[{"ddc":["000"],"citation":{"ista":"Iofinova EB. 2026. On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria.","apa":"Iofinova, E. B. (2026). On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21854","mla":"Iofinova, Eugenia B. On the Utility and Effects of Efficiency in Artificial Neural Networks. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21854.","chicago":"Iofinova, Eugenia B. “On the Utility and Effects of Efficiency in Artificial Neural Networks.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21854.","short":"E.B. Iofinova, On the Utility and Effects of Efficiency in Artificial Neural Networks, Institute of Science and Technology Austria, 2026.","ama":"Iofinova EB. On the utility and effects of efficiency in artificial neural networks. 2026. doi:10.15479/AT-ISTA-21854","ieee":"E. B. Iofinova, “On the utility and effects of efficiency in artificial neural networks,” Institute of Science and Technology Austria, 2026."},"type":"dissertation","language":[{"iso":"eng"}],"acknowledgement":"The research in this Ph.D. was funded in whole\r\nor in part by the Austrian Science Fund (FWF) W1260-N35 (Vienna Graduate School for\r\nComputational Optimization). For open access purposes the author has applied a CC BY\r\npublic copyright license to any author accepted manuscript version arising from this submission\r\nwherever possible. Additionally, I am grateful to Alois Schlögl, Waleed Khalid, and the rest of\r\nthe ISTA Scientific Computing team for building and maintaining the infrastructure I used\r\nto run experiments. I’m also deeply grateful to the Alistarh group’s administrative assistant,\r\nChristine Francois, who always deals with our nonsense with common sense and a smile.\r\n","doi":"10.15479/AT-ISTA-21854","date_published":"2026-05-11T00:00:00Z","day":"11","_id":"21854","das_tickbox":"1","supervisor":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-07-27T12:50:04Z","year":"2026","OA_place":"publisher","month":"05","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2663-337X"]},"file":[{"file_size":28479571,"file_id":"21856","date_updated":"2026-05-11T08:36:01Z","checksum":"2e148dad920e3f9b7c32796e0ba2e5f7","date_created":"2026-05-11T08:36:01Z","access_level":"closed","creator":"eiofinov","relation":"source_file","file_name":"EIofinova_thesis_FinalVersion.zip","content_type":"application/zip"},{"access_level":"open_access","date_created":"2026-05-13T13:10:48Z","success":1,"checksum":"b10c2933f386f532b2dbf28b19c5525c","relation":"main_file","content_type":"application/pdf","file_name":"2026_Iofinova_Eugenia_Thesis.pdf","creator":"eiofinov","file_id":"21877","file_size":18137757,"date_updated":"2026-05-13T13:10:48Z"}],"page":"237","abstract":[{"lang":"eng","text":"As neural-network-based models grow both in size and popularity, interest has grown in making the models smaller and more efficient to train. To that end, many methods have been proposed to prune models by reducing their number of nonzero parameters. Additionally, parameter-efficient fine-tuning, in which a much smaller number of parameters than the total contained in the model is updated during training, has become very popular, especially in the space of Large Language Models. At the same time, the increasingly routine deployment of machine learning in real-world applications has spurred a drive to make them more trustworthy - in the sense of, among other things, being unbiased, interpretable, and editable. In this thesis, we examine the interplay between efficiency and trustworthiness.\r\n\r\nFirst, we analyze the effects of model pruning on bias in computer vision models, demonstrating that increased sparsity leads to greater bias, largely as a function of increased model uncertainty in marginal cases. Based on this observation, we propose several bias mitigation techniques. Then, we demonstrate that example-specific model pruning can improve model interpretation methods while improving pruning efficiency to make example-specific model pruning feasible in real time. Then, we investigate the effectiveness of parameter-efficient and data-efficient model personalization via fine-tuning, demonstrating that it is highly feasible with very small computational and data resources. Finally, we consider efficiency in editing model knowledge using a custom synthetic data framework, demonstrating that parameter-efficient, low-rank fine-tuning frequently outperforms full-rank fine-tuning, and, additionally, that restricting which model blocks are fine-tuned frequently improves results. Together, the results in this thesis provide new insights and techniques for combining trustworthiness and efficiency during neural network inference and training.\r\n\r\n"}],"degree_awarded":"PhD","publisher_comment":"In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of ISTA's products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.","file_date_updated":"2026-05-13T13:10:48Z","doi_confirm":"1","publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14771"},{"id":"18121","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"21858"},{"id":"21859","relation":"part_of_dissertation","status":"public"},{"id":"21857","relation":"part_of_dissertation","status":"public"}]},"date_created":"2026-05-11T08:43:22Z","oa_version":"Published Version","title":"On the utility and effects of efficiency in artificial neural networks","article_processing_charge":"No","status":"public","has_accepted_license":"1","oa":1,"corr_author":"1","author":[{"orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B","last_name":"Iofinova","first_name":"Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117"}],"project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publisher":"Institute of Science and Technology Austria"},{"date_created":"2026-05-11T08:50:28Z","oa_version":"Accepted Version","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"21854"}]},"article_processing_charge":"No","title":"Panza: Investigating the feasibility of fully-local personalized text generation","OA_type":"green","keyword":["LLMs","PEFT","LoRA","personalization","efficient ML"],"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"The availability of powerful open-source large language models (LLMs) opens exciting use cases, such as using personal data to fine-tune these models to imitate a user’s unique writing style. Two key requirements for this functionality are personalization–in the sense that the output should recognizably reflect the user’s own writing style—and privacy–users may justifiably be wary of uploading extremely personal data, such as their email archive, to a third-party service. In this paper, we demonstrate the feasibility of training and running such an assistant, which we call Panza, on commodity hardware, for the specific use case of email generation. Panza’s personalization features are based on a combination of parameter-efficient fine-tuning using a variant of the Reverse Instructions technique [1] and Retrieval-Augmented Generation (RAG) [2]. We demonstrate that this combination allows us to fine-tune an LLM to reflect a user’s writing style using limited data, while executing on extremely limited resources, e.g. on a free Google Colab instance. Our key methodological contribution is the first detailed study of evaluation metrics for this task, and\r\nof how different choices of system components–the use of RAG and of different fine-tuning approaches–impact the system’s performance. Additionally, we demonstrate that very little data - under 100 email samples - are sufficient to create models that convincingly imitate humans, showcasing a previously unknown attack vector in language models. We are releasing the full Panza code as well as three new email datasets licensed for research use.","lang":"eng"}],"publisher":"OpenReview","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"author":[{"full_name":"Nicolicioiu, Armand","last_name":"Nicolicioiu","first_name":"Armand"},{"id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","first_name":"Eugenia B","last_name":"Iofinova","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B"},{"full_name":"Jovanovic, Andrej","last_name":"Jovanovic","first_name":"Andrej"},{"last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar"},{"id":"66374281-f394-11eb-9cf6-869147deecc0","first_name":"Mahdi","last_name":"Nikdan","full_name":"Nikdan, Mahdi"},{"full_name":"Panferov, Andrei","last_name":"Panferov","first_name":"Andrei","id":"2c18daae-4dbe-11ef-8491-98ce2d960f09"},{"last_name":"Markov","first_name":"Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia"},{"first_name":"Nir","last_name":"Shavit","full_name":"Shavit, Nir"},{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"corr_author":"1","oa":1,"conference":{"location":"Tübíngen, Germany","start_date":"2026-03-23","end_date":"2026-03-26","name":"CPAL: Conference on Parsimony and Learning"},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","date_published":"2026-03-06T00:00:00Z","article_number":"81","main_file_link":[{"url":"https://openreview.net/pdf?id=soFWnTqd23","open_access":"1"}],"day":"06","language":[{"iso":"eng"}],"quality_controlled":"1","publication":"Third Conference on Parsimony and Learning (Proceedings Track)","citation":{"ieee":"A. Nicolicioiu et al., Panza: Investigating the feasibility of fully-local personalized text generation. OpenReview, 2026.","chicago":"Nicolicioiu, Armand, Eugenia B Iofinova, Andrej Jovanovic, Eldar Kurtic, Mahdi Nikdan, Andrei Panferov, Ilia Markov, Nir Shavit, and Dan-Adrian Alistarh. Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation. Third Conference on Parsimony and Learning (Proceedings Track). OpenReview, 2026.","mla":"Nicolicioiu, Armand, et al. “Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation.” Third Conference on Parsimony and Learning (Proceedings Track), 81, OpenReview, 2026.","ama":"Nicolicioiu A, Iofinova EB, Jovanovic A, et al. Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation. OpenReview; 2026.","short":"A. Nicolicioiu, E.B. Iofinova, A. Jovanovic, E. Kurtic, M. Nikdan, A. Panferov, I. Markov, N. Shavit, D.-A. Alistarh, Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation, OpenReview, 2026.","apa":"Nicolicioiu, A., Iofinova, E. B., Jovanovic, A., Kurtic, E., Nikdan, M., Panferov, A., … Alistarh, D.-A. (2026). Panza: Investigating the feasibility of fully-local personalized text generation. Third Conference on Parsimony and Learning (Proceedings Track). Tübíngen, Germany: OpenReview.","ista":"Nicolicioiu A, Iofinova EB, Jovanovic A, Kurtic E, Nikdan M, Panferov A, Markov I, Shavit N, Alistarh D-A. 2026. Panza: Investigating the feasibility of fully-local personalized text generation, OpenReview,p."},"type":"conference_poster","month":"03","year":"2026","OA_place":"publisher","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"21857","date_updated":"2026-07-27T12:50:03Z"},{"month":"01","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"21859","date_updated":"2026-07-27T12:50:03Z","year":"2026","OA_place":"repository","doi":"10.48550/arXiv.2601.23153","date_published":"2026-01-30T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2601.23153","open_access":"1"}],"day":"30","type":"preprint","citation":{"short":"E.B. Iofinova, D.-A. Alistarh, ArXiv (n.d.).","ama":"Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv. doi:10.48550/arXiv.2601.23153","chicago":"Iofinova, Eugenia B, and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2601.23153.","mla":"Iofinova, Eugenia B., and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” ArXiv, doi:10.48550/arXiv.2601.23153.","ieee":"E. B. Iofinova and D.-A. Alistarh, “Behemoth: Benchmarking unlearning in LLMs using fully synthetic data,” arXiv. .","ista":"Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv, 10.48550/arXiv.2601.23153.","apa":"Iofinova, E. B., & Alistarh, D.-A. (n.d.). Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv. https://doi.org/10.48550/arXiv.2601.23153"},"language":[{"iso":"eng"}],"publication":"arXiv","acknowledgement":"EI thanks Weiwei Yang, Janardhan Kulkani, and Kate Lytvynets for their advice and support in\r\ndeveloping an earlier version of the Behemoth library. This research was supported by the Scientific\r\nService Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).\r\nEI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35.\r\n","project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":"W1260-N35","name":"Vienna Graduate School on Computational Optimization"}],"author":[{"id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","first_name":"Eugenia B","last_name":"Iofinova","full_name":"Iofinova, Eugenia B","orcid":"0000-0002-7778-3221"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"status":"public","oa":1,"OA_type":"green","date_created":"2026-05-11T08:58:07Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"21854"}]},"publication_status":"draft","oa_version":"Preprint","article_processing_charge":"No","title":"Behemoth: Benchmarking unlearning in LLMs using fully synthetic data","arxiv":1,"abstract":[{"lang":"eng","text":"As artificial neural networks, and specifically large language models, have improved rapidly in capabilities and quality, they have increasingly been deployed in real-world applications, from customer service to Google search, despite the fact that they frequently make factually incorrect or undesirable statements. This trend has inspired practical and academic interest in model editing, that is, in adjusting the weights of the model to modify its likely outputs for queries relating to a specific fact or set of facts. This may be done either to amend a fact or set of facts, for instance, to fix a frequent error in the training data, or to suppress a fact or set of facts entirely, for instance, in case of dangerous knowledge. Multiple methods have been proposed to do such edits. However, at the same time, it has been shown that such model editing can be brittle and incomplete. Moreover the effectiveness of any model editing method necessarily depends on the data on which the model is trained, and, therefore, a good understanding of the interaction of the training data distribution and the way it is stored in the network is necessary and helpful to reliably perform model editing. However, working with large language models trained on real-world data does not allow us to understand this relationship or fully measure the effects of model editing. We therefore propose Behemoth, a fully synthetic data generation framework. To demonstrate the practical insights from the framework, we explore model editing in the context of simple tabular data, demonstrating surprising findings that, in some cases, echo real-world results, for instance, that in some cases restricting the update rank results in a more effective update."}],"external_id":{"arxiv":["2601.23153"]}},{"OA_place":"repository","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2026","oa":1,"date_updated":"2026-07-27T13:59:27Z","_id":"21422","status":"public","has_accepted_license":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","department":[{"_id":"VeSu"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","month":"03","author":[{"last_name":"Sunko","first_name":"Veronika","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523","full_name":"Sunko, Veronika"}],"file_date_updated":"2026-03-11T10:28:37Z","citation":{"ieee":"V. Sunko, “Data underpinning ‘Magneto-optical Kerr effect in an A-type antiferromagnet.’” Institute of Science and Technology Austria, 2026.","chicago":"Sunko, Veronika. “Data Underpinning ‘Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21422.","mla":"Sunko, Veronika. Data Underpinning “Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21422.","short":"V. Sunko, (2026).","ama":"Sunko V. Data underpinning “Magneto-optical Kerr effect in an A-type antiferromagnet.” 2026. doi:10.15479/AT-ISTA-21422","apa":"Sunko, V. (2026). Data underpinning “Magneto-optical Kerr effect in an A-type antiferromagnet.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21422","ista":"Sunko V. 2026. Data underpinning ‘Magneto-optical Kerr effect in an A-type antiferromagnet’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21422."},"type":"research_data","file":[{"creator":"vsunko","file_name":"MBT_Data_Paper.zip","relation":"main_file","content_type":"application/zip","success":1,"date_created":"2026-03-11T10:28:34Z","access_level":"open_access","checksum":"54db0b68f0cf919009317fd3da8f733b","date_updated":"2026-03-11T10:28:34Z","file_id":"21429","file_size":85004},{"checksum":"df1785b7ada7cd07f76a441ee4f52266","success":1,"date_created":"2026-03-11T10:28:37Z","access_level":"open_access","creator":"vsunko","relation":"main_file","content_type":"text/plain","file_name":"README.txt","file_size":2593,"file_id":"21430","date_updated":"2026-03-11T10:28:37Z"}],"day":"11","article_processing_charge":"No","title":"Data underpinning \"Magneto-optical Kerr effect in an A-type antiferromagnet\"","related_material":{"record":[{"id":"21872","status":"public","relation":"used_in_publication"}]},"date_published":"2026-03-11T00:00:00Z","oa_version":"Published Version","date_created":"2026-03-11T07:04:26Z","doi":"10.15479/AT-ISTA-21422"},{"project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"corr_author":"1","author":[{"full_name":"Mascolo, Elia","orcid":"0000-0003-2977-7844","last_name":"Mascolo","first_name":"Elia","id":"776a6ed0-a053-11f0-8635-80b95e0e0d53"},{"last_name":"Körei","first_name":"Reka E","id":"50FDE43E-AA30-11E9-A72B-8A12E6697425","full_name":"Körei, Reka E"},{"first_name":"Noa O.","last_name":"Borst","full_name":"Borst, Noa O."},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Crocker","first_name":"Justin","full_name":"Crocker, Justin"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik"}],"supplementarymaterial":"no","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Elsevier","has_accepted_license":"1","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","OA_type":"hybrid","title":"Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges","article_processing_charge":"Yes (via OA deal)","date_created":"2026-04-26T22:01:46Z","publication_status":"published","oa_version":"Published Version","abstract":[{"text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype-phenotype (GP) map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the second of a two-part series, we review the application of evolutionary concepts — epistasis, robustness, evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene regulatory sequences. We then evaluate the potential for a unifying theory for the evolution of regulatory sequences and identify key open challenges.","lang":"eng"}],"file":[{"access_level":"open_access","success":1,"date_created":"2026-07-27T13:39:59Z","checksum":"ac8bbee61717bfe7116e312cc6825259","relation":"main_file","content_type":"application/pdf","file_name":"2026_CurrentOpinionGeneticsDev_Mascolo.pdf","creator":"dernst","file_id":"22590","file_size":3190001,"date_updated":"2026-07-27T13:39:59Z"}],"article_type":"review","file_date_updated":"2026-07-27T13:39:59Z","dataavailabilitystatement":"No data were used for the research described in the article.","month":"06","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"date_updated":"2026-07-27T13:40:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","das_tickbox":"1","_id":"21759","PlanS_conform":"1","OA_place":"publisher","year":"2026","researchdata_availability":"no","doi":"10.1016/j.gde.2026.102472","day":"01","date_published":"2026-06-01T00:00:00Z","article_number":"102472","type":"journal_article","citation":{"ieee":"E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,” Current Opinion in Genetics and Development, vol. 98. Elsevier, 2026.","chicago":"Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” Current Opinion in Genetics and Development. Elsevier, 2026. https://doi.org/10.1016/j.gde.2026.102472.","mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” Current Opinion in Genetics and Development, vol. 98, 102472, Elsevier, 2026, doi:10.1016/j.gde.2026.102472.","short":"E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current Opinion in Genetics and Development 98 (2026).","ama":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 2026;98. doi:10.1016/j.gde.2026.102472","apa":"Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., & Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2026.102472","ista":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 98, 102472."},"ddc":["570"],"volume":98,"intvolume":" 98","publication":"Current Opinion in Genetics and Development","acknowledgement":"We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant 101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European Molecular Biology Laboratory (N.O.B., J.C.).","language":[{"iso":"eng"}],"quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"21849","das_tickbox":"1","date_updated":"2026-07-27T13:56:09Z","year":"2026","PlanS_conform":"1","OA_place":"publisher","month":"06","ec_funded":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"ddc":["570"],"volume":22,"type":"journal_article","citation":{"ieee":"F. Olmeda et al., “Scaling and self-similarity in the formation of the embryonic epigenome,” Nature Physics, vol. 22. Springer Nature, pp. 931–940, 2026.","ama":"Olmeda F, Lohoff T, Kafetzopoulos I, et al. Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. 2026;22:931-940. doi:10.1038/s41567-026-03263-x","short":"F. Olmeda, T. Lohoff, I. Kafetzopoulos, S.J. Clark, L. Benson, F. Santos, F. Krueger, S. Walker, W. Reik, S. Rulands, Nature Physics 22 (2026) 931–940.","mla":"Olmeda, Fabrizio, et al. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” Nature Physics, vol. 22, Springer Nature, 2026, pp. 931–40, doi:10.1038/s41567-026-03263-x.","chicago":"Olmeda, Fabrizio, Tim Lohoff, Ioannis Kafetzopoulos, Stephen J. Clark, Laura Benson, Fatima Santos, Felix Krueger, Simon Walker, Wolf Reik, and Steffen Rulands. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-026-03263-x.","apa":"Olmeda, F., Lohoff, T., Kafetzopoulos, I., Clark, S. J., Benson, L., Santos, F., … Rulands, S. (2026). Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-026-03263-x","ista":"Olmeda F, Lohoff T, Kafetzopoulos I, Clark SJ, Benson L, Santos F, Krueger F, Walker S, Reik W, Rulands S. 2026. Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. 22, 931–940."},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":" 22","publication":"Nature Physics","acknowledgement":"We thank all members of the W.R. and S.R. laboratories, F. Piazza, B. D. Simons, and F. Jülicher for helpful discussions. We thank M. Ciarchi for providing annotations for the chromatin compartments. S.R. is a member of the Center for Nano Science (CeNS). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 950349). Research in W.R.’s laboratory was supported by the Biotechnology and Biological Sciences Research Council (BB/K010867/1), Wellcome (095645/Z/11/Z) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (EpiCell lineage 882798). F.O. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. Open access funding provided by Max Planck Society.","doi":"10.1038/s41567-026-03263-x","researchdata_availability":"yes","date_published":"2026-06-01T00:00:00Z","day":"01","status":"public","has_accepted_license":"1","oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"author":[{"full_name":"Olmeda, Fabrizio","first_name":"Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","last_name":"Olmeda"},{"full_name":"Lohoff, Tim","first_name":"Tim","last_name":"Lohoff"},{"last_name":"Kafetzopoulos","first_name":"Ioannis","full_name":"Kafetzopoulos, Ioannis"},{"full_name":"Clark, Stephen J.","first_name":"Stephen J.","last_name":"Clark"},{"last_name":"Benson","first_name":"Laura","full_name":"Benson, Laura"},{"full_name":"Santos, Fatima","last_name":"Santos","first_name":"Fatima"},{"full_name":"Krueger, Felix","last_name":"Krueger","first_name":"Felix"},{"last_name":"Walker","first_name":"Simon","full_name":"Walker, Simon"},{"full_name":"Reik, Wolf","first_name":"Wolf","last_name":"Reik"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"}],"publisher":"Springer Nature","department":[{"_id":"EdHa"}],"supplementarymaterial":"yes","pmid":1,"file":[{"access_level":"open_access","success":1,"date_created":"2026-07-27T13:54:58Z","checksum":"58e7734f1ebaf6def642140cb489f08f","relation":"main_file","file_name":"2026_NaturePhysics_Olmeda.pdf","content_type":"application/pdf","creator":"dernst","file_id":"22591","file_size":7932222,"date_updated":"2026-07-27T13:54:58Z"}],"abstract":[{"text":"The development of complex tissues relies on the precise assignment of cell identity. At the molecular scale, this process depends on the deposition of epigenetic modifications—such as methylation—that are regulated by complex biochemical networks and occur at specific regions on the DNA and chromatin. Here we show that despite the complexity of epigenetic regulation, dynamical scaling and self-similarity of DNA methylation marks emerge in embryonic development. Drawing on single-cell multi-omics experiments, super-resolution microscopy and statistical physics, we demonstrate that these phenomena originate in dynamical feedback between DNA methylation and the formation of nanoscale dynamic chromatin aggregates. These nanoscale processes lead to genome-wide increase in DNA methylation marks following a power law and self-similar correlation functions. Using this framework, we identify methylation patterns that precede gene expression changes in embryonic symmetry breaking. Our work identifies linear sequencing measurements as a laboratory to study mesoscopic biophysical processes in vivo.","lang":"eng"}],"external_id":{"pmid":["42318073"]},"page":"931-940","article_type":"original","dataavailabilitystatement":"All sequencing datasets reported in this paper are available on Gene Expression Omnibus (GEO) under accession GSE166226. STORM localization data are available on Zenodo (https://doi.org/10.5281/zenodo.18965309)57. Raw images are available upon request. Code for computing the correlation functions and STORM analysis are available via GitHub at https://github.com/srulands/inference_of_spatio-temporal_processes.","file_date_updated":"2026-07-27T13:54:58Z","OA_type":"hybrid","date_created":"2026-05-10T22:02:16Z","oa_version":"Published Version","publication_status":"published","title":"Scaling and self-similarity in the formation of the embryonic epigenome","article_processing_charge":"Yes (via OA deal)"},{"year":"2026","PlanS_conform":"1","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","das_tickbox":"0","_id":"21883","date_updated":"2026-07-27T14:02:46Z","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"month":"06","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":" 302","acknowledgement":"This work was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Imaging & Optics Facility (IOF) and the MiBa Machine Shop. Specifically; Robert Hauschild (IOF), sharing designs, insights and pioneering 3D printing activities at the Imaging and Optics Facility; Bernhard Hochreiter (IOF), for support and testing of anoxic chamber. We also thank Ana Rita Carvalho Faria and Oliver Biehlmaier (Biozentrum University of Basel, Imaging Core Facility) for sharing the design of the adopted power meter.\r\nOpen Access funding provided by Institute of Science and Technology Austria.","publication":"Journal of Microscopy","ddc":["600"],"volume":302,"type":"journal_article","citation":{"ista":"Goudarzi M, Schuster M, Milberger A, Gunkel M, Terjung S, Krens G. 2026. 3D printing in core facilities – Low pain, high gain. Journal of Microscopy. 302(3), 382–395.","apa":"Goudarzi, M., Schuster, M., Milberger, A., Gunkel, M., Terjung, S., & Krens, G. (2026). 3D printing in core facilities – Low pain, high gain. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.70106","chicago":"Goudarzi, Mohammad, Maximilian Schuster, Arthur Milberger, Manuel Gunkel, Stefan Terjung, and Gabriel Krens. “3D Printing in Core Facilities – Low Pain, High Gain.” Journal of Microscopy. Wiley, 2026. https://doi.org/10.1111/jmi.70106.","mla":"Goudarzi, Mohammad, et al. “3D Printing in Core Facilities – Low Pain, High Gain.” Journal of Microscopy, vol. 302, no. 3, Wiley, 2026, pp. 382–95, doi:10.1111/jmi.70106.","short":"M. Goudarzi, M. Schuster, A. Milberger, M. Gunkel, S. Terjung, G. Krens, Journal of Microscopy 302 (2026) 382–395.","ama":"Goudarzi M, Schuster M, Milberger A, Gunkel M, Terjung S, Krens G. 3D printing in core facilities – Low pain, high gain. Journal of Microscopy. 2026;302(3):382-395. doi:10.1111/jmi.70106","ieee":"M. Goudarzi, M. Schuster, A. Milberger, M. Gunkel, S. Terjung, and G. Krens, “3D printing in core facilities – Low pain, high gain,” Journal of Microscopy, vol. 302, no. 3. Wiley, pp. 382–395, 2026."},"date_published":"2026-06-01T00:00:00Z","day":"01","researchdata_availability":"no","doi":"10.1111/jmi.70106","oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public","department":[{"_id":"Bio"}],"publisher":"Wiley","supplementarymaterial":"no","corr_author":"1","author":[{"id":"3384113A-F248-11E8-B48F-1D18A9856A87","first_name":"Mohammad","last_name":"Goudarzi","full_name":"Goudarzi, Mohammad"},{"last_name":"Schuster","first_name":"Maximilian","id":"37e65def-d415-11eb-ae59-a7b67be103db","full_name":"Schuster, Maximilian"},{"full_name":"Milberger, Arthur","last_name":"Milberger","first_name":"Arthur"},{"full_name":"Gunkel, Manuel","first_name":"Manuel","last_name":"Gunkel"},{"full_name":"Terjung, Stefan","first_name":"Stefan","last_name":"Terjung"},{"last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"}],"article_type":"original","file_date_updated":"2026-07-27T14:01:34Z","pmid":1,"file":[{"file_name":"2026_JourMicroscopy_Goudarzi.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2026-07-27T14:01:34Z","success":1,"checksum":"06dfad92b1465ed614a1201b4129960a","date_updated":"2026-07-27T14:01:34Z","file_id":"22593","file_size":4625767}],"external_id":{"pmid":["42104760"]},"abstract":[{"text":"Three-dimensional (3D) printing has rapidly developed from a niche hobbyist activity into a widely accessible and indispensable technology across multiple scientific disciplines. Within microscopy, optical engineering laboratories and imaging core facilities, 3D printing enables creating customised solutions for sample holders, optical components and everyday laboratory tools that traditionally required specialised machining. By providing rapid prototyping, low-cost production and reproducibility, 3D printing facilitates innovation and efficiency in facility operations. This article provides a perspective on the possibilities, challenges, and practical aspects of implementing 3D printing within microscopy core facilities. Instead of providing technical review about 3D printing, we focus on service organisation, user engagement, resource management and community-driven repositories for design dissemination. Our aim is to share insights with those considering the implementation of 3D printing as a service for developing add-on components to ease the operation of different aspects of the machine-park driven services and those who are managing advanced instrumentation within research groups.","lang":"eng"}],"page":"382-395","oa_version":"Published Version","publication_status":"published","date_created":"2026-05-17T22:02:11Z","title":"3D printing in core facilities – Low pain, high gain","article_processing_charge":"Yes (via OA deal)","issue":"3","OA_type":"hybrid"},{"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":" 17","acknowledgement":"We thank Christine Kuntscher for providing optical conductivity and reflectance data published in ref. 33, and Nicola Spaldin, Joel Moore and Bevin Huang for useful discussions. V.S. and J.O. received support from the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4537 awarded to J.O. at UC Berkeley. Experimental and theoretical work at LBNL and UC Berkeley was funded by the Quantum Materials (KC2202) program under the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division under Contract No. DE-AC02-05CH11231. Work at the University of Kansas was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, EPSCoR, and Materials Sciences and Engineering Division under Award No. DE-SC0025319. Parts of device fabrication were performed in the KU Nanofabrication Facility, which is supported by the National Institutes of Health NIGMS P30GM145499. Work at ORNL was supported by the U. S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division. For the DFT calculations we used resources provided by the Swedish National Infrastructure for Computing (SNIC) at C3SE. We acknowledge support from the US National Science Foundation (NSF) Grant Number 2201516 under the Accelnet program of Office of International Science and Engineering (OISE). This publication is funded in part by a QuantEmX grant from ICAM and the Gordon and Betty Moore Foundation through Grant GBMF9616 to S. K.","publication":"Nature Communications","ddc":["530"],"volume":17,"type":"journal_article","citation":{"ieee":"V. Sunko et al., “Magneto-optical Kerr effect in an A-type antiferromagnet,” Nature Communications, vol. 17. Springer Nature, 2026.","chicago":"Sunko, Veronika, Salman Ahsanullah, Vivek Jain, Sophie Weber, Sivaloganathan Kumaran, Jiaqiang Yan, Joseph Orenstein, and Dmitry Ovchinnikov. “Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.” Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-72577-4.","mla":"Sunko, Veronika, et al. “Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.” Nature Communications, vol. 17, 7364, Springer Nature, 2026, doi:10.1038/s41467-026-72577-4.","ama":"Sunko V, Ahsanullah S, Jain V, et al. Magneto-optical Kerr effect in an A-type antiferromagnet. Nature Communications. 2026;17. doi:10.1038/s41467-026-72577-4","short":"V. Sunko, S. Ahsanullah, V. Jain, S. Weber, S. Kumaran, J. Yan, J. Orenstein, D. Ovchinnikov, Nature Communications 17 (2026).","apa":"Sunko, V., Ahsanullah, S., Jain, V., Weber, S., Kumaran, S., Yan, J., … Ovchinnikov, D. (2026). Magneto-optical Kerr effect in an A-type antiferromagnet. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-026-72577-4","ista":"Sunko V, Ahsanullah S, Jain V, Weber S, Kumaran S, Yan J, Orenstein J, Ovchinnikov D. 2026. Magneto-optical Kerr effect in an A-type antiferromagnet. Nature Communications. 17, 7364."},"article_number":"7364","date_published":"2026-07-27T00:00:00Z","day":"27","doi":"10.1038/s41467-026-72577-4","researchdata_availability":"yes","DOAJ_listed":"1","year":"2026","PlanS_conform":"1","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","das_tickbox":"1","_id":"21872","date_updated":"2026-07-27T13:59:27Z","publication_identifier":{"eissn":["2041-1723"]},"month":"07","article_type":"original","dataavailabilitystatement":"The datasets generated and analyzed during the study of “Magneto-optical Kerr effect in an A-type antiferromagnet\" are available in the ISTA REx repository with https://doi.org/10.15479/AT-ISTA-21422.","file_date_updated":"2026-07-27T13:58:06Z","file":[{"file_size":1054779,"file_id":"22592","date_updated":"2026-07-27T13:58:06Z","checksum":"bde19c4342933c05fe801c2bef7dc732","success":1,"date_created":"2026-07-27T13:58:06Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2026_NatureComm_Sunko.pdf","content_type":"application/pdf"}],"external_id":{"arxiv":["2504.16167"]},"abstract":[{"lang":"eng","text":"Magneto-optic Kerr effect (MOKE) is a powerful probe of broken time-reversal symmetry (T), typically used to study ferromagnets. While MOKE has been observed in some antiferromagnets (AFMs) with vanishing magnetization, it is often associated with structures whose symmetry is lower than basic collinear, bipartite order. In contrast, theory predicts a mechanism for MOKE intrinsic to all AFMs of A-type, i.e. layered AFMs in which ferromagnetic layers are antiferromagnetically aligned. Here we report the experimental confirmation of this mechanism in a bulk AFM. We achieve this by measuring the imaginary component of MOKE as a function of photon energy in MnBi2Te4, an A-type AFM where T is preserved in combination with a translation, and comparing the experimental results with model calculations. Our model suggests that observable MOKE should be expected in all collinear A-type AFMs with out-of-plane spin order, thus enabling optical detection of AFM domains and expanding the scope of MOKE to few-layer AFMs."