[{"publication_identifier":{"isbn":["9783032262196"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication":"27th International Symposium on Formal Methods","date_created":"2026-06-14T22:01:44Z","abstract":[{"text":"Runtime monitoring checks, during execution, whether a partial signal produced by a hybrid system satisfies its specification. Signal First-Order Logic (SFO) offers expressive real-time specifications over such signals, but currently comes only with Boolean semantics and has no tool support. We provide the first robustness-based quantitative semantics for SFO, enabling the expression and evaluation of rich real-time properties beyond the scope of existing formalisms such as Signal Temporal Logic. To enable online monitoring, we identify a past-time fragment of SFO and give a pastification procedure that transforms bounded-response SFO formulas into equisatisfiable formulas in this fragment. We then develop an efficient runtime monitoring algorithm for this past-time fragment and evaluate its performance on a set of benchmarks, demonstrating the practicality and effectiveness of our approach. To the best of our knowledge, this is the first publicly available prototype for online quantitative monitoring of full SFO.","lang":"eng"}],"date_updated":"2026-06-22T08:21:09Z","type":"conference","file_date_updated":"2026-06-22T08:18:41Z","OA_type":"hybrid","title":"Quantitative monitoring of Signal First-Order logic","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","oa":1,"has_accepted_license":"1","conference":{"start_date":"2026-05-18","name":"FM: Formal Methods","end_date":"2026-05-22","location":"Tokyo, Japan"},"keyword":["Signal first-order logic","Robustness-based quantitative semantics","Online runtime monitoring"],"citation":{"ista":"Chalupa M, Henzinger TA, Sarac NE, Yu E. 2026. Quantitative monitoring of Signal First-Order logic. 27th International Symposium on Formal Methods. FM: Formal Methods, LNCS, vol. 16557, 214–233.","short":"M. Chalupa, T.A. Henzinger, N.E. Sarac, E. Yu, in:, 27th International Symposium on Formal Methods, Springer Nature, 2026, pp. 214–233.","chicago":"Chalupa, Marek, Thomas A Henzinger, Naci E Sarac, and Emily Yu. “Quantitative Monitoring of Signal First-Order Logic.” In 27th International Symposium on Formal Methods, 16557:214–33. Springer Nature, 2026. https://doi.org/10.1007/978-3-032-26220-2_11.","mla":"Chalupa, Marek, et al. “Quantitative Monitoring of Signal First-Order Logic.” 27th International Symposium on Formal Methods, vol. 16557, Springer Nature, 2026, pp. 214–33, doi:10.1007/978-3-032-26220-2_11.","apa":"Chalupa, M., Henzinger, T. A., Sarac, N. E., & Yu, E. (2026). Quantitative monitoring of Signal First-Order logic. In 27th International Symposium on Formal Methods (Vol. 16557, pp. 214–233). Tokyo, Japan: Springer Nature. https://doi.org/10.1007/978-3-032-26220-2_11","ama":"Chalupa M, Henzinger TA, Sarac NE, Yu E. Quantitative monitoring of Signal First-Order logic. In: 27th International Symposium on Formal Methods. Vol 16557. Springer Nature; 2026:214-233. doi:10.1007/978-3-032-26220-2_11","ieee":"M. Chalupa, T. A. Henzinger, N. E. Sarac, and E. Yu, “Quantitative monitoring of Signal First-Order logic,” in 27th International Symposium on Formal Methods, Tokyo, Japan, 2026, vol. 16557, pp. 214–233."},"file":[{"file_size":849237,"creator":"dernst","date_updated":"2026-06-22T08:18:41Z","file_name":"2026_LNCS_Chalupa.pdf","file_id":"22113","date_created":"2026-06-22T08:18:41Z","relation":"main_file","checksum":"7055199ecb985e9e2e272f4988827067","content_type":"application/pdf","success":1,"access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"das_tickbox":"0","status":"public","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported by the European Research Council (ERC) Grants VAMOS (No. 101020093) and HYPER (No. 101055412), and by the Advanced Research and Invention Agency under the Safeguarded AI programme (MSAI-PR01-P047).","scopus_import":"1","doi":"10.1007/978-3-032-26220-2_11","day":"18","ec_funded":1,"publication_status":"published","department":[{"_id":"ToHe"}],"month":"05","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"arxiv":1,"intvolume":" 16557","volume":16557,"_id":"22006","external_id":{"arxiv":["2603.00728"]},"alternative_title":["LNCS"],"author":[{"first_name":"Marek","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac"},{"first_name":"Zhengqi","orcid":"0000-0002-4993-773X","id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342","full_name":"Yu, Zhengqi","last_name":"Yu"}],"ddc":["000"],"publisher":"Springer Nature","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"year":"2026","date_published":"2026-05-18T00:00:00Z","page":"214-233","article_processing_charge":"No"},{"year":"2026","article_number":"201","ddc":["530"],"project":[{"_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3","name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","grant_number":"F100403"},{"_id":"8fa7db46-16d5-11f0-9cad-917600954daf","grant_number":"12078","name":"Polarons in Lead Halide Perovskites"}],"publisher":"Springer Nature","article_processing_charge":"Yes","date_published":"2026-04-14T00:00:00Z","volume":9,"intvolume":" 9","supplementarymaterial":"yes","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding authors upon request. The computational codes that were used to generate the figures presented in this study are available from the corresponding authors upon request.","author":[{"first_name":"Jinglun","last_name":"Li","id":"ff19510a-0d2c-11ef-b018-c338ad2f4325","full_name":"Li, Jinglun"},{"first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","full_name":"Koutentakis, Georgios","last_name":"Koutentakis"},{"id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d","full_name":"Hrast, Mateja","last_name":"Hrast","first_name":"Mateja"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"full_name":"Schindewolf, Andreas","last_name":"Schindewolf","first_name":"Andreas"},{"last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e","full_name":"Al Hyder, Ragheed","first_name":"Ragheed"}],"external_id":{"arxiv":["2506.23318"]},"_id":"22100","acknowledgement":"J.-L.Li thanks Gaoren Wang for valuable discussions on the absorbing boundary condition. G.M.K. thanks P. Giannakeas for fruitful discussions during the initial stages of this study. G.M.K. was funded by the Austrian Science Fund (FWF) [10.55776/F1004]. R.A. received funding from the Austrian Academy of Science ÖAW grant No. PR1029OEAW03. A.S. acknowledges funding from the European Union’s Horizon Europe research and innovation programme under grant agreement No. 101219560.","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","success":1,"checksum":"3bf5852b54b9f13ec1679056a5f58c3a","relation":"main_file","content_type":"application/pdf","file_name":"2026_CommunicationsPhysics_Li.pdf","file_id":"22133","date_created":"2026-06-24T06:09:35Z","creator":"dernst","file_size":1161879,"date_updated":"2026-06-24T06:09:35Z"}],"citation":{"ieee":"J. Li, G. Koutentakis, M. Hrast, M. Lemeshko, A. Schindewolf, and R. Al Hyder, “Tunable field-linked s-wave interactions in dipolar fermi mixtures,” Communications Physics, vol. 9. Springer Nature, 2026.","ama":"Li J, Koutentakis G, Hrast M, Lemeshko M, Schindewolf A, Al Hyder R. Tunable field-linked s-wave interactions in dipolar fermi mixtures. Communications Physics. 2026;9. doi:10.1038/s42005-026-02578-8","apa":"Li, J., Koutentakis, G., Hrast, M., Lemeshko, M., Schindewolf, A., & Al Hyder, R. (2026). Tunable field-linked s-wave interactions in dipolar fermi mixtures. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-026-02578-8","mla":"Li, Jinglun, et al. “Tunable Field-Linked s-Wave Interactions in Dipolar Fermi Mixtures.” Communications Physics, vol. 9, 201, Springer Nature, 2026, doi:10.1038/s42005-026-02578-8.","chicago":"Li, Jinglun, Georgios Koutentakis, Mateja Hrast, Mikhail Lemeshko, Andreas Schindewolf, and Ragheed Al Hyder. “Tunable Field-Linked s-Wave Interactions in Dipolar Fermi Mixtures.” Communications Physics. Springer Nature, 2026. https://doi.org/10.1038/s42005-026-02578-8.","short":"J. Li, G. Koutentakis, M. Hrast, M. Lemeshko, A. Schindewolf, R. Al Hyder, Communications Physics 9 (2026).","ista":"Li J, Koutentakis G, Hrast M, Lemeshko M, Schindewolf A, Al Hyder R. 2026. Tunable field-linked s-wave interactions in dipolar fermi mixtures. Communications Physics. 9, 201."},"das_tickbox":"1","status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"publication_status":"published","department":[{"_id":"MiLe"}],"day":"14","doi":"10.1038/s42005-026-02578-8","corr_author":"1","month":"04","DOAJ_listed":"1","type":"journal_article","date_updated":"2026-06-24T06:10:44Z","file_date_updated":"2026-06-24T06:09:35Z","PlanS_conform":"1","publication":"Communications Physics","date_created":"2026-06-21T22:02:58Z","publication_identifier":{"eissn":["2399-3650"]},"abstract":[{"text":"Spin mixtures of degenerate fermions are a cornerstone of quantum many-body physics, enabling superfluidity, polarons, and rich spin dynamics through s-wave scattering resonances. Combining them with strong, long-range dipolar interactions provides highly flexible control schemes promising even more exotic quantum phases. Recently, microwave shielding gave access to spin-polarized degenerate samples of dipolar fermionic molecules, where tunable p-wave interactions were enabled by field-linked resonances available only by compromising the shielding (due to experimental limitations). Here, we study the scattering properties of a fermionic dipolar spin mixture and show that a universal s-wave resonance is readily accessible without compromising the shielding. We develop a universal description of the tunable s-wave interaction and weakly bound tetratomic states based on the microwave-field parameters. The s-wave resonance paves the way to stable, controllable and strongly-interacting dipolar spin mixtures of deeply degenerate fermions and supports favorable conditions to reach this regime via evaporative cooling.","lang":"eng"}],"has_accepted_license":"1","oa":1,"title":"Tunable field-linked s-wave interactions in dipolar fermi mixtures","researchdata_availability":"upon request","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","article_type":"original","OA_place":"publisher"},{"file":[{"relation":"main_file","checksum":"994bf21d6269dabccf1e1091e02962c5","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":858595,"creator":"dernst","date_updated":"2026-06-24T06:19:56Z","file_name":"2026_ProcACMProgrammingLanguages_Chatterjee.pdf","file_id":"22135","date_created":"2026-06-24T06:19:56Z"}],"citation":{"ista":"Chatterjee K, Goharshady E, Zikelic D. 2026. SuperDP: Differential privacy refutation via supermartingales. Proceedings of the ACM on Programming Languages. 10(PLDI), 218.","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, and Dorde Zikelic. “SuperDP: Differential Privacy Refutation via Supermartingales.