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Finally, we prove that there exist arbitrarily large primes $\\ell$ for which some abelian surface\r\n$A/\\mathbb{Q}$ fails the local-global principle for isogenies of degree $\\ell$."}],"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","author":[{"first_name":"Davide","full_name":"Lombardo, Davide","last_name":"Lombardo"},{"first_name":"Matteo","orcid":"0000-0002-0854-0306","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","last_name":"Verzobio","full_name":"Verzobio, Matteo"}],"month":"01","article_number":"18"},{"status":"public","article_type":"comment","quality_controlled":"1","file":[{"date_created":"2024-02-06T13:56:15Z","relation":"main_file","checksum":"32b3788f7085cf44a84108d8faaff3ce","creator":"dernst","file_id":"14944","content_type":"application/pdf","access_level":"open_access","file_size":5942467,"file_name":"2024_Neuron_Cheung.pdf","date_updated":"2024-02-06T13:56:15Z","success":1}],"ddc":["570"],"abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"date_published":"2024-01-17T00:00:00Z","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","month":"01","author":[{"last_name":"Cheung","full_name":"Cheung, Giselle T","first_name":"Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","last_name":"Pauler","full_name":"Pauler, Florian"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"last_name":"Krausgruber","full_name":"Krausgruber, Thomas","first_name":"Thomas"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher"},{"id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","first_name":"Martin","full_name":"Schrammel, Martin","last_name":"Schrammel"},{"last_name":"Özgen","full_name":"Özgen, Natalie Y","first_name":"Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090"},{"last_name":"Ivec","full_name":"Ivec, Alexis","first_name":"Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"has_accepted_license":"1","doi":"10.1016/j.neuron.2023.11.009","page":"230-246.e11","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issnl":["1234-5678"],"eisbn":["1234995621"],"issn":["0896-6273"]},"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/"}]},"language":[{"iso":"eng"}],"publication":"Neuron","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Elsevier","intvolume":"       112","external_id":{"pmid":["38096816"]},"title":"Multipotent progenitors instruct ontogeny of the superior colliculus","day":"17","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","volume":112,"year":"2024","issue":"2","date_updated":"2025-05-14T09:39:37Z","_id":"12875","file_date_updated":"2024-02-06T13:56:15Z","project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"}],"department":[{"_id":"SiHi"},{"_id":"RySh"}],"publication_status":"published","date_created":"2023-04-27T09:41:48Z","pmid":1,"license":"https://creativecommons.org/licenses/by/4.0/"},{"external_id":{"arxiv":["2304.01430"]},"status":"public","title":"Divided attention: Unsupervised multi-object discovery with contextually separated slots","day":"03","quality_controlled":"1","file":[{"success":1,"date_updated":"2024-02-12T08:40:36Z","file_name":"2024_CPAL_Lao.pdf","file_size":8038511,"access_level":"open_access","content_type":"application/pdf","file_id":"14978","creator":"dernst","checksum":"8fad894c34f1b3d5a14fb8ffb12f7277","relation":"main_file","date_created":"2024-02-12T08:40:36Z"}],"abstract":[{"lang":"eng","text":"We introduce a method to segment the visual field into independently moving regions, trained with no ground truth or supervision. It consists of an adversarial conditional encoder-decoder architecture based on Slot Attention, modified to use the image as context to decode optical flow without attempting to reconstruct the image itself. In the resulting multi-modal representation, one modality (flow) feeds the encoder to produce separate latent codes (slots), whereas the other modality (image) conditions the decoder to generate the first (flow) from the slots. This design frees the representation from having to encode complex nuisance variability in the image due to, for instance, illumination and reflectance properties of the scene. Since customary autoencoding based on minimizing the reconstruction error does not preclude the entire flow from being encoded into a single slot, we modify the loss to an adversarial criterion based on Contextual Information Separation. The resulting min-max optimization fosters the separation of objects and their assignment to different attention slots, leading to Divided Attention, or DivA. DivA outperforms recent unsupervised multi-object motion segmentation methods while tripling run-time speed up to 104FPS and reducing the performance gap from supervised methods to 12% or less. DivA can handle different numbers of objects and different image sizes at training and test time, is invariant to permutation of object labels, and does not require explicit regularization."