}],"publication_status":"published","date_created":"2026-05-12T21:31:27Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"21422"}]},"oa_version":"Published Version","article_processing_charge":"Yes","title":"Magneto-optical Kerr effect in an A-type antiferromagnet","arxiv":1,"OA_type":"gold","oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public","department":[{"_id":"VeSu"}],"publisher":"Springer Nature","supplementarymaterial":"yes","author":[{"orcid":"0000-0003-2724-3523","full_name":"Sunko, Veronika","last_name":"Sunko","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","first_name":"Veronika"},{"first_name":"Salman","last_name":"Ahsanullah","full_name":"Ahsanullah, Salman"},{"full_name":"Jain, Vivek","first_name":"Vivek","last_name":"Jain"},{"full_name":"Weber, Sophie","first_name":"Sophie","last_name":"Weber"},{"full_name":"Kumaran, Sivaloganathan","first_name":"Sivaloganathan","last_name":"Kumaran"},{"last_name":"Yan","first_name":"Jiaqiang","full_name":"Yan, Jiaqiang"},{"first_name":"Joseph","last_name":"Orenstein","full_name":"Orenstein, Joseph"},{"first_name":"Dmitry","last_name":"Ovchinnikov","full_name":"Ovchinnikov, Dmitry"}],"corr_author":"1"},{"issue":"4","OA_type":"closed access","oa_version":"None","publication_status":"published","date_created":"2026-06-07T22:01:36Z","article_processing_charge":"No","title":"Emerging bioethical conflicts: One Health and animal experimentation","pmid":1,"page":"226-235","external_id":{"pmid":["42185081"]},"abstract":[{"text":"One Health initiatives are modern paradigms for research and health care practices in various fields. Concrete definitions of the One Health framework, however, remain heterogeneous, leading to conceptual problems and uncertainties in the application of the framework. This article discusses several approaches to the One Health concept, and their associated consequences, with special focus on animal experimentation. The first issue addressed is how One Health should be defined, as well as what (and who) should be considered within a One Health approach. In order to shed further light on this, we explore the history of animals in biomedical science, highlighting historical milestones in the use of animal models, as well as the development and current state of ethical considerations in the field of animal experimentation. The second issue comes with the inclusion of animal experimentation per se as part of the One Health concept. Therefore, particular attention is paid to bioethical principles and the resulting problems that can arise when applying them to the One Health concept. Arguments such as the idea of inequality between humans and non-human animals, and the premise that all actions are done for the benefit of humans, are raised and then used to explore the question of whether the One Health concept is compatible with existing bioethical principles. Based on the bioethical principles of protecting the environment, the biodiversity and biosphere, this paper seeks an inclusive perspective of the One Health concept. Successful solutions will be based on this concept, which embraces all living beings. The authors conclude that a multispecies ethics approach could help create a more ethical ecosystem that is aligned with the wellbeing of all life on a shared planet.","lang":"eng"}],"article_type":"original","author":[{"full_name":"Ulman, Yesim Isil","first_name":"Yesim Isil","last_name":"Ulman"},{"full_name":"Kostomitsopoulos, Nikos","last_name":"Kostomitsopoulos","first_name":"Nikos"},{"full_name":"Camenzind, Samuel","first_name":"Samuel","last_name":"Camenzind"},{"last_name":"Kitsara","first_name":"Maria","full_name":"Kitsara, Maria"},{"full_name":"Pavone, Ilja Richard","first_name":"Ilja Richard","last_name":"Pavone"},{"full_name":"Schober, Sophie","last_name":"Schober","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie"}],"corr_author":"1","publisher":"SAGE Publications","department":[{"_id":"PreCl"}],"status":"public","scopus_import":"1","doi":"10.1177/02611929261453330","date_published":"2026-07-01T00:00:00Z","day":"01","volume":54,"type":"journal_article","citation":{"ista":"Ulman YI, Kostomitsopoulos N, Camenzind S, Kitsara M, Pavone IR, Schober S. 2026. Emerging bioethical conflicts: One Health and animal experimentation. Alternatives to Laboratory Animals. 54(4), 226–235.","apa":"Ulman, Y. I., Kostomitsopoulos, N., Camenzind, S., Kitsara, M., Pavone, I. R., & Schober, S. (2026). Emerging bioethical conflicts: One Health and animal experimentation. Alternatives to Laboratory Animals. SAGE Publications. https://doi.org/10.1177/02611929261453330","mla":"Ulman, Yesim Isil, et al. “Emerging Bioethical Conflicts: One Health and Animal Experimentation.” Alternatives to Laboratory Animals, vol. 54, no. 4, SAGE Publications, 2026, pp. 226–35, doi:10.1177/02611929261453330.","chicago":"Ulman, Yesim Isil, Nikos Kostomitsopoulos, Samuel Camenzind, Maria Kitsara, Ilja Richard Pavone, and Sophie Schober. “Emerging Bioethical Conflicts: One Health and Animal Experimentation.” Alternatives to Laboratory Animals. SAGE Publications, 2026. https://doi.org/10.1177/02611929261453330.","short":"Y.I. Ulman, N. Kostomitsopoulos, S. Camenzind, M. Kitsara, I.R. Pavone, S. Schober, Alternatives to Laboratory Animals 54 (2026) 226–235.","ama":"Ulman YI, Kostomitsopoulos N, Camenzind S, Kitsara M, Pavone IR, Schober S. Emerging bioethical conflicts: One Health and animal experimentation. Alternatives to Laboratory Animals. 2026;54(4):226-235. doi:10.1177/02611929261453330","ieee":"Y. I. Ulman, N. Kostomitsopoulos, S. Camenzind, M. Kitsara, I. R. Pavone, and S. Schober, “Emerging bioethical conflicts: One Health and animal experimentation,” Alternatives to Laboratory Animals, vol. 54, no. 4. SAGE Publications, pp. 226–235, 2026."},"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Alternatives to Laboratory Animals","intvolume":" 54","month":"07","publication_identifier":{"issn":["0261-1929"],"eissn":["2632-3559"]},"_id":"21950","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-27T14:13:17Z","year":"2026"},{"type":"journal_article","citation":{"ieee":"F. Ruzicka, “Reverse genetics of sexual antagonism,” Nature Ecology & Evolution, vol. 10. Springer Nature, pp. 1035–1036, 2026.","mla":"Ruzicka, Filip. “Reverse Genetics of Sexual Antagonism.” Nature Ecology & Evolution, vol. 10, Springer Nature, 2026, pp. 1035–36, doi:10.1038/s41559-026-03036-y.","chicago":"Ruzicka, Filip. “Reverse Genetics of Sexual Antagonism.” Nature Ecology & Evolution. Springer Nature, 2026. https://doi.org/10.1038/s41559-026-03036-y.","short":"F. Ruzicka, Nature Ecology & Evolution 10 (2026) 1035–1036.","ama":"Ruzicka F. Reverse genetics of sexual antagonism. Nature Ecology & Evolution. 2026;10:1035-1036. doi:10.1038/s41559-026-03036-y","apa":"Ruzicka, F. (2026). Reverse genetics of sexual antagonism. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-026-03036-y","ista":"Ruzicka F. 2026. Reverse genetics of sexual antagonism. Nature Ecology & Evolution. 10, 1035–1036."},"volume":10,"publication":"Nature Ecology & Evolution","intvolume":" 10","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1038/s41559-026-03036-y","researchdata_availability":"no","day":"01","date_published":"2026-06-01T00:00:00Z","date_updated":"2026-07-27T14:05:02Z","das_tickbox":"0","_id":"21900","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","month":"06","publication_identifier":{"eissn":["2397-334X"]},"page":"1035-1036","abstract":[{"lang":"eng","text":"Individually silencing 125 fruit fly genes reveals opposing fitness effects of mutations between females and males, as well as between germline and somatic tissues."}],"external_id":{"pmid":["42067637 "]},"pmid":1,"article_type":"comment","OA_type":"closed access","title":"Reverse genetics of sexual antagonism","article_processing_charge":"No","date_created":"2026-05-20T14:36:45Z","publication_status":"published","oa_version":"None","status":"public","scopus_import":"1","corr_author":"1","author":[{"last_name":"Ruzicka","id":"347955dd-57b0-11ee-9095-c28bdd368f4b","first_name":"Filip","full_name":"Ruzicka, Filip"}],"supplementarymaterial":"no","publisher":"Springer Nature","department":[{"_id":"BeVi"}]},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"project":[{"grant_number":"W1260-N35","name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"corr_author":"1","author":[{"first_name":"Jeferson","id":"00223538-AF8F-11E9-A4C7-F729E6697425","last_name":"Zapata","full_name":"Zapata, Jeferson"}],"doi_confirm":"1","file_date_updated":"2026-06-10T13:33:25Z","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"This thesis investigates algorithmic certification and approximation methods for degenerate semidefinite programs (SDPs) and the singular roots of polynomial systems. In the first part, we present a hybrid symbolic-numeric algorithm for certifying the feasibility of weakly feasible, degenerate SDPs. By reformulating linear matrix inequalities (LMIs) into a structured polynomial system via facial reduction and incidence varieties, we guarantee the existence of an isolated exact solution. This algebraic reduction enables the certification of maximum-rank numerical approximations using methods from algebraic geometry.\r\n\r\nIn the second part, we address the severe ill-conditioning and loss of quadratic convergence that plague standard path-tracking methods near isolated singular roots. To overcome this, we propose tracking algorithms that achieve superlinear convergence without the computational bloat characteristic of classical deflation techniques. By modeling the solution path as a generalized fractional Puiseux series, our approach combines an explicitly derived algebraic predictor with a localized hyperplane desingularization phase during the corrector step. Furthermore, we introduce a continuous path-limit method and an extension of the geometric sequence rule to directly extract exact fractional exponents. This bypasses traditional heuristic trial-and-error methods and explicitly accommodates sparse series expansions. Numerical experiments confirm that our method significantly reduces the cumulative number of matrix inversions while achieving high-accuracy root approximations, even for heavily degenerate systems exhibiting higher coranks."}],"page":"89","file":[{"file_id":"21958","file_size":40811933,"date_updated":"2026-06-08T13:20:02Z","date_created":"2026-06-08T13:20:02Z","access_level":"closed","checksum":"b11a959e99d3dcf61040282b5c837141","creator":"jzapata","content_type":"application/zip","file_name":"istaustriathesis_JZapata.zip","relation":"source_file"},{"file_size":2207892,"file_id":"21992","date_updated":"2026-06-10T13:33:25Z","checksum":"edf1e5899b2e31505cd1aa3fe8bd4b7f","success":1,"date_created":"2026-06-10T13:33:25Z","access_level":"open_access","creator":"jzapata","content_type":"application/pdf","relation":"main_file","file_name":"4_Final_Thesis_JZapata_REX.pdf"}],"article_processing_charge":"No","title":"Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"21144"}]},"oa_version":"Published Version","publication_status":"published","date_created":"2026-06-08T13:29:52Z","OA_place":"publisher","year":"2026","date_updated":"2026-07-27T14:30:42Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"21957","supervisor":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"das_tickbox":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-079-4"]},"month":"06","acknowledgement":"Funding: Vienna Graduate School on Computational Optimization (FWF), grant DOI: 10.55776/W1260.","language":[{"iso":"eng"}],"citation":{"apa":"Zapata, J. (2026). Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21957","ista":"Zapata J. 2026. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria.","ieee":"J. Zapata, “Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames,” Institute of Science and Technology Austria, 2026.","ama":"Zapata J. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. 2026. doi:10.15479/AT-ISTA-21957","short":"J. Zapata, Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames, Institute of Science and Technology Austria, 2026.","chicago":"Zapata, Jeferson. “Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21957.","mla":"Zapata, Jeferson. Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21957."},"type":"dissertation","ddc":["500"],"day":"09","date_published":"2026-06-09T00:00:00Z","doi":"10.15479/AT-ISTA-21957"},{"month":"02","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"issn":["2663-337X"]},"_id":"21360","das_tickbox":"1","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-07-27T14:30:08Z","year":"2026","OA_place":"repository","doi":"10.15479/AT-ISTA-21360","date_published":"2026-02-26T00:00:00Z","day":"26","ddc":["570","575","583"],"type":"dissertation","citation":{"ista":"Riegler S. 2026. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. Institute of Science and Technology Austria.","apa":"Riegler, S. (2026). Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21360","short":"S. Riegler, Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species, Institute of Science and Technology Austria, 2026.","ama":"Riegler S. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. 2026. doi:10.15479/AT-ISTA-21360","chicago":"Riegler, Stefan. “Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21360.","mla":"Riegler, Stefan. Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21360.","ieee":"S. Riegler, “Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species,” Institute of Science and Technology Austria, 2026."},"language":[{"iso":"eng"}],"acknowledgement":"I would like to acknowledge the Austrian Academy of Sciences (ÖAW) and European\r\nResearch Executive Agency (REA) for funding my research (DOC ÖAW Fellowship\r\n26130, Horizon Europe BOLERO Project 101060393). ","corr_author":"1","author":[{"last_name":"Riegler","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan","full_name":"Riegler, Stefan","orcid":"0000-0003-3413-1343"}],"project":[{"grant_number":"101060393","name":"Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks","_id":"34afa094-11ca-11ed-8bc3-a375845a59fb"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","status":"public","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"related_material":{"record":[{"status":"public","relation":"research_data","id":"21363"}]},"oa_version":"Published Version","publication_status":"published","date_created":"2026-02-27T09:08:14Z","title":"Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species","article_processing_charge":"No","file":[{"access_level":"closed","date_created":"2026-03-02T10:59:50Z","checksum":"2f1f44e8536c2538f94a440217452c9f","content_type":"application/x-zip-compressed","relation":"source_file","file_name":"2026_Riegler_Stefan_Thesis.zip","creator":"sriegler","file_id":"21386","file_size":31430022,"date_updated":"2026-03-02T10:59:50Z"},{"embargo":"2027-02-27","creator":"sriegler","file_name":"2026_Riegler_Stefan_Thesis.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2026-03-02T10:59:49Z","embargo_to":"open_access","access_level":"closed","checksum":"2e8dc39640bc26ae5684c944c619719b","date_updated":"2026-03-02T10:59:49Z","file_id":"21387","file_size":11635090}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","page":"185","degree_awarded":"PhD","file_date_updated":"2026-03-02T10:59:50Z","doi_confirm":"1"},{"doi":"10.15479/AT-ISTA-21363","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"21360"}]},"oa_version":"Published Version","date_published":"2026-02-27T00:00:00Z","date_created":"2026-02-27T09:18:41Z","day":"27","article_processing_charge":"No","title":"Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species","file":[{"creator":"sriegler","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_name":"SupplementaryTables.xlsx","embargo":"2027-02-27","checksum":"de9145fa166a28c588b5184a2d3d4fee","embargo_to":"open_access","date_created":"2026-02-27T09:11:33Z","access_level":"closed","date_updated":"2026-02-27T09:11:33Z","file_size":63749444,"file_id":"21364"},{"date_updated":"2026-02-27T09:13:11Z","file_size":124,"file_id":"21365","relation":"main_file","content_type":"text/plain","file_name":"ReadMe.txt","creator":"sriegler","embargo":"2027-02-27","checksum":"ce1f163551c96cee45943a8ea29720b6","access_level":"closed","embargo_to":"open_access","date_created":"2026-02-27T09:13:11Z"}],"ddc":["575"],"type":"research_data","citation":{"apa":"Riegler, S. (2026). Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21363","ista":"Riegler S. 2026. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21363.","ieee":"S. Riegler, “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species.” Institute of Science and Technology Austria, 2026.","short":"S. Riegler, (2026).","ama":"Riegler S. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species. 2026. doi:10.15479/AT-ISTA-21363","chicago":"Riegler, Stefan. “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21363.","mla":"Riegler, Stefan. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21363."},"abstract":[{"text":"The data contains information on coffee differential gene expression as well as co-expression and trait correlations in two separate experiments. First, contrasting nitrogen supply, second, intra- and interspecific grafting.","lang":"eng"}],"file_date_updated":"2026-02-27T09:13:11Z","author":[{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan","last_name":"Riegler","orcid":"0000-0003-3413-1343","full_name":"Riegler, Stefan"}],"corr_author":"1","month":"02","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"_id":"21363","has_accepted_license":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","status":"public","contributor":[{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","contributor_type":"supervisor"}],"date_updated":"2026-07-27T14:30:07Z","year":"2026","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"}},{"researchdata_availability":"yes","doi":"10.1021/acs.est.5c08400","day":"17","article_number":"5c08400","date_published":"2026-02-17T00:00:00Z","citation":{"apa":"Ibarra-Espinosa, S., Dias de Freitas, E., Gaubert, B., Lichtig, P., Ropkins, K., da Silva, I., … Brasseur, G. (2026). A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science & Technology. American Chemical Society. https://doi.org/10.1021/acs.est.5c08400","ista":"Ibarra-Espinosa S, Dias de Freitas E, Gaubert B, Lichtig P, Ropkins K, da Silva I, Martins Pereira G, Schuch D, Nascimento J, Hoinaski L, Martins LD, Gavidia-Calderón M, Vara-Vela A, Toledo de Almeida Albuquerque T, Ynoue RY, Diez S, Mera Z, Casallas Garcia A, Vallejo F, Diaz V, Pedruzzi R, Abrutzky R, Franco MA, Huneeus N, Jorquera H, Belalcázar-Cerón LC, Rojas NY, de Fatima Andrade M, Emmons L, Brasseur G. 2026. A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science & Technology. 60(6), 5c08400.","ieee":"S. Ibarra-Espinosa et al., “A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality,” Environmental Science & Technology, vol. 60, no. 6. American Chemical Society, 2026.","mla":"Ibarra-Espinosa, Sergio, et al. “A Century of Vehicular Emissions in Brazil: Unveiling the Impacts of Unique Fuel Mix on Air Quality.” Environmental Science & Technology, vol. 60, no. 6, 5c08400, American Chemical Society, 2026, doi:10.1021/acs.est.5c08400.","chicago":"Ibarra-Espinosa, Sergio, Edmilson Dias de Freitas, Benjamin Gaubert, Pablo Lichtig, Karl Ropkins, Iara da Silva, Guilherme Martins Pereira, et al. “A Century of Vehicular Emissions in Brazil: Unveiling the Impacts of Unique Fuel Mix on Air Quality.” Environmental Science & Technology. American Chemical Society, 2026. https://doi.org/10.1021/acs.est.5c08400.","short":"S. Ibarra-Espinosa, E. Dias de Freitas, B. Gaubert, P. Lichtig, K. Ropkins, I. da Silva, G. Martins Pereira, D. Schuch, J. Nascimento, L. Hoinaski, L.D. Martins, M. Gavidia-Calderón, A. Vara-Vela, T. Toledo de Almeida Albuquerque, R.Y. Ynoue, S. Diez, Z. Mera, A. Casallas Garcia, F. Vallejo, V. Diaz, R. Pedruzzi, R. Abrutzky, M.A. Franco, N. Huneeus, H. Jorquera, L.C. Belalcázar-Cerón, N.Y. Rojas, M. de Fatima Andrade, L. Emmons, G. Brasseur, Environmental Science & Technology 60 (2026).","ama":"Ibarra-Espinosa S, Dias de Freitas E, Gaubert B, et al. A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science & Technology. 2026;60(6). doi:10.1021/acs.est.5c08400"},"type":"journal_article","volume":60,"ddc":["550"],"publication":"Environmental Science & Technology","acknowledgement":"Part of this material is based upon work supported by the NSF National Center for Atmospheric Research, which is a major facility sponsored by the National Science Foundation under Cooperative Agreement No. 1852977. Casallas was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. E. D. Freitas thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 313210/2022–5). Silva gratefully acknowledges the financial support from the National Council for Scientific and Technological Development (CNPq), process number 140512/2021–7. P. Lichtig was supported by base funding from the National Commission for Atomic Energy (CNEA, Arg.) and by NSF NCAR. R.Y. Ynoue thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 406728/2022–4). M. A. Franco thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 407752/2023–4). G. M. Pereira thanks the support by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; Process numbers 2018/07848–9, 2016/18438–0, and 2019/01316–80) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES; Process number 88887.103225/2025–00). M.F. Andrade thanks the support by FAPESP (Process number 2016/18438–0) and CNPQ (Klimapolis INCT).","intvolume":" 60","quality_controlled":"1","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1520-5851"],"issn":["0013-936X"]},"ec_funded":1,"date_updated":"2026-07-28T07:03:54Z","_id":"21164","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","OA_type":"closed access","issue":"6","title":"A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality","article_processing_charge":"No","publication_status":"published","date_created":"2026-02-09T06:54:10Z","oa_version":"None","external_id":{"pmid":["41636708"]},"abstract":[{"lang":"eng","text":"Global emission inventories often fail to capture the complexities of vehicular pollution in regions with unique fuel mixes, such as Brazil’s extensive biofuel use, leading to significant uncertainties in atmospheric modeling. This study presents a century-long (1960–2100) bottom-up vehicular emission inventory for Brazil, leveraging locally derived emission factors. Our estimates reveal substantial discrepancies in magnitude, timing, and speciation of non-CO2 pollutants (CO, NMHC, PM2.5) compared to leading global inventories (EDGAR, CEDS, CAMS), highlighting critical inaccuracies in widely used data sets. More critically, future projections under Shared Socioeconomic Pathways (SSPs) uncover a novel positive feedback mechanism: rising temperatures significantly enhance vehicular evaporative nonmethane hydrocarbon (NMHC) emissions. This temperature-dependent increase and subsequent NMHC oxidation to CO2 suggest an overlooked pathway that could amplify climate warming and air pollution globally, particularly after a breakpoint around 2050 (p < 0.05). While historical emissions peaked in the 1990s–2000s, nonexhaust PM becomes increasingly important. Air quality simulations using our inventory in the MUSICA model show good regional PM2.5 agreement but highlight challenges in resolving local primary pollutant peaks. This comprehensive inventory provides crucial data for Brazil and uncovers globally relevant climate–chemistry interactions, urging a re-evaluation of regional specificities in global emission assessments."