hz. We demonstrate laser cooling its motion from room temperature to 240~microkelvins, surpassing by over 20-fold the coldest motions attained for oscillators ranging from micrograms to kilograms. We quantify and contrast the utility of the current approach with other platforms. The achieved performance and large improvement potential highlight milligram-scale torsional pendulums as a powerful platform for precision measurements relevant to future studies at the quantum-gravity interface. article_processing_charge: No author: - first_name: Sofya full_name: Agafonova, Sofya id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80 last_name: Agafonova orcid: 0000-0003-0582-2946 citation: ama: 'Agafonova S. Research Data for: “One-milligram torsional pendulum toward experiments at the quantum-gravity interface.” 2025. doi:10.15479/AT-ISTA-20842' apa: 'Agafonova, S. (2025). Research Data for: “One-milligram torsional pendulum toward experiments at the quantum-gravity interface.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20842' chicago: 'Agafonova, Sofia. “Research Data for: ‘One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20842.' ieee: 'S. Agafonova, “Research Data for: ‘One-milligram torsional pendulum toward experiments at the quantum-gravity interface.’” Institute of Science and Technology Austria, 2025.' ista: 'Agafonova S. 2025. Research Data for: ‘One-milligram torsional pendulum toward experiments at the quantum-gravity interface’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20842.' mla: 'Agafonova, Sofia. Research Data for: “One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20842.' short: S. Agafonova, (2025). contributor: - first_name: Pere last_name: Rosello - first_name: Manuel last_name: Mekonnen - contributor_type: supervisor first_name: Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X corr_author: '1' date_created: 2025-12-21T14:23:50Z date_published: 2025-12-22T00:00:00Z date_updated: 2026-06-10T08:36:07Z day: '22' department: - _id: GradSch - _id: OnHo doi: 10.15479/AT-ISTA-20842 file: - access_level: open_access checksum: 7af34e4226a00cdcb7f154272050e217 content_type: application/x-zip-compressed creator: sagafono date_created: 2025-12-22T13:45:30Z date_updated: 2025-12-22T13:45:30Z file_id: '20854' file_name: AllData.zip file_size: 146656591 relation: main_file success: 1 - access_level: open_access checksum: 71806a2ef9fb26ad7b78e04c6754ee4e content_type: application/x-zip-compressed creator: sagafono date_created: 2025-12-22T13:45:33Z date_updated: 2025-12-22T13:45:33Z file_id: '20855' file_name: SourceData.zip file_size: 93470129 relation: main_file success: 1 - access_level: open_access checksum: 08facd1b4a102f83e4d99d48a85b258d content_type: text/plain creator: sagafono date_created: 2025-12-22T13:51:09Z date_updated: 2025-12-22T13:51:09Z file_id: '20856' file_name: readme.txt file_size: 461 relation: main_file success: 1 file_date_updated: 2025-12-22T13:51:09Z fulldoi: https://doi.org/10.15479/AT-ISTA-20842 has_accepted_license: '1' month: '12' oa: 1 oa_version: Published Version project: - _id: bdb2a702-d553-11ed-ba76-f12e3e5a3bc6 grant_number: '101087907' name: 'A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics' publisher: Institute of Science and Technology Austria related_material: record: - id: '20840' relation: used_in_publication status: public status: public title: 'Research Data for: ''One-milligram torsional pendulum toward experiments at the quantum-gravity interface''' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '21020' abstract: - lang: eng text: "Runtime verification offers scalable solutions to improve the safety and reliability of systems. However, systems that require verification or monitoring by a third party to ensure compliance with a specification might contain sensitive information, causing privacy concerns when usual runtime verification approaches are used. Privacy is compromised if protected information about the system, or sensitive data that is processed by the system, is revealed. In addition, revealing the specification being monitored may undermine the essence of third-party verification.