}],"ddc":["000"],"date_published":"2024-01-03T00:00:00Z","article_processing_charge":"No","month":"01","author":[{"last_name":"Lao","full_name":"Lao, Dong","first_name":"Dong"},{"last_name":"Hu","full_name":"Hu, Zhengyang","first_name":"Zhengyang"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello"},{"full_name":"Yang, Yanchao","last_name":"Yang","first_name":"Yanchao"},{"last_name":"Soatto","full_name":"Soatto, Stefano","first_name":"Stefano"}],"year":"2024","has_accepted_license":"1","date_updated":"2025-02-13T08:10:28Z","_id":"14213","type":"conference","file_date_updated":"2024-02-12T08:40:36Z","publication_identifier":{"issnl":["1234-4321"]},"conference":{"location":"Hong Kong, China","start_date":"2024-01-03","end_date":"2024-01-03","name":"CPAL: Conference on Parsimony and Learning"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"oa_version":"Published Version","publication":"1st Conference on Parsimony and Learning","arxiv":1,"publication_status":"published","date_created":"2023-08-22T14:19:59Z","oa":1},{"publication_status":"published","pmid":1,"date_created":"2023-09-01T11:32:02Z","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"file_date_updated":"2024-01-30T12:59:57Z","date_updated":"2025-07-02T12:51:02Z","_id":"14251","department":[{"_id":"JiFr"}],"citation":{"ieee":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, and J. Friml, “Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution,” <i>Plant Communications</i>, vol. 5, no. 1. Elsevier, 2024.","short":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, J. Friml, Plant Communications 5 (2024).","apa":"Tang, H., Lu, K., Zhang, Y., Cheng, Y., Tu, S., &#38; Friml, J. (2024). Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>","ista":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. 2024. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 5(1), 100669.","chicago":"Tang, Han, KJ Lu, Y Zhang, YL Cheng, SL Tu, and Jiří Friml. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>.","ama":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>","mla":"Tang, Han, et al. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>, vol. 5, no. 1, 100669, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>."},"year":"2024","issue":"1","title":"Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution","day":"08","external_id":{"pmid":["37528584"]},"acknowledgement":"This work was supported by the ERC grant (PR1023ERC02) to H. T. and J. F., and by the ministry of science and technology (grant number 110-2636-B-005-001) to K. J. L.","volume":5,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         5","oa":1,"publisher":"Elsevier","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2590-3462"],"issnl":["1234-4567"]},"doi":"10.1016/j.xplc.2023.100669","language":[{"iso":"eng"}],"ec_funded":1,"publication":"Plant Communications","oa_version":"Published Version","month":"01","author":[{"id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","orcid":"0000-0001-6152-6637","first_name":"Han","full_name":"Tang, Han","last_name":"Tang"},{"first_name":"KJ","full_name":"Lu, KJ","last_name":"Lu"},{"full_name":"Zhang, Y","last_name":"Zhang","first_name":"Y"},{"full_name":"Cheng, YL","last_name":"Cheng","first_name":"YL"},{"first_name":"SL","last_name":"Tu","full_name":"Tu, SL"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"}],"article_processing_charge":"Yes","scopus_import":"1","has_accepted_license":"1","article_number":"100669","quality_controlled":"1","status":"public","article_type":"original","ddc":["580"],"abstract":[{"text":"The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms.","lang":"eng"}],"date_published":"2024-01-08T00:00:00Z","file":[{"date_created":"2024-01-30T12:59:57Z","relation":"main_file","creator":"dernst","checksum":"edbc44c6d4a394d2bf70f92fdbb08f0a","access_level":"open_access","file_size":2825565,"file_id":"14911","content_type":"application/pdf","success":1,"date_updated":"2024-01-30T12:59:57Z","file_name":"2023_PlantCommunications_Tang.pdf"}]},{"date_updated":"2026-03-18T11:15:21Z","_id":"14479","supplementarymaterial":"yes","department":[{"_id":"SyCr"}],"citation":{"short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>.","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. 2024;34(4):902-909.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>","ieee":"E. Csata <i>et al.