}],"pmid":1,"dataavailabilitystatement":"Scripts available here https://github.com/ibarraespinosa/musica_vein and here https://github.com/atmoschem/vein.","article_type":"original","author":[{"first_name":"Sergio","last_name":"Ibarra-Espinosa","full_name":"Ibarra-Espinosa, Sergio"},{"full_name":"Dias de Freitas, Edmilson","last_name":"Dias de Freitas","first_name":"Edmilson"},{"last_name":"Gaubert","first_name":"Benjamin","full_name":"Gaubert, Benjamin"},{"first_name":"Pablo","last_name":"Lichtig","full_name":"Lichtig, Pablo"},{"full_name":"Ropkins, Karl","first_name":"Karl","last_name":"Ropkins"},{"first_name":"Iara","last_name":"da Silva","full_name":"da Silva, Iara"},{"first_name":"Guilherme","last_name":"Martins Pereira","full_name":"Martins Pereira, Guilherme"},{"full_name":"Schuch, Daniel","first_name":"Daniel","last_name":"Schuch"},{"first_name":"Janaina","last_name":"Nascimento","full_name":"Nascimento, Janaina"},{"full_name":"Hoinaski, Leonardo","last_name":"Hoinaski","first_name":"Leonardo"},{"last_name":"Martins","first_name":"Leila Droprinchinski","full_name":"Martins, Leila Droprinchinski"},{"full_name":"Gavidia-Calderón, Mario","last_name":"Gavidia-Calderón","first_name":"Mario"},{"last_name":"Vara-Vela","first_name":"Angel","full_name":"Vara-Vela, Angel"},{"last_name":"Toledo de Almeida Albuquerque","first_name":"Taciana","full_name":"Toledo de Almeida Albuquerque, Taciana"},{"full_name":"Ynoue, Rita Yuri","first_name":"Rita Yuri","last_name":"Ynoue"},{"last_name":"Diez","first_name":"Sebastian","full_name":"Diez, Sebastian"},{"last_name":"Mera","first_name":"Zamir","full_name":"Mera, Zamir"},{"full_name":"Casallas Garcia, Alejandro","orcid":"0000-0002-1988-5035","first_name":"Alejandro","id":"92081129-2d75-11ef-a48d-b04dd7a2385a","last_name":"Casallas Garcia"},{"full_name":"Vallejo, Fidel","last_name":"Vallejo","first_name":"Fidel"},{"full_name":"Diaz, Valeria","last_name":"Diaz","first_name":"Valeria"},{"last_name":"Pedruzzi","first_name":"Rizzieri","full_name":"Pedruzzi, Rizzieri"},{"full_name":"Abrutzky, Rosana","first_name":"Rosana","last_name":"Abrutzky"},{"last_name":"Franco","first_name":"Marco A.","full_name":"Franco, Marco A."},{"first_name":"Nicolas","last_name":"Huneeus","full_name":"Huneeus, Nicolas"},{"first_name":"Hector","last_name":"Jorquera","full_name":"Jorquera, Hector"},{"full_name":"Belalcázar-Cerón, Luis Carlos","first_name":"Luis Carlos","last_name":"Belalcázar-Cerón"},{"first_name":"Néstor Y.","last_name":"Rojas","full_name":"Rojas, Néstor Y."},{"full_name":"de Fatima Andrade, Maria","first_name":"Maria","last_name":"de Fatima Andrade"},{"first_name":"Louisa","last_name":"Emmons","full_name":"Emmons, Louisa"},{"first_name":"Guy","last_name":"Brasseur","full_name":"Brasseur, Guy"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"supplementarymaterial":"yes","department":[{"_id":"CaMu"}],"publisher":"American Chemical Society","has_accepted_license":"1","status":"public","scopus_import":"1"},{"PlanS_conform":"1","OA_place":"publisher","year":"2026","date_updated":"2026-07-28T06:49:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","das_tickbox":"1","_id":"20971","publication_identifier":{"eissn":["1944-9208"],"issn":["8755-1209"]},"ec_funded":1,"month":"03","intvolume":" 64","publication":"Reviews of Geophysics","acknowledgement":"This work is the result of collaboration and discussions within HEFEX II, and we are grateful to all colleagues who have contributed to and enriched these discussions in various ways. T. Sauter acknowledges funding from the German Research Foundation (DFG) (Grant 543257843). This research was funded in part by the Austrian Science Fund (FWF) (Grant https://doi.org/10.55776/P36624 and https://doi.org/10.55776/P36306) for which E. Collier and R. Prinz are grateful. A. R. Groos, T. E. Shaw, R. Mott and M. Haugeneder acknowledge Transnational Access from the European Union's H2020 project INTERACT III (Grant 871120) for participation in the HEFEX II campaign and working group. I. Stiperski (Grant Agreement No. 101001691) and A. R. Groos (Grant Agreement No. 948290) acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program. R. Mott acknowledges funding from the Swiss National Science Foundation (SNSF) (Grant 200021_219918). B. Goger is supported by EXCLAIM, a project funded by ETH Zurich. J.E. Sicart acknowledges LabEx OSUG@2020 (Investissements d'avenir - ANR10 LABX56) for participation in the HEFEX II campaign and working group. T. E. Shaw acknowledges funding from the EU Horizon 2020 Marie Skłodowska-Curie Grant 101026058 and 101034413. K. F. Haualand and T. Sauter are supported by the JOSTICE project funded by the Research Council of Norway (RCN Grant 302458).","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"apa":"Sauter, T., Brock, B. W., Collier, E., Goger, B., Groos, A. R., Haualand, K. F., … Voordendag, A. (2026). Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. Reviews of Geophysics. Wiley. https://doi.org/10.1029/2024RG000869","ista":"Sauter T, Brock BW, Collier E, Goger B, Groos AR, Haualand KF, Mott R, Nicholson L, Prinz R, Shaw T, Stiperski I, Georgi A, Haugeneder M, Mandal A, Reynolds D, Saigger M, Sicart JE, Voordendag A. 2026. Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. Reviews of Geophysics. 64(1), e2024RG000869.","ieee":"T. Sauter et al., “Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review,” Reviews of Geophysics, vol. 64, no. 1. Wiley, 2026.","ama":"Sauter T, Brock BW, Collier E, et al. Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. Reviews of Geophysics. 2026;64(1). doi:10.1029/2024RG000869","short":"T. Sauter, B.W. Brock, E. Collier, B. Goger, A.R. Groos, K.F. Haualand, R. Mott, L. Nicholson, R. Prinz, T. Shaw, I. Stiperski, A. Georgi, M. Haugeneder, A. Mandal, D. Reynolds, M. Saigger, J.E. Sicart, A. Voordendag, Reviews of Geophysics 64 (2026).","chicago":"Sauter, T., B. W. Brock, E. Collier, B. Goger, A. R. Groos, K. F. Haualand, R. Mott, et al. “Glacier-Atmosphere Interactions and Feedbacks in High-Mountain Regions - A Review.” Reviews of Geophysics. Wiley, 2026. https://doi.org/10.1029/2024RG000869.","mla":"Sauter, T., et al. “Glacier-Atmosphere Interactions and Feedbacks in High-Mountain Regions - A Review.” Reviews of Geophysics, vol. 64, no. 1, e2024RG000869, Wiley, 2026, doi:10.1029/2024RG000869."},"ddc":["550"],"volume":64,"day":"01","article_number":"e2024RG000869","date_published":"2026-03-01T00:00:00Z","researchdata_availability":"no","doi":"10.1029/2024RG000869","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","has_accepted_license":"1","status":"public","supplementarymaterial":"no","publisher":"Wiley","department":[{"_id":"FrPe"}],"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"author":[{"full_name":"Sauter, T.","first_name":"T.","last_name":"Sauter"},{"last_name":"Brock","first_name":"B. W.","full_name":"Brock, B. W."},{"full_name":"Collier, E.","last_name":"Collier","first_name":"E."},{"last_name":"Goger","first_name":"B.","full_name":"Goger, B."},{"first_name":"A. R.","last_name":"Groos","full_name":"Groos, A. R."},{"first_name":"K. F.","last_name":"Haualand","full_name":"Haualand, K. F."},{"full_name":"Mott, R.","last_name":"Mott","first_name":"R."},{"full_name":"Nicholson, L.","last_name":"Nicholson","first_name":"L."},{"first_name":"R.","last_name":"Prinz","full_name":"Prinz, R."},{"orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas","last_name":"Shaw","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas"},{"full_name":"Stiperski, I.","first_name":"I.","last_name":"Stiperski"},{"full_name":"Georgi, A.","last_name":"Georgi","first_name":"A."},{"full_name":"Haugeneder, M.","last_name":"Haugeneder","first_name":"M."},{"full_name":"Mandal, A.","last_name":"Mandal","first_name":"A."},{"last_name":"Reynolds","first_name":"D.","full_name":"Reynolds, D."},{"last_name":"Saigger","first_name":"M.","full_name":"Saigger, M."},{"first_name":"J. E.","last_name":"Sicart","full_name":"Sicart, J. E."},{"first_name":"A.","last_name":"Voordendag","full_name":"Voordendag, A."}],"article_type":"original","file_date_updated":"2026-07-28T06:48:08Z","dataavailabilitystatement":"Data were not used, nor created for this research. Software (other than for typesetting) was not used for this research.","abstract":[{"text":"Mountain glaciers are among the natural systems most vulnerable to climate change. However, their interactions with the atmosphere are complex and not fully understood. These interactions can trigger rapid adjustments and climate feedbacks that either amplify or attenuate atmospheric signals, influencing both glacier response and large-scale atmospheric circulation. Observing this functional coupling in nature is challenging because the key processes occur over a wide range of spatial and temporal scales. However, recent advances in observational techniques and modeling have provided new insights into these interactions. In this review, we summarize the current state of knowledge on glacier-atmosphere interactions in high-mountain regions at different scales, and highlight recent advances in observational and numerical modeling. We also highlight important knowledge gaps and outline future research directions to improve the prediction of glacier change in a warming world.","lang":"eng"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2026_ReviewsGeophysics_Sauter.pdf","creator":"dernst","access_level":"open_access","success":1,"date_created":"2026-07-28T06:48:08Z","checksum":"9d46167619be91210c45ee9e1f187395","date_updated":"2026-07-28T06:48:08Z","file_id":"22594","file_size":3012737}],"article_processing_charge":"Yes (in subscription journal)","title":"Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review","oa_version":"Published Version","publication_status":"published","date_created":"2026-01-11T23:01:33Z","OA_type":"hybrid","issue":"1"},{"volume":86,"ddc":["570"],"type":"journal_article","citation":{"ieee":"R. Kelley et al., “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” Molecular Cell, vol. 86, no. 1. Elsevier, p. 213–230.e7, 2026.","short":"R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S. Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty, L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P. Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular Cell 86 (2026) 213–230.e7.","ama":"Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. 2026;86(1):213-230.e7. doi:10.1016/j.molcel.2025.11.029","mla":"Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell, vol. 86, no. 1, Elsevier, 2026, p. 213–230.e7, doi:10.1016/j.molcel.2025.11.029.","chicago":"Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell. Elsevier, 2026. https://doi.org/10.1016/j.molcel.2025.11.029.","apa":"Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X., … Kotecha, A. (2026). Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2025.11.029","ista":"Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG, Plitzko JM, Engel BD, Kotecha A. 2026. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. 86(1), 213–230.e7."