\r\nIn this work, we propose two novel protocols for the privacy-preserving runtime verification of systems against formal sequential specifications. In our first protocol, the monitor verifies whether the system satisfies the specification without learning anything else, though both parties are aware of the specification. Our second protocol ensures that the system remains oblivious to the monitored specification, while the monitor learns only whether the system satisfies the specification and nothing more. Our protocols adapt and improve existing techniques used in cryptography, and more specifically, multi-party computation.\r\nThe sequential specification defines the observation step of the monitor, whose granularity depends on the situation (e.g., banks may be monitored on a daily basis). Our protocols exchange a single message per observation step, after an initialisation phase. This design minimises communication overhead, enabling relatively lightweight privacy-preserving monitoring. We implement our approach for monitoring specifications described by register automata and evaluate it experimentally." acknowledgement: This work is a part of projects VAMOS that has received fund-ing from the European Research Council (ERC), grant agreementNo 101020093 and the Austrian Science Fund (FWF) SFB projectSpyCoDe F8502.We thank anonymous reviewers for pointing us to related work [ 3] and for their valuable suggestions that improved this paper. article_processing_charge: Yes (via OA deal) arxiv: 1 author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Mahyar full_name: Karimi, Mahyar id: 6e5417ba-5355-11ee-ae5a-94c2e510b26b last_name: Karimi orcid: 0009-0005-0820-1696 - first_name: K. S. full_name: Thejaswini, K. S. id: 3807fb92-fdc1-11ee-bb4a-b4d8a431c753 last_name: Thejaswini citation: ama: 'Henzinger TA, Karimi M, Thejaswini KS. Privacy-preserving runtime verification. In: Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security. Association for Computing Machinery; 2025:2774-2787. doi:10.1145/3719027.3765137' apa: 'Henzinger, T. A., Karimi, M., & Thejaswini, K. S. (2025). Privacy-preserving runtime verification. In Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security (pp. 2774–2787). Taipei, Taiwan: Association for Computing Machinery. https://doi.org/10.1145/3719027.3765137' chicago: Henzinger, Thomas A, Mahyar Karimi, and K. S. Thejaswini. “Privacy-Preserving Runtime Verification.” In Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security, 2774–87. Association for Computing Machinery, 2025. https://doi.org/10.1145/3719027.3765137. ieee: T. A. Henzinger, M. Karimi, and K. S. Thejaswini, “Privacy-preserving runtime verification,” in Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security, Taipei, Taiwan, 2025, pp. 2774–2787. ista: 'Henzinger TA, Karimi M, Thejaswini KS. 2025. Privacy-preserving runtime verification. Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 2774–2787.' mla: Henzinger, Thomas A., et al. “Privacy-Preserving Runtime Verification.” Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2025, pp. 2774–87, doi:10.1145/3719027.3765137. short: T.A. Henzinger, M. Karimi, K.S. Thejaswini, in:, Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2025, pp. 2774–2787. conference: end_date: 2025-10-17 location: Taipei, Taiwan name: 'CCS: Conference on Computer and Communications Security' start_date: 2025-10-13 corr_author: '1' date_created: 2026-01-20T10:17:10Z date_published: 2025-11-22T00:00:00Z date_updated: 2026-03-13T13:37:19Z day: '22' ddc: - '000' department: - _id: ToHe - _id: GradSch doi: 10.1145/3719027.3765137 ec_funded: 1 external_id: arxiv: - '2505.09276' file: - access_level: open_access checksum: 615ffddab6c7285158c2953acec6fa6f content_type: application/pdf creator: dernst date_created: 2026-01-21T07:34:58Z date_updated: 2026-01-21T07:34:58Z file_id: '21024' file_name: 2025_CCS_HenzingerT.pdf file_size: 1241912 relation: main_file success: 1 file_date_updated: 2026-01-21T07:34:58Z fulldoi: https://doi.org/10.1145/3719027.3765137 has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 2774-2787 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software - _id: 34a1b658-11ca-11ed-8bc3-c75229f0241e grant_number: F8502 name: Interface Theory for Security and Privacy publication: Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security publication_identifier: isbn: - '9798400715259' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '21401' relation: dissertation_contains status: public scopus_import: '1' status: public title: Privacy-preserving runtime verification tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '21136' abstract: - lang: eng text: The