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2026. https://doi.org/10.1145/3808296.","mla":"Chatterjee, Krishnendu, et al. “SuperDP: Differential Privacy Refutation via Supermartingales.” Proceedings of the ACM on Programming Languages, vol. 10, no. PLDI, 218, Association for Computing Machinery, 2026, doi:10.1145/3808296.","short":"K. Chatterjee, E. Goharshady, D. Zikelic, Proceedings of the ACM on Programming Languages 10 (2026).","ama":"Chatterjee K, Goharshady E, Zikelic D. SuperDP: Differential privacy refutation via supermartingales. Proceedings of the ACM on Programming Languages. 2026;10(PLDI). doi:10.1145/3808296","apa":"Chatterjee, K., Goharshady, E., & Zikelic, D. (2026). SuperDP: Differential privacy refutation via supermartingales. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3808296","ieee":"K. Chatterjee, E. Goharshady, and D. Zikelic, “SuperDP: Differential privacy refutation via supermartingales,” Proceedings of the ACM on Programming Languages, vol. 10, no. PLDI. Association for Computing Machinery, 2026."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"das_tickbox":"1","status":"public","scopus_import":"1","acknowledgement":"The authors would like to thank Petr Novotný for valuable discussions that helped shape this work.\r\nThis research was supported by the Singapore Ministry of Education (MOE) Academic Research\r\nFund (AcRF) Tier 1 grant (Proposal ID: 25-SIS-SMU-009), Vienna Science and Technology Fund\r\n(WWTF), State of Lower Austria [Grant ID 10.47379/ICT25017], ERC CoG 863818 (ForM-SMArt),\r\nand Austrian Science Fund (FWF) 10.55776/COE12.","ec_funded":1,"day":"08","doi":"10.1145/3808296","department":[{"_id":"KrCh"}],"publication_status":"published","month":"06","corr_author":"1","related_material":{"record":[{"status":"public","id":"22134","relation":"research_data"}]},"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","arxiv":1,"publication_identifier":{"eissn":["2475-1421"]},"date_created":"2026-06-21T22:02:59Z","publication":"Proceedings of the ACM on Programming Languages","abstract":[{"text":"Differential privacy (DP) has established itself as one of the standards for ensuring privacy of individual data. However, reasoning about DP is a challenging and error-prone task, hence methods for formal verification and refutation of DP properties have received significant interest in recent years. In this work, we present a novel method for automated formal refutation of є-DP. Our method refutes є-DP by searching for a pair of inputs together with a non-negative function over outputs whose expected value on these two inputs differs by a significant amount. The two inputs and the non-negative function over outputs are computed simultaneously, by utilizing upper expectation supermartingales and lower expectation submartingales from probabilistic program analysis, which we leverage to introduce a sound and complete proof rule for є-DP refutation. To the best of our knowledge, our method is the first method for є-DP refutation to offer the following four desirable features: (1) it is fully automated, (2) it is applicable to stochastic mechanisms with sampling instructions from both discrete and continuous distributions, (3) it provides soundness guarantees, and (4) it provides semi-completeness guarantees. Our experiments show that our prototype tool SuperDP achieves superior performance compared to the state of the art and manages to refute є-DP for a number of challenging examples collected from the literature, including ones that were out of the reach of prior methods.","lang":"eng"}],"date_updated":"2026-06-24T06:39:37Z","type":"journal_article","PlanS_conform":"1","file_date_updated":"2026-06-24T06:19:56Z","OA_type":"gold","title":"SuperDP: Differential privacy refutation via supermartingales","researchdata_availability":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","article_type":"original","has_accepted_license":"1","oa":1,"keyword":["Static Program Analysis","Differential Privacy","Probabilistic Programming","Martingales"],"ddc":["000"],"publisher":"Association for Computing Machinery","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"article_number":"218","year":"2026","date_published":"2026-06-08T00:00:00Z","article_processing_charge":"Yes","intvolume":" 10","volume":10,"_id":"22102","issue":"PLDI","external_id":{"arxiv":["2603.26215"]},"dataavailabilitystatement":"The artifact supporting the findings of this study, which includes the underlying datasets, software\r\ncode, and experiments, is publicly available in Zenodo https://zenodo.org/records/19399862.","supplementarymaterial":"no","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Kafshdar Goharshadi, Ehsan","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","last_name":"Kafshdar Goharshadi","orcid":"0000-0002-8595-0587","first_name":"Ehsan"},{"first_name":"Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}]},{"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","corr_author":"1","month":"06","department":[{"_id":"ChWo"},{"_id":"GradSch"}],"publication_status":"accepted","doi":"10.1111/cgf.70516","day":"24","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"mla":"Wei, Ziyu, et al. “Circles of Confidence for Multi-Label Geometry Completion.” Computer Graphics Forum, vol. 45, no. 5, Wiley, doi:10.1111/cgf.70516.","chicago":"Wei, Ziyu , Christian Hafner, Aleksei Kalinov, Peter Synak, and Chris Wojtan. “Circles of Confidence for Multi-Label Geometry Completion.” In Computer Graphics Forum, Vol. 45. Wiley, n.d. https://doi.org/10.1111/cgf.70516.","short":"Z. Wei, C. Hafner, A. Kalinov, P. Synak, C. Wojtan, in:, Computer Graphics Forum, Wiley, n.d.","ista":"Wei Z, Hafner C, Kalinov A, Synak P, Wojtan C. Circles of confidence for multi-label geometry completion. Computer Graphics Forum. Eurographics: Symposium on Geometry Processing vol. 45.","ieee":"Z. Wei, C. Hafner, A. Kalinov, P. Synak, and C. Wojtan, “Circles of confidence for multi-label geometry completion,” in Computer Graphics Forum, Bern, Switzerland, vol. 45, no. 5.","apa":"Wei, Z., Hafner, C., Kalinov, A., Synak, P., & Wojtan, C. (n.d.). Circles of confidence for multi-label geometry completion. In Computer Graphics Forum (Vol. 45). Bern, Switzerland: Wiley. https://doi.org/10.1111/cgf.70516","ama":"Wei Z, Hafner C, Kalinov A, Synak P, Wojtan C. Circles of confidence for multi-label geometry completion. In: Computer Graphics Forum. Vol 45. Wiley. doi:10.1111/cgf.70516"},"file":[{"file_name":"document(3).pdf","file_id":"22132","date_created":"2026-06-23T09:07:22Z","creator":"mly","file_size":14536575,"date_updated":"2026-06-23T09:07:22Z","access_level":"open_access","success":1,"checksum":"365f986db34e3fbce74089207599253b","relation":"main_file","content_type":"application/pdf"}],"conference":{"end_date":"2026-07-03","location":"Bern, Switzerland","start_date":"2026-07-01","name":"Eurographics: Symposium on Geometry Processing"},"oa":1,"has_accepted_license":"1","OA_place":"publisher","title":"Circles of confidence for multi-label geometry completion","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","file_date_updated":"2026-06-23T09:07:22Z","type":"conference","date_updated":"2026-06-24T05:49:08Z","abstract":[{"text":"Inside–outside classification is widely used for geometry processing tasks such as surface reconstruction, geometry completion,\r\nand calculating signed distance fields. We introduce a new integral formulation of this problem, which assigns confidence\r\nscores that points are inside or outside, given incomplete boundary geometry. Even though our geometric construction does\r\nnot appear in previous work, we show that it is unexpectedly linked to both the well-established generalized winding number\r\n(GWN) and pseudonormal methods for geometry completion, and it provably reduces to either one of them for specific values\r\nof a control parameter. The results obtained with our method frequently outperform screened Poisson surface reconstruction\r\n(PSR), GWN, and the pseudonormal method in terms of quality, and are at least on par with them on all of our examples. Unlike\r\nthese methods, our algorithm naturally extends to the multi-label setting, in which regions with an arbitrary number of colors\r\nor physical materials can be reconstructed, and non-manifold features such as T-junctions may appear in the interface and\r\nboundary geometry","lang":"eng"}],"date_created":"2026-06-23T09:08:41Z","publication":"Computer Graphics Forum","article_processing_charge":"No","date_published":"2026-06-24T00:00:00Z","year":"2026","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"publisher":"Wiley","ddc":["005"],"author":[{"last_name":"Wei","full_name":"Wei, Ziyu ","first_name":"Ziyu "},{"first_name":"Christian","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner"},{"full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","orcid":"0000-0003-2189-3904","first_name":"Aleksei"},{"first_name":"Peter","last_name":"Synak","full_name":"Synak, Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"issue":"5","_id":"22129","volume":45,"intvolume":" 45"},{"type":"research_data_reference","date_updated":"2026-06-24T06:39:38Z","date_created":"2026-06-24T06:25:29Z","abstract":[{"text":"This artifact provides the source code, benchmarks, and scripts necessary to build and reproduce the experimental results for `SuperDP` (Accepted at PLDI 2026). It also includes instructions for running the tool on user-provided inputs.","lang":"eng"}],"has_accepted_license":"1","oa":1,"author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Kafshdar Goharshadi","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","full_name":"Kafshdar Goharshadi, Ehsan","first_name":"Ehsan","orcid":"0000-0002-8595-0587"},{"last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","first_name":"Dorde","orcid":"0000-0002-4681-1699"}],"title":"SuperDP: Differential Privacy Refutation via Supermartingales","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","_id":"22134","OA_place":"repository","year":"2026","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ddc":["000"],"citation":{"short":"K. Chatterjee, E. Goharshady, D. Zikelic, (2026).","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, and Dorde Zikelic. “SuperDP: Differential Privacy Refutation via Supermartingales.” Zenodo, 2026. https://doi.org/10.5281/ZENODO.18930113.","mla":"Chatterjee, Krishnendu, et al. SuperDP: Differential Privacy Refutation via Supermartingales. Zenodo, 2026, doi:10.5281/ZENODO.18930113.","ista":"Chatterjee K, Goharshady E, Zikelic D. 2026. SuperDP: Differential Privacy Refutation via Supermartingales, Zenodo, 10.5281/ZENODO.18930113.","ieee":"K. Chatterjee, E. Goharshady, and D. Zikelic, “SuperDP: Differential Privacy Refutation via Supermartingales.” Zenodo, 2026.","apa":"Chatterjee, K., Goharshady, E., & Zikelic, D. (2026). SuperDP: Differential Privacy Refutation via Supermartingales. Zenodo. https://doi.org/10.5281/ZENODO.18930113","ama":"Chatterjee K, Goharshady E, Zikelic D. SuperDP: Differential Privacy Refutation via Supermartingales. 