[{"publication_status":"published","publisher":"AAAS","OA_type":"gold","date_created":"2026-08-02T22:01:53Z","date_published":"2026-07-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication":"Science Advances","_id":"22620","page":"1-11","day":"17","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 12","has_accepted_license":"1","external_id":{"pmid":["42467783"]},"license":"https://creativecommons.org/licenses/by/4.0/","month":"07","quality_controlled":"1","title":"Shaping of developmental gradients through selection on multiple loci in Antirrhinum","das_tickbox":"1","file_date_updated":"2026-08-03T09:44:40Z","type":"journal_article","status":"public","volume":12,"article_type":"original","department":[{"_id":"NiBa"}],"issue":"29","article_processing_charge":"Yes","citation":{"apa":"Bradley, D., Boell, L., Richardson, D., Copsey, L., Whibley, A., Xu, T., … Coen, E. (2026). Shaping of developmental gradients through selection on multiple loci in Antirrhinum. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adx2011","ista":"Bradley D, Boell L, Richardson D, Copsey L, Whibley A, Xu T, Zhang Y, Xue Y, Field D, Coen E. 2026. Shaping of developmental gradients through selection on multiple loci in Antirrhinum. Science Advances. 12(29), 1–11.","ama":"Bradley D, Boell L, Richardson D, et al. Shaping of developmental gradients through selection on multiple loci in Antirrhinum. Science Advances. 2026;12(29):1-11. doi:10.1126/sciadv.adx2011","ieee":"D. Bradley et al., “Shaping of developmental gradients through selection on multiple loci in Antirrhinum,” Science Advances, vol. 12, no. 29. AAAS, pp. 1–11, 2026.","short":"D. Bradley, L. Boell, D. Richardson, L. Copsey, A. Whibley, T. Xu, Y. Zhang, Y. Xue, D. Field, E. Coen, Science Advances 12 (2026) 1–11.","mla":"Bradley, Desmond, et al. “Shaping of Developmental Gradients through Selection on Multiple Loci in Antirrhinum.” Science Advances, vol. 12, no. 29, AAAS, 2026, pp. 1–11, doi:10.1126/sciadv.adx2011.","chicago":"Bradley, Desmond, Louis Boell, Daniel Richardson, Lucy Copsey, Annabel Whibley, Ting Xu, Yu’E Zhang, Yongbiao Xue, David Field, and Enrico Coen. “Shaping of Developmental Gradients through Selection on Multiple Loci in Antirrhinum.” Science Advances. AAAS, 2026. https://doi.org/10.1126/sciadv.adx2011."},"scopus_import":"1","abstract":[{"text":"Development depends on precise shaping of molecular gradients, but how natural selection acts to establish precision is unknown. Here, we analyze genes that control differences in the gradient of yellow flower color between two varieties of snapdragon (Antirrhinum). We show that these differences depend, in part, on cis-regulatory variation in the pigment biosynthetic gene, FLAVIA (FLA). FLA interacts multiplicatively with three other loci, one of which is a trans-acting regulator of FLA, to further shape the yellow gradient. All the loci exhibit clines at a hybrid zone, with widths that correlate with phenotypic effect, showing how selection can hone gradient shape with remarkable precision by acting on cis and trans variation at multiple loci.","lang":"eng"}],"year":"2026","acknowledgement":"We thank C. Taylor for plant care, N. Barton for sharing SNP data and useful comments, H. Tavares for useful discussions and bioinformatics, M. Couchman for field and data archiving, T. Li for help with photography and phenotyping, J. Chan for help with ImageJ analyses, and X. Rebocho for organization of field experiments. This work was supported by Biotechnology and Biological Sciences Research Council grants BB/S009256/1 (to E.C.), BB/G009325/1 (to E.C.), BBS/E/JI/230002C (to E.C.), and BBS/E/J/000PR9773 (to E.C.); Biotechnology Biological Sciences Research Council Norwich Research Park Biosciences Doctoral Training Partnership grant BB/M011216/1 (to D.R.); and Natural Science Foundation of China grant 32030007 (to Y.X.)","doi":"10.1126/sciadv.adx2011","ddc":["570"],"dataavailabilitystatement":"All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials. All materials generated in this study are described in Materials and Methods and are available on request from E.C. (enrico.coen@jic.ac.uk).","pmid":1,"oa":1,"PlanS_conform":"1","language":[{"iso":"eng"}],"DOAJ_listed":"1","author":[{"last_name":"Bradley","first_name":"Desmond","full_name":"Bradley, Desmond"},{"last_name":"Boell","first_name":"Louis","full_name":"Boell, Louis"},{"full_name":"Richardson, Daniel","last_name":"Richardson","first_name":"Daniel"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"full_name":"Whibley, Annabel","last_name":"Whibley","first_name":"Annabel"},{"last_name":"Xu","first_name":"Ting","full_name":"Xu, Ting"},{"full_name":"Zhang, Yu’E","first_name":"Yu’E","last_name":"Zhang"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"date_updated":"2026-08-03T09:52:37Z","supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1126/sciadv.adx2011","researchdata_availability":"no","oa_version":"Published Version","corr_author":"1","file":[{"relation":"main_file","success":1,"file_id":"22635","file_name":"2026_ScienceAdv_Bradley.pdf","content_type":"application/pdf","date_created":"2026-08-03T09:44:40Z","creator":"dernst","checksum":"f9155dc2d9273e43c0caf78dffa96864","file_size":916329,"access_level":"open_access","date_updated":"2026-08-03T09:44:40Z"}],"publication_identifier":{"eissn":["2375-2548"]}},{"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2602.21363"}],"issue":"3","department":[{"_id":"GeKa"},{"_id":"GradSch"},{"_id":"NanoFab"}],"volume":129,"project":[{"name":"Quantum bits with Kitaev Transmons","_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811","grant_number":"101115315"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors"},{"grant_number":"PAT 7682124","_id":"5b9e579c-ab3d-11f0-914f-88754c5b5a3f","name":"Superconducting spin qubits in planar Ge"},{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"name":"Realization and Manipulation of a Planar hybrid superconducting Andreev spin qubit in Germanium","_id":"8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3","grant_number":"101150858"}],"article_type":"original","doi":"10.1063/5.0333142","dataavailabilitystatement":"The data that support the findings of this study are openly available in Institute of Science and Technology repository at http://doi.org/10.15479/AT-ISTA-22242, Ref. 50.","arxiv":1,"scopus_import":"1","acknowledgement":"We sincerely thank Nick van Loo, Greg Mazur, Dhananjay Joshi, and Srijit Goswami for their inputs on low-temperature HfOx deposition; Matias Urdampilleta and Daniel Jirovec for discussions; and Kristen Léonard for the careful reading of the manuscript. This research was supported by the Scientific Service Units of ISTA through resources provided by the Miba Machine Shop and the Nanofabrication facility. The authors acknowledge support from the NOMIS Foundation; the European Innovation Council Pathfinder Grant No. 101115315 (QuKiT); the FWF Projects with DOI:10.55776/F86, DOI:10.55776/PAT7682124, and DOI:10.55776/P36507; and the HE-MSCA-PF project with DOI:10.3030/101150858. ICN2 is supported by the Severo Ochoa Program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Program/Generalitat de Catalunya. ICN2 acknowledges funding from Generalitat de Catalunya (No. 2021SGR00457). We acknowledge support from the CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+).","year":"2026","abstract":[{"text":"Planar germanium is currently the only semiconducting platform where high-coherence spin qubits and proximity-induced superconductivity have each been demonstrated. Recent research into spin qubits in Ge/SiGe heterostructures has focused on increasing the thickness of the SiGe capping layer, reporting improvements in the electrostatic noise levels. Meanwhile, heterostructures with thinner capping layers remain rather unexplored, despite the potential advantages for proximity-induced superconductivity. Here, we study a Ge/SiGe heterostructure with a thin SiGe cap d - 4nm and investigate its viability to host low-noise quantum dots. To keep the thermal budget compatible with superconducting layers, low-temperature oxide deposition processes were developed and implemented for the gate dielectrics. The charge noise level of the fabricated devices is estimated to be 1.8 +- 1.0 μeV/ square HZ, comparable to devices fabricated on shallow heterostructures ( d - 20nm) with high-temperature deposited oxides. Low charge noise levels, together with the straightforward integration of superconductors, make this heterostructure an attractive platform for prototyping hybrid semiconducting–superconducting devices.","lang":"eng"}],"citation":{"mla":"Borovkov, Maksim, et al. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices.” Applied Physics Letters, vol. 129, no. 3, 033505, AIP Publishing, 2026, doi:10.1063/5.0333142.","short":"M. Borovkov, Y.A. Schell, D. Sokolova, K.E.R. Roux, P. Falthansl-Scheinecker, G. Fabris, D.C. Shah, J. Saez Mollejo, R. Previdi, I. Taha, A. Genç, J. Arbiol, S. Calcaterra, A.D.C. Oliveira, D. Chrastina, G. Isella, A. Bubis, G. Katsaros, Applied Physics Letters 129 (2026).","chicago":"Borovkov, Maksim, Yona A Schell, Dina Sokolova, Kevin Etienne Robert Roux, Paul Falthansl-Scheinecker, Giorgio Fabris, Devashish C Shah, et al. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices.” Applied Physics Letters. AIP Publishing, 2026. https://doi.org/10.1063/5.0333142.","ama":"Borovkov M, Schell YA, Sokolova D, et al. Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices. Applied Physics Letters. 2026;129(3). doi:10.1063/5.0333142","ista":"Borovkov M, Schell YA, Sokolova D, Roux KER, Falthansl-Scheinecker P, Fabris G, Shah DC, Saez Mollejo J, Previdi R, Taha I, Genç A, Arbiol J, Calcaterra S, Oliveira ADC, Chrastina D, Isella G, Bubis A, Katsaros G. 2026. Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices. Applied Physics Letters. 129(3), 033505.","apa":"Borovkov, M., Schell, Y. A., Sokolova, D., Roux, K. E. R., Falthansl-Scheinecker, P., Fabris, G., … Katsaros, G. (2026). Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0333142","ieee":"M. Borovkov et al., “Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices,” Applied Physics Letters, vol. 129, no. 3. AIP Publishing, 2026."},"date_updated":"2026-08-03T11:08:39Z","author":[{"last_name":"Borovkov","id":"1fd0975f-8b61-11ed-b69e-d149334f28c5","first_name":"Maksim","full_name":"Borovkov, Maksim"},{"last_name":"Schell","id":"fe39122d-06bb-11ec-a33b-9e22b40e40a5","first_name":"Yona A","full_name":"Schell, Yona A"},{"first_name":"Dina","last_name":"Sokolova","id":"2d2d62f8-72f0-11ef-b75a-8ec3e8a60032","full_name":"Sokolova, Dina"},{"full_name":"Roux, Kevin Etienne Robert","last_name":"Roux","id":"53f93ea2-803f-11ed-ab7e-b283135794ef","first_name":"Kevin Etienne Robert"},{"full_name":"Falthansl-Scheinecker, Paul","last_name":"Falthansl-Scheinecker","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","first_name":"Paul"},{"full_name":"Fabris, Giorgio","first_name":"Giorgio","last_name":"Fabris","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352"},{"first_name":"Devashish C","last_name":"Shah","id":"de191434-4e7e-11ef-bf4b-9a056fc19fc3","orcid":"0009-0007-5829-7707","full_name":"Shah, Devashish C"},{"first_name":"Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime"},{"full_name":"Previdi, Rodolfo","first_name":"Rodolfo","id":"bc4ea1dc-00ce-11ec-8a4e-b325ca8b9876","last_name":"Previdi"},{"full_name":"Taha, Inas","first_name":"Inas","last_name":"Taha"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"full_name":"Oliveira, Afonso De Cerdeira","last_name":"Oliveira","first_name":"Afonso De Cerdeira"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Bubis, Anton","first_name":"Anton","id":"1f6212b5-f795-11ec-9c0c-de4780302890","last_name":"Bubis"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"}],"supplementarymaterial":"yes","language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"eissn":["1077-3118"],"issn":["0003-6951"]},"article_number":"033505","corr_author":"1","fulldoi":"https://doi.org/10.1063/5.0333142","researchdata_availability":"yes","oa_version":"Preprint","date_created":"2026-08-02T22:01:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-07-20T00:00:00Z","OA_type":"green","publication_status":"published","publisher":"AIP Publishing","day":"20","related_material":{"record":[{"id":"22242","status":"public","relation":"research_data"}]},"publication":"Applied Physics Letters","_id":"22619","OA_place":"repository","external_id":{"arxiv":["2602.21363"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"intvolume":" 129","status":"public","title":"Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices","type":"journal_article","das_tickbox":"1","month":"07","quality_controlled":"1"},{"status":"public","title":"Sums of three cubes over a function field","das_tickbox":"0","type":"journal_article","file_date_updated":"2026-08-03T12:12:03Z","quality_controlled":"1","month":"07","external_id":{"arxiv":["2402.07146"]},"has_accepted_license":"1","intvolume":" 14","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"22","publication":"Forum of Mathematics Sigma","_id":"22618","OA_place":"publisher","date_created":"2026-08-02T22:01:52Z","date_published":"2026-07-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","publication_status":"published","publisher":"Cambridge University Press","publication_identifier":{"eissn":["2050-5094"]},"article_number":"e112","file":[{"content_type":"application/pdf","file_id":"22636","file_name":"2026_ForumMathematics_Browning.pdf","access_level":"open_access","checksum":"e92a762e03f832bdca8c106a9a88ef9b","date_created":"2026-08-03T12:12:03Z","date_updated":"2026-08-03T12:12:03Z","creator":"dernst","file_size":810718,"relation":"main_file","success":1}],"ec_funded":1,"researchdata_availability":"no","fulldoi":"https://doi.org/10.1017/fms.2026.10259","oa_version":"Published Version","corr_author":"1","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glas","id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb","first_name":"Jakob","full_name":"Glas, Jakob"},{"first_name":"Victor","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","last_name":"Wang","full_name":"Wang, Victor","orcid":"0000-0002-0704-7026"}],"date_updated":"2026-08-03T12:13:59Z","supplementarymaterial":"no","language":[{"iso":"eng"}],"DOAJ_listed":"1","oa":1,"PlanS_conform":"1","ddc":["500"],"doi":"10.1017/fms.2026.10259","arxiv":1,"scopus_import":"1","acknowledgement":"While working on this paper the first two authors were supported by FWF grant (DOI 10.55776/P36278) and the third author was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413, and by the National Science and Technology Council Project Grant 114-2115-M-001-010-MY2.","abstract":[{"lang":"eng","text":"We use a function field version of the circle method to prove that a positive proportion of elements in 𝔽𝑞[𝑡] are representable as a sum of three cubes of minimal degree from 𝔽𝑞[𝑡], assuming a suitable form of the Ratios Conjecture and that char(𝔽𝑞) >3. The analogue of this conjecture for quadratic Dirichlet L-functions is known for large fixed q, via recent developments in homological stability."