plant hormone auxin regulates growth and development through at least two distinct signaling pathways. The nuclear pathway, involving TIR1/AFB receptors, mediates transcription; whereas the cell surface ABP1-TMK1 auxin perception triggers global ultrafast phosphorylation response. Here, we revisit the rich history of the disputed ABP1 auxin receptor, highlighting recent findings of the involvement of TMKs and other molecular components and focusing on their role in auxin canalization-mediated development. acknowledgement: We gratefully acknowledge the funding by the Austrian Science Fund (FWF; I 6123-B and P 37051-B) and the European Research Council (ERC; 101142681 CYNIPS).We would like to thank Lukas Fiedler for his significant input and thoughtful revision of this manuscript. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Monzer A, Friml J. Historical and mechanistic perspective on ABP1-TMK1-mediated cell surface auxin signaling. npj Science of Plants. 2025;1(1):2. doi:10.1038/s44383-025-00002-8 apa: Monzer, A., & Friml, J. (2025). Historical and mechanistic perspective on ABP1-TMK1-mediated cell surface auxin signaling. Npj Science of Plants. Springer Nature. https://doi.org/10.1038/s44383-025-00002-8 chicago: Monzer, Aline, and Jiří Friml. “Historical and Mechanistic Perspective on ABP1-TMK1-Mediated Cell Surface Auxin Signaling.” Npj Science of Plants. Springer Nature, 2025. https://doi.org/10.1038/s44383-025-00002-8. ieee: A. Monzer and J. Friml, “Historical and mechanistic perspective on ABP1-TMK1-mediated cell surface auxin signaling.,” npj Science of Plants, vol. 1, no. 1. Springer Nature, p. 2, 2025. ista: Monzer A, Friml J. 2025. Historical and mechanistic perspective on ABP1-TMK1-mediated cell surface auxin signaling. npj Science of Plants. 1(1), 2. mla: Monzer, Aline, and Jiří Friml. “Historical and Mechanistic Perspective on ABP1-TMK1-Mediated Cell Surface Auxin Signaling.” Npj Science of Plants, vol. 1, no. 1, Springer Nature, 2025, p. 2, doi:10.1038/s44383-025-00002-8. short: A. Monzer, J. Friml, Npj Science of Plants 1 (2025) 2. corr_author: '1' date_created: 2026-02-03T13:03:53Z date_published: 2025-07-01T00:00:00Z date_updated: 2026-02-10T09:39:20Z day: '01' ddc: - '580' department: - _id: JiFr - _id: GradSch doi: 10.1038/s44383-025-00002-8 external_id: pmid: - '40630787' file: - access_level: open_access checksum: 6c190faacf0e3bef98311dc8a12132d4 content_type: application/pdf creator: dernst date_created: 2026-02-10T09:35:43Z date_updated: 2026-02-10T09:35:43Z file_id: '21208' file_name: 2025_NPJSciencePlants_Monzer.pdf file_size: 974106 relation: main_file success: 1 file_date_updated: 2026-02-10T09:35:43Z fulldoi: https://doi.org/10.1038/s44383-025-00002-8 has_accepted_license: '1' intvolume: ' 1' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '2' pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants publication: npj Science of Plants publication_identifier: eissn: - 3005-1401 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Historical and mechanistic perspective on ABP1-TMK1-mediated cell surface auxin signaling. tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21248' abstract: - lang: eng text: Camera-type eyes in vertebrates and cephalopods are striking examples of parallel evolution of a complex structure. While comparisons have focused on these two groups, camera-type eyes with likely high functionality are also found in other invertebrate phyla with simpler brains. Employing single-cell RNA sequencing, we identify neurogenic cells in the adult eyes and brain of the marine annelid worm Platynereis dumerilii. Distinct neural stem cells in the camera-type adult eyes, located at the edge of the cup-shaped retina, and adjacent to the glass body/lens, produce radial lines of cells, reminiscent of stem cells in ciliary marginal zones of vertebrate eyes exhibiting life-long growth. Normal proliferation in the eye depends on ambient light, a phenomenon that depends on the integrity of the photoreceptor gene c-opsin1, which is present in emerging rhabdomeric photoreceptors, and impacts on their differentiation. During reproductive maturation, proliferation in the eye as well as the entire brain sharply declines, while cells upregulate molecular characteristics of mammalian adult neural stem cell quiescence. Our data provide insights into the development and modulation of annelid head and brain cells, revealing similarities and differences to vertebrate eye development, neurogenesis and brain plasticity. acknowledgement: 'We are grateful to Andrij Belokurov, Margaryta Borysova and Netsanet Getachew for routine worm cultures and genotyping support, Lena Stumbauer for practical help, as well as all members of the Tessmar-Raible and Raible labs for constructive discussions. This work was supported by, Helmholtz Society, distinguished professorship by the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (K.T.