2026. doi:10.5281/ZENODO.18930113"},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.18930113"}],"publisher":"Zenodo","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"KrCh"}],"day":"09","doi":"10.5281/ZENODO.18930113","related_material":{"record":[{"status":"public","id":"22102","relation":"used_in_publication"}]},"date_published":"2026-03-09T00:00:00Z","corr_author":"1","month":"03"},{"date_updated":"2026-06-10T09:21:49Z","type":"research_data","file_date_updated":"2026-01-08T01:35:08Z","date_created":"2025-12-17T10:10:57Z","abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}],"oa":1,"has_accepted_license":"1","author":[{"orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra","last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","first_name":"Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"_id":"20833","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","title":"Research Data for 'Causes and consequences of sex-chromosome turnovers in Diptera'","year":"2026","file":[{"relation":"main_file","checksum":"0b79be6229f2ad9ac117ef00fc4f5c0e","content_type":"text/plain","success":1,"access_level":"open_access","file_size":1201,"creator":"llayanaf","date_updated":"2025-12-17T10:09:25Z","file_name":"README.txt","file_id":"20834","date_created":"2025-12-17T10:09:25Z"},{"file_name":"Supplementary_Datasets.zip","date_created":"2025-12-17T10:10:11Z","file_id":"20835","file_size":19052849,"creator":"llayanaf","date_updated":"2025-12-17T10:10:11Z","success":1,"access_level":"open_access","relation":"main_file","checksum":"daf1c03149dd170b14e5c8e109ee3c77","content_type":"application/zip"},{"date_updated":"2025-12-17T10:12:05Z","creator":"llayanaf","file_size":4575,"file_id":"20837","date_created":"2025-12-17T10:12:05Z","file_name":"Perl_scripts.zip","content_type":"application/zip","checksum":"251e7aab01917c2ad2fbccf465492ea1","relation":"main_file","access_level":"open_access","success":1},{"date_updated":"2026-01-08T01:35:08Z","file_size":572362,"creator":"llayanaf","date_created":"2026-01-08T01:35:08Z","file_id":"20959","file_name":"Supplementary_Tables.zip","content_type":"application/zip","relation":"main_file","checksum":"3cabf143b8cd286eae48c598da2b03bd","success":1,"access_level":"open_access"}],"citation":{"ista":"Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20833.","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20833.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).","mla":"Layana Franco, Lorena Alexandra, et al. Research Data for “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20833.","apa":"Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20833","ama":"Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” 2026. doi:10.15479/AT-ISTA-20833","ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science and Technology Austria, 2026."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"publisher":"Institute of Science and Technology Austria","status":"public","oa_version":"Published Version","article_processing_charge":"No","day":"8","doi":"10.15479/AT-ISTA-20833","department":[{"_id":"BeVi"}],"date_published":"2026-01-08T00:00:00Z","corr_author":"1","month":"01"},{"related_material":{"record":[{"id":"20842","relation":"research_data","status":"public"}]},"month":"03","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"publication_status":"published","day":"04","doi":"10.1038/s42005-026-02514-w","arxiv":1,"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_id":"21457","date_created":"2026-03-16T10:07:46Z","file_name":"2026_CommunicationsPhysics_Agafonova.pdf","date_updated":"2026-03-16T10:07:46Z","creator":"dernst","file_size":1901772,"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"62e2175e7e3ad49260ae6a7b4e0860a2","relation":"main_file"}],"citation":{"apa":"Agafonova, S., Rosello, P., Mekonnen, M., & Hosten, O. (2026). One-milligram torsional pendulum toward experiments at the quantum-gravity interface. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-026-02514-w","ama":"Agafonova S, Rosello P, Mekonnen M, Hosten O. One-milligram torsional pendulum toward experiments at the quantum-gravity interface. Communications Physics. 2026;9. doi:10.1038/s42005-026-02514-w","ieee":"S. Agafonova, P. Rosello, M. Mekonnen, and O. Hosten, “One-milligram torsional pendulum toward experiments at the quantum-gravity interface,” Communications Physics, vol. 9. Springer Nature, 2026.","ista":"Agafonova S, Rosello P, Mekonnen M, Hosten O. 2026. One-milligram torsional pendulum toward experiments at the quantum-gravity interface. Communications Physics. 9, 80.","short":"S. Agafonova, P. Rosello, M. Mekonnen, O. Hosten, Communications Physics 9 (2026).","mla":"Agafonova, Sofia, et al. “One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” Communications Physics, vol. 9, 80, Springer Nature, 2026, doi:10.1038/s42005-026-02514-w.","chicago":"Agafonova, Sofia, Pere Rosello, Manuel Mekonnen, and Onur Hosten. “One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” Communications Physics. Springer Nature, 2026. https://doi.org/10.1038/s42005-026-02514-w."},"acknowledgement":"We thank Gerard Higgins, Andrei Militaru, Nikolai Kiesel, and Markus Aspelmeyer for useful discussions on the topic of the figure-of-merit. We thank Teodor Strömberg for helping with the additional characterizations of the optical lever noise. We thank Johannes Fink and Scott Waitukaitis for their helpful feedback on the manuscript. This work was supported by Institute of Science and Technology Austria and the European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).","scopus_import":"1","article_type":"original","OA_place":"publisher","title":"One-milligram torsional pendulum toward experiments at the quantum-gravity interface","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","oa":1,"has_accepted_license":"1","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."}],"date_created":"2025-12-21T11:39:04Z","publication":"Communications Physics","publication_identifier":{"eissn":["2399-3650"]},"file_date_updated":"2026-03-16T10:07:46Z","PlanS_conform":"1","DOAJ_listed":"1","type":"journal_article","date_updated":"2026-06-10T08:36:06Z","date_published":"2026-03-04T00:00:00Z","article_processing_charge":"Yes","project":[{"grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6"}],"publisher":"Springer Nature","ddc":["530"],"year":"2026","article_number":"80","external_id":{"arxiv":["2408.09445"]},"_id":"20840","author":[{"orcid":"0000-0003-0582-2946","first_name":"Sofya","last_name":"Agafonova","full_name":"Agafonova, Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80"},{"full_name":"Rosello, Pere","last_name":"Rosello","first_name":"Pere"},{"first_name":"Manuel","last_name":"Mekonnen","full_name":"Mekonnen, Manuel"},{"orcid":"0000-0002-2031-204X","first_name":"Onur","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten"}],"intvolume":" 9","volume":9},{"citation":{"apa":"Quattrocchi, F. (2026). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. Calculus of Variations and Partial Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-025-03193-1","ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. Calculus of Variations and Partial Differential Equations. 2026;65(1). doi:10.1007/s00526-025-03193-1","ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” Calculus of Variations and Partial Differential Equations, vol. 65, no. 1. Springer Nature, 2026.","ista":"Quattrocchi F. 2026. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. Calculus of Variations and Partial Differential Equations. 65(1), 23.","mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” Calculus of Variations and Partial Differential Equations, vol. 65, no. 1, 23, Springer Nature, 2026, doi:10.1007/s00526-025-03193-1.","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” Calculus of Variations and Partial Differential Equations. Springer Nature, 2026. https://doi.org/10.1007/s00526-025-03193-1.","short":"F. Quattrocchi, Calculus of Variations and Partial Differential Equations 65 (2026)."},"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"635370d64abaf444f50f5cca60bba1be","success":1,"access_level":"open_access","date_updated":"2026-01-05T12:36:39Z","file_size":958382,"creator":"dernst","file_id":"20945","date_created":"2026-01-05T12:36:39Z","file_name":"2026_CalculusVariations_Quattrocchi.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful comments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, Oliver Tse for pointing out the reference [10], and the anonymous reviewer for carefully reading this manuscript and providing valuable suggestions. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.Open access funding provided by Institute of Science and Technology (IST Austria).","scopus_import":"1","doi":"10.1007/s00526-025-03193-1","day":"01","department":[{"_id":"JaMa"}],"publication_status":"published","month":"01","corr_author":"1","related_material":{"record":[{"id":"20571","relation":"earlier_version","status":"public"}]},"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"publication_identifier":{"eissn":["1432-0835"],"issn":["0944-2669"]},"publication":"Calculus of Variations and Partial Differential Equations","date_created":"2025-12-29T12:06:26Z","abstract":[{"lang":"eng","text":"We prove the convergence of a modified Jordan–Kinderlehrer–Otto scheme to a solution\r\nto the Fokker–Planck equation in Ω e R^d with general—strictly positive and temporally\r\nconstant—Dirichlet boundary conditions. We work under mild assumptions on the domain,\r\nthe drift, and the initial datum. In the special case where Ω is an interval in R1, we prove\r\nthat such a solution is a gradient flow—curve of maximal slope—within a suitable space of\r\nmeasures, endowed with a modified Wasserstein distance. Our discrete scheme and modified\r\ndistance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures\r\nAppl. 94, (2010), pp. 107–130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41–88]\r\non an optimal-transport approach to evolution equations with Dirichlet boundary conditions.\r\nSimilarly to these works, we allow the mass to flow from/to the boundary ∂Ω throughout\r\nthe evolution. However, our leading idea is to also keep track of the mass at the boundary\r\nby working with measures defined on the whole closure Ω . The driving functional is a\r\nmodification of the classical relative entropy that also makes use of the information at the\r\nboundary. As an intermediate result, when Ω is an interval in R1, we find a formula for the\r\ndescending slope of this geodesically nonconvex functional."}],"date_updated":"2026-04-07T08:37:46Z","type":"journal_article","file_date_updated":"2026-01-05T12:36:39Z","PlanS_conform":"1","OA_type":"hybrid","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","OA_place":"publisher","article_type":"original","has_accepted_license":"1","oa":1,"ddc":["510"],"publisher":"Springer Nature","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"article_number":"23","year":"2026","date_published":"2026-01-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","intvolume":" 65","volume":65,"external_id":{"arxiv":["2403.07803"]},"_id":"20865","issue":"1","author":[{"id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi","first_name":"Filippo","orcid":"0009-0000-9773-1931"}]},{"author":[{"last_name":"Dmytrenko","full_name":"Dmytrenko, Oleg","first_name":"Oleg"},{"last_name":"Yuan","full_name":"Yuan, Biao","first_name":"Biao"},{"last_name":"Crosby","full_name":"Crosby, Kadin T.","first_name":"Kadin T."