}],"year":"2026","citation":{"ieee":"T. D. Browning, J. Glas, and V. Wang, “Sums of three cubes over a function field,” Forum of Mathematics Sigma, vol. 14. Cambridge University Press, 2026.","apa":"Browning, T. D., Glas, J., & Wang, V. (2026). Sums of three cubes over a function field. Forum of Mathematics Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2026.10259","ama":"Browning TD, Glas J, Wang V. Sums of three cubes over a function field. Forum of Mathematics Sigma. 2026;14. doi:10.1017/fms.2026.10259","ista":"Browning TD, Glas J, Wang V. 2026. Sums of three cubes over a function field. Forum of Mathematics Sigma. 14, e112.","chicago":"Browning, Timothy D, Jakob Glas, and Victor Wang. “Sums of Three Cubes over a Function Field.” Forum of Mathematics Sigma. Cambridge University Press, 2026. https://doi.org/10.1017/fms.2026.10259.","short":"T.D. Browning, J. Glas, V. Wang, Forum of Mathematics Sigma 14 (2026).","mla":"Browning, Timothy D., et al. “Sums of Three Cubes over a Function Field.” Forum of Mathematics Sigma, vol. 14, e112, Cambridge University Press, 2026, doi:10.1017/fms.2026.10259."},"article_processing_charge":"Yes","department":[{"_id":"TiBr"},{"_id":"GradSch"}],"article_type":"original","volume":14,"project":[{"_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278","name":"Rational curves via function field analytic number theory"},{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}]},{"doi_confirm":"1","oa":1,"author":[{"id":"1fd0975f-8b61-11ed-b69e-d149334f28c5","last_name":"Borovkov","first_name":"Maksim","full_name":"Borovkov, Maksim"}],"date_updated":"2026-08-03T11:08:38Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-22242","corr_author":"1","oa_version":"Published Version","file":[{"file_name":"noise_paper_public_deposit.zip","file_id":"22243","content_type":"application/x-zip-compressed","access_level":"open_access","checksum":"2a1ea297e01a7a202a6b144d69a46eef","file_size":3082596099,"creator":"mborovko","date_created":"2026-07-04T17:28:49Z","date_updated":"2026-07-04T17:28:49Z","relation":"main_file","success":1}],"project":[{"name":"Quantum bits with Kitaev Transmons","grant_number":"101115315","_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"name":"Realization and Manipulation of a Planar hybrid superconducting Andreev spin qubit in Germanium","_id":"8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3","grant_number":"101150858"},{"name":"Superconducting spin qubits in planar Ge","_id":"5b9e579c-ab3d-11f0-914f-88754c5b5a3f","grant_number":"PAT 7682124"}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"article_processing_charge":"No","citation":{"mla":"Borovkov, Maksim. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22242.","short":"M. Borovkov, (2026).","chicago":"Borovkov, Maksim. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22242.","ista":"Borovkov M. 2026. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices, Institute of Science and Technology Austria, 10.15479/AT-ISTA-22242.","ama":"Borovkov M. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. 2026. doi:10.15479/AT-ISTA-22242","apa":"Borovkov, M. (2026). Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22242","ieee":"M. Borovkov, “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026."},"abstract":[{"lang":"eng","text":"This deposit contains the data and analysis code accompanying the publication \"Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices\" (Borovkov et al.). The deposit includes the raw transport and current-noise measurements of three gate-defined quantum-dot devices as QCodes SQLite databases, the master table of the charge-noise (flank-method) analysis with the pointers linking every analyzed PSD trace to the raw data, the toy-model noise simulation datasets behind the supplementary figures, the archived analysis figures (PSD fits and lever-arm extractions), and the Python code reproducing the full analysis and all figures. The code is also maintained at https://github.com/ISTA-Nanoelectronics/noise_paper_public; instructions are provided in the README files."}],"year":"2026","ddc":["530"],"doi":"10.15479/AT-ISTA-22242","contributor":[{"contributor_type":"contact_person","id":"1fd0975f-8b61-11ed-b69e-d149334f28c5","last_name":"Borovkov","first_name":"Maksim"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"has_accepted_license":"1","month":"07","title":"Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices","type":"research_data","file_date_updated":"2026-07-04T17:28:49Z","status":"public","publisher":"Institute of Science and Technology Austria","date_created":"2026-07-04T17:32:27Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_published":"2026-07-04T00:00:00Z","OA_place":"repository","_id":"22242","day":"04","related_material":{"record":[{"relation":"used_in_publication","id":"22619","status":"public"}],"link":[{"relation":"research_data","url":"https://github.com/ISTA-Nanoelectronics/noise_paper_public"}]}},{"publication_status":"published","publisher":"American Geophysical Union","date_created":"2026-07-27T12:30:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-04-28T00:00:00Z","OA_type":"gold","publication":"Geophysical Research Letters","_id":"22449","OA_place":"publisher","day":"28","intvolume":" 53","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","month":"04","quality_controlled":"1","status":"public","title":"Transpiration changes with soil warming: Insights from a mechanistic model","type":"journal_article","das_tickbox":"1","volume":53,"article_type":"letter_note","article_processing_charge":"No","main_file_link":[{"url":" https://doi.org/10.1029/2025GL120046","open_access":"1"}],"extern":"1","issue":"8","citation":{"ista":"Luo Z, Ren J, Zhuang Q, Fatichi S. 2026. Transpiration changes with soil warming: Insights from a mechanistic model. Geophysical Research Letters. 53(8), e2025GL120046.","ama":"Luo Z, Ren J, Zhuang Q, Fatichi S. Transpiration changes with soil warming: Insights from a mechanistic model. Geophysical Research Letters. 2026;53(8). doi:10.1029/2025gl120046","apa":"Luo, Z., Ren, J., Zhuang, Q., & Fatichi, S. (2026). Transpiration changes with soil warming: Insights from a mechanistic model. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2025gl120046","ieee":"Z. Luo, J. Ren, Q. Zhuang, and S. Fatichi, “Transpiration changes with soil warming: Insights from a mechanistic model,” Geophysical Research Letters, vol. 53, no. 8. American Geophysical Union, 2026.","mla":"Luo, Zhaoyang, et al. “Transpiration Changes with Soil Warming: Insights from a Mechanistic Model.” Geophysical Research Letters, vol. 53, no. 8, e2025GL120046, American Geophysical Union, 2026, doi:10.1029/2025gl120046.","short":"Z. Luo, J. Ren, Q. Zhuang, S. Fatichi, Geophysical Research Letters 53 (2026).","chicago":"Luo, Zhaoyang, Jianning Ren, Qi Zhuang, and Simone Fatichi. “Transpiration Changes with Soil Warming: Insights from a Mechanistic Model.” Geophysical Research Letters. American Geophysical Union, 2026. https://doi.org/10.1029/2025gl120046."},"ddc":["550"],"doi":"10.1029/2025gl120046","scopus_import":"1","abstract":[{"text":"Transpiration (T) connects water, energy, and carbon cycles within ecosystems. While T has often been reported to increase with soil warming, underlying reasons remain poorly understood. Here, using a mechanistic ecohydrological model, T&C‐BG, we simulated T responses to soil warming at 30 sites spanning various biomes and climates. Consistent with observations, the numerical model reproduces negative, insignificant, and predominantly positive T responses under soil warming. Numerical results show that soil warming generally increases T for sites with a small Bowen ratio. The main mechanisms leading to positive T responses to soil warming are complex changes in energy partitioning with modifications of canopy surface temperature and aerodynamic, stomatal, and leaf boundary layer conductance. However, soil warming can also affect phenology, which might result in either increased or decreased T. Our findings shed light on how T changes with warmer soil and help interpret outcomes of warming experiments.","lang":"eng"}],"year":"2026","oa":1,"author":[{"last_name":"Luo","first_name":"Zhaoyang","full_name":"Luo, Zhaoyang"},{"full_name":"Ren, Jianning","last_name":"Ren","first_name":"Jianning"},{"last_name":"Zhuang","first_name":"Qi","full_name":"Zhuang, Qi"},{"full_name":"Fatichi, Simone","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi"}],"date_updated":"2026-08-03T13:37:39Z","language":[{"iso":"eng"}],"DOAJ_listed":"1","oa_version":"Published Version","fulldoi":"https://doi.org/10.1029/2025gl120046","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"article_number":"e2025GL120046"},{"external_id":{"pmid":["41812348"]},"has_accepted_license":"1","intvolume":" 209","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","title":"Tree canopy configuration and Swiss adult mortality at the municipal level: A nationwide ecological study","type":"journal_article","das_tickbox":"1","quality_controlled":"1","month":"03","date_created":"2026-07-27T12:30:23Z","date_published":"2026-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","publication_status":"published","publisher":"Elsevier","day":"01","keyword":["Aggregation","Fragmentation","Green space exposure","Green space morphology","Green space structure","Landscape metrics","Shape complexity"],"publication":"Environment International","_id":"22480","OA_place":"publisher","author":[{"full_name":"Chi, Dengkai","last_name":"Chi","first_name":"Dengkai"},{"full_name":"Manoli, Gabriele","last_name":"Manoli","first_name":"Gabriele"},{"full_name":"Yang, Jun","last_name":"Yang","first_name":"Jun"},{"last_name":"Richards","first_name":"Daniel","full_name":"Richards, Daniel"},{"last_name":"Hahs","first_name":"Amy","full_name":"Hahs, Amy"},{"full_name":"Lin, Brenda","first_name":"Brenda","last_name":"Lin"},{"last_name":"McDonnell","first_name":"Mark J.","full_name":"McDonnell, Mark J."},{"full_name":"Zhang, Ye","last_name":"Zhang","first_name":"Ye"},{"full_name":"Zhu, Yue","first_name":"Yue","last_name":"Zhu"},{"full_name":"Qiu, Yeshan","first_name":"Yeshan","last_name":"Qiu"},{"last_name":"Wang","first_name":"Jing","full_name":"Wang, Jing"},{"first_name":"Xing","last_name":"Zheng","full_name":"Zheng, Xing"},{"last_name":"Burlando","first_name":"Paolo","full_name":"Burlando, Paolo"},{"full_name":"Fatichi, Simone","last_name":"Fatichi","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone"},{"full_name":"Tan, Puay Yok","last_name":"Tan","first_name":"Puay Yok"}],"date_updated":"2026-08-03T14:17:29Z","language":[{"iso":"eng"}],"DOAJ_listed":"1","oa":1,"pmid":1,"publication_identifier":{"issn":["0160-4120"],"eissn":["1873-6750"]},"article_number":"110188","oa_version":"Published Version","fulldoi":"https://doi.org/10.1016/j.envint.2026.110188","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1016/j.envint.2026.110188","open_access":"1"}],"extern":"1","article_type":"original","volume":209,"doi":"10.1016/j.envint.2026.110188","ddc":["550"],"scopus_import":"1","abstract":[{"lang":"eng","text":"Background:\r\nThe spatial distribution of tree canopies influences ecological functions and residents’ exposure to green spaces. Although several studies have examined green space configuration at neighborhood scales, evidence on tree canopy configuration at the municipal scale, an operational unit for urban planning, remains limited.