-R.), H2020 European Research Council, ERC Grant Agreement #819952 (K.T.-R.), Austrian Science Funds (FWF), SFB F78 (F.R., K.T-R; https://doi.org/10.55776/F78), the Human Frontier Science Program (HFSP), #RGP021/2024, https://doi.org/10.52044/HFSP.RGP0212024.pc.gr.194174 (KT-R), University of Vienna Research Platform SinCeReSt (F.R.), For open access purposes, K.T.-R. has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. We acknowledge support by the Open Access publication fund of Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung. None of the funding bodies was involved in the design of the study, the collection, analysis, and interpretation of data or in writing the manuscript. Open Access funding enabled and organized by Projekt DEAL.' article_number: '9861' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nadja full_name: Milivojev, Nadja last_name: Milivojev - first_name: Federico full_name: Scaramuzza, Federico last_name: Scaramuzza - first_name: Pedro Ozório full_name: Brum, Pedro Ozório last_name: Brum - first_name: Camila L full_name: Velastegui Gamboa, Camila L id: 625aea67-91c1-11f0-aad8-f71452b4174d last_name: Velastegui Gamboa - first_name: Gabriele full_name: Andreatta, Gabriele last_name: Andreatta - first_name: Florian full_name: Raible, Florian last_name: Raible - first_name: Kristin full_name: Tessmar-Raible, Kristin last_name: Tessmar-Raible citation: ama: Milivojev N, Scaramuzza F, Brum PO, et al. Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity. Nature Communications. 2025;16. doi:10.1038/s41467-025-65631-0 apa: Milivojev, N., Scaramuzza, F., Brum, P. O., Velastegui Gamboa, C. L., Andreatta, G., Raible, F., & Tessmar-Raible, K. (2025). Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65631-0 chicago: Milivojev, Nadja, Federico Scaramuzza, Pedro Ozório Brum, Camila L Velastegui Gamboa, Gabriele Andreatta, Florian Raible, and Kristin Tessmar-Raible. “Light-Modulated Stem Cells in the Camera-Type Eye of an Annelid Model for Adult Brain Plasticity.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65631-0. ieee: N. Milivojev et al., “Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Milivojev N, Scaramuzza F, Brum PO, Velastegui Gamboa CL, Andreatta G, Raible F, Tessmar-Raible K. 2025. Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity. Nature Communications. 16, 9861. mla: Milivojev, Nadja, et al. “Light-Modulated Stem Cells in the Camera-Type Eye of an Annelid Model for Adult Brain Plasticity.” Nature Communications, vol. 16, 9861, Springer Nature, 2025, doi:10.1038/s41467-025-65631-0. short: N. Milivojev, F. Scaramuzza, P.O. Brum, C.L. Velastegui Gamboa, G. Andreatta, F. Raible, K. Tessmar-Raible, Nature Communications 16 (2025). date_created: 2026-02-16T15:38:11Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-06-18T18:30:32Z day: '01' ddc: - '570' department: - _id: GradSch doi: 10.1038/s41467-025-65631-0 fulldoi: https://doi.org/10.1038/s41467-025-65631-0 intvolume: ' 16' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-025-65631-0 month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: publisher OA_type: gold _id: '21250' abstract: - lang: eng text: We investigate the step complexity of the Leader Election problem (and implementing the corresponding test-and-set object) in asynchronous shared memory, where processes communicate through registers supporting atomic read and write and must coordinate so that a single process becomes the leader. Determining tight step complexity bounds for solving this problem is one of the key open problems in the theory of shared memory distributed computing. The best known algorithm is a randomized tournament-tree, which has worst-case expected step complexity O(log N) for N processes. There are provably no deterministic wait-free algorithms, and only restricted lower bounds are known for obstruction-free and randomized wait-free algorithms. We introduce