},{"last_name":"Krebel","full_name":"Krebel, Max","first_name":"Max"},{"last_name":"Chen","full_name":"Chen, Xiye","first_name":"Xiye"},{"first_name":"Jakub S.","last_name":"Nowak","full_name":"Nowak, Jakub S."},{"full_name":"Chramiec-Głąbik, Andrzej","last_name":"Chramiec-Głąbik","first_name":"Andrzej"},{"last_name":"Filani","full_name":"Filani, Bamidele","first_name":"Bamidele"},{"first_name":"Anne-Sophie","last_name":"Gribling-Burrer","full_name":"Gribling-Burrer, Anne-Sophie"},{"first_name":"Wiep","full_name":"van der Toorn, Wiep","last_name":"van der Toorn"},{"last_name":"von Kleist","full_name":"von Kleist, Max","first_name":"Max"},{"last_name":"Achmedov","full_name":"Achmedov, Tatjana","first_name":"Tatjana"},{"first_name":"Redmond P.","last_name":"Smyth","full_name":"Smyth, Redmond P."},{"full_name":"Glatt, Sebastian","last_name":"Glatt","first_name":"Sebastian"},{"orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo"},{"first_name":"Dirk W.","last_name":"Heinz","full_name":"Heinz, Dirk W."},{"first_name":"Ryan N.","last_name":"Jackson","full_name":"Jackson, Ryan N."},{"last_name":"Beisel","full_name":"Beisel, Chase L.","first_name":"Chase L."}],"_id":"20963","external_id":{"pmid":["41501459"]},"year":"2026","ddc":["570"],"publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","date_published":"2026-01-07T00:00:00Z","pmid":1,"date_updated":"2026-01-12T10:13:56Z","type":"journal_article","PlanS_conform":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","date_created":"2026-01-08T07:57:17Z","abstract":[{"text":"In all domains of life, tRNAs mediate the transfer of genetic information from mRNAs to proteins. As their depletion suppresses translation and, consequently, viral replication, tRNAs represent long-standing and increasingly recognized targets of innate immunity1,2,3,4,5. Here we report Cas12a3 effector nucleases from type V CRISPR–Cas adaptive immune systems in bacteria that preferentially cleave tRNAs after recognition of target RNA. Cas12a3 orthologues belong to one of two previously unreported nuclease clades that exhibit RNA-mediated cleavage of non-target RNA, and are distinct from all other known type V systems. Through cell-based and biochemical assays and direct RNA sequencing, we demonstrate that recognition of a complementary target RNA by the CRISPR RNA triggers Cas12a3 to cleave the conserved 5′-CCA-3′ tail of diverse tRNAs to drive growth arrest and anti-phage defence. Cryogenic electron microscopy structures further revealed a distinct tRNA-loading domain that positions the tRNA tail in the RuvC active site of the nuclease. By designing synthetic reporters that mimic the tRNA acceptor stem and tail, we expanded the capacity of current CRISPR-based diagnostics for multiplexed RNA detection. Overall, these findings reveal widespread tRNA inactivation as a previously unrecognized CRISPR-based immune strategy that broadens the application space of the existing CRISPR toolbox.","lang":"eng"}],"has_accepted_license":"1","oa":1,"OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity","OA_place":"publisher","article_type":"original","scopus_import":"1","acknowledgement":"We thank Ł. Koziej for processing of the initial cryo-EM datasets, S. Schmelz for support in cryo-EM, A. Gatzemeier for assistance in the purification of dBa1Cas12a3, R. Rarose for support with the in vitro RNA experiments, M. Kaminski for providing purified PsmCas13b protein, L. Schönemann for protein purification, and C. Krempl and S. Backesfor providing the RSV and influenza A transcript-encoding plasmids. This work was supported through funding by the European Research Council (101001394 to S.G.; 865973 and 101158249 to C.L.B.), the R. Gaurth Hansen Family (to R.N.J.), the National Institutes of Health (R35GM138080 to R.N.J.), the PostDoc Plus Program from the Graduate School of Life Sciences at Julius-Maximilians-Universität Würzburg (to O.D.), and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy–The Berlin Mathematics Research Center MATH+ (EXC−2046/1, project ID: 390685689 to M.v.K.). Open access funding provided by Helmholtz-Zentrum für Infektionsforschung GmbH (HZI).","citation":{"apa":"Dmytrenko, O., Yuan, B., Crosby, K. T., Krebel, M., Chen, X., Nowak, J. S., … Beisel, C. L. (2026). RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-09852-9","ama":"Dmytrenko O, Yuan B, Crosby KT, et al. RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity. Nature. 2026. doi:10.1038/s41586-025-09852-9","ieee":"O. Dmytrenko et al., “RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity,” Nature. Springer Nature, 2026.","ista":"Dmytrenko O, Yuan B, Crosby KT, Krebel M, Chen X, Nowak JS, Chramiec-Głąbik A, Filani B, Gribling-Burrer A-S, van der Toorn W, von Kleist M, Achmedov T, Smyth RP, Glatt S, Bravo JPK, Heinz DW, Jackson RN, Beisel CL. 2026. RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity. Nature.","short":"O. Dmytrenko, B. Yuan, K.T. Crosby, M. Krebel, X. Chen, J.S. Nowak, A. Chramiec-Głąbik, B. Filani, A.-S. Gribling-Burrer, W. van der Toorn, M. von Kleist, T. Achmedov, R.P. Smyth, S. Glatt, J.P.K. Bravo, D.W. Heinz, R.N. Jackson, C.L. Beisel, Nature (2026).","mla":"Dmytrenko, Oleg, et al. “RNA-Triggered Cas12a3 Cleaves TRNA Tails to Execute Bacterial Immunity.” Nature, Springer Nature, 2026, doi:10.1038/s41586-025-09852-9.","chicago":"Dmytrenko, Oleg, Biao Yuan, Kadin T. Crosby, Max Krebel, Xiye Chen, Jakub S. Nowak, Andrzej Chramiec-Głąbik, et al. “RNA-Triggered Cas12a3 Cleaves TRNA Tails to Execute Bacterial Immunity.” Nature. Springer Nature, 2026. https://doi.org/10.1038/s41586-025-09852-9."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","main_file_link":[{"url":"https://doi.org/10.1038/s41586-025-09852-9","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.1038/s41586-025-09852-9","day":"07","publication_status":"epub_ahead","department":[{"_id":"JaBr"}],"month":"01"},{"publication_identifier":{"issn":["2791-4585"]},"date_created":"2026-01-09T09:22:48Z","supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"}],"file_date_updated":"2026-01-28T12:38:19Z","date_updated":"2026-04-07T11:41:44Z","type":"dissertation","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels","has_accepted_license":"1","status":"public","file":[{"creator":"dvladimi","file_size":2867531,"embargo":"2027-01-01","date_updated":"2026-01-21T14:12:13Z","file_name":"2026_Vladimirtsev_Dmitrii_Thesis.pdf","file_id":"21033","date_created":"2026-01-21T14:12:13Z","checksum":"812857b2fbe3f6113bef22fd04bccd3e","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed"},{"access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","checksum":"2b969f97f8d7461bea3d255f48c2219c","date_created":"2026-01-21T14:41:58Z","file_id":"21034","file_name":"Source Files.zip","date_updated":"2026-01-28T12:38:19Z","file_size":25023066,"creator":"dvladimi"}],"citation":{"ieee":"D. Vladimirtsev, “Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels,” Institute of Science and Technology Austria, 2026.","ama":"Vladimirtsev D. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. 2026. doi:10.15479/AT-ISTA-20964","apa":"Vladimirtsev, D. (2026). Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20964","short":"D. Vladimirtsev, Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels, Institute of Science and Technology Austria, 2026.","mla":"Vladimirtsev, Dmitrii. Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20964.","chicago":"Vladimirtsev, Dmitrii. “Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20964.","ista":"Vladimirtsev D. 2026. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. Institute of Science and Technology Austria."},"month":"01","corr_author":"1","related_material":{"record":[{"id":"20982","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/AT-ISTA-20964","day":"14","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"20964","alternative_title":["ISTA Master’s Thesis"],"author":[{"first_name":"Dmitrii","last_name":"Vladimirtsev","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","full_name":"Vladimirtsev, Dmitrii"}],"publisher":"Institute of Science and Technology Austria","project":[{"grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"ddc":["570"],"degree_awarded":"MS","year":"2026","date_published":"2026-01-14T00:00:00Z","article_processing_charge":"No","page":"22"},{"ec_funded":1,"day":"05","doi":"10.1029/2024RG000869","publication_status":"epub_ahead","department":[{"_id":"FrPe"}],"month":"01","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ista":"Sauter T, Brock BW, Collier E, Goger B, Groos AR, Haualand KF, Mott R, Nicholson L, Prinz R, Shaw T, Stiperski I, Georgi A, Haugeneder M, Mandal A, Reynolds D, Saigger M, Sicart JE, Voordendag A. 2026. Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. Reviews of Geophysics. 64(1), e2024RG000869.","mla":"Sauter, T., et al. “Glacier-Atmosphere Interactions and Feedbacks in High-Mountain Regions - A Review.” Reviews of Geophysics, vol. 64, no. 1, e2024RG000869, 2026, doi:10.1029/2024RG000869.","short":"T. Sauter, B.W. Brock, E. Collier, B. Goger, A.R. Groos, K.F. Haualand, R. Mott, L. Nicholson, R. Prinz, T. Shaw, I. Stiperski, A. Georgi, M. Haugeneder, A. Mandal, D. Reynolds, M. Saigger, J.E. Sicart, A. Voordendag, Reviews of Geophysics 64 (2026).","chicago":"Sauter, T., B. W. Brock, E. Collier, B. Goger, A. R. Groos, K. F. Haualand, R. Mott, et al. “Glacier-Atmosphere Interactions and Feedbacks in High-Mountain Regions - A Review.” Reviews of Geophysics, 2026. https://doi.org/10.1029/2024RG000869.","ama":"Sauter T, Brock BW, Collier E, et al. Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. Reviews of Geophysics. 2026;64(1). doi:10.1029/2024RG000869","apa":"Sauter, T., Brock, B. W., Collier, E., Goger, B., Groos, A. R., Haualand, K. F., … Voordendag, A. (2026). Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. Reviews of Geophysics. https://doi.org/10.1029/2024RG000869","ieee":"T. Sauter et al., “Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review,” Reviews of Geophysics, vol. 64, no. 1. 2026."