\r\nMethods:\r\nWe conducted a nationwide ecological study of 2,136 Swiss municipalities. Tree canopy coverage (PLAND), aggregation (AI, reflecting how tightly green patches are grouped together), patch density (PD, a measure of fragmentation), and area-weighted mean shape index (SHAPE_AM, a measure of shape complexity) were derived from 1-m canopy maps within municipality-specific populated areas. Natural-cause, cardiovascular, and cancer mortality (2017–2019) were obtained from the Swiss National Cohort. Fully adjusted negative binomial regression models estimated associations between canopy metric and mortality for each IQR increase in the metrics.\r\nResults:\r\nHolding configuration constant, each IQR increase in canopy coverage (∼18%) was associated with a 3.6% [B: −0.036; 95% CI: −0.078 – 0.005] reduction in cardiovascular mortality. Higher aggregation corresponded to a 4.3% [B: 0.043; 95% CI: 0.026–0.061], an 8.9% [B: 0.089; 95% CI: 0.059–0.119], and a 2.1% [B: 0.021; 95% CI: 0–0.042] higher number of natural-cause, cardiovascular, and cancer deaths respectively. Higher fragmentation was associated with a 3.3% [B: 0.033; 95% CI: 0.016–0.050], a 4.9% [B: 0.049; 95% CI: 0.020–0.078], and a 2.2% [B: 0.022; 95% CI: 0.001–0.043] increase in these causes respectively. No meaningful associations were observed between shape complexity and any mortality outcomes. Associations for aggregation and fragmentation were generally stronger in highly urbanized municipalities.\r\nConclusions:\r\nAt the municipal scale, mortality was lower where tree canopy was distributed across several moderately sized, spatially balanced patches rather than highly aggregated or highly fragmented structures. These findings suggest that urban greening strategies should optimize its spatial configuration to maximize health benefits."}],"year":"2026","citation":{"chicago":"Chi, Dengkai, Gabriele Manoli, Jun Yang, Daniel Richards, Amy Hahs, Brenda Lin, Mark J. McDonnell, et al. “Tree Canopy Configuration and Swiss Adult Mortality at the Municipal Level: A Nationwide Ecological Study.” Environment International. Elsevier, 2026. https://doi.org/10.1016/j.envint.2026.110188.","short":"D. Chi, G. Manoli, J. Yang, D. Richards, A. Hahs, B. Lin, M.J. McDonnell, Y. Zhang, Y. Zhu, Y. Qiu, J. Wang, X. Zheng, P. Burlando, S. Fatichi, P.Y. Tan, Environment International 209 (2026).","mla":"Chi, Dengkai, et al. “Tree Canopy Configuration and Swiss Adult Mortality at the Municipal Level: A Nationwide Ecological Study.” Environment International, vol. 209, 110188, Elsevier, 2026, doi:10.1016/j.envint.2026.110188.","ieee":"D. Chi et al., “Tree canopy configuration and Swiss adult mortality at the municipal level: A nationwide ecological study,” Environment International, vol. 209. Elsevier, 2026.","apa":"Chi, D., Manoli, G., Yang, J., Richards, D., Hahs, A., Lin, B., … Tan, P. Y. (2026). Tree canopy configuration and Swiss adult mortality at the municipal level: A nationwide ecological study. Environment International. Elsevier. https://doi.org/10.1016/j.envint.2026.110188","ista":"Chi D, Manoli G, Yang J, Richards D, Hahs A, Lin B, McDonnell MJ, Zhang Y, Zhu Y, Qiu Y, Wang J, Zheng X, Burlando P, Fatichi S, Tan PY. 2026. Tree canopy configuration and Swiss adult mortality at the municipal level: A nationwide ecological study. Environment International. 209, 110188.","ama":"Chi D, Manoli G, Yang J, et al. Tree canopy configuration and Swiss adult mortality at the municipal level: A nationwide ecological study. Environment International. 2026;209. doi:10.1016/j.envint.2026.110188"}},{"date_created":"2026-08-04T06:29:31Z","date_published":"2026-07-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","publication_status":"published","publisher":"American Chemical Society","page":"31245-31252","day":"15","publication":"Journal of the AmericanChemical Society","_id":"22645","OA_place":"publisher","has_accepted_license":"1","external_id":{"pmid":["42532904"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"intvolume":" 148","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","title":"Reaction medium asan architect of nanocrystal superlattices","file_date_updated":"2026-08-04T06:40:17Z","type":"journal_article","das_tickbox":"0","quality_controlled":"1","month":"07","article_processing_charge":"Yes (via OA deal)","issue":"29","department":[{"_id":"MaIb"},{"_id":"LifeSc"},{"_id":"GradSch"},{"_id":"CaGo"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"article_type":"original","volume":148,"ddc":["540"],"doi":"10.1021/jacs.6c07859","scopus_import":"1","year":"2026","abstract":[{"lang":"eng","text":"Nanocrystal superlattices are commonly formed by changing concentration, solvent conditions, or particle surface chemistry. Although effective, these approaches alter multiple contributions to the interparticle potential simultaneously, making it difficult to isolate the interactions responsible for ordering or to control assembly in chemically complex environments. Here, we show that oligomeric species present in a nanocrystal reaction medium drive superlattice formation through a depletion mechanism. Using PbTe nanocrystals as a model system, we identify Pb–oleate oligomers in the crude reaction mixture, characterize their solution structure, and quantify their contribution to the interparticle potential, establishing depletion as the dominant short-range interaction governing spontaneous body-centered cubic superlattice formation. We then confirm the depletion origin of ordering by showing that varying depletant concentration predictably shifts the order–disorder boundary and produces a thermally reversible transition between dispersed and ordered states ─ behavior that is inconsistent with van der Waals or ligand-mediated mechanisms but is a direct consequence of depletion control. Having established and validated the mechanism, we demonstrate that the same depletion framework can be deliberately activated in purified dispersions and transferred across nanocrystal systems of different composition and shape, including anisotropic and binary assemblies. These results establish precursor-derived depletion as a general and chemically grounded mechanism for nanocrystal superlattice formation, and show that collective ordering can be programmed through the surrounding medium rather than through particle surface modification."}],"acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility, and the Lab Support Facility (LSF). M.E. acknowledges financial support from Deutsche Forschungsgemeinschaft through Collaborative Research Centre 1411. We thank Dr. Tommaso Constanzo and Tobias Kleinhanns for assistance with high-quality electron microscope image acquisition, Dr. Jeonghyun Park for providing NCs, Dr. Mariano Calcabrini for assistance with the NMR study, and Prof. Jonathan De Roo for fruitful discussions. This work benefited from the use of the SasView application, originally developed under NSF award DMR-0520547. SasView contains code developed with funding from the European Union’s Horizon 2020 research and innovation program under the SINE2020 project, grant agreement No. 654000.","citation":{"chicago":"Lee, Seungho, Daniel Balazs, Aiswarya Rayaroth Puthiyaveettil, Sharona Horta, Carl Peter Goodrich, Michael Engel, Ihor Cherniukh, and Maria Ibáñez. “Reaction Medium Asan Architect of Nanocrystal Superlattices.” Journal of the AmericanChemical Society. American Chemical Society, 2026. https://doi.org/10.1021/jacs.6c07859.","mla":"Lee, Seungho, et al. “Reaction Medium Asan Architect of Nanocrystal Superlattices.” Journal of the AmericanChemical Society, vol. 148, no. 29, American Chemical Society, 2026, pp. 31245–52, doi:10.1021/jacs.6c07859.","short":"S. Lee, D. Balazs, A. Rayaroth Puthiyaveettil, S. Horta, C.P. Goodrich, M. Engel, I. Cherniukh, M. Ibáñez, Journal of the AmericanChemical Society 148 (2026) 31245–31252.","ieee":"S. Lee et al., “Reaction medium asan architect of nanocrystal superlattices,” Journal of the AmericanChemical Society, vol. 148, no. 29. American Chemical Society, pp. 31245–31252, 2026.","ista":"Lee S, Balazs D, Rayaroth Puthiyaveettil A, Horta S, Goodrich CP, Engel M, Cherniukh I, Ibáñez M. 2026. Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. 148(29), 31245–31252.","ama":"Lee S, Balazs D, Rayaroth Puthiyaveettil A, et al. Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. 2026;148(29):31245-31252. doi:10.1021/jacs.6c07859","apa":"Lee, S., Balazs, D., Rayaroth Puthiyaveettil, A., Horta, S., Goodrich, C. P., Engel, M., … Ibáñez, M. (2026). Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. American Chemical Society. https://doi.org/10.1021/jacs.6c07859"},"date_updated":"2026-08-04T06:47:13Z","author":[{"first_name":"Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs"},{"full_name":"Rayaroth Puthiyaveettil, Aiswarya","first_name":"Aiswarya","last_name":"Rayaroth Puthiyaveettil","id":"8aceb01b-8972-11ed-ae7b-d5fe53775add"},{"full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"full_name":"Engel, Michael","first_name":"Michael","last_name":"Engel"},{"id":"d03b62b2-5976-11ef-a8d7-9525504b7895","last_name":"Cherniukh","first_name":"Ihor","full_name":"Cherniukh, Ihor"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"supplementarymaterial":"yes","language":[{"iso":"eng"}],"PlanS_conform":"1","oa":1,"pmid":1,"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"file":[{"content_type":"application/pdf","file_id":"22646","file_name":"2026_JACS_Lee.pdf","date_created":"2026-08-04T06:40:17Z","file_size":6564594,"creator":"dernst","access_level":"open_access","checksum":"063314ae5ac4225ebd4436aa8707d113","date_updated":"2026-08-04T06:40:17Z","relation":"main_file","success":1}],"researchdata_availability":"no","fulldoi":"https://doi.org/10.1021/jacs.6c07859","corr_author":"1","oa_version":"Published Version"},{"intvolume":" 114","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2512.14528"]},"has_accepted_license":"1","quality_controlled":"1","month":"08","status":"public","title":"Continuous accumulation of cold atoms in an optical cavity","type":"journal_article","file_date_updated":"2026-08-04T06:03:14Z","das_tickbox":"1","publication_status":"published","publisher":"American Physical Society","date_created":"2026-08-04T05:58:23Z","date_published":"2026-08-03T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","publication":"Physical Review A","_id":"22642","OA_place":"publisher","day":"03","PlanS_conform":"1","oa":1,"author":[{"full_name":"Gheorghita, Edward-Fulbright","id":"e664a051-133f-11ed-8f02-a05999ad0822","last_name":"Gheorghita","first_name":"Edward-Fulbright"},{"last_name":"Wald","id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","full_name":"Wald, Sebastian","orcid":"0000-0002-5869-1604"},{"full_name":"Pupić, Andrea","first_name":"Andrea","last_name":"Pupić","id":"ef9c50a4-5335-11ef-8b9b-8ce03e6380ed"},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-08-04T06:07:20Z","supplementarymaterial":"yes","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1103/71f2-sq4p","oa_version":"Published Version","corr_author":"1","researchdata_availability":"upon request","article_number":"023302","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"file":[{"content_type":"application/pdf","file_name":"2026_PhysicalReviewA_Gheorghita.pdf","file_id":"22643","date_created":"2026-08-04T06:03:14Z","file_size":959463,"checksum":"fdecc394b734b56e1b3b151a816bbe14","creator":"dernst","date_updated":"2026-08-04T06:03:14Z","access_level":"open_access","relation":"main_file","success":1}],"department":[{"_id":"OnHo"},{"_id":"GradSch"}],"volume":114,"project":[{"_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","issue":"2","citation":{"ieee":"E.-F. Gheorghita, S. Wald, A. Pupić, and O. Hosten, “Continuous accumulation of cold atoms in an optical cavity,” Physical Review A, vol. 114, no. 2. American Physical Society, 2026.","apa":"Gheorghita, E.-F., Wald, S., Pupić, A., & Hosten, O. (2026). Continuous accumulation of cold atoms in an optical cavity. Physical Review A. American Physical Society. https://doi.org/10.1103/71f2-sq4p","ista":"Gheorghita E-F, Wald S, Pupić A, Hosten O. 2026. Continuous accumulation of cold atoms in an optical cavity. Physical Review A. 114(2), 023302.","ama":"Gheorghita E-F, Wald S, Pupić A, Hosten O. Continuous accumulation of cold atoms in an optical cavity. Physical Review A. 2026;114(2). doi:10.1103/71f2-sq4p","chicago":"Gheorghita, Edward-Fulbright, Sebastian Wald, Andrea Pupić, and Onur Hosten. “Continuous Accumulation of Cold Atoms in an Optical Cavity.” Physical Review A. American Physical Society, 2026. https://doi.org/10.1103/71f2-sq4p.","short":"E.-F. Gheorghita, S. Wald, A. Pupić, O. Hosten, Physical Review A 114 (2026).","mla":"Gheorghita, Edward-Fulbright, et al. “Continuous Accumulation of Cold Atoms in an Optical Cavity.” Physical Review A, vol. 114, no. 2, 023302, American Physical Society, 2026, doi:10.1103/71f2-sq4p."},"doi":"10.1103/71f2-sq4p","ddc":["530"],"dataavailabilitystatement":"There are no publicly available research data or software\r\nsupporting this manuscript. Requests for further information\r\nor data should be sent to the authors.","scopus_import":"1","arxiv":1,"year":"2026","acknowledgement":"The authors thank Vyacheslav Li for his earlier contributions to the development of the setup utilized in this work.