a new lower bound that establishes an Ω((log N)/(log log N + log Q)) step complexity for any obstruction-free Leader Election algorithm, where N is the number of processes, and 2 ≤ Q ≤ N is a bound on the value contention, which we define as the maximum number of different values that processes can be simultaneously poised to write to the same register in any execution of the algorithm. Our result is strictly stronger than previous bounds based on write contention. In particular, it implies new lower bounds on step complexity that depend on register size. acknowledgement: The work of Dan Alistarh is supported by grants from ERC, Austrian FWF, and the Google and NVIDIA corporations. Faith Ellen was supported in part by the Natural Science and Engineering Research Council of Canada (NSERC) grant RGPIN-2020-04178. alternative_title: - LIPIcs article_processing_charge: Yes author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Faith full_name: Ellen, Faith last_name: Ellen - first_name: Alexander full_name: Fedorov, Alexander id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6 last_name: Fedorov citation: ama: 'Alistarh D-A, Ellen F, Fedorov A. An almost-logarithmic lower bound for leader election with bounded value contention. In: 39th International Symposium on Distributed Computing. Vol 356. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025:3:1-3:16. doi:10.4230/LIPIcs.DISC.2025.3' apa: 'Alistarh, D.-A., Ellen, F., & Fedorov, A. (2025). An almost-logarithmic lower bound for leader election with bounded value contention. In 39th International Symposium on Distributed Computing (Vol. 356, p. 3:1-3:16). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2025.3' chicago: Alistarh, Dan-Adrian, Faith Ellen, and Alexander Fedorov. “An Almost-Logarithmic Lower Bound for Leader Election with Bounded Value Contention.” In 39th International Symposium on Distributed Computing, 356:3:1-3:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. https://doi.org/10.4230/LIPIcs.DISC.2025.3. ieee: D.-A. Alistarh, F. Ellen, and A. Fedorov, “An almost-logarithmic lower bound for leader election with bounded value contention,” in 39th International Symposium on Distributed Computing, Berlin, Germany, 2025, vol. 356, p. 3:1-3:16. ista: 'Alistarh D-A, Ellen F, Fedorov A. 2025. An almost-logarithmic lower bound for leader election with bounded value contention. 39th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 356, 3:1-3:16.' mla: Alistarh, Dan-Adrian, et al. “An Almost-Logarithmic Lower Bound for Leader Election with Bounded Value Contention.” 39th International Symposium on Distributed Computing, vol. 356, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, p. 3:1-3:16, doi:10.4230/LIPIcs.DISC.2025.3. short: D.-A. Alistarh, F. Ellen, A. Fedorov, in:, 39th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, p. 3:1-3:16. conference: end_date: 2025-10-31 location: Berlin, Germany name: 'DISC: Symposium on Distributed Computing' start_date: 2025-10-27 corr_author: '1' date_created: 2026-02-16T15:41:15Z date_published: 2025-10-22T00:00:00Z date_updated: 2026-02-18T06:49:38Z day: '22' ddc: - '000' department: - _id: DaAl - _id: GradSch doi: 10.4230/LIPIcs.DISC.2025.3 file: - access_level: open_access checksum: 3825a0e6e6a05503e842a59f95528bd9 content_type: application/pdf creator: dernst date_created: 2026-02-18T06:46:02Z date_updated: 2026-02-18T06:46:02Z file_id: '21310' file_name: 2025_LIPIcs_Alistarh.pdf file_size: 1492189 relation: main_file success: 1 file_date_updated: 2026-02-18T06:46:02Z fulldoi: https://doi.org/10.4230/LIPIcs.DISC.2025.3 has_accepted_license: '1' intvolume: ' 356' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 3:1-3:16 publication: 39th International Symposium on Distributed Computing publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' status: public title: An almost-logarithmic lower bound for leader election with bounded value contention tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 356 year: '2025' ... --- OA_place: repository OA_type: green _id: '21257' abstract: - lang: eng text: 'We investigate the problem of accurate sparse fine-tuning of large language models (LLMs), that is, fine-tuning pre-trained LLMs on specialized tasks, while inducing sparsity in their weights. Our work is motivated by experiments showing that standard loss-based fine-tuning methods are not able to achieve high accuracy in this