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2024RG000869"}],"acknowledgement":"This work is the result of collaboration and discussions within HEFEX II, and we are grateful to all colleagues who have contributed to and enriched these discussions in various ways. T. Sauter acknowledges funding from the German Research Foundation (DFG) (Grant 543257843). This research was funded in part by the Austrian Science Fund (FWF) (Grant https://doi.org/10.55776/P36624 and https://doi.org/10.55776/P36306) for which E. Collier and R. Prinz are grateful. A. R. Groos, T. E. Shaw, R. Mott and M. Haugeneder acknowledge Transnational Access from the European Union's H2020 project INTERACT III (Grant 871120) for participation in the HEFEX II campaign and working group. I. Stiperski (Grant Agreement No. 101001691) and A. R. Groos (Grant Agreement No. 948290) acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program. R. Mott acknowledges funding from the Swiss National Science Foundation (SNSF) (Grant 200021_219918). B. Goger is supported by EXCLAIM, a project funded by ETH Zurich. J.E. Sicart acknowledges LabEx OSUG@2020 (Investissements d'avenir - ANR10 LABX56) for participation in the HEFEX II campaign and working group. T. E. Shaw acknowledges funding from the EU Horizon 2020 Marie Skłodowska-Curie Grant 101026058 and 101034413. K. F. Haualand and T. Sauter are supported by the JOSTICE project funded by the Research Council of Norway (RCN Grant 302458).","scopus_import":"1","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review","OA_place":"publisher","article_type":"original","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["8755-1209"],"eissn":["1944-9208"]},"date_created":"2026-01-11T23:01:33Z","publication":"Reviews of Geophysics","abstract":[{"text":"Mountain glaciers are among the natural systems most vulnerable to climate change. However, their interactions with the atmosphere are complex and not fully understood. These interactions can trigger rapid adjustments and climate feedbacks that either amplify or attenuate atmospheric signals, influencing both glacier response and large-scale atmospheric circulation. Observing this functional coupling in nature is challenging because the key processes occur over a wide range of spatial and temporal scales. However, recent advances in observational techniques and modeling have provided new insights into these interactions. In this review, we summarize the current state of knowledge on glacier-atmosphere interactions in high-mountain regions at different scales, and highlight recent advances in observational and numerical modeling. We also highlight important knowledge gaps and outline future research directions to improve the prediction of glacier change in a warming world.","lang":"eng"}],"date_updated":"2026-01-12T10:04:17Z","type":"journal_article","PlanS_conform":"1","date_published":"2026-01-05T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","ddc":["550"],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"article_number":"e2024RG000869","year":"2026","issue":"1","_id":"20971","author":[{"first_name":"T.","full_name":"Sauter, T.","last_name":"Sauter"},{"full_name":"Brock, B. W.","last_name":"Brock","first_name":"B. W."},{"first_name":"E.","full_name":"Collier, E.","last_name":"Collier"},{"full_name":"Goger, B.","last_name":"Goger","first_name":"B."},{"first_name":"A. R.","full_name":"Groos, A. R.","last_name":"Groos"},{"full_name":"Haualand, K. F.","last_name":"Haualand","first_name":"K. F."},{"full_name":"Mott, R.","last_name":"Mott","first_name":"R."},{"first_name":"L.","full_name":"Nicholson, L.","last_name":"Nicholson"},{"last_name":"Prinz","full_name":"Prinz, R.","first_name":"R."},{"last_name":"Shaw","full_name":"Shaw, Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","orcid":"0000-0001-7640-6152","first_name":"Thomas"},{"first_name":"I.","full_name":"Stiperski, I.","last_name":"Stiperski"},{"full_name":"Georgi, A.","last_name":"Georgi","first_name":"A."},{"first_name":"M.","full_name":"Haugeneder, M.","last_name":"Haugeneder"},{"first_name":"A.","last_name":"Mandal","full_name":"Mandal, A."},{"last_name":"Reynolds","full_name":"Reynolds, D.","first_name":"D."},{"first_name":"M.","full_name":"Saigger, M.","last_name":"Saigger"},{"last_name":"Sicart","full_name":"Sicart, J. E.","first_name":"J. E."},{"last_name":"Voordendag","full_name":"Voordendag, A.","first_name":"A."}],"intvolume":" 64","volume":64},{"citation":{"chicago":"Kücükdereli, Hakan, and Amelia M. Douglass. “Neuroscience: What Doesn’t Kill You Makes You Stronger.” Current Biology. Elsevier, 2026. https://doi.org/10.1016/j.cub.2025.11.056.","short":"H. Kücükdereli, A.M. Douglass, Current Biology 36 (2026) R27–R29.","mla":"Kücükdereli, Hakan, and Amelia M. Douglass. “Neuroscience: What Doesn’t Kill You Makes You Stronger.” Current Biology, vol. 36, no. 1, Elsevier, 2026, pp. R27–29, doi:10.1016/j.cub.2025.11.056.","ista":"Kücükdereli H, Douglass AM. 2026. Neuroscience: What doesn’t kill you makes you stronger. Current Biology. 36(1), R27–R29.","ieee":"H. Kücükdereli and A. M. Douglass, “Neuroscience: What doesn’t kill you makes you stronger,” Current Biology, vol. 36, no. 1. Elsevier, pp. R27–R29, 2026.","apa":"Kücükdereli, H., & Douglass, A. M. (2026). Neuroscience: What doesn’t kill you makes you stronger. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2025.11.056","ama":"Kücükdereli H, Douglass AM. Neuroscience: What doesn’t kill you makes you stronger. Current Biology. 2026;36(1):R27-R29. doi:10.1016/j.cub.2025.11.056"},"status":"public","scopus_import":"1","day":"05","doi":"10.1016/j.cub.2025.11.056","department":[{"_id":"AmDo"},{"_id":"SiHi"}],"month":"01","corr_author":"1","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"None","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"publication":"Current Biology","date_created":"2026-01-11T23:01:33Z","abstract":[{"lang":"eng","text":"Small amounts of stress are thought to have beneficial effects. A new study reports a mechanism by which the psychedelic drug, psilocybin, causes acute release of stress hormones, despite its known long-term anti-anxiety effects."}],"date_updated":"2026-01-12T10:09:13Z","type":"journal_article","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Neuroscience: What doesn’t kill you makes you stronger","article_type":"letter_note","publisher":"Elsevier","year":"2026","pmid":1,"date_published":"2026-01-05T00:00:00Z","page":"R27-R29","article_processing_charge":"No","intvolume":" 36","volume":36,"_id":"20972","issue":"1","external_id":{"pmid":["41494523"]},"author":[{"first_name":"Hakan","id":"5d5f6ea4-ef9e-11f0-a10a-85e12a3552af","full_name":"Kücükdereli, Hakan","last_name":"Kücükdereli"},{"last_name":"Douglass","full_name":"Douglass, Amelia May Barnett","id":"de5f6fda-80fb-11ef-996f-a8c4ecd8e289","orcid":"0000-0001-5398-6473","first_name":"Amelia May Barnett"}]},{"article_number":"staf2219","year":"2026","publisher":"Oxford University Press","ddc":["520"],"article_processing_charge":"Yes","date_published":"2026-01-01T00:00:00Z","volume":545,"intvolume":" 545","author":[{"first_name":"Timo","full_name":"Kist, Timo","last_name":"Kist"},{"first_name":"Joseph F.","last_name":"Hennawi","full_name":"Hennawi, Joseph F."},{"first_name":"Frederick B.","full_name":"Davies, Frederick B.","last_name":"Davies"},{"first_name":"Eduardo","last_name":"Bañados","full_name":"Bañados, Eduardo"},{"full_name":"Bosman, Sarah E.I.","last_name":"Bosman","first_name":"Sarah E.I."},{"first_name":"Zheng","last_name":"Cai","full_name":"Cai, Zheng"},{"first_name":"Anna Christina","full_name":"Eilers, Anna Christina","last_name":"Eilers"},{"first_name":"Xiaohui","full_name":"Fan, Xiaohui","last_name":"Fan"},{"orcid":"0000-0003-3633-5403","first_name":"Zoltán","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman"},{"last_name":"Jun","full_name":"Jun, Hyunsung D.","first_name":"Hyunsung D."},{"first_name":"Yichen","full_name":"Liu, Yichen","last_name":"Liu"},{"first_name":"Jinyi","full_name":"Yang, Jinyi","last_name":"Yang"},{"last_name":"Wang","full_name":"Wang, Feige","first_name":"Feige"}],"external_id":{"arxiv":["2508.21818"]},"_id":"20974","issue":"3","scopus_import":"1","acknowledgement":"We acknowledge helpful conversations with the ENIGMA group at UC Santa Barbara and Leiden University. This work is based on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programmes #1219 and #1764. This work made use of numpy (C. R. Harris et al. 2020), scipy (P. Virtanen et al. 2020), jax (J. Bradbury et al. 2018), numpyro (E. Bingham et al. 2018; D. Phan, N. Pradhan & M. Jankowiak 2019), sklearn (F. Pedregosa et al. 2011), astropy (Astropy Collaboration 2013, 2018, 2022), PypeIt (J. Prochaska et al. 2020), skycalc_ipy (K. Leschinski 2021), h5py (A. Collette 2013), matplotlib (J. D. Hunter 2007), corner.py (D. Foreman-Mackey 2016), and IPython (F. Pérez & B. E. Granger 2007). TK and JFH acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 885301). JFH acknowledges support from NSF grant no. 2307180. SEIB was supported by the Deutsche Forschungsgemeinschaft (DFG) under Emmy Noether grant number BO 5771/1-1. FW acknowledges support from NSF award AST-2513040.","status":"public","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"68f04ab0fdcee4f12341d116c5f794cd","success":1,"access_level":"open_access","date_updated":"2026-01-12T09:43:07Z","file_size":2174272,"creator":"dernst","date_created":"2026-01-12T09:43:07Z","file_id":"20979","file_name":"2026_MonthNoticesRAS_Kist.pdf"}],"citation":{"short":"T. Kist, J.F. Hennawi, F.B. Davies, E. Bañados, S.E.I. Bosman, Z. Cai, A.C. Eilers, X. Fan, Z. Haiman, H.D. Jun, Y. Liu, J. Yang, F. Wang, Monthly Notices of the Royal Astronomical Society 545 (2026).","chicago":"Kist, Timo, Joseph F. Hennawi, Frederick B. Davies, Eduardo Bañados, Sarah E.I. Bosman, Zheng Cai, Anna Christina Eilers, et al. “First Constraints on the Local Ionization Topology in Front of Two Quasars at z ∼ 7.5.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2026. https://doi.org/10.1093/mnras/staf2219.","mla":"Kist, Timo, et al. “First Constraints on the Local Ionization Topology in Front of Two Quasars at z ∼ 7.5.” Monthly Notices of the Royal Astronomical Society, vol. 545, no. 3, staf2219, Oxford University Press, 2026, doi:10.1093/mnras/staf2219.","ista":"Kist T, Hennawi JF, Davies FB, Bañados E, Bosman SEI, Cai Z, Eilers AC, Fan X, Haiman Z, Jun HD, Liu Y, Yang J, Wang F. 2026. First constraints on the local ionization topology in front of two quasars at z ∼ 7.5. Monthly Notices of the Royal Astronomical Society. 545(3), staf2219.","ieee":"T. Kist et al., “First constraints on the local ionization topology in front of two quasars at z ∼ 7.5,” Monthly Notices of the Royal Astronomical Society, vol. 545, no. 3. Oxford University Press, 2026.","ama":"Kist T, Hennawi JF, Davies FB, et al. First constraints on the local ionization topology in front of two quasars at z ∼ 7.5. Monthly Notices of the Royal Astronomical Society. 2026;545(3). doi:10.1093/mnras/staf2219","apa":"Kist, T., Hennawi, J. F., Davies, F. B., Bañados, E., Bosman, S. E. I., Cai, Z., … Wang, F. (2026). First constraints on the local ionization topology in front of two quasars at z ∼ 7.5. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staf2219"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"arxiv":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","month":"01","doi":"10.1093/mnras/staf2219","day":"01","department":[{"_id":"ZoHa"}],"publication_status":"published","file_date_updated":"2026-01-12T09:43:07Z","PlanS_conform":"1","date_updated":"2026-01-12T09:45:54Z","DOAJ_listed":"1","type":"journal_article","abstract":[{"text":"Thus far, Lyman-α damping wings towards quasars have been used to probe the global ionization state of the foreground intergalactic medium (IGM). A new parametrization has demonstrated that the damping wing signature also carries local information about the distribution of neutral hydrogen (H I) in front of the quasar before it started shining. Leveraging a recently introduced Bayesian JAX-based Hamiltonian Monte Carlo inference framework, we derive constraints on the Lorentzian-weighted H I column density NDW H I , the quasar’s distance rpatch to the first neutral patch, and its lifetime tQ based on James Webb Space\r\nTelescope (JWST) Near Infrared Spectrograph (NIRSpec) spectra of the two z ∼ 7.5 quasars J1007+2115 and J1342+0928. After folding in model-dependent topology information, we find that J1007+2115 (and J1342+0928) is most likely to reside in a (xH1)= 0.32+0.22 −0.20 (0.58+0.23 −0.23) neutral IGM while shining for a remarkably short lifetime of log10 tQ/yr = 4.14+0.74 −0.18 (an intermediate lifetime of 5.64+0.25 −0.43) along a sightline with log10 NDW\r\nH I /cm−2 = 19.70+0.35 −0.86 (20.24+0.25 −0.22) and rpatch = 28.9+54.0 −14.4 cMpc\r\n(10.9+5.6−5.9 cMpc). In light of the potential presence of local absorbers in the foreground of J1342+0928 as has been recently suggested, we also demonstrate how the Lorentzian-weighted column density NDW H I provides a natural means for quantifying their contribution to the observed damping wing signal.","lang":"eng"}],"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication":"Monthly Notices of the Royal Astronomical Society","date_created":"2026-01-11T23:01:34Z","has_accepted_license":"1","oa":1,"OA_place":"publisher","article_type":"original","OA_type":"gold","title":"First constraints on the local ionization topology in front of two quasars at z ∼ 7.5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2026-01-11T23:01:34Z","publication":"Nature Astronomy","publication_identifier":{"eissn":["2397-3366"]},"abstract":[{"text":"Galaxy clusters are the most massive, gravitationally bound structures in the Universe. They emerged through hierarchical structure formation of large-scale dark matter and baryon overdensities. Early galaxy ‘proto-clusters’ are believed to have substantially contributed to the cosmic star-formation rate density and served as ‘hotspots’ for the reionization of the intergalactic medium. Our understanding of the formation of these structures at the earliest cosmic epochs is, however, limited to sparse observations of their galaxy members or is based on phenomenological models and cosmological simulations. Here we report the detection of a large and coherent structure of neutral atomic hydrogen gas (H i) extending from a galaxy proto-cluster at redshift z = 5.4, one billion years after the Big Bang. The presence of this H i gas is revealed by strong damped Lyman-α absorption features observed in several background-galaxy spectra. Although the sight lines overall probe a large range in H i column densities, NHI = 1020 cm−2 to 1023.5 cm−2, they are similar across nearby sight lines, demonstrating that they probe the same dense neutral gas. This observation of a dense large-scale overdensity of cold neutral gas challenges current cosmological simulations and has strong implications for the reionization topology of the Universe.","lang":"eng"}],"type":"journal_article","date_updated":"2026-01-12T09:53:21Z","title":"A dense web of neutral gas in a galaxy proto-cluster post-reionization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","_id":"20975","article_type":"original","author":[{"first_name":"Kasper E.","full_name":"Heintz, Kasper E.","last_name":"Heintz"},{"full_name":"Bennett, Jake S.","last_name":"Bennett","first_name":"Jake S."},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"first_name":"Albert","full_name":"Sneppen, Albert","last_name":"Sneppen"},{"full_name":"Rennehan, Douglas","last_name":"Rennehan","first_name":"Douglas"},{"full_name":"Pollock, Clara L.","last_name":"Pollock","first_name":"Clara L."},{"first_name":"Joris","last_name":"Witstok","full_name":"Witstok, Joris"},{"first_name":"Renske","full_name":"Smit, Renske","last_name":"Smit"},{"last_name":"Vejlgaard","full_name":"Vejlgaard, Simone","first_name":"Simone"},{"first_name":"Chamilla","last_name":"Terp","full_name":"Terp, Chamilla"},{"first_name":"Umran S.","full_name":"Koca, Umran S.","last_name":"Koca"},{"first_name":"Gabriel B.","last_name":"Brammer","full_name":"Brammer, Gabriel B."},{"last_name":"Finlator","full_name":"Finlator, Kristian","first_name":"Kristian"},{"first_name":"Matthew J.","last_name":"Hayes","full_name":"Hayes, Matthew J."},{"last_name":"Sijacki","full_name":"Sijacki, Debora","first_name":"Debora"},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"Francesco","last_name":"Valentino","full_name":"Valentino, Francesco"},{"first_name":"Nial R.","full_name":"Tanvir, Nial R.","last_name":"Tanvir"},{"full_name":"Jakobsson, Páll","last_name":"Jakobsson","first_name":"Páll"},{"last_name":"Laursen","full_name":"Laursen, Peter","first_name":"Peter"},{"first_name":"Darach J.","last_name":"Watson","full_name":"Watson, Darach J."},{"first_name":"Romeel","last_name":"Davé","full_name":"Davé, Romeel"},{"first_name":"Laura C.","last_name":"Keating","full_name":"Keating, Laura C."},{"first_name":"Alba","last_name":"Covelo-Paz","full_name":"Covelo-Paz, Alba"}],"citation":{"ista":"Heintz KE, Bennett JS, Oesch PA, Sneppen A, Rennehan D, Pollock CL, Witstok J, Smit R, Vejlgaard S, Terp C, Koca US, Brammer GB, Finlator K, Hayes MJ, Sijacki D, Naidu RP, Matthee JJ, Valentino F, Tanvir NR, Jakobsson P, Laursen P, Watson DJ, Davé R, Keating LC, Covelo-Paz A. 2026. A dense web of neutral gas in a galaxy proto-cluster post-reionization. Nature Astronomy.","short":"K.E. Heintz, J.S. Bennett, P.A. Oesch, A. Sneppen, D. Rennehan, C.L. Pollock, J. Witstok, R. Smit, S. Vejlgaard, C. Terp, U.S. Koca, G.B. Brammer, K. Finlator, M.J. Hayes, D. Sijacki, R.P. Naidu, J.J. Matthee, F. Valentino, N.R. Tanvir, P. Jakobsson, P. Laursen, D.J. Watson, R. Davé, L.C. Keating, A. Covelo-Paz, Nature Astronomy (2026).","mla":"Heintz, Kasper E., et al. “A Dense Web of Neutral Gas in a Galaxy Proto-Cluster Post-Reionization.” Nature Astronomy, Springer Nature, 2026, doi:10.1038/s41550-025-02745-x.","chicago":"Heintz, Kasper E., Jake S. Bennett, Pascal A. Oesch, Albert Sneppen, Douglas Rennehan, Clara L. Pollock, Joris Witstok, et al. “A Dense Web of Neutral Gas in a Galaxy Proto-Cluster Post-Reionization.” Nature Astronomy. Springer Nature, 2026. https://doi.org/10.1038/s41550-025-02745-x.","apa":"Heintz, K. E., Bennett, J. S., Oesch, P. A., Sneppen, A., Rennehan, D., Pollock, C. L., … Covelo-Paz, A. (2026). A dense web of neutral gas in a galaxy proto-cluster post-reionization. Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-025-02745-x","ama":"Heintz KE, Bennett JS, Oesch PA, et al. A dense web of neutral gas in a galaxy proto-cluster post-reionization. Nature Astronomy. 2026. doi:10.1038/s41550-025-02745-x","ieee":"K. E. Heintz et al., “A dense web of neutral gas in a galaxy proto-cluster post-reionization,” Nature Astronomy. Springer Nature, 2026."},"status":"public","publisher":"Springer Nature","year":"2026","scopus_import":"1","acknowledgement":"This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (Contract No. MB22.00072). The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation (Grant No. DNRF140). The data products presented herein were retrieved from the DJA, which is an initiative of the Cosmic Dawn Center. This work is based on observations made with the NASA/ESA/CSA JWST. The data were obtained from MAST at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. J.S.B. acknowledges support from the Simons Collaboration on Learning the Universe. J.S.B.’s simulations used resources from the Cambridge Service for Data Driven Discovery operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using tier 2 funding from the Engineering and Physical Sciences Research Council (Capital Grant No. EP/P020259/1). K.F. gratefully acknowledges support from the National Science Foundation (Award No. 2006550). M.J.H. is fellow of the Knut & Alice Wallenberg Foundation. D.S. acknowledges support from the Science and Technology Facilities Council. U.S.K. was partially funded by the Summer Undergraduate Research Fellowships programme at Caltech.","publication_status":"epub_ahead","department":[{"_id":"JoMa"}],"day":"02","doi":"10.1038/s41550-025-02745-x","date_published":"2026-01-02T00:00:00Z","month":"01","quality_controlled":"1","oa_version":"None","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"OA_place":"repository","article_type":"original","OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Computing a connection matrix and persistence efficiently from a morse decomposition","oa":1,"abstract":[{"text":"Morse decompositions partition the flows in a vector field into equivalent structures. Given such a decomposition, one can define a further summary of its flow structure by what is called a connection matrix. These matrices, a generalization of Morse boundary operators from classical Morse theory, capture the connections made by the flows among the critical structures—such as attractors, repellers, and orbits—in a vector field. Recently, in the context of combinatorial dynamics, an efficient persistence-like algorithm to compute connection matrices has been proposed in Dey, Lipiński, Mrozek, and Slechta [SIAM J. Appl. Dyn. Syst., 23 (2024), pp. 81–97]. We show that, actually, the classical persistence algorithm with exhaustive reduction retrieves connection matrices, both simplifying the algorithm of Dey et al. and bringing the theory of persistence closer to combinatorial dynamical systems. We supplement this main result with an observation: the concept of persistence as defined for scalar fields naturally adapts to Morse decompositions whose Morse sets are filtered with a Lyapunov function. We conclude by presenting preliminary experimental results.","lang":"eng"}],"publication_identifier":{"issn":["1536-0040"]},"date_created":"2026-01-12T11:17:06Z","publication":"SIAM Journal on Applied Dynamical Systems","date_updated":"2026-01-20T07:40:39Z","type":"journal_article","month":"01","day":"01","ec_funded":1,"doi":"10.1137/25m1739406","department":[{"_id":"HeEd"}],"publication_status":"published","arxiv":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2502.19369","open_access":"1"}],"status":"public","citation":{"ieee":"T. K. Dey, A. Haas, and M. Lipiński, “Computing a connection matrix and persistence efficiently from a morse decomposition,” SIAM Journal on Applied Dynamical Systems, vol. 25, no. 1. Society for Industrial & Applied Mathematics, pp. 108–130, 2026.","apa":"Dey, T. K., Haas, A., & Lipiński, M. (2026). Computing a connection matrix and persistence efficiently from a morse decomposition. SIAM Journal on Applied Dynamical Systems. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/25m1739406","ama":"Dey TK, Haas A, Lipiński M. Computing a connection matrix and persistence efficiently from a morse decomposition. SIAM Journal on Applied Dynamical Systems. 2026;25(1):108-130. doi:10.1137/25m1739406","chicago":"Dey, Tamal K., Andrew Haas, and Michał Lipiński. “Computing a Connection Matrix and Persistence Efficiently from a Morse Decomposition.” SIAM Journal on Applied Dynamical Systems. Society for Industrial & Applied Mathematics, 2026. https://doi.org/10.1137/25m1739406.","mla":"Dey, Tamal K., et al. “Computing a Connection Matrix and Persistence Efficiently from a Morse Decomposition.” SIAM Journal on Applied Dynamical Systems, vol. 25, no. 1, Society for Industrial & Applied Mathematics, 2026, pp. 108–30, doi:10.1137/25m1739406.","short":"T.K. Dey, A. Haas, M. Lipiński, SIAM Journal on Applied Dynamical Systems 25 (2026) 108–130.","ista":"Dey TK, Haas A, Lipiński M. 2026. Computing a connection matrix and persistence efficiently from a morse decomposition. SIAM Journal on Applied Dynamical Systems. 