\r\nThis work was supported by the Institute of Science and Technology Austria (ISTA); E.G. was supported by the European Research Council under Grant No. 101087907 (ERC CoG\r\nQuHAMP).","abstract":[{"lang":"eng","text":"Continuously operating atom-light interfaces represent a key prerequisite for steady-state quantum sensors and efficient quantum processors. Here, we demonstrate continuous accumulation of sub-Doppler-cooled atoms in a shallow intracavity dipole trap, realizing this regime. The key ingredient is a light-shift manipulation that creates spatially varying cooling parameters, enabling efficient capture and accumulation of atoms within a cavity mode. Demonstrated with rubidium atoms, a continuous flux from a source cell is funneled through the magneto-optical trap into the cavity mode, where the atoms are cooled and maintained below 10µK in steady state without time-sequenced operation. We characterize the resulting continuously maintained ensemble of millions of atoms and its collective coupling to the cavity field, establishing a route toward continuously operated cavity-QED systems and long-duration atomic and hybrid quantum sensors."}]},{"external_id":{"pmid":["42477503"]},"title":"The role of clathrin in post‐Golgi secretion in plant cells","type":"journal_article","das_tickbox":"1","status":"public","quality_controlled":"1","month":"07","OA_type":"hybrid","date_created":"2026-08-04T06:48:41Z","date_published":"2026-07-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"epub_ahead","publisher":"Wiley","day":"20","OA_place":"publisher","publication":"New Phytologist","_id":"22647","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"full_name":"Gackowski, Adam","first_name":"Adam","last_name":"Gackowski"},{"first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana"},{"first_name":"Saqer S.","last_name":"Alotaibi","full_name":"Alotaibi, Saqer S."},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"date_updated":"2026-08-04T07:58:27Z","supplementarymaterial":"yes","pmid":1,"oa":1,"article_number":"nph.71454","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"fulldoi":"https://doi.org/10.1111/nph.71454","corr_author":"1","oa_version":"Published Version","researchdata_availability":"yes","article_processing_charge":"Yes (via OA deal)","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.71454"}],"article_type":"original","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"GradSch"}],"scopus_import":"1","acknowledgement":"The authors wish to acknowledge Dr. Paweł Baster for cloning PIN1-GFP-2/pDONR221, Ms. Aline Monzer and Dr. Mingyue Li for help with CHC protein level evaluation, Dr. Michał Rychłowski for help with confocal microscopy, Prof. Ari Pekka Mähönen for sharing the p1R4-pUBQ10:XVE plasmid, and Prof. Ying Gu for sharing seeds of the sec5 mutant. M.A. would like to thank Dr. Xixi Zhang and Prof. Sebastian Bednarek for inspiring discussions. This work was supported by the Taif University Researchers Supporting Project, TURSP-HC2022/02 to JF and SA and Austrian Science Fund (FWF): I 3630-B25 to JF. Open Access funding provided by Institute of Science and Technology Austria.","year":"2026","abstract":[{"lang":"eng","text":"Within the plant endomembrane system, the vesicle coat protein clathrin localizes to the plasma membrane (PM) and the trans-Golgi Network/early endosome (TGN/EE). While the role of clathrin in endocytosis at the PM is well established, its function at TGN/EE, presumably in late secretion (trafficking from the TGN/EE to the cell surface) or en route to the vacuole, is debated. Similarly debated are potential homeostatic mechanisms balancing the trafficking routes, especially endocytosis and late secretion.\r\nWe address these questions in Arabidopsis thaliana using conditional silencing of CLATHRIN HEAVY CHAIN (CHC), conditional overexpression of the clathrin uncoating factor AUXILIN-LIKE1, and secretory mutants.\r\nCHC silencing interferes with trafficking of cargoes destined for the apoplast and the PM, supporting a function of clathrin in late secretion. The secretory cargoes become abnormally rerouted from the TGN/EE to the vacuole. Unlike CHC silencing, overexpression of AUXILIN-LIKE1 selectively inhibits clathrin-mediated endocytosis while secretion continues normally at early points of induction. Conversely, secretory mutants exhibit a reduced PM recruitment of clathrin, and variably, of the TPLATE endocytic component.\r\nTogether, our data show a role of clathrin in secretion and suggest secretion as a fundamental trafficking process to which endocytosis is adjusted by a weak homeostatic mechanism."}],"dataavailabilitystatement":"Original data associated with this study have been deposited in Dataset S1. The accession nos. of A. thaliana genes used in this study are as follows: CHC1 (AT3G11130), CHC2 (AT3G08530), CLC2 (AT2G40060), TPLATE (AT3G01780), AP2A1 (AT5G22770), DRP1C (AT1G14830), GNOM-LIKE1 (AT5G39500), BEN3/BIG2 (AT3G60860), TMK4 (AT3G23750), PIN1 (AT1G73590), AUXILIN-LIKE1 (AT4G12780), AP1M2 (AT1G60780), ECHIDNA (AT1G09330), SEC5A (AT1G76850), SEC5B (AT1G21170), TUB2 (AT5G62690), and PP2AA3 (AT1G13320).","doi":"10.1111/nph.71454","citation":{"chicago":"Adamowski, Maciek, Adam Gackowski, Ivana Matijevic, Saqer S. Alotaibi, and Jiří Friml. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71454.","short":"M. Adamowski, A. Gackowski, I. Matijevic, S.S. Alotaibi, J. Friml, New Phytologist (2026).","mla":"Adamowski, Maciek, et al. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist, nph. 71454, Wiley, 2026, doi:10.1111/nph.71454.","ieee":"M. Adamowski, A. Gackowski, I. Matijevic, S. S. Alotaibi, and J. Friml, “The role of clathrin in post‐Golgi secretion in plant cells,” New Phytologist. Wiley, 2026.","apa":"Adamowski, M., Gackowski, A., Matijevic, I., Alotaibi, S. S., & Friml, J. (2026). The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. Wiley. https://doi.org/10.1111/nph.71454","ama":"Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. 2026. doi:10.1111/nph.71454","ista":"Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. 2026. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist., nph. 71454."}},{"supplementarymaterial":"no","author":[{"id":"ea10a57b-23f6-11ef-9085-80d8596d52ef","last_name":"Desio","first_name":"Davide","orcid":"0000-0001-9840-3809","full_name":"Desio, Davide"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"date_updated":"2026-08-04T05:57:21Z","language":[{"iso":"eng"}],"oa":1,"PlanS_conform":"1","article_number":"87","publication_identifier":{"issn":["1573-0530"]},"file":[{"content_type":"application/pdf","file_id":"22641","file_name":"2026_LettersMathPhysics_Desio.pdf","date_created":"2026-08-04T05:55:58Z","date_updated":"2026-08-04T05:55:58Z","access_level":"open_access","checksum":"1b90ff7da16b9604d6fe2c6281493456","creator":"dernst","file_size":371840,"relation":"main_file","success":1}],"fulldoi":"https://doi.org/10.1007/s11005-026-02107-2","oa_version":"Published Version","corr_author":"1","researchdata_availability":"no","article_processing_charge":"Yes (via OA deal)","issue":"4","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"volume":116,"article_type":"original","doi":"10.1007/s11005-026-02107-2","ddc":["510"],"abstract":[{"lang":"eng","text":"We present an abstract Dyson expansion for perturbations that are merely relatively form-bounded, and apply it to the polaron problem. For a large class of polaron-type models, including the Fröhlich and Nelson models, we prove that the vacuum expectation value of the heat semi-group is a completely monotone function of the square of the total momentum. Consequently, the ground-state energy is a concave function of the square of the momentum, a result recently proved for the Fröhlich model in [14] using a probabilistic approach via Wiener integrals."}],"year":"2026","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","scopus_import":"1","arxiv":1,"citation":{"chicago":"Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded Perturbations and Applications to the Polaron Problem.” Letters in Mathematical Physics. Springer Nature, 2026. https://doi.org/10.1007/s11005-026-02107-2.","short":"D. Desio, R. Seiringer, Letters in Mathematical Physics 116 (2026).","mla":"Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded Perturbations and Applications to the Polaron Problem.” Letters in Mathematical Physics, vol. 116, no. 4, 87, Springer Nature, 2026, doi:10.1007/s11005-026-02107-2.","ieee":"D. Desio and R. Seiringer, “Dyson expansion for form-bounded perturbations and applications to the polaron problem,” Letters in Mathematical Physics, vol. 116, no. 4. Springer Nature, 2026.","apa":"Desio, D., & Seiringer, R. (2026). Dyson expansion for form-bounded perturbations and applications to the polaron problem. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-026-02107-2","ama":"Desio D, Seiringer R. Dyson expansion for form-bounded perturbations and applications to the polaron problem. Letters in Mathematical Physics. 2026;116(4). doi:10.1007/s11005-026-02107-2","ista":"Desio D, Seiringer R. 2026. Dyson expansion for form-bounded perturbations and applications to the polaron problem. Letters in Mathematical Physics. 116(4), 87."},"has_accepted_license":"1","external_id":{"arxiv":["2512.13443"]},"intvolume":" 116","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","das_tickbox":"0","file_date_updated":"2026-08-04T05:55:58Z","type":"journal_article","title":"Dyson expansion for form-bounded perturbations and applications to the polaron problem","quality_controlled":"1","month":"07","date_published":"2026-07-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-08-03T13:21:14Z","OA_type":"hybrid","publisher":"Springer Nature","publication_status":"published","day":"17","_id":"22639","publication":"Letters in Mathematical Physics","OA_place":"publisher"},{"pmid":1,"author":[{"first_name":"Alons","last_name":"Lends","full_name":"Lends, Alons"},{"last_name":"Lamon","first_name":"Gaelle","full_name":"Lamon, Gaelle"},{"last_name":"Vallet","first_name":"Alicia","full_name":"Vallet, Alicia"},{"first_name":"Axelle","last_name":"Grélard","full_name":"Grélard, Axelle"},{"last_name":"Morvan","first_name":"Estelle","full_name":"Morvan, Estelle"},{"first_name":"Vishukumar","last_name":"Aimanianda","full_name":"Aimanianda, Vishukumar"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"},{"first_name":"Antoine","last_name":"Loquet","full_name":"Loquet, Antoine"}],"date_updated":"2026-08-04T05:52:13Z","supplementarymaterial":"yes","language":[{"iso":"eng"}],"researchdata_availability":"no","fulldoi":"https://doi.org/10.1021/jacs.6c06064","oa_version":"None","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"department":[{"_id":"PaSc"}],"article_type":"original","volume":148,"article_processing_charge":"No","issue":"27","citation":{"short":"A. Lends, G. Lamon, A. Vallet, A. Grélard, E. Morvan, V. Aimanianda, P. Schanda, A. Loquet, Journal of the American Chemical Society 148 (2026) 28037–28042.","mla":"Lends, Alons, et al. “On-Cell Detection of Polysaccharide One-Bond1Jch Couplings by Proton-Detected Solid-State NMR.” Journal of the American Chemical Society, vol. 148, no. 27, American Chemical Society, 2026, pp. 28037–42, doi:10.1021/jacs.6c06064.","chicago":"Lends, Alons, Gaelle Lamon, Alicia Vallet, Axelle Grélard, Estelle Morvan, Vishukumar Aimanianda, Paul Schanda, and Antoine Loquet. “On-Cell Detection of Polysaccharide One-Bond1Jch Couplings by Proton-Detected Solid-State NMR.” Journal of the American Chemical Society. American Chemical Society, 2026. https://doi.org/10.1021/jacs.6c06064.","apa":"Lends, A., Lamon, G., Vallet, A., Grélard, A., Morvan, E., Aimanianda, V., … Loquet, A. (2026). On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.6c06064","ama":"Lends A, Lamon G, Vallet A, et al. On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR. Journal of the American Chemical Society. 2026;148(27):28037-28042. doi:10.1021/jacs.6c06064","ista":"Lends A, Lamon G, Vallet A, Grélard A, Morvan E, Aimanianda V, Schanda P, Loquet A. 2026. On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR. Journal of the American Chemical Society. 148(27), 28037–28042.","ieee":"A. Lends et al., “On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR,” Journal of the American Chemical Society, vol. 148, no. 27. American Chemical Society, pp. 28037–28042, 2026."},"doi":"10.1021/jacs.6c06064","scopus_import":"1","year":"2026","acknowledgement":"We thank the ANR (ANR-16-CE11-0020-02 to A. Loquet and V.A. and ANR-21-CE17-0032 to V.A.) as well as the Swiss National Science Foundation for early postdoc mobility project P2EZP2_184258 to A. Lends. This work has benefited from the Biophysical and Structural Chemistry Platform at Institut Européen de Chimie et Biologie IECB, Centre National de la Recherche Scientifique CNRS Unité d’Appui et de Recherche UAR 3033, INSERM US001, and the CNRS (IR-RMN FR3050 and Infranalytics FR2054).","abstract":[{"lang":"eng","text":"The one-bond proton-carbon coupling constant (1JCH) is an insightful probe of carbohydrate configuration. Equatorial and axial protons at the C1 position typically exhibit distinct 1JCH values, enabling NMR measurements to distinguish α- and β-configurations in carbohydrates. In principle, such measurements could provide insights into carbohydrates in the cell walls of intact microbes. However, traditionally, these measurements are performed by solution NMR with carbohydrates that were extracted, solubilized and fractionated, leaving the biological relevance of the measurements uncertain. Here, we demonstrate that 1H-detected solid-state NMR with fast magic-angle spinning allows quantitative measurements of 1JCH couplings for mobile capsular polysaccharides, directly on submilligram amounts of pathogenic cells. Our approach is demonstrated on intact cells of the pathogenic yeast Cryptococcus neoformans. High-resolution proton-detected spectra enabled the determination of coupling constants for five mobile polysaccharide units of the cryptococcal capsule, revealing their native configurations and confirming previous solution NMR-based anomeric configuration assignments."