setting, especially at high sparsity targets. To address this issue, we perform a detailed study of knowledge distillation losses for fine-tuning of sparse models. We determine an L2-based distillation approach that we term ‘SquareHead’, which enables accurate recovery even at higher sparsities. Investigating the question of efficient inference, we show that sparse LLMs can be executed faster by taking advantage of sparsity. Specifically, we exhibit end-to-end results showing speedups enabled by sparsity, while recovering accuracy, on the following models and tasks, respectively: T5 for language translation, Whisper for speech translation, and open GPT-type models such as the Mosaic Pre-Trained Transformer (MPT) and Llama-2 models for text generation. In particular, for popular generative tasks, we show for the first time that sparse fine-tuning can reach 75% sparsity without drops in accuracy, and provide notable end-to-end speedups for inference on CPUs. Moreover, we also highlight that sparsity is compatible with other compression approaches, such as quantization.' acknowledgement: We would like to thank Eugenia Iofinova for useful comments on an earlier version of this draft, and Artur Niederfahrenhorst for useful suggestions regarding fine-tuning on the GSM8k dataset. alternative_title: - 'Machine Translation: Technologies and Applications' article_processing_charge: No arxiv: 1 author: - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Denis full_name: Kuznedelev, Denis last_name: Kuznedelev - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Michael full_name: Goinv, Michael last_name: Goinv - first_name: Shubhra full_name: Pandit, Shubhra last_name: Pandit - first_name: Abhinav full_name: Agarwalla, Abhinav last_name: Agarwalla - first_name: Tuan full_name: Nguyen, Tuan last_name: Nguyen - first_name: Alexandre full_name: Marques, Alexandre last_name: Marques - first_name: Mark full_name: Kurtz, Mark last_name: Kurtz - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Kurtic E, Kuznedelev D, Frantar E, et al. Sparse Fine-Tuning for Inference Acceleration of Large Language Models. In: Passban P, Way A, Rezagholizadeh M, eds. Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques. Springer Nature; 2025:83-97. doi:10.1007/978-3-031-85747-8_6' apa: Kurtic, E., Kuznedelev, D., Frantar, E., Goinv, M., Pandit, S., Agarwalla, A., … Alistarh, D.-A. (2025). Sparse Fine-Tuning for Inference Acceleration of Large Language Models. In P. Passban, A. Way, & M. Rezagholizadeh (Eds.), Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques (pp. 83–97). Springer Nature. https://doi.org/10.1007/978-3-031-85747-8_6 chicago: Kurtic, Eldar, Denis Kuznedelev, Elias Frantar, Michael Goinv, Shubhra Pandit, Abhinav Agarwalla, Tuan Nguyen, Alexandre Marques, Mark Kurtz, and Dan-Adrian Alistarh. “Sparse Fine-Tuning for Inference Acceleration of Large Language Models.” In Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques, edited by Peyman Passban, Andy Way, and Mehdi Rezagholizadeh, 83–97. Springer Nature, 2025. https://doi.org/10.1007/978-3-031-85747-8_6. ieee: E. Kurtic et al., “Sparse Fine-Tuning for Inference Acceleration of Large Language Models,” in Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques, P. Passban, A. Way, and M. Rezagholizadeh, Eds. Springer Nature, 2025, pp. 83–97. ista: 'Kurtic E, Kuznedelev D, Frantar E, Goinv M, Pandit S, Agarwalla A, Nguyen T, Marques A, Kurtz M, Alistarh D-A. 2025.Sparse Fine-Tuning for Inference Acceleration of Large Language Models. In: Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques. Machine Translation: Technologies and Applications, , 83–97.' mla: Kurtic, Eldar, et al. “Sparse Fine-Tuning for Inference Acceleration of Large Language Models.” Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques, edited by Peyman Passban et al., Springer Nature, 2025, pp. 83–97, doi:10.1007/978-3-031-85747-8_6. short: E. Kurtic, D. Kuznedelev, E. Frantar, M. Goinv, S. Pandit, A. Agarwalla, T. Nguyen, A. Marques, M. Kurtz, D.