25(1), 108–130."},"acknowledgement":"This research was supported by NSF grants DMS-2301360 and CCF-2437030 as well as from the European Union's Horizon 2020 research and innovation programme under Marie Sk\\lodowska-Curie grant 101034413.\r\n","scopus_import":"1","_id":"20980","issue":"1","external_id":{"arxiv":["2502.19369"]},"author":[{"first_name":"Tamal K.","full_name":"Dey, Tamal K.","last_name":"Dey"},{"full_name":"Haas, Andrew","last_name":"Haas","first_name":"Andrew"},{"last_name":"Lipiński","id":"dfffb474-4317-11ee-8f5c-fe3fc95a425e","full_name":"Lipiński, Michał","first_name":"Michał","orcid":"0000-0001-9789-9750"}],"intvolume":" 25","volume":25,"date_published":"2026-01-01T00:00:00Z","article_processing_charge":"No","page":"108-130","publisher":"Society for Industrial & Applied Mathematics","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"ddc":["510"],"year":"2026"},{"article_processing_charge":"Yes (in subscription journal)","date_published":"2026-01-12T00:00:00Z","year":"2026","ddc":["570","577"],"publisher":"Elsevier","project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"author":[{"first_name":"Juan Sebastian","id":"1271b54b-dbcd-11ea-9d1d-d92da838fe2c","full_name":"Calderon Garcia, Juan Sebastian","last_name":"Calderon Garcia"},{"full_name":"Costalunga, Giacomo","last_name":"Costalunga","first_name":"Giacomo"},{"last_name":"Vogels","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P"},{"last_name":"Vallentin","full_name":"Vallentin, Daniela","first_name":"Daniela"}],"_id":"20986","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"12","doi":"10.1016/j.cub.2025.12.025","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"publication_status":"epub_ahead","month":"01","scopus_import":"1","acknowledgement":"We would like to thank J. Benichov and N. Hein for their help with fieldwork; M. Ramadas for helping with the segmentation analysis; T. Eliav, C. Chintaluri, G. Tkacik, and A. Navas for providing helpful comments to the project and manuscript; and A. Costalunga for the drawings of nightingales. Funding sources: The Joachim Herz Stiftung Add-on Fellowships for Interdisciplinary Life Science, awarded to G.C.; the ERC Consolidator Grant 819603 SYNAPSEEK, awarded to T.P.V.; and DFG Research Unit 5768–532521431, DFG Research Grant-547921981, DFG SFB 1315–327654276, and the ERC Starting Grant 757459 MIDNIGHT, awarded to D.V.","citation":{"ama":"Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. Interplay between syllable duration and pitch during whistle matching in wild nightingales. Current Biology. 2026. doi:10.1016/j.cub.2025.12.025","apa":"Calderon Garcia, J. S., Costalunga, G., Vogels, T. P., & Vallentin, D. (2026). Interplay between syllable duration and pitch during whistle matching in wild nightingales. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2025.12.025","ieee":"J. S. Calderon Garcia, G. Costalunga, T. P. Vogels, and D. Vallentin, “Interplay between syllable duration and pitch during whistle matching in wild nightingales,” Current Biology. Elsevier, 2026.","ista":"Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. 2026. Interplay between syllable duration and pitch during whistle matching in wild nightingales. Current Biology.","short":"J.S. Calderon Garcia, G. Costalunga, T.P. Vogels, D. Vallentin, Current Biology (2026).","chicago":"Calderon Garcia, Juan Sebastian, Giacomo Costalunga, Tim P Vogels, and Daniela Vallentin. “Interplay between Syllable Duration and Pitch during Whistle Matching in Wild Nightingales.” Current Biology. Elsevier, 2026. https://doi.org/10.1016/j.cub.2025.12.025.","mla":"Calderon Garcia, Juan Sebastian, et al. “Interplay between Syllable Duration and Pitch during Whistle Matching in Wild Nightingales.” Current Biology, Elsevier, 2026, doi:10.1016/j.cub.2025.12.025."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2025.12.025","open_access":"1"}],"oa":1,"has_accepted_license":"1","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Interplay between syllable duration and pitch during whistle matching in wild nightingales","OA_place":"publisher","article_type":"original","date_updated":"2026-01-20T07:33:32Z","type":"journal_article","PlanS_conform":"1","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"date_created":"2026-01-14T12:00:29Z","publication":"Current Biology","abstract":[{"lang":"eng","text":"During complex vocal interactions, different features of acoustic stimuli are integrated to produce appropriate vocal responses,1 such as copying sounds during vocal matching behavior in some animals.2,3,4,5,6,7,8,9,10,11,12 However, little is known about the interplay and possible trade-offs between the different temporal and spectral acoustic features during these vocal exchanges.2,13,14 Nightingales can flexibly match the pitch of their tonal “whistle songs” in real time during counter-singing duels.15,16 Here, we show that the syllable duration of whistle playbacks could alter the song responses of wild nightingales, causing their whistle duration distribution to shift toward the presented stimulus duration. When exposed to whistle playbacks featuring unnatural combinations of pitch and duration, nightingales demonstrate a flexible trade-off between pitch matching and temporal imitation, yet they are constrained by their vocal repertoire. They selectively adapted their vocal responses to approximate these novel stimuli, aligning them with their natural whistle repertoire. We developed a computational model of nightingale whistle-matching behavior that revealed a hierarchical organization of acoustic feature production. During whistle matching, the feature integration process is constrained by the duration of syllables, and pitch matching follows within this temporal framework, forcing a trade-off between the two features. Our findings reveal a complex interplay between the spectral and temporal domains that shapes song-matching behavior."}]},{"oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_status":"published","doi":"10.15479/AT-ISTA-20991","day":"16","related_material":{"record":[{"status":"public","relation":"research_data","id":"18498"},{"status":"public","id":"18491","relation":"part_of_dissertation"}]},"month":"01","corr_author":"1","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)","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"citation":{"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.","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.","short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026.","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","ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi: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."},"file":[{"file_size":22456421,"creator":"dgarciac","date_updated":"2026-01-16T12:25:13Z","file_name":"2026_Garcia_Diego_Thesis.docx","file_id":"20996","date_created":"2026-01-16T12:25:13Z","relation":"source_file","checksum":"841f1bc073d667125729b2a017f8c37a","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"relation":"main_file","checksum":"a1f33d4f183ce7072eee42a6ccf5340b","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":9556719,"creator":"dgarciac","date_updated":"2026-01-16T12:25:13Z","file_name":"2026_Garcia_Diego_Thesis.pdf","file_id":"20997","date_created":"2026-01-16T12:25:13Z"},{"file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar","file_id":"20998","date_created":"2026-01-16T13:08:14Z","creator":"dgarciac","file_size":54491433,"date_updated":"2026-01-16T13:08:14Z","access_level":"closed","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.","checksum":"98a80691067174c30fe53f38ce7344e6","relation":"supplementary_material","content_type":"application/x-compressed"},{"file_size":7982811,"creator":"dgarciac","date_updated":"2026-01-16T13:08:14Z","file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar","date_created":"2026-01-16T13:08:14Z","file_id":"20999","relation":"supplementary_material","checksum":"99a3cab2fa36666b9a92eefc27d586da","content_type":"application/x-compressed","access_level":"open_access"},{"access_level":"open_access","content_type":"text/plain","checksum":"255fdf56b2932c46bf27c63aa6106a4f","relation":"supplementary_material","file_id":"21000","date_created":"2026-01-16T13:08:59Z","file_name":"README.txt","date_updated":"2026-01-16T13:08:59Z","creator":"dgarciac","file_size":732}],"status":"public","has_accepted_license":"1","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"The genomic architecture of local adaptation in introduced populations","OA_place":"publisher","type":"dissertation","date_updated":"2026-04-16T12:20:37Z","file_date_updated":"2026-01-16T13:08:59Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969"}],"date_created":"2026-01-16T09:47:59Z","publication_identifier":{"isbn":["978-3-99078-077-0"],"issn":["2663-337X"]},"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."}],"page":"199","article_processing_charge":"No","date_published":"2026-01-16T00:00:00Z","year":"2026","degree_awarded":"PhD","ddc":["576"],"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","full_name":"Garcia Castillo, Diego Fernando","first_name":"Diego Fernando"}],"alternative_title":["ISTA Thesis"],"_id":"20991"},{"date_published":"2026-01-09T00:00:00Z","page":"481-488","article_processing_charge":"No","publisher":"American Chemical Society","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"year":"2026","_id":"21001","issue":"1","author":[{"first_name":"Niraj Nitish","full_name":"Patil, Niraj Nitish","last_name":"Patil"},{"last_name":"Wu","full_name":"Wu, Ruiqi","first_name":"Ruiqi"},{"id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine","last_name":"Fiedler","first_name":"Christine"},{"first_name":"Nilotpal","full_name":"Kapuria, Nilotpal","last_name":"Kapuria"},{"first_name":"Bingfei","last_name":"Nan","full_name":"Nan, Bingfei"},{"last_name":"Navita","full_name":"Navita, Navita","id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4","orcid":"0000-0001-7408-8197","first_name":"Navita"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez"},{"last_name":"Ryan","full_name":"Ryan, Kevin M.","first_name":"Kevin M."},{"full_name":"Ganose, Alex M.","last_name":"Ganose","first_name":"Alex M."},{"first_name":"Shalini","full_name":"Singh, Shalini","last_name":"Singh"}],"intvolume":" 11","volume":11,"day":"09","doi":"10.1021/acsenergylett.5c02909","department":[{"_id":"MaIb"},{"_id":"GradSch"}],"publication_status":"published","month":"01","language":[{"iso":"eng"}],"oa_version":"None","quality_controlled":"1","citation":{"ieee":"N. N. Patil et al., “Layered alkali-copper selenides: Deciphering thermoelectric properties and reaction pathways for nanostructuring β-CsCu5Se3,” ACS Energy Letters, vol. 11, no. 1. American Chemical Society, pp. 481–488, 2026.","apa":"Patil, N. N., Wu, R., Fiedler, C., Kapuria, N., Nan, B., Jakhar, N., … Singh, S. (2026). Layered alkali-copper selenides: Deciphering thermoelectric properties and reaction pathways for nanostructuring β-CsCu5Se3. ACS Energy Letters. American Chemical Society. https://doi.org/10.1021/acsenergylett.5c02909","ama":"Patil NN, Wu R, Fiedler C, et al. Layered alkali-copper selenides: Deciphering thermoelectric properties and reaction pathways for nanostructuring β-CsCu5Se3. ACS Energy Letters. 