}],"intvolume":" 148","external_id":{"pmid":["42377973"]},"month":"06","quality_controlled":"1","status":"public","title":"On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR","das_tickbox":"0","type":"journal_article","publication_status":"published","publisher":"American Chemical Society","date_created":"2026-08-03T13:20:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-06-15T00:00:00Z","OA_type":"closed access","publication":"Journal of the American Chemical Society","_id":"22638","page":"28037-28042","day":"15"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2506.18065"]},"has_accepted_license":"1","month":"07","quality_controlled":"1","status":"public","das_tickbox":"0","type":"journal_article","title":"Liouville function, von Mangoldt function, and norm forms at random binary forms","publisher":"Cambridge University Press","publication_status":"epub_ahead","mathsc":["11N32","11N37","11D57","11G35"],"date_published":"2026-07-21T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-08-04T06:15:04Z","OA_type":"hybrid","_id":"22644","publication":"Glasgow Mathematical Journal","OA_place":"publisher","day":"21","page":"1-34","PlanS_conform":"1","oa":1,"supplementarymaterial":"no","author":[{"orcid":"0000-0002-4989-5330","full_name":"Diao, Yijie","last_name":"Diao","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","first_name":"Yijie"}],"date_updated":"2026-08-04T06:28:01Z","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1017/s0017089526101074","researchdata_availability":"no","corr_author":"1","oa_version":"Published Version","publication_identifier":{"eissn":["1469-509X"],"issn":["0017-0895"]},"department":[{"_id":"TiBr"},{"_id":"GradSch"}],"article_type":"original","main_file_link":[{"url":"https://doi.org/10.1017/S0017089526101074","open_access":"1"}],"article_processing_charge":"Yes (via OA deal)","citation":{"ieee":"Y. Diao, “Liouville function, von Mangoldt function, and norm forms at random binary forms,” Glasgow Mathematical Journal. Cambridge University Press, pp. 1–34, 2026.","apa":"Diao, Y. (2026). Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal. Cambridge University Press. https://doi.org/10.1017/s0017089526101074","ista":"Diao Y. 2026. Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal., 1–34.","ama":"Diao Y. Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal. 2026:1-34. doi:10.1017/s0017089526101074","chicago":"Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms at Random Binary Forms.” Glasgow Mathematical Journal. Cambridge University Press, 2026. https://doi.org/10.1017/s0017089526101074.","short":"Y. Diao, Glasgow Mathematical Journal (2026) 1–34.","mla":"Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms at Random Binary Forms.” Glasgow Mathematical Journal, Cambridge University Press, 2026, pp. 1–34, doi:10.1017/s0017089526101074."},"ddc":["500"],"doi":"10.1017/s0017089526101074","acknowledgement":"I am deeply grateful to my advisor Tim Browning for suggesting this problem and for the many valuable discussions that shaped this work. I would also like to thank Efthymios Sofos, Matteo Verzobio, and Shuntaro Yamagishi for discussions and insights that contributed to this paper. I am also very grateful to the anonymous referee for their careful reading and for the considerable effort they put into improving the manuscript.","year":"2026","abstract":[{"lang":"eng","text":"We analyze the average behavior of various arithmetic functions at the values of degree 𝑑 binary forms ordered by height, with probability 1. This approach yields averaged versions of the Chowla conjecture and the Bateman–Horn conjecture for random binary forms. Furthermore, we show that the rational Hasse principle holds for almost all Châtelet varieties defined by a fixed norm form of degree 𝑒 and by varying binary forms of fixed degree 𝑑, provided 𝑒 divides 𝑑. This proves an average version of a conjecture of Colliot-Thélène."}],"arxiv":1,"scopus_import":"1"},{"month":"07","quality_controlled":"1","title":"Physics-inspired procedural texturing of extremely deformable surfaces","file_date_updated":"2026-05-29T13:19:37Z","type":"journal_article","das_tickbox":"0","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 45","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","OA_place":"publisher","publication":"ACM Transactions on Graphics","_id":"21923","day":"01","related_material":{"link":[{"url":"https://ista.ac.at/en/news/infinite-deformation-and-shape-computation/","relation":"press_release","description":"News on ISTA website"}]},"keyword":["Procedural animation"],"publication_status":"published","publisher":"Association for Computing Machinery","OA_type":"gold","date_created":"2026-05-29T13:25:16Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2026-07-01T00:00:00Z","corr_author":"1","fulldoi":"https://doi.org/10.1145/3811353","oa_version":"Published Version","researchdata_availability":"no","file":[{"relation":"main_file","success":1,"content_type":"video/mp4","file_name":"tog454-article154-supplemental.mp4","file_id":"21924","creator":"akalinov","access_level":"open_access","checksum":"ea165bf731ddd3045f83878dcb833672","file_size":77337231,"date_updated":"2026-05-29T13:19:33Z","date_created":"2026-05-29T13:19:33Z"},{"file_size":226633977,"date_created":"2026-05-29T13:19:37Z","access_level":"open_access","creator":"akalinov","checksum":"6274cfb15ea5ba7324b74afc7b0d9629","date_updated":"2026-05-29T13:19:37Z","file_name":"tog454-article154-video.mp4","file_id":"21925","content_type":"video/mp4","success":1,"relation":"main_file"},{"success":1,"relation":"main_file","creator":"akalinov","access_level":"open_access","checksum":"9d41b322a7876be9a3311017b9973183","date_updated":"2026-05-29T13:19:33Z","date_created":"2026-05-29T13:19:33Z","file_size":6793867,"content_type":"application/pdf","file_id":"21926","file_name":"tog454-article154-supplemental.pdf"},{"success":1,"relation":"main_file","date_created":"2026-05-29T13:19:36Z","checksum":"51bc60d2de867fbfa570652dec7993b4","file_size":84173392,"creator":"akalinov","access_level":"open_access","date_updated":"2026-05-29T13:19:36Z","file_name":"tog454-article154-main-1.pdf","file_id":"21927","content_type":"application/pdf"}],"article_number":"154","publication_identifier":{"issn":["0730-0301"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2026-07-23","start_date":"2026-07-19","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","location":"Los Angeles, CA, United States"},"date_updated":"2026-08-04T09:07:44Z","author":[{"first_name":"Aleksei","last_name":"Kalinov","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","orcid":"0000-0003-2189-3904","full_name":"Kalinov, Aleksei"},{"first_name":"Mickaël","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","full_name":"Ly, Mickaël"},{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","first_name":"Christian","full_name":"Hafner, Christian"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"supplementarymaterial":"yes","citation":{"apa":"Kalinov, A., Ly, M., Hafner, C., & Wojtan, C. (2026). Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3811353","ista":"Kalinov A, Ly M, Hafner C, Wojtan C. 2026. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 45(4), 154.","ama":"Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 2026;45(4). doi:10.1145/3811353","ieee":"A. Kalinov, M. Ly, C. Hafner, and C. Wojtan, “Physics-inspired procedural texturing of extremely deformable surfaces,” ACM Transactions on Graphics, vol. 45, no. 4. Association for Computing Machinery, 2026.","short":"A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45 (2026).","mla":"Kalinov, Aleksei, et al. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on Graphics, vol. 45, no. 4, 154, Association for Computing Machinery, 2026, doi:10.1145/3811353.","chicago":"Kalinov, Aleksei, Mickaël Ly, Christian Hafner, and Chris Wojtan. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2026. https://doi.org/10.1145/3811353."},"scopus_import":"1","acknowledgement":"We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback. We also thank Jonathan Gagnon for their help with running the Lapped Textures codes and SideFX for the Houdini Education software licenses.\r\nImages in Fig. 2 by Kisoulou and Vultured on Unsplash, Michal Jarmoluk and Public Domain Pictures from Pixabay and Hawai‘i Volcanoes NPS on flickr. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","year":"2026","abstract":[{"text":"The appearance of simulated natural phenomena heavily depends on the way surfaces are textured. However, applying texture maps to dynamic deformable surfaces presents a significant challenge, due to ever-shifting differences in length scales involved. When these surfaces move and advect the texture along with them, their final appearance degrades as deformed regions dramatically distort their texture map. Modifications to the texture directly at the pixel level in response to the deformation may introduce ghosting artifacts and look unnatural. In the real world, the appearance of surface details on a deforming material changes through the interplay of physical processes such as rupturing, exposure of internal structure, or wrinkling. Motivated by these behaviors, in this work we explore how physical principles can guide the texturing methods based on the measure of surface deformation.\r\nWe present two novel wave-based procedural texturing algorithms which reproduce common physical properties like advection and self-similarity, enabling the plausible animation of deforming objects with extreme texture map distortions. Our algorithms are fully procedural, require no actual physics simulation, and store no state or history of deformation besides the input UV map, making them highly parallelizable on the GPU and efficient enough for real-time applications. We show the versatility of the method by animating physical phenomena with extreme deformations such as flowing lava, stretching putty and outpouring sludge.","lang":"eng"}],"ddc":["006"],"doi":"10.1145/3811353","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"article_type":"original","volume":45,"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"issue":"4","article_processing_charge":"Yes"},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","_id":"22363","OA_place":"publisher","day":"14","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/the-art-of-proper-flickering/"}]},"publication_status":"published","publisher":"National Academy of Sciences","date_created":"2026-07-19T22:01:46Z","date_published":"2026-07-14T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_type":"hybrid","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"07","status":"public","title":"Invariant nonequilibrium dynamics in gene regulation optimize information flow","type":"journal_article","file_date_updated":"2026-07-20T13:12:47Z","das_tickbox":"1","intvolume":" 123","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"external_id":{"pmid":["42406962"]},"has_accepted_license":"1","citation":{"ieee":"B. Zoller, A. Benichou, T. Gregor, and G. Tkačik, “Invariant nonequilibrium dynamics in gene regulation optimize information flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 123, no. 28. National Academy of Sciences, 2026.","apa":"Zoller, B., Benichou, A., Gregor, T., & Tkačik, G. (2026). Invariant nonequilibrium dynamics in gene regulation optimize information flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2524855123","ama":"Zoller B, Benichou A, Gregor T, Tkačik G. Invariant nonequilibrium dynamics in gene regulation optimize information flow. Proceedings of the National Academy of Sciences of the United States of America. 2026;123(28). doi:10.1073/pnas.2524855123","ista":"Zoller B, Benichou A, Gregor T, Tkačik G. 2026. Invariant nonequilibrium dynamics in gene regulation optimize information flow. Proceedings of the National Academy of Sciences of the United States of America. 123(28), e2524855123.","chicago":"Zoller, Benjamin, Alexis Benichou, Thomas Gregor, and Gašper Tkačik. “Invariant Nonequilibrium Dynamics in Gene Regulation Optimize Information Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2026. https://doi.org/10.1073/pnas.2524855123.","short":"B. Zoller, A. Benichou, T. Gregor, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 123 (2026).","mla":"Zoller, Benjamin, et al. “Invariant Nonequilibrium Dynamics in Gene Regulation Optimize Information Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 123, no. 28, e2524855123, National Academy of Sciences, 2026, doi:10.1073/pnas.2524855123."