-A. Alistarh, in:, P. Passban, A. Way, M. Rezagholizadeh (Eds.), Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques, Springer Nature, 2025, pp. 83–97. corr_author: '1' date_created: 2026-02-16T15:57:53Z date_published: 2025-07-05T00:00:00Z date_updated: 2026-02-19T09:26:54Z day: '05' department: - _id: DaAl - _id: GradSch doi: 10.1007/978-3-031-85747-8_6 editor: - first_name: Peyman full_name: Passban, Peyman last_name: Passban - first_name: Andy full_name: Way, Andy last_name: Way - first_name: Mehdi full_name: Rezagholizadeh, Mehdi last_name: Rezagholizadeh external_id: arxiv: - '2310.06927' fulldoi: https://doi.org/10.1007/978-3-031-85747-8_6 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2310.06927 month: '07' oa: 1 oa_version: Preprint page: 83-97 publication: Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques publication_identifier: eisbn: - '9783031857478' eissn: - 2522-803X isbn: - '9783031857461' issn: - 2522-8021 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Sparse Fine-Tuning for Inference Acceleration of Large Language Models type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher OA_type: gold _id: '21327' abstract: - lang: eng text: Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational heterogeneity revealed by diverse experimental modalities. Here, we present a framework for building experiment-grounded protein structure generative models that infer conformational ensembles consistent with measured experimental data. The key idea is to treat stateof-the-art protein structure predictors (e.g., AlphaFold3) as sequence-conditioned structural priors, and cast ensemble modeling as posterior inference of protein structures given experimental measurements. Through extensive real-data experiments, we demonstrate the generality of our method to incorporate a variety of experimental measurements. In particular, our framework uncovers previously unmodeled conformational heterogeneity from crystallographic densities, and generates high-accuracy NMR ensembles orders of magnitude faster than the status quo. Notably, we demonstrate that our ensembles outperform AlphaFold3 (Abramson et al., 2024) and sometimes better fit experimental data than publicly deposited structures to the Protein Data Bank (PDB, Burley et al. (2017)). We believe that this approach will unlock building predictive models that fully embrace experimentally observed conformational diversity. acknowledged_ssus: - _id: ScienComp acknowledgement: 'This work was supported by the Israeli Science Foundation (ISF) grant number 1834/24. We acknowledge support from the Austrian Science Fund (FWF, grant numbers I5812-B and I6223) and the financial support of the Helmsley Fellowships Program for Sustainability and Health. This research uses resources of the Institute of Science and Technology Austria’s scientific computing cluster. ' alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Sai A full_name: Maddipatla, Sai A id: e957f5e5-91c9-11f0-a95f-e090f66ecb4d last_name: Maddipatla - first_name: Nadav E full_name: Sellam, Nadav E id: ef280fe0-91c9-11f0-a95f-8dea3f5bc513 last_name: Sellam - first_name: Meital I full_name: Bojan, Meital I id: 11d88cf5-91ca-11f0-a95f-edf9f08f47b7 last_name: Bojan - first_name: Sanketh full_name: Vedula, Sanketh id: 94f2fe44-70fa-11f0-b76b-92922c09452b last_name: Vedula - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Ailie full_name: Marx, Ailie last_name: Marx - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: 'Maddipatla SA, Sellam NE, Bojan MI, et al. Inverse problems with experiment-guided AlphaFold. In: Proceedings of the 42nd International Conference on Machine Learning. Vol 267. ML Research Press; 2025:42366-42393.' apa: 'Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Vedula, S., Schanda, P., Marx, A., & Bronstein, A. M. (2025). Inverse problems with experiment-guided AlphaFold. In Proceedings of the 42nd International Conference on Machine Learning (Vol. 267, pp. 42366–42393). Vancouver, Canada: ML Research Press.' chicago: Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Sanketh Vedula, Paul Schanda, Ailie Marx, and Alex M. Bronstein. “Inverse Problems with Experiment-Guided AlphaFold.” In Proceedings of the 42nd International Conference on Machine Learning, 267:42366–93. ML Research Press, 2025. ieee: S. A. Maddipatla et al., “Inverse problems with experiment-guided AlphaFold,” in Proceedings of the 42nd International Conference on Machine Learning, Vancouver, Canada, 2025, vol. 267, pp. 42366–42393. ista: 'Maddipatla SA, Sellam NE, Bojan MI, Vedula S, Schanda P, Marx A, Bronstein AM. 2025. Inverse problems with experiment-guided AlphaFold. Proceedings of the 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 42366–42393.' mla: Maddipatla, Sai A., et al. “Inverse Problems with