},"quality_controlled":"1","language":[{"iso":"eng"}],"acknowledgement":"Calculations were performed at the Max Planck Institute of Biochemistry and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF) in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing center at the University of Basel, Switzerland; and at Thermo Fisher Scientific, in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific. All lamella preparations and tilt-series collections used in this work were conducted at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios microscopes. This work was also supported by the ERC consolidator grant “cryOcean” (fulfilled by the Swiss State Secretariat for Education, Research and Innovation, M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E. and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T., an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.","publication":"Molecular Cell","intvolume":" 86","doi":"10.1016/j.molcel.2025.11.029","researchdata_availability":"yes","date_published":"2026-01-08T00:00:00Z","day":"08","_id":"20935","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T07:39:23Z","year":"2026","OA_place":"publisher","PlanS_conform":"1","month":"01","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"file":[{"date_updated":"2026-07-28T07:38:45Z","file_size":26749637,"file_id":"22599","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2026_MolecularCell_Kelley.pdf","checksum":"96a2f8519124d1a0d9de8d2594bf7147","success":1,"date_created":"2026-07-28T07:38:45Z","access_level":"open_access"}],"page":"213-230.e7","abstract":[{"text":"In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics.","lang":"eng"}],"file_date_updated":"2026-07-28T07:38:45Z","dataavailabilitystatement":"Raw EM data are available at the EMPIAR under accession code EMPIAR: EMPIAR-11830. Annotation and processing information for all 1,829 tomograms are provided in spreadsheet format.153 The following subtomogram averages have been deposited at the Electron Microscopy Data Bank (EMDB): 80S ribosome (EMDB: EMD-51847), nucleosome (EMDB: EMD-19906), PSII (EMDB: EMD-51731), Rubisco (EMDB: EMD-51848), microtubule (EMDB: EMD-51804), clathrin (EMDB: EMD-51789), and ATP synthase (EMDB: EMD-51802). Segmentations shown in Figures 2 and 3 are deposited on Zenodo (https://doi.org/10.5281/zenodo.15875785). Particle positions and orientations used for STA, along with all resources derived from this work, are available on GitHub (https://github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations). Reconstructed tomograms and annotations are also available to explore interactively at the CZII Cryo-ET Data Portal (DS-10302, https://cryoetdataportal.czscience.com/datasets/10302/). Raw data for cryo-PFIB/SEM slice-and-view of a whole C. reinhardtii cell has also been deposited (EMPIAR: EMPIAR-11275).\r\n\r\nThis paper does not report original code.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","article_type":"original","issue":"1","OA_type":"hybrid","oa_version":"Published Version","date_created":"2026-01-04T23:01:36Z","publication_status":"published","title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","article_processing_charge":"Yes (in subscription journal)","status":"public","has_accepted_license":"1","scopus_import":"1","oa":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Ron","last_name":"Kelley","full_name":"Kelley, Ron"},{"full_name":"Khavnekar, Sagar","last_name":"Khavnekar","first_name":"Sagar"},{"first_name":"Ricardo D.","last_name":"Righetto","full_name":"Righetto, Ricardo D."},{"full_name":"Heebner, Jessica","first_name":"Jessica","last_name":"Heebner"},{"full_name":"Obr, Martin","orcid":"0000-0003-1756-6564","last_name":"Obr","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xianjun","last_name":"Zhang","full_name":"Zhang, Xianjun"},{"first_name":"Saikat","last_name":"Chakraborty","full_name":"Chakraborty, Saikat"},{"full_name":"Tagiltsev, Grigory","last_name":"Tagiltsev","first_name":"Grigory"},{"orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","first_name":"Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"full_name":"Van Dorst, Sofie","last_name":"Van Dorst","first_name":"Sofie"},{"full_name":"Waltz, Florent","last_name":"Waltz","first_name":"Florent"},{"full_name":"Mccafferty, Caitlyn L.","first_name":"Caitlyn L.","last_name":"Mccafferty"},{"last_name":"Lamm","first_name":"Lorenz","full_name":"Lamm, Lorenz"},{"last_name":"Zufferey","first_name":"Simon","full_name":"Zufferey, Simon"},{"full_name":"Van Der Stappen, Philippe","first_name":"Philippe","last_name":"Van Der Stappen"},{"last_name":"Van Den Hoek","first_name":"Hugo","full_name":"Van Den Hoek, Hugo"},{"last_name":"Wietrzynski","first_name":"Wojciech","full_name":"Wietrzynski, Wojciech"},{"orcid":"0000-0001-5206-1794","full_name":"Harar, Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","first_name":"Pavol","last_name":"Harar"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"full_name":"Briggs, John A.G.","first_name":"John A.G.","last_name":"Briggs"},{"last_name":"Plitzko","first_name":"Jürgen M.","full_name":"Plitzko, Jürgen M."},{"full_name":"Engel, Benjamin D.","last_name":"Engel","first_name":"Benjamin D."},{"full_name":"Kotecha, Abhay","first_name":"Abhay","last_name":"Kotecha"}],"publisher":"Elsevier","department":[{"_id":"AlMi"}],"supplementarymaterial":"yes"},{"main_file_link":[{"url":"https://doi.org/10.1101/2025.05.05.652195","open_access":"1"}],"date_published":"2026-01-07T00:00:00Z","day":"07","researchdata_availability":"upon request","doi":"10.1016/j.ymthe.2025.10.008","quality_controlled":"1","language":[{"iso":"eng"}],"acknowledgement":"This project was generously supported by Seedfinancing (grant no. P2282679) of the Austrian Bundesministerium für Digitalisierung und Wirtschaftsstandort and the Bundesministerium für Klimaschutz, Umwelt, Energie, Mobilität, Innovation, und Technologie, handled by the Austrian Wirtschaftsservice (aws), as well as by Life Science Call 2022 (grant no. FO999896442) of the Austrian Research Promotion Agency (FFG). We thank Mag. Michael Schunn from the PCF of the Institute of Science and Technology Austria for his continuous technical support.","publication":"Molecular Therapy","biorxivid":1,"intvolume":" 34","volume":34,"citation":{"apa":"Rica, R., Klein, K., Johnson, L., Carta, G., Sarcevic, M., Langer, F., … Sparber, F. (2026). Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2025.10.008","ista":"Rica R, Klein K, Johnson L, Carta G, Sarcevic M, Langer F, Rademacher C, Wawrzinek R, Quattrone F, Sparber F. 2026. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. Molecular Therapy. 34(1), 397–406.","ieee":"R. Rica et al., “Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response,” Molecular Therapy, vol. 34, no. 1. Elsevier, pp. 397–406, 2026.","chicago":"Rica, Ramona, Klara Klein, Litty Johnson, Gabriele Carta, Mirza Sarcevic, Freyja Langer, Christoph Rademacher, Robert Wawrzinek, Federica Quattrone, and Florian Sparber. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” Molecular Therapy. Elsevier, 2026. https://doi.org/10.1016/j.ymthe.2025.10.008.","mla":"Rica, Ramona, et al. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” Molecular Therapy, vol. 34, no. 1, Elsevier, 2026, pp. 397–406, doi:10.1016/j.ymthe.2025.10.008.","ama":"Rica R, Klein K, Johnson L, et al. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. Molecular Therapy. 2026;34(1):397-406. doi:10.1016/j.ymthe.2025.10.008","short":"R. Rica, K. Klein, L. Johnson, G. Carta, M. Sarcevic, F. Langer, C. Rademacher, R. Wawrzinek, F. Quattrone, F. Sparber, Molecular Therapy 34 (2026) 397–406."},"type":"journal_article","publication_identifier":{"eissn":["1525-0024"],"issn":["1525-0016"]},"month":"01","year":"2026","OA_place":"repository","_id":"20858","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T07:37:08Z","date_created":"2025-12-28T23:01:26Z","oa_version":"Preprint","publication_status":"published","article_processing_charge":"No","title":"Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response","issue":"1","OA_type":"green","dataavailabilitystatement":"The data that support the findings of this study are available on request from the corresponding authors.","article_type":"original","page":"397-406","abstract":[{"text":"Targeted antigen delivery to immune cells, particularly dendritic cells, has emerged as a promising strategy to enhance therapeutic efficacy of vaccines, while minimizing adverse effects associated with conventional immunization. In this study, we use our previously described small glycomimetic molecule that is selectively recognized by the Langerhans cell (LC)-specific surface receptor Langerin and demonstrate specific delivery of protein antigens to these specialized dendritic cells. Our results show that Langerin-mediated antigen delivery significantly enhances the immune response in vivo, resulting in increased expansion and activation of antigen-specific T cells, compared to immunization with unmodified antigen. We demonstrate the feasibility of our LC-targeted platform for immune cell-specific immunization with protein antigen and underscore the potential of LCs as an access point for next-generation vaccines and immunotherapies.","lang":"eng"}],"external_id":{"biorxivid":["10.1101/2025.05.05.652195"]},"department":[{"_id":"PreCl"}],"publisher":"Elsevier","supplementarymaterial":"yes","author":[{"first_name":"Ramona","last_name":"Rica","full_name":"Rica, Ramona"},{"first_name":"Klara","last_name":"Klein","full_name":"Klein, Klara"},{"full_name":"Johnson, Litty","last_name":"Johnson","first_name":"Litty"},{"full_name":"Carta, Gabriele","first_name":"Gabriele","last_name":"Carta"},{"full_name":"Sarcevic, Mirza","first_name":"Mirza","last_name":"Sarcevic"},{"full_name":"Langer, Freyja","id":"3C1BE782-F248-11E8-B48F-1D18A9856A87","first_name":"Freyja","last_name":"Langer"},{"first_name":"Christoph","last_name":"Rademacher","full_name":"Rademacher, Christoph"},{"full_name":"Wawrzinek, Robert","last_name":"Wawrzinek","first_name":"Robert"},{"first_name":"Federica","last_name":"Quattrone","full_name":"Quattrone, Federica"},{"last_name":"Sparber","first_name":"Florian","full_name":"Sparber, Florian"}],"scopus_import":"1","oa":1,"status":"public"},{"day":"01","date_published":"2026-01-01T00:00:00Z","doi":"10.1055/a-2690-9269","publication":"Synlett","intvolume":" 37","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","citation":{"apa":"Pieber, B. (2026). Photochemical cross-couplings using semiconducting materials. Synlett. Georg Thieme Verlag. https://doi.org/10.1055/a-2690-9269","ista":"Pieber B. 2026. Photochemical cross-couplings using semiconducting materials. Synlett. 37(1), 43–54.","ieee":"B. Pieber, “Photochemical cross-couplings using semiconducting materials,” Synlett, vol. 37, no. 1. Georg Thieme Verlag, pp. 43–54, 2026.","mla":"Pieber, Bartholomäus. “Photochemical Cross-Couplings Using Semiconducting Materials.” Synlett, vol. 37, no. 1, Georg Thieme Verlag, 2026, pp. 43–54, doi:10.1055/a-2690-9269.","chicago":"Pieber, Bartholomäus. “Photochemical Cross-Couplings Using Semiconducting Materials.” Synlett. Georg Thieme Verlag, 2026. https://doi.org/10.1055/a-2690-9269.","ama":"Pieber B. Photochemical cross-couplings using semiconducting materials. Synlett. 2026;37(1):43-54. doi:10.1055/a-2690-9269","short":"B. Pieber, Synlett 37 (2026) 43–54."