},"ddc":["570"],"doi":"10.1073/pnas.2524855123","dataavailabilitystatement":"Software code data have been deposited in Institute Pasteur GitHub (https://gitlab.pasteur.fr/tglab/invariantpromoterdynamicspaper) (51).","scopus_import":"1","year":"2026","abstract":[{"text":"Eukaryotic gene regulation relies on stochastic yet controlled promoter switching, in which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies have revealed a surprising invariance of the “switching correlation time” (TC)—the characteristic decay time of the autocorrelation function of promoter activity fluctuations—across gene expression levels in multiple genes and organisms. A biophysically plausible explanation for this invariance has so far been lacking. Here, we show that this empirical constraint imposes stringent requirements on minimal yet realistic models of transcriptional regulation. Specifically, reproducing TC–invariance requires regulatory architectures with at least four internal states and nonequilibrium dynamics that break detailed balance. Using Bayesian inference on Drosophila gap gene expression data, we demonstrate that such models i) quantitatively reproduce the observed TC–invariance, ii) remain robust to parameter perturbations, and iii) maximize information transmission from transcription factor concentration to gene expression. Remarkably, the TC-invariant modulation strategy we identify as optimal closely parallels contemporary control-theoretic results on the modulation of stochastic switching systems. Taken together, our results suggest that eukaryotic transcriptional regulation operates in a nonequilibrium regime to balance precision, reaction-rate limitations, and energy dissipation, thereby achieving near-optimal information transmission under fundamental physical constraints.","lang":"eng"}],"acknowledgement":"This work was supported by the French NationalResearch Agency (ANR-20-CE12-0028 “ChroDynE” and ANR-23-CE13-0021“GastruCyp” and ANR-10 LABX-73 “Revive;” all T.G.), and by funding from theEuropean Research Council (ERC-2023-SyG, “Dynatrans,” 101118866, T.G. andG.T.). This work was also supported in part by the U.S. NSF, through the Centerfor the Physics of Biological Function (PHY-1734030, T.G.), and by NIH GrantsR01GM097275, U01DA047730, and U01DK127429 (T.G.)","department":[{"_id":"GaTk"}],"article_type":"original","volume":123,"project":[{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"article_processing_charge":"Yes","issue":"28","oa_version":"Published Version","fulldoi":"https://doi.org/10.1073/pnas.2524855123","corr_author":"1","researchdata_availability":"yes","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_number":"e2524855123","file":[{"date_created":"2026-07-20T13:12:47Z","file_size":24580098,"creator":"dernst","access_level":"open_access","checksum":"f4d82dd706ff1629db68d71190288350","date_updated":"2026-07-20T13:12:47Z","file_name":"2026_PNAS_Zoller.pdf","file_id":"22376","content_type":"application/pdf","success":1,"relation":"main_file"}],"oa":1,"pmid":1,"date_updated":"2026-08-04T09:21:10Z","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Benichou, Alexis","first_name":"Alexis","last_name":"Benichou","id":"3a67230c-5fc0-11ef-a673-de9a2ffadafe"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"supplementarymaterial":"yes","language":[{"iso":"eng"}]},{"title":"Roots navigate around decay regions by sensing local pH gradients","das_tickbox":"1","type":"journal_article","status":"public","quality_controlled":"1","month":"07","external_id":{"pmid":["42424472"]},"intvolume":" 393","day":"09","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/roots-steer-clear-of-plant-rot/"}]},"publication":"Science","_id":"22315","OA_type":"closed access","date_created":"2026-07-13T14:57:10Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2026-07-09T00:00:00Z","publication_status":"published","publisher":"American Association for the Advancement of Science","article_number":"eadw6568","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"fulldoi":"https://doi.org/10.1126/science.adw6568","researchdata_availability":"yes","oa_version":"None","language":[{"iso":"eng"}],"date_updated":"2026-08-04T09:22:49Z","author":[{"full_name":"Bao, Zhulatai","first_name":"Zhulatai","last_name":"Bao"},{"full_name":"Wang, Huihui","last_name":"Wang","first_name":"Huihui"},{"full_name":"Zhang, Ai","first_name":"Ai","last_name":"Zhang"},{"last_name":"Gao","first_name":"Ruxi","full_name":"Gao, Ruxi"},{"last_name":"Gu","first_name":"Wen","full_name":"Gu, Wen"},{"last_name":"Fan","first_name":"Ni","full_name":"Fan, Ni"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"last_name":"Zhang","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"}],"supplementarymaterial":"yes","pmid":1,"scopus_import":"1","acknowledgement":"We are grateful to H. Guo and L. Liu (Department of Biology, Southern University of Science and Technology) for providing the rgf1/2/3, rgi1/2/3/4, tpst-1, and pepr1/2 lines. We thank K.-h. Liu (College of Life Science, Northwest A&F University) for generously providing the ABA biosensor nlsABACUS2-400n. We also thank J. Li and J. Chang (School of Life Sciences, Lanzhou University) for providing the ahk2-5/cre1-2, ahp1/2/3, arr16/arr17, and pTCSn::GFP lines. Our thanks further extend to D. Qian, also from the School of Life Sciences at Lanzhou University, for sharing Arabidopsis line pTUB6::mCherry-TUB6. We are grateful to Y. Zhao (CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) for providing nced3/5, snrk2.2/2.3/2.6, and pyl duodecuple mutants. We also acknowledge the Teaching and Research Core Facility at the College of Life Sciences, Northwest A&F University, particularly N. Fan, for their invaluable technical assistance. We also thank Life Science Research Core Services (LSRCS), Northwest A&F University, for helping with characterization, including CLSM (X. Liu). Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China JYB2025XDXM706 (Y.Z.); Qin Chuangyuan High-level Innovation and Entrepreneurship Talent Program QCYRCXM-2022-237 (Y.Z.); Fundamental Research Funds for the Central Universities K20200168 (Y.Z.); National Natural Science Foundation of China 32570375 (Y.Z.); National Natural Science Foundation of China 32400699 (A.Z.); European Research Council (ERC, CYNIPS) 101142681 (J.F.); Austrian Science Fund (FWF): P 37051-B (J.F.).","year":"2026","abstract":[{"lang":"eng","text":"Plant tropisms enable roots to navigate complex soils by responding to directional environmental cues. Biological decay, although central to nutrient cycling, also creates microbially active and potentially hostile niches. In this work, we identified “saprotropism,” a previously unrecognized growth response that enables roots to actively bend away from decaying plant-derived matter. Fungal-driven microbial decomposition released organic acids and formed stable pH gradients in surrounding soil, allowing roots to pinpoint decay without direct contact. Root epidermal cells sensed this acidic gradient through the root meristem growth factor peptide-receptor module, converting external pH asymmetry into asymmetric abscisic acid (ABA) distribution. ABA asymmetry drove microtubule reorganization, which was decoded into decay-avoidant root bending. Together, these findings establish microbial decay–derived chemical gradients as an instructive signal for root navigation and expand the framework of microbe-soil-plant communication."}],"doi":"10.1126/science.adw6568","dataavailabilitystatement":"All data are available in the manuscript or the supplementary materials. The raw RNA-seq data have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE315473. Microbiome sequencing data have been deposited in the Sequence Read Archive (SRA) under BioProject number PRJNA1397137. Materials are available upon request from the corresponding author.","citation":{"mla":"Bao, Zhulatai, et al. “Roots Navigate around Decay Regions by Sensing Local PH Gradients.” Science, vol. 393, no. 6807, eadw6568, American Association for the Advancement of Science, 2026, doi:10.1126/science.adw6568.","short":"Z. Bao, H. Wang, A. Zhang, R. Gao, W. Gu, N. Fan, J. Friml, Y. Zhang, Science 393 (2026).","chicago":"Bao, Zhulatai, Huihui Wang, Ai Zhang, Ruxi Gao, Wen Gu, Ni Fan, Jiří Friml, and Yuzhou Zhang. “Roots Navigate around Decay Regions by Sensing Local PH Gradients.” Science. American Association for the Advancement of Science, 2026. https://doi.org/10.1126/science.adw6568.","ama":"Bao Z, Wang H, Zhang A, et al. Roots navigate around decay regions by sensing local pH gradients. Science. 2026;393(6807). doi:10.1126/science.adw6568","ista":"Bao Z, Wang H, Zhang A, Gao R, Gu W, Fan N, Friml J, Zhang Y. 2026. Roots navigate around decay regions by sensing local pH gradients. Science. 393(6807), eadw6568.","apa":"Bao, Z., Wang, H., Zhang, A., Gao, R., Gu, W., Fan, N., … Zhang, Y. (2026). Roots navigate around decay regions by sensing local pH gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adw6568","ieee":"Z. Bao et al., “Roots navigate around decay regions by sensing local pH gradients,” Science, vol. 393, no. 6807. American Association for the Advancement of Science, 2026."},"issue":"6807","article_processing_charge":"No","article_type":"original","volume":393,"project":[{"grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"department":[{"_id":"JiFr"}]},{"day":"17","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/patterns-in-genetic-chaos/"}]},"OA_place":"publisher","publication":"Nature","_id":"22295","OA_type":"hybrid","date_created":"2026-07-13T09:47:21Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2026-06-17T00:00:00Z","publication_status":"epub_ahead","publisher":"Springer Nature","title":"Cortical development dynamics across autism spectrum disorder mouse models","type":"journal_article","status":"public","quality_controlled":"1","month":"06","has_accepted_license":"1","external_id":{"pmid":["42310454"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Despite the functional diversity of over 100 causal genes1,2,3, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD."}],"year":"2026","acknowledgement":"We thank F. Freeman, V. Voronin and M. Ladron de Guevara for technical assistance; A. Stichelberger and S. Liegenfeld for the management of our animal colony; M. Schunn, C. Gold and the Preclinical Facility team for technical assistance; C. Jansen and the Scientific Computing Facility for bioinformatics support and technical assistance; the Biomedical Sequencing Facility at CeMM for assistance with next-generation sequencing; and J. Lin and T. Krausgruber in the laboratory of C. Bock for support with flow cytometry; J. Kirchner for illustrating the multi-omics approach depicted in Fig. 1; and all members of the laboratory of G.N. for their support and discussions. This study was supported by the Scientific Service Units of ISTA through resources provided by the Imaging & Optics Facility and the Laboratory Support Facility. Bulk RNA-seq was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities, member of the Vienna BioCenter. This work was supported by a European Research Council Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the Austrian Science Fund (PE1028W1232 and PR1028FG1803) to G.N. Open access funding provided by Institute of Science and Technology (IST Austria).","ddc":["570"],"dataavailabilitystatement":"Single-nucleus multiomics data are available from the Gene Expression Omnibus (GSE328363). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). Single-cell data can be accessed and visualized through a CELLxGENE database (https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/.2026_Nature_Schwarz). Source data are provided with this paper. Scripts and analyses that support the main findings of this study are accessible in a GitHub repository (https://git.ista.ac.at/research-sofware/mouseome).","doi":"10.1038/s41586-026-10679-1","citation":{"ama":"Schwarz LA, Dotter C, Isaev S, et al. Cortical development dynamics across autism spectrum disorder mouse models. Nature. 2026. doi:10.1038/s41586-026-10679-1","ista":"Schwarz LA, Dotter C, Isaev S, Lisi M, Malzl D, Büschl C, Ladstätter S, Oliveira B, Barel M, Basilico B, Chintaluri C, Gorkiewicz S, Goudarzi M, Belinova T, Reichl S, Sendžikaitė G, Arcot Jayaram S, Koppensteiner P, Sommer CM, Vogels TP, Menche J, Adameyko I, Kharchenko PV, Bock C, Novarino G. 2026. Cortical development dynamics across autism spectrum disorder mouse models. Nature.","apa":"Schwarz, L. A., Dotter, C., Isaev, S., Lisi, M., Malzl, D., Büschl, C., … Novarino, G. (2026). Cortical development dynamics across autism spectrum disorder mouse models. Nature. Springer Nature. https://doi.org/10.1038/s41586-026-10679-1","ieee":"L. A. Schwarz et al., “Cortical development dynamics across autism spectrum disorder mouse models,” Nature. Springer Nature, 2026.","mla":"Schwarz, Lena A., et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” Nature, Springer Nature, 2026, doi:10.1038/s41586-026-10679-1.","short":"L.A. Schwarz, C. Dotter, S. Isaev, M. Lisi, D. Malzl, C. Büschl, S. Ladstätter, B. Oliveira, M. Barel, B. Basilico, C. Chintaluri, S. Gorkiewicz, M. Goudarzi, T. Belinova, S. Reichl, G. Sendžikaitė, S. Arcot Jayaram, P. Koppensteiner, C.M. Sommer, T.P. Vogels, J. Menche, I. Adameyko, P.V. Kharchenko, C. Bock, G. Novarino, Nature (2026).","chicago":"Schwarz, Lena A, Christoph Dotter, Sergey Isaev, Michela Lisi, Daniel Malzl, Christoph Büschl, Sabrina Ladstätter, et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” Nature. Springer Nature, 2026. https://doi.org/10.1038/s41586-026-10679-1."