Experiment-Guided AlphaFold.” Proceedings of the 42nd International Conference on Machine Learning, vol. 267, ML Research Press, 2025, pp. 42366–93. short: S.A. Maddipatla, N.E. Sellam, M.I. Bojan, S. Vedula, P. Schanda, A. Marx, A.M. Bronstein, in:, Proceedings of the 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 42366–42393. conference: end_date: 2025-07-19 location: Vancouver, Canada name: 'ICML: International Conference on Machine Learning' start_date: 2025-07-13 corr_author: '1' date_created: 2026-02-18T12:11:17Z date_published: 2025-07-30T00:00:00Z date_updated: 2026-02-19T08:56:43Z day: '30' ddc: - '000' - '540' department: - _id: PaSc - _id: AlBr - _id: GradSch external_id: arxiv: - '2502.09372' file: - access_level: open_access checksum: f33230a6d59b7978d4cd72795e4e9059 content_type: application/pdf creator: dernst date_created: 2026-02-19T08:56:10Z date_updated: 2026-02-19T08:56:10Z file_id: '21338' file_name: 2025_ICML_Maddipatla.pdf file_size: 1924177 relation: main_file success: 1 file_date_updated: 2026-02-19T08:56:10Z has_accepted_license: '1' intvolume: ' 267' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 42366 - 42393 project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery - _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0 grant_number: I06223 name: Structure and mechanism of the mitochondrial MIM insertase publication: Proceedings of the 42nd International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: Inverse problems with experiment-guided AlphaFold tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 267 year: '2025' ... --- OA_place: repository OA_type: green _id: '15128' abstract: - lang: eng text: We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\zeta)$ and a general class of related quantities involving two resolvents at nearby spectral parameters. - lang: fre text: "On établit un théorème limite central universel pour les statistiques linéaires mésoscopiques des valeurs propres d’une matrice de type Wigner au milieu du spectre, avec des fonctions de classe \r\n et à support compact. La principale nouveauté de cette approche est qu’elle repose sur une loi locale optimale pour la fonction à deux points $T(z,\\zeta)$ , ainsi que pour une classe plus générale d’observables impliquant deux résolvantes évaluées en des paramètres proches." acknowledgement: "I would like to express my gratitude to László Erdős for suggesting the project and supervising my work. I am also thankful to Yuanyuan Xu and Oleksii Kolupaiev for many helpful discussions. Furthermore, I am grateful to Guillaume Dubach for translating the abstract into French.\r\nThe author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Volodymyr full_name: Riabov, Volodymyr id: 1949f904-edfb-11eb-afb5-e2dfddabb93b last_name: Riabov citation: ama: Riabov V. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2025;61(1):129-154. doi:10.1214/23-AIHP1438 apa: Riabov, V. (2025). Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AIHP1438 chicago: Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2025. https://doi.org/10.1214/23-AIHP1438. ieee: V. Riabov, “Mesoscopic eigenvalue statistics for Wigner-type matrices,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 61, no. 1. Institute of Mathematical Statistics, pp. 129–154, 2025. ista: Riabov V. 2025. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 61(1), 129–154. mla: Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 61, no. 1, Institute of Mathematical Statistics, 2025, pp. 129–54, doi:10.1214/23-AIHP1438. short: V. Riabov, Annales de l’institut Henri Poincare (B) Probability and Statistics 61 (2025) 129–154. corr_author: '1' date_created: 2024-03-20T09:41:04Z date_published: 2025-02-01T00:00:00Z date_updated: 2025-05-19T13:54:31Z day: '01' department: - _id: GradSch - _id: LaEr doi: 10.1214/23-AIHP1438 ec_funded: 1 external_id: arxiv: - '2301.01712' isi: - '001427953600004' fulldoi: https://doi.org/10.1214/23-AIHP1438 intvolume: ' 61' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.01712 month: '02' oa: 1 oa_version: Preprint page: 129-154 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Annales de l'institut Henri Poincare (B) Probability and Statistics publication_identifier: issn: - 0246-0203 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Mesoscopic eigenvalue statistics for Wigner-type matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2025' ...