},"volume":37,"publication_identifier":{"eissn":["1437-2096"],"issn":["0936-5214"]},"month":"01","year":"2026","date_updated":"2026-07-28T07:42:47Z","_id":"20537","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","title":"Photochemical cross-couplings using semiconducting materials","publication_status":"published","oa_version":"None","date_created":"2025-10-26T23:01:35Z","OA_type":"closed access","issue":"1","article_type":"original","page":"43-54","abstract":[{"text":"In this personal account, I describe the work performed in my research group on the development of methods that harness heterogeneous photocatalysts for light-mediated nickel-catalyzed cross-couplings. This includes catalytic systems using carbon nitride materials, dye-sensitized TiO₂, covalent organic frameworks (COFs), and conjugated polymers. The rationale behind the selection of materials and how their use led to the identification of catalyst deactivation, structure–activity relationships, and future opportunities is discussed.","lang":"eng"}],"external_id":{"isi":["001582268500001"]},"isi":1,"department":[{"_id":"BaPi"}],"publisher":"Georg Thieme Verlag","corr_author":"1","author":[{"full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus"}],"scopus_import":"1","status":"public"},{"status":"public","has_accepted_license":"1","oa":1,"author":[{"full_name":"Depope, Al","last_name":"Depope","first_name":"Al","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830"}],"corr_author":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","grant_number":"101161364","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits"},{"name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MaRo"},{"_id":"MaMo"}],"publisher":"Institute of Science and Technology Austria","file":[{"checksum":"9ab386790515628d957a194f30a7ccb4","date_created":"2026-07-13T14:52:19Z","access_level":"open_access","creator":"adepope","relation":"main_file","file_name":"2026_Depope_Al_Thesis.pdf","content_type":"application/pdf","file_size":25109878,"file_id":"22316","date_updated":"2026-07-13T14:52:19Z"},{"file_size":1203199939,"file_id":"22317","date_updated":"2026-07-13T14:56:41Z","checksum":"8ed8fb63f76a695d5b6fec35343f4b90","access_level":"closed","date_created":"2026-07-13T14:56:41Z","content_type":"application/zip","file_name":"2026_Depope_Al_Thesis.zip","relation":"source_file","creator":"adepope"}],"page":"169","abstract":[{"text":"Uncovering the genetic architecture of complex traits and pinpointing causal molecular drivers require the ability to distinguish true signals from noise within massive, high-dimensional omics datasets. To extract meaningful biological insights from these datasets, such as identifying causal genetic variants and proteins, scalable and accurate inference methods are essential. To this end, this thesis develops novel Bayesian inference frameworks based on Vector Approximate Message Passing and demonstrates their effectiveness in the modeling of disease onset times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that enables the joint modeling of quantitative complex traits across millions of genetic variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample polygenic risk prediction compared to state-of-the-art approaches. We model human height using 17 million whole-genome sequence variants from the UK Biobank, incorporating a vast number of rare variants and revealing novel associations. gVAMP achieves a prediction accuracy of approximately 46% for human height, representing the highest reported performance for this trait to date. \r\n\r\nSecond, we present vampW, a Bayesian framework for survival analysis applied to proteomic data. By effectively handling right-censoring and complex protein dependencies within the UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations across 24 disease outcomes, the majority of which are not among the top marginal discoveries. We further adjust protein levels for exponential age effects, yielding 1,308 associations and highlighting the sensitivity of the analysis to the chosen age-correction methodology. Finally, vampW improves upon the variable selection capabilities of the commonly used (penalized) variants of the Cox proportional hazards model and delivers state-of-the-art out-of-sample prediction of disease onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting the genetic architecture of complex traits and the proteomic drivers of disease onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions of onset times, this work advances the capabilities of personalized medicine and clinical risk stratification.","lang":"eng"}],"degree_awarded":"PhD","keyword":["Approximate Message Passing","GWAS","Genomics","Proteomics","Survival modeling"],"file_date_updated":"2026-07-13T14:56:41Z","doi_confirm":"1","related_material":{"record":[{"id":"21488","status":"public","relation":"part_of_dissertation"}]},"date_created":"2026-07-10T13:27:20Z","oa_version":"Published Version","publication_status":"published","title":"From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics","article_processing_charge":"No","supervisor":[{"last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"_id":"22258","das_tickbox":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-07-28T07:08:15Z","year":"2026","OA_place":"publisher","month":"07","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2663-337X"]},"ddc":["576","610","006"],"citation":{"ieee":"A. Depope, “From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics,” Institute of Science and Technology Austria, 2026.","ama":"Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:10.15479/AT-ISTA-22258","short":"A. Depope, From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science and Technology Austria, 2026.","mla":"Depope, Al. From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22258.","chicago":"Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22258.","apa":"Depope, A. (2026). From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22258","ista":"Depope A. 2026. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria."},"type":"dissertation","language":[{"iso":"eng"}],"acknowledgement":"This work was supported in part by the Swiss National Science Foundation through the\r\nEccellenza Grant \"Improving estimation and prediction of common complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n","doi":"10.15479/AT-ISTA-22258","date_published":"2026-07-11T00:00:00Z","day":"11"},{"DOAJ_listed":"1","researchdata_availability":"yes","doi":"10.1016/j.xgen.2026.101162","day":"13","article_number":"101162","date_published":"2026-05-13T00:00:00Z","citation":{"ista":"Depope A, Bajzik J, Mondelli M, Robinson MR. 2026. Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. 6(5), 101162.","apa":"Depope, A., Bajzik, J., Mondelli, M., & Robinson, M. R. (2026). Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. Elsevier. https://doi.org/10.1016/j.xgen.2026.101162","ama":"Depope A, Bajzik J, Mondelli M, Robinson MR. Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. 2026;6(5). doi:10.1016/j.xgen.2026.101162","short":"A. Depope, J. Bajzik, M. Mondelli, M.R. Robinson, Cell Genomics 6 (2026).","chicago":"Depope, Al, Jakub Bajzik, Marco Mondelli, and Matthew Richard Robinson. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” Cell Genomics. Elsevier, 2026. https://doi.org/10.1016/j.xgen.2026.101162.","mla":"Depope, Al, et al. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” Cell Genomics, vol. 6, no. 5, 101162, Elsevier, 2026, doi:10.1016/j.xgen.2026.101162.","ieee":"A. Depope, J. Bajzik, M. Mondelli, and M. R. Robinson, “Joint modeling of whole-genome sequencing data for human height via approximate message passing,” Cell Genomics, vol. 6, no. 5. Elsevier, 2026."},"type":"journal_article","volume":6,"ddc":["000","570"],"publication":"Cell Genomics","acknowledgement":"We thank Malgorzata Borczyk for creating the gene burden scores. We thank Robin Beaumont, Amedeo Roberto Esposito, Gareth Hawkes, Philip Schniter, Matthew Stephens, Pragya Sur, Peter Visscher, Michael Weedon, and Harry Wright for providing valuable suggestions and comments on earlier versions of the work. This project was funded by a Lopez-Loreta Prize to M.M., an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181), an ERC Starting Grant to M.M. (INF2, project number 101161364), and core funding from ISTA. High-performance computing was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We would like to acknowledge the participants and investigators of the UK Biobank study. We gratefully acknowledge the All of Us participants for their contributions, without whom this research would not have been possible. We also thank the National Institutes of Health All of Us Research Program for making available the participant data (and/or samples and/or cohort) examined in this study.","intvolume":" 6","quality_controlled":"1","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["2666-979X"]},"date_updated":"2026-07-28T07:08:15Z","_id":"21488","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","year":"2026","OA_type":"gold","issue":"5","title":"Joint modeling of whole-genome sequencing data for human height via approximate message passing","article_processing_charge":"Yes","oa_version":"Published Version","publication_status":"published","date_created":"2026-03-23T15:10:03Z","related_material":{"record":[{"id":"22258","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/big-data-and-human-height/","relation":"press_release","description":"News on ISTA website"}]},"abstract":[{"lang":"eng","text":"Human height is a model for the genetic analysis of complex traits, and recent studies suggest the presence of thousands of common genetic variant associations and hundreds of low-frequency/rare variants. Here, we develop a new algorithmic paradigm based on approximate message passing (genomic vector approximate message passing [gVAMP]) for identifying DNA sequence variants associated with complex traits and common diseases in large-scale whole-genome sequencing (WGS) data. We show that gVAMP accurately localizes associations to variants with the correct frequency and position in the DNA, outperforming existing fine-mapping methods in selecting the appropriate genetic variants within WGS data. We then apply gVAMP to jointly model the relationship of tens of millions of WGS variants with human height in hundreds of thousands of UK Biobank individuals. We identify 59 rare variants and gene burden scores alongside many hundreds of DNA regions containing common variant associations and show that understanding the genetic basis of complex traits will require the joint analysis of hundreds of millions of variables measured on millions of people. The polygenic risk scores obtained from gVAMP have high accuracy (including a prediction accuracy of ∼46% for human height) and outperform current methods for downstream tasks such as mixed linear model association testing across 13 UK Biobank traits. In conclusion, gVAMP offers a scalable foundation for a wider range of analyses in WGS data."}],"external_id":{"pmid":["41713425"]},"file":[{"file_id":"22596","file_size":3736705,"date_updated":"2026-07-28T07:06:26Z","date_created":"2026-07-28T07:06:26Z","success":1,"access_level":"open_access","checksum":"6b59686f8d9733add4f23d23f3dd9df0","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2026_CellGenomics_Depope.pdf"}],"pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2026-07-28T07:06:26Z","dataavailabilitystatement":"This project uses the UK Biobank data under project number 35520. UK Biobank genotypic and phenotypic data are available through a formal request at http://www.ukbiobank.ac.uk. It also uses genotypic and phenotypic data from the All of Us study, which are also available through a formal request at https://www.researchallofus.org/data-tools/data-access/. All summary statistic estimates are released publicly on Dryad: https://doi.org/10.5061/dryad.cz8w9gjjc.\r\n•\r\nThe gVAMP code developed in this work is open source and has been deposited on GitHub, where it is publicly available at https://github.com/medical-genomics-group/gVAMP, and the code used to generate the data in the manuscript are available from Zenodo https://doi.org/10.5281/zenodo.17935521. The URLs of other software used are listed in the key resources table.","article_type":"original","author":[{"full_name":"Depope, Al","last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","first_name":"Al"},{"last_name":"Bajzik","first_name":"Jakub","id":"b995e25b-8c4b-11ed-a6d8-f71b7bcd6122","full_name":"Bajzik, Jakub"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"}],"corr_author":"1","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","grant_number":"101161364","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits"},{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"}],"supplementarymaterial":"yes","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"publisher":"Elsevier","status":"public","has_accepted_license":"1","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"scopus_import":"1","oa":1}]