},"article_processing_charge":"Yes (via OA deal)","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-026-10679-1"}],"article_type":"original","project":[{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865"},{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"FG1803 49015","_id":"ebb38b5d-77a9-11ec-83b8-a42e08120a88","name":"Neurobiology of anxiety in autism spectrum disorders"}],"department":[{"_id":"AnKi"},{"_id":"GaNo"},{"_id":"TiVo"},{"_id":"ScienComp"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"fulldoi":"https://doi.org/10.1038/s41586-026-10679-1","researchdata_availability":"yes","corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"author":[{"full_name":"Schwarz, Lena A","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz"},{"first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph"},{"last_name":"Isaev","first_name":"Sergey","full_name":"Isaev, Sergey"},{"full_name":"Lisi, Michela","first_name":"Michela","id":"39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c","last_name":"Lisi"},{"first_name":"Daniel","last_name":"Malzl","full_name":"Malzl, Daniel"},{"full_name":"Büschl, Christoph","id":"2a8c054c-0913-11ee-9159-f8ef515809ed","last_name":"Büschl","first_name":"Christoph"},{"first_name":"Sabrina","last_name":"Ladstätter","full_name":"Ladstätter, Sabrina"},{"full_name":"Oliveira, Bárbara","first_name":"Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira"},{"full_name":"Barel, Matteo","first_name":"Matteo","last_name":"Barel","id":"8959927b-2236-11ed-bd6e-ea83d94ade0e"},{"full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette"},{"orcid":"0000-0003-4252-1608","full_name":"Chintaluri, Chaitanya","first_name":"Chaitanya","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","last_name":"Chintaluri"},{"full_name":"Gorkiewicz, Sarah","first_name":"Sarah","last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","first_name":"Mohammad","full_name":"Goudarzi, Mohammad"},{"first_name":"Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","last_name":"Belinova","full_name":"Belinova, Tereza"},{"first_name":"Stephan","last_name":"Reichl","full_name":"Reichl, Stephan"},{"first_name":"Gintarė","last_name":"Sendžikaitė","id":"dd6d52f2-c50d-11eb-9548-bcf0ff82b344","full_name":"Sendžikaitė, Gintarė"},{"orcid":"0000-0002-2479-2669","full_name":"Arcot Jayaram, Satish","first_name":"Satish","last_name":"Arcot Jayaram","id":"b0bbee33-09f7-11eb-909c-8b358058d28a"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"},{"last_name":"Kharchenko","id":"0095641e-7eb7-11f1-8665-aec51a2ab5e0","first_name":"Peter Vasili","full_name":"Kharchenko, Peter Vasili"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"date_updated":"2026-08-04T09:29:55Z","supplementarymaterial":"yes","pmid":1,"oa":1,"PlanS_conform":"1"},{"publication_status":"epub_ahead","publisher":"Springer Nature","date_created":"2026-07-12T22:02:19Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2026-06-29T00:00:00Z","OA_type":"hybrid","publication":"Nature Biotechnology","_id":"22268","OA_place":"publisher","day":"29","related_material":{"link":[{"url":"https://ista.ac.at/en/news/toward-experiment-guided-alphafold/","relation":"press_release","description":"News on ISTA website"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["42374114"]},"has_accepted_license":"1","quality_controlled":"1","month":"06","status":"public","title":"Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles","das_tickbox":"1","type":"journal_article","department":[{"_id":"PaSc"},{"_id":"AlBr"},{"_id":"GradSch"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","main_file_link":[{"url":"https://doi.org/10.1038/s41587-026-03166-5","open_access":"1"}],"citation":{"mla":"Maddipatla, Sai A., et al. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” Nature Biotechnology, Springer Nature, 2026, doi:10.1038/s41587-026-03166-5.","short":"S.A. Maddipatla, N.E. Sellam, M.I. Bojan, V. Masalitin, S. Vedula, P. Schanda, A. Marx, A.M. Bronstein, Nature Biotechnology (2026).","chicago":"Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Vova Masalitin, Sanketh Vedula, Paul Schanda, Ailie Marx, and Alex M. Bronstein. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” Nature Biotechnology. Springer Nature, 2026. https://doi.org/10.1038/s41587-026-03166-5.","ama":"Maddipatla SA, Sellam NE, Bojan MI, et al. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology. 2026. doi:10.1038/s41587-026-03166-5","ista":"Maddipatla SA, Sellam NE, Bojan MI, Masalitin V, Vedula S, Schanda P, Marx A, Bronstein AM. 2026. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology.","apa":"Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Masalitin, V., Vedula, S., Schanda, P., … Bronstein, A. M. (2026). Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-026-03166-5","ieee":"S. A. Maddipatla et al., “Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles,” Nature Biotechnology. Springer Nature, 2026."},"ddc":["570"],"doi":"10.1038/s41587-026-03166-5","dataavailabilitystatement":"All structures and metrics reported in this paper are openly available on Harvard Dataverse - https://doi.org/10.7910/DVN/PLYUHN. All code is openly available on GitHub (https://github.com/sai-advaith/guided_alphafold); the version used for this paper (version 0.9.1) is permanently archived on Zenodo https://doi.org/10.5281/zenodo.17307005","scopus_import":"1","year":"2026","acknowledgement":"A. Marx acknowledges the financial support of the Helmsley Fellowships Program for Sustainability and Health. A.M.B. and P.S. are supported by the Institute of Science and Technology Austria Internal Project Call grant Generative Protein NMR. S.V. was supported in part by funding from the Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard. Open access funding provided by Institute of Science and Technology (IST Austria).","abstract":[{"text":"AlphaFold3 predicts highly accurate protein structures from sequence but tends to collapse to a single dominant conformation, even when the underlying structure is inherently heterogeneous. Moreover, its predictions are oblivious to experimental conditions that can alter local sequence conformation. In this work, we show that AlphaFold3 can be guided to match data obtained by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and cryogenic electron microscopy (cryo-EM) experiments and combinations thereof. Our approach can also incorporate data that explicitly report on dynamics, such as site-resolved order parameters. We demonstrate that this methodology generates compact structural ensembles whose ensemble-averaged observables agree with experiment, with fewer distance restraint violations than traditionally resolved NMR structures and with unmodeled alternate conformations uncovered in electron density. This methodology paves the way for experimentally aware predictive models that generate structural ensembles consistent with the measurements, potentially over multiple modalities, and that can be further refined toward thermodynamically grounded ensembles by incorporating energetics.","lang":"eng"}],"oa":1,"PlanS_conform":"1","pmid":1,"date_updated":"2026-08-04T09:25:18Z","author":[{"full_name":"Maddipatla, Sai A","first_name":"Sai A","last_name":"Maddipatla","id":"e957f5e5-91c9-11f0-a95f-e090f66ecb4d"},{"id":"ef280fe0-91c9-11f0-a95f-8dea3f5bc513","last_name":"Sellam","first_name":"Nadav E","full_name":"Sellam, Nadav E"},{"full_name":"Bojan, Meital I","first_name":"Meital I","id":"11d88cf5-91ca-11f0-a95f-edf9f08f47b7","last_name":"Bojan"},{"full_name":"Masalitin, Vova","id":"ff7958eb-91c9-11f0-a95f-f3bf65828cf6","last_name":"Masalitin","first_name":"Vova"},{"full_name":"Vedula, Sanketh","last_name":"Vedula","first_name":"Sanketh"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"},{"first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"}],"supplementarymaterial":"yes","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41587-026-03166-5","oa_version":"Published Version","corr_author":"1","researchdata_availability":"yes","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]}},{"author":[{"orcid":"0000-0002-5636-9259","full_name":"Krätschmer, Ilse","first_name":"Ilse","last_name":"Krätschmer","id":"30d4014e-7753-11eb-b44b-db6d61112e73"},{"full_name":"Hegemann, Laura","first_name":"Laura","last_name":"Hegemann"},{"first_name":"Robin J.","last_name":"Hofmeister","full_name":"Hofmeister, Robin J."},{"last_name":"Corfield","first_name":"Elizabeth C.","full_name":"Corfield, Elizabeth C."},{"full_name":"Mahmoudi, Mahdi","last_name":"Mahmoudi","first_name":"Mahdi"},{"full_name":"Delaneau, Olivier","last_name":"Delaneau","first_name":"Olivier"},{"first_name":"Ole A.","last_name":"Andreassen","full_name":"Andreassen, Ole A."},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Hayward","first_name":"Caroline","full_name":"Hayward, Caroline"},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."},{"last_name":"Ystrom","first_name":"Eivind","full_name":"Ystrom, Eivind"},{"last_name":"Havdahl","first_name":"Alexandra","full_name":"Havdahl, Alexandra"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"}],"date_updated":"2026-08-04T09:34:08Z","supplementarymaterial":"yes","language":[{"iso":"eng"}],"DOAJ_listed":"1","oa":1,"pmid":1,"publication_identifier":{"eissn":["2666-979X"]},"article_number":"101277","file":[{"relation":"main_file","success":1,"file_name":"2026_CellGenomics_Kraetschmer.pdf","file_id":"22597","content_type":"application/pdf","access_level":"open_access","date_created":"2026-07-28T07:24:50Z","file_size":3679297,"creator":"dernst","checksum":"f896b510480d2d4e4a7fd46c2e2761f4","date_updated":"2026-07-28T07:24:50Z"}],"corr_author":"1","fulldoi":"https://doi.org/10.1016/j.xgen.2026.101277","oa_version":"Published Version","researchdata_availability":"yes","article_processing_charge":"Yes","issue":"7","department":[{"_id":"MaRo"}],"article_type":"original","volume":6,"project":[{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"}],"ddc":["570"],"doi":"10.1016/j.xgen.2026.101277","dataavailabilitystatement":"Information on how to access the MoBaPsychGen post-imputation QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this project. For access to be granted to the Estonian Biobank genotypic and corresponding phenotypic data, a preliminary application must be presented to the oversight committee, who must first approve the project. Ethics permission must then be obtained from the Estonian Committee on Bioethics and Human Research. Finally, a full project must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation Scotland data is available with appropriate permission from the Generation Scotland Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe code for JODIE developed in this work is open source and is publicly available on zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729) are available by application to a Data Access Committee (DAC) of the Wellcome Trust Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org.","scopus_import":"1","acknowledgement":"We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father, and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. We thank the Norwegian Institute of Public Health (NIPH) for generating high-quality genomic data. The research is part of the HARVEST collaboration, supported by the Research Council of Norway (#229624). We also thank the NORMENT Center for providing genotype data, funded by the Research Council of Norway (#223273), South East Norway Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration with deCODE Genetics. We further thank the Center for Diabetes Research, the University of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED, Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for Sensitive Data) facilities, owned by the University of Oslo, operated and developed by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no). E.Y. is supported by the European Union (grant numbers 101045526 and 101073237) and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe would like to acknowledge the participants and investigators of the Generation Scotland Cohort study. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank and acknowledge the participants and investigators of the Estonian Biobank (EstBB) study. The research was conducted using the Estonian Center of Genomics/Roadmap II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses were performed on resources provided by Sigma2 - the National Infrastructure for High-Performance Computing and Data Storage in Norway. Estonian Data analysis was carried out in the High-Performance Computing Center cloud provided by University of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained from the other analyses was conducted at IST Austria and is supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","year":"2026","abstract":[{"text":"We introduce JODIE, a genetic joint modeling approach that estimates how DNA loci influence human traits by partitioning genetic effects into four components: direct effects (from a child’s alleles), indirect maternal and paternal effects (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental transmission of alleles), while uniquely accounting for assortative mating. We analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood educational test scores. We find direct effects to be the largest contributor to trait variation, but combined, indirect parental and PofO effects are similarly substantial. We support our results by within-family genome-wide association testing and identify 276 independently associated DNA regions with a complex interplay between direct, indirect, and PofO effects. By joint modeling, we show that direct, indirect, and PofO effects collectively shape human phenotypic variation across loci genome-wide.","lang":"eng"}],"citation":{"ieee":"I. Krätschmer et al., “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” Cell Genomics, vol. 6, no. 7. Elsevier, 2026.","ama":"Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 2026;6(7). doi:10.1016/j.xgen.2026.101277","ista":"Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 6(7), 101277.","apa":"Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. Elsevier. https://doi.org/10.1016/j.xgen.2026.101277","chicago":"Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” Cell Genomics. Elsevier, 2026. https://doi.org/10.1016/j.xgen.2026.101277.","mla":"Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” Cell Genomics, vol. 6, no. 7, 101277, Elsevier, 2026, doi:10.1016/j.xgen.2026.101277.","short":"I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi, O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom, A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026)."