2026;11(1):481-488. doi:10.1021/acsenergylett.5c02909","mla":"Patil, Niraj Nitish, et al. “Layered Alkali-Copper Selenides: Deciphering Thermoelectric Properties and Reaction Pathways for Nanostructuring β-CsCu5Se3.” ACS Energy Letters, vol. 11, no. 1, American Chemical Society, 2026, pp. 481–88, doi:10.1021/acsenergylett.5c02909.","chicago":"Patil, Niraj Nitish, Ruiqi Wu, Christine Fiedler, Nilotpal Kapuria, Bingfei Nan, Navita Jakhar, Andreu Cabot, et al. “Layered Alkali-Copper Selenides: Deciphering Thermoelectric Properties and Reaction Pathways for Nanostructuring β-CsCu5Se3.” ACS Energy Letters. American Chemical Society, 2026. https://doi.org/10.1021/acsenergylett.5c02909.","short":"N.N. Patil, R. Wu, C. Fiedler, N. Kapuria, B. Nan, N. Jakhar, A. Cabot, M. Ibáñez, K.M. Ryan, A.M. Ganose, S. Singh, ACS Energy Letters 11 (2026) 481–488.","ista":"Patil NN, Wu R, Fiedler C, Kapuria N, Nan B, Jakhar N, Cabot A, Ibáñez M, Ryan KM, Ganose AM, Singh S. 2026. Layered alkali-copper selenides: Deciphering thermoelectric properties and reaction pathways for nanostructuring β-CsCu5Se3. ACS Energy Letters. 11(1), 481–488."},"status":"public","scopus_import":"1","acknowledgement":"This publication has emanated from research conducted with the financial support of Taighde Éireann-Research Ireland under Grant number 22/FFP-P/11591. C.F. and M.I. would like to acknowledge the financial support of ISTA and the Werner Siemens Foundation. N.N.P. acknowledges the financial support of AMBER under grant number 12/rc/2278_p2.","OA_type":"closed access","title":"Layered alkali-copper selenides: Deciphering thermoelectric properties and reaction pathways for nanostructuring β-CsCu5Se3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"letter_note","publication_identifier":{"eissn":["2380-8195"]},"publication":"ACS Energy Letters","date_created":"2026-01-18T23:02:43Z","abstract":[{"lang":"eng","text":"Copper chalcogenides offer high charge mobility and low lattice thermal conductivity but suffer from structural instability due to dynamic Cu+ migration. Here, we report a colloidal hot-injection synthesis of ternary cesium copper selenide (CsCu5Se3) nanocrystals (NCs), achieving precise control over phase, size, and morphology through tailored precursor-ligand modulation. This strategy enabled systematic exploration of stable and metastable Cs–Cu–Se phases and mechanistic investigation of nucleation and growth, providing insight into phase modulation and dimensional control at the nanoscale. CsCu5Se3 NCs exhibit low lattice thermal conductivity (∼0.5 Wm–1K–1) and an experimental zT of 0.27 at 718 K. Complementary first-principles calculations, consistent with experimental electronic and optical responses, predict a zT of 1.05 at 1000 K. These findings elucidate the formation dynamics of CsCu5Se3 and establish ABZ (A = alkali, B = metal, Z = chalcogen) NCs as tunable platforms for advanced functional applications."}],"date_updated":"2026-01-19T08:43:21Z","type":"journal_article"},{"volume":113,"intvolume":" 113","author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177","first_name":"Timothy D"}],"issue":"1","_id":"21002","article_number":"e70371","year":"2026","publisher":"Wiley","project":[{"grant_number":"P36278","name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3"}],"ddc":["510"],"article_processing_charge":"Yes (via OA deal)","date_published":"2026-01-06T00:00:00Z","PlanS_conform":"1","file_date_updated":"2026-01-19T08:19:46Z","date_updated":"2026-01-19T08:23:15Z","type":"journal_article","abstract":[{"text":"The Davenport–Heilbronn method is a version of the circle method that was developed for studying Diophantine inequalities in the paper (Davenport and Heilbronn, J. Lond. Math. Soc. (1) 21 (1946), 185–193). We discuss the main ideas in the paper, together with an account of the development of the subject in the intervening 80 years.","lang":"eng"}],"publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"publication":"Journal of the London Mathematical Society","date_created":"2026-01-18T23:02:44Z","has_accepted_license":"1","oa":1,"OA_place":"publisher","article_type":"original","OA_type":"hybrid","title":"The Davenport–Heilbronn method: 80 years on","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The author is very grateful to Jörg Brüdern, Simon Rydin Myerson and Trevor Wooley for their help and advice with preparing this survey, in addition to Vinay Kumaraswamy, Victor Wang and the anonymous referee for useful comments on an earlier draft. This work was supported by a FWF Grant (DOI 10.55776/P36278).\r\nOpen Access funding provided by Institute of Science and Technology Austria/KEMÖ.","scopus_import":"1","status":"public","citation":{"short":"T.D. Browning, Journal of the London Mathematical Society 113 (2026).","chicago":"Browning, Timothy D. “The Davenport–Heilbronn Method: 80 Years On.” Journal of the London Mathematical Society. Wiley, 2026. https://doi.org/10.1112/jlms.70371.","mla":"Browning, Timothy D. “The Davenport–Heilbronn Method: 80 Years On.” Journal of the London Mathematical Society, vol. 113, no. 1, e70371, Wiley, 2026, doi:10.1112/jlms.70371.","ista":"Browning TD. 2026. The Davenport–Heilbronn method: 80 years on. Journal of the London Mathematical Society. 113(1), e70371.","ieee":"T. D. Browning, “The Davenport–Heilbronn method: 80 years on,” Journal of the London Mathematical Society, vol. 113, no. 1. Wiley, 2026.","apa":"Browning, T. D. (2026). The Davenport–Heilbronn method: 80 years on. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.70371","ama":"Browning TD. The Davenport–Heilbronn method: 80 years on. Journal of the London Mathematical Society. 2026;113(1). doi:10.1112/jlms.70371"},"file":[{"access_level":"open_access","success":1,"checksum":"3b05bd625c81d038259a14f7e2ddd57c","relation":"main_file","content_type":"application/pdf","file_name":"2026_JourLondonMathSoc_Browning.pdf","date_created":"2026-01-19T08:19:46Z","file_id":"21004","creator":"dernst","file_size":235238,"date_updated":"2026-01-19T08:19:46Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"month":"01","corr_author":"1","day":"06","doi":"10.1112/jlms.70371","department":[{"_id":"TiBr"}],"publication_status":"published"},{"ddc":["570","540"],"project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"publisher":"Springer Nature","year":"2026","date_published":"2026-01-08T00:00:00Z","article_processing_charge":"Yes (via OA deal)","_id":"21006","author":[{"last_name":"Hübl","full_name":"Hübl, Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","first_name":"Maximilian"},{"first_name":"Thomas E.","last_name":"Videbæk","full_name":"Videbæk, Thomas E."},{"first_name":"Daichi","last_name":"Hayakawa","full_name":"Hayakawa, Daichi"},{"full_name":"Rogers, W. Benjamin","last_name":"Rogers","first_name":"W. Benjamin"},{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. 2026. A polyhedral structure controls programmable self-assembly. Nature Physics.","chicago":"Hübl, Maximilian, Thomas E. Videbæk, Daichi Hayakawa, W. Benjamin Rogers, and Carl Peter Goodrich. “A Polyhedral Structure Controls Programmable Self-Assembly.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-025-03120-3.","mla":"Hübl, Maximilian, et al. “A Polyhedral Structure Controls Programmable Self-Assembly.” Nature Physics, Springer Nature, 2026, doi:10.1038/s41567-025-03120-3.","short":"M. Hübl, T.E. Videbæk, D. Hayakawa, W.B. Rogers, C.P. Goodrich, Nature Physics (2026).","ama":"Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. A polyhedral structure controls programmable self-assembly. Nature Physics. 2026. doi:10.1038/s41567-025-03120-3","apa":"Hübl, M., Videbæk, T. E., Hayakawa, D., Rogers, W. B., & Goodrich, C. P. (2026). A polyhedral structure controls programmable self-assembly. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03120-3","ieee":"M. Hübl, T. E. Videbæk, D. Hayakawa, W. B. Rogers, and C. P. Goodrich, “A polyhedral structure controls programmable self-assembly,” Nature Physics. Springer Nature, 2026."},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41567-025-03120-3"}],"acknowledgement":"We thank B. Isaac and A. Tiano for their technical support with the electron microscopy and S. Waitukaitis for helpful comments on the manuscript. The TEM images were prepared and imaged at the Brandeis Electron Microscopy facility. This work was supported by the Gesellschaft für Forschungsförderung Niederösterreich under project FTI23-G-011 (M.C.H. and C.P.G.), the Brandeis University Materials Research Science and Engineering Center (MRSEC) under grant number NSF DMR-2011846 (T.E.V., D.H. and W.B.R.) and the Smith Family Foundation (W.B.R.). Open access funding provided by Institute of Science and Technology (IST Austria).","scopus_import":"1","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"publication_status":"epub_ahead","day":"08","doi":"10.1038/s41567-025-03120-3","related_material":{"link":[{"url":"https://ista.ac.at/en/news/behind-natures-blueprints/","relation":"press_release","description":"News on ISTA website"}]},"corr_author":"1","month":"01","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","publication":"Nature Physics","date_created":"2026-01-20T10:02:19Z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"abstract":[{"text":"Modern experimental methods in programmable self-assembly make it possible to precisely design particle concentrations, shapes and interactions. However, more physical insight is needed before we can take full advantage of this vast design space to assemble nanostructures with complex form and function. Here we show how a substantial part of this design space can be quickly and comprehensively understood by identifying a class of thermodynamic constraints that act on it. These thermodynamic constraints form a high-dimensional convex polyhedron that determines which nanostructures can be assembled at high equilibrium yield and reveals limitations that govern the coexistence of structures. We validate our predictions through detailed, quantitative assembly experiments of nanoscale particles synthesized using DNA origami. Our results uncover physical relationships underpinning many-component programmable self-assembly in equilibrium and form the basis for robust inverse design, applicable to various systems from biological protein complexes to synthetic nanomachines.","lang":"eng"}],"type":"journal_article","date_updated":"2026-04-28T11:56:45Z","PlanS_conform":"1","title":"A polyhedral structure controls programmable self-assembly","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_type":"hybrid","article_type":"original","OA_place":"publisher","oa":1,"has_accepted_license":"1"}]