},"external_id":{"pmid":["40909755"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 6","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","title":"Separating direct, indirect, and parent-of-origin genetic effects in the human population","das_tickbox":"1","file_date_updated":"2026-07-28T07:24:50Z","type":"journal_article","quality_controlled":"1","month":"07","date_created":"2026-06-10T07:39:08Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2026-07-08T00:00:00Z","OA_type":"gold","publication_status":"published","publisher":"Elsevier","day":"08","keyword":["direct genetic effects","DGE","indirect genetic effects","IGE","parent-of-origin effects","phenotypic variation","assortative mating","within-family GWAS","MoBa","EstBB"],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/","relation":"press_release","description":"News on ISTA website"}]},"publication":"Cell Genomics","_id":"21987","OA_place":"publisher"},{"oa":1,"doi_confirm":"1","date_updated":"2026-08-04T09:32:45Z","author":[{"orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22334","oa_version":"Published Version","corr_author":"1","publication_identifier":{"isbn":["978-3-99078-084-8"],"issn":["2663-337X"]},"file":[{"relation":"source_file","date_updated":"2026-07-16T09:17:08Z","access_level":"closed","checksum":"8b85114eff543916c0e1445cd2189555","creator":"lbecker","date_created":"2026-07-16T09:17:08Z","file_size":99472908,"file_name":"2026_Becker_Lea_source_files.zip","file_id":"22346","content_type":"application/zip"},{"success":1,"relation":"main_file","access_level":"open_access","date_updated":"2026-07-16T09:17:05Z","checksum":"6c526862bc6dbd1e4c80ecb34580bc58","creator":"lbecker","file_size":74647289,"date_created":"2026-07-16T09:17:05Z","content_type":"application/pdf","file_name":"2026_Becker_Lea_Thesis.pdf","file_id":"22347"}],"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"project":[{"name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"citation":{"short":"L.M. Becker, Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR, Institute of Science and Technology Austria, 2026.","mla":"Becker, Lea Marie. Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22334.","chicago":"Becker, Lea Marie. “Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22334.","apa":"Becker, L. M. (2026). Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22334","ama":"Becker LM. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. 2026. doi:10.15479/AT-ISTA-22334","ista":"Becker LM. 2026. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria.","ieee":"L. M. Becker, “Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR,” Institute of Science and Technology Austria, 2026."},"doi":"10.15479/AT-ISTA-22334","ddc":["572"],"year":"2026","abstract":[{"lang":"eng","text":"Characterizing protein dynamics at the atomic level is essential for our understanding of biological mechanisms. Whether it is to facilitate metabolite transport, catalyze reactions, transmit signals, or regulate metabolism – proteins are constantly in motion and sample multiple conformational states to fulfill their function. Nuclear magnetic resonance (NMR) spectroscopy is particularly well suited to elucidate the dynamics of biomolecules on their complex free-energy landscape. In particular, solid-state magic-angle spinning (MAS) NMR enables the study of large molecular assemblies, protein crystals, or insoluble proteins at atomic resolution without an inherent molecular size limitation. MAS NMR experiments to probe protein dynamics are extremely versatile and sensitive to motional timescales from picoseconds to seconds. Over the past decades, technological advances, developments in experimental design, and new isotope-labeling approaches have further expanded the possibilities of this technique and significantly improved the accuracy of the determined motional parameters.\r\nFunctionally important sites of proteins often contain aromatic residues. Their side-chain motions have therefore long served as valuable indicators of mechanistically relevant dynamics in NMR studies. In this thesis, site-specifically labeled aromatic residues act as sensitive reporters for MAS NMR studies of protein dynamics. The first part addresses how different environments impact side-chain motion by probing ring flips of phenylalanines and tyrosines in crystalline proteins and amyloid fibrils. It provides important insights for the analysis of dynamics obtained in non-native protein environments and emphasizes the complex factors that determine the timescale of internal dynamics. In the second part, the focus shifts towards methodological questions regarding the investigation of protein dynamics by 19F MAS NMR. The fluorine nucleus exhibits promising characteristics for NMR studies but also presents significant challenges, which is why the full methodological potential of 19F MAS NMR has not been fully realized yet. This work demonstrates that paramagnetic doping can considerably reduce the measurement time and improve the sensitivity of fluorinated samples. Finally, 19F MAS NMR is evaluated as a tool for studying protein side-chain dynamics on the example of tryptophans. The results illustrate the challenges in analyzing such experiments and lay the foundation for further development of 19F MAS NMR relaxation studies.\r\nTaken together, this thesis highlights the potential of combining specific isotope labeling, MAS NMR, and complementary methods such as crystallography and computational simulations to elucidate internal protein dynamics. The further development of such integrative approaches will be crucial to improving our understanding of complex mechanisms and protein function.\r\n"}],"acknowledgement":"During the work on this thesis, I was the recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01).","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"NMR"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"has_accepted_license":"1","month":"07","status":"public","file_date_updated":"2026-07-16T09:17:08Z","das_tickbox":"1","type":"dissertation","title":"Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"}],"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2026-07-13T00:00:00Z","date_created":"2026-07-14T08:08:51Z","degree_awarded":"PhD","_id":"22334","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"12675","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"21777","status":"public"},{"status":"public","id":"12114","relation":"part_of_dissertation"},{"id":"22105","status":"public","relation":"part_of_dissertation"}]},"day":"13","page":"205"},{"pmid":1,"PlanS_conform":"1","oa":1,"language":[{"iso":"eng"}],"supplementarymaterial":"yes","author":[{"full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","first_name":"Lea Marie"},{"full_name":"Fu, Haohao","last_name":"Fu","first_name":"Haohao"},{"id":"71cda2f3-e604-11ee-a1df-da10587eda3f","last_name":"Tatman","first_name":"Benjamin","full_name":"Tatman, Benjamin"},{"full_name":"Dreydoppel, Matthias","first_name":"Matthias","last_name":"Dreydoppel"},{"id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","last_name":"Kapitonova","first_name":"Anna","full_name":"Kapitonova, Anna"},{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"full_name":"Weininger, Ulrich","last_name":"Weininger","first_name":"Ulrich"},{"full_name":"Engilberge, Sylvain","first_name":"Sylvain","last_name":"Engilberge"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"date_updated":"2026-08-04T09:32:45Z","oa_version":"Published Version","fulldoi":"https://doi.org/10.1038/s41557-026-02155-0","corr_author":"1","researchdata_availability":"yes","file":[{"success":1,"relation":"main_file","file_size":2618184,"date_created":"2026-07-28T06:58:35Z","creator":"dernst","date_updated":"2026-07-28T06:58:35Z","access_level":"open_access","checksum":"1069fb27949fd2cb641b043b3a96a580","content_type":"application/pdf","file_name":"2026_NatureChemistry_Becker.pdf","file_id":"22595"}],"publication_identifier":{"issn":["17554330"],"eissn":["17554349"]},"project":[{"name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0"}],"article_type":"original","volume":18,"department":[{"_id":"PaSc"},{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","citation":{"ieee":"L. M. Becker et al., “Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes,” Nature Chemistry, vol. 18. Springer Nature, pp. 1221–1230, 2026.","apa":"Becker, L. M., Fu, H., Tatman, B., Dreydoppel, M., Kapitonova, A., Balazs, D., … Schanda, P. (2026). Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-026-02155-0","ista":"Becker LM, Fu H, Tatman B, Dreydoppel M, Kapitonova A, Balazs D, Weininger U, Engilberge S, Chipot C, Schanda P. 2026. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry. 18, 1221–1230.","ama":"Becker LM, Fu H, Tatman B, et al. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry. 2026;18:1221-1230. doi:10.1038/s41557-026-02155-0","chicago":"Becker, Lea Marie, Haohao Fu, Benjamin Tatman, Matthias Dreydoppel, Anna Kapitonova, Daniel Balazs, Ulrich Weininger, Sylvain Engilberge, Christophe Chipot, and Paul Schanda. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Nature Chemistry. Springer Nature, 2026. https://doi.org/10.1038/s41557-026-02155-0.","short":"L.M. Becker, H. Fu, B. Tatman, M. Dreydoppel, A. Kapitonova, D. Balazs, U. Weininger, S. Engilberge, C. Chipot, P. Schanda, Nature Chemistry 18 (2026) 1221–1230.","mla":"Becker, Lea Marie, et al. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Nature Chemistry, vol. 18, Springer Nature, 2026, pp. 1221–30, doi:10.1038/s41557-026-02155-0."},"year":"2026","acknowledgement":"We thank N. R. Skrynnikov and O. O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to T. Schubeis (Lyon) for advice on GB1 crystallization and R. Schmid for initial crystallization trials. We thank C. Mueller-Dieckmann for assistance with room-temperature X-ray crystallography data collection on beamline ID30B at the ESRF, which is acknowledged for providing beamtime through its In-House Research programme. We thank S. Falkner for assistance with constructing the structural model of the IgG:GB1 complex. We thank J. Lewandowski for providing feedback on the paper and granting access to backbone relaxation data of IgG:GB1T2Q and GB1T2Q microcrystals. This research was supported by the Scientific Service Units (SSU) of the Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank P. Rovó and M. V. Falcón for excellent support of the NMR facility. L.M.B. is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant number PR10660EAW01). C.C. acknowledges the European Research Council (grant project 101097272 ‘MilliInMicro’) and the Métropole du Grand Nancy (grant project ‘ARC’). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.Open access funding provided by Institute of Science and Technology (IST Austria).","abstract":[{"text":"Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein–protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labelling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a crystal structure of a GB1 variant reported in this work, reproduce these elevated barriers and reveal how the crystal restrains motions.","lang":"eng"}],"scopus_import":"1","doi":"10.1038/s41557-026-02155-0","dataavailabilitystatement":"The cryo and room-temperature crystal structures of GB1QDD are deposited at the PDB under the access codes 9I2I and 9T8Z, respectively. The solid-state NMR backbone assignment of GB1QDD is deposited at the BMRB under the access code 53330. NMR spectra, analysis scripts and raw data are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-20641)120. Files to reproduce the enhanced-sampling MD simulations are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-21145)121.","ddc":["540"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"intvolume":" 18","has_accepted_license":"1","external_id":{"pmid":["42271006"]},"quality_controlled":"1","month":"07","type":"journal_article","das_tickbox":"1","file_date_updated":"2026-07-28T06:58:35Z","title":"Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes","status":"public","publisher":"Springer Nature","publication_status":"published","OA_type":"hybrid","date_published":"2026-07-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2026-06-21T22:03:01Z","OA_place":"publisher","_id":"22105","publication":"Nature Chemistry","related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-proteins-breathe/","description":"News on ISTA website","relation":"research_data"}],"record":[{"status":"public","id":"20641","relation":"research_data"},{"status":"public","id":"21145","relation":"research_data"},{"relation":"dissertation_contains","id":"22334","status":"public"}]},"day":"01","page":"1221-1230"}]