</i>, “Fungal infection alters collective nutritional intake of ant colonies,” <i>Current Biology</i>, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.26.564092"}],"publication_status":"published","date_created":"2023-10-31T13:30:20Z","pmid":1,"external_id":{"pmid":["38307022"]},"title":"Fungal infection alters collective nutritional intake of ant colonies","day":"26","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","volume":34,"researchdata_availability":"unclear","dataavailabilitystatement":"no DAS","year":"2024","issue":"4","doi":"10.1016/j.cub.2024.01.017","page":"902-909.e6","type":"journal_article","publication_identifier":{"issnl":["1234-5678"],"issn":["0960-9822"],"eissn":["1879-0445"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa_version":"Preprint","publication":"Current Biology","publisher":"Elsevier","oa":1,"intvolume":"        34","status":"public","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication."}],"date_published":"2024-02-26T00:00:00Z","article_processing_charge":"No","scopus_import":"1","month":"02","author":[{"last_name":"Csata","full_name":"Csata, Eniko","first_name":"Eniko"},{"first_name":"Alfonso","full_name":"Perez-Escudero, Alfonso","last_name":"Perez-Escudero"},{"full_name":"Laury, Emmanuel","last_name":"Laury","first_name":"Emmanuel"},{"id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna","full_name":"Leitner, Hanna","last_name":"Leitner"},{"first_name":"Gerard","last_name":"Latil","full_name":"Latil, Gerard"},{"first_name":"Juerge","full_name":"Heinze, Juerge","last_name":"Heinze"},{"first_name":"Stephen","last_name":"Simpson","full_name":"Simpson, Stephen"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"}]},{"related_material":{"record":[{"relation":"used_in_publication","id":"15009","status":"public"}]},"citation":{"ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","short":"M.N. Elkrewi, (2024).","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>.","mla":"Elkrewi, Marwan N. <i>Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>"},"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"doi":"10.15479/AT:ISTA:14705","_id":"14705","date_updated":"2026-05-18T12:46:40Z","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"first_name":"Vincent K","contributor_type":"researcher","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"contributor_type":"project_member","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"last_name":"Vicoso","first_name":"Beatriz","contributor_type":"supervisor","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","contributor_type":"researcher","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"type":"research_data","project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"date_created":"2023-12-22T13:40:48Z","publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2024-01-02T00:00:00Z","ddc":["576"],"abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"status":"public","day":"02","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","year":"2024","has_accepted_license":"1","retracted":"1","article_processing_charge":"No","author":[{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"month":"01"},{"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"grant_number":"26380","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","name":"Polygenic Adaptation in a Metapopulation"}],"file_date_updated":"2024-01-03T18:31:34Z","_id":"14711","date_updated":"2025-05-26T09:05:10Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_created":"2023-12-26T22:49:53Z","day":"19","title":"Local adaptation, genetic load and extinction in metapopulations","supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"last_name":"Polechova","full_name":"Polechova, Jitka","first_name":"Jitka"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}],"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2663 - 337X"]},"acknowledged_ssus":[{"_id":"SSU"}],"type":"dissertation","page":"183","doi":"10.15479/at:ista:14711","degree_awarded":"MS","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10658"},{"status":"public","relation":"part_of_dissertation","id":"10787"},{"status":"public","relation":"part_of_dissertation","id":"14732"}]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","date_published":"2024-01-19T00:00:00Z","abstract":[{"lang":"eng","text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management."}],"ddc":["576"],"file":[{"relation":"source_file","date_created":"2024-01-03T18:30:13Z","checksum":"de179b1c6758f182ff0c70d8b38c1501","creator":"oolusany","content_type":"application/zip","file_id":"14730","file_size":16986244,"access_level":"closed","date_updated":"2024-01-03T18:30:13Z","file_name":"FinalSubmission_Thesis_OLUSANYA.zip"},{"content_type":"application/pdf","file_id":"14731","file_size":6460403,"access_level":"open_access","date_updated":"2024-01-03T18:31:34Z","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","success":1,"relation":"main_file","date_created":"2024-01-03T18:31:34Z","checksum":"0e331585e3cd4823320aab4e69e64ccf","creator":"oolusany"}],"author":[{"first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya","full_name":"Olusanya, Oluwafunmilola O"}],"month":"01","article_processing_charge":"No","has_accepted_license":"1"},{"year":"2024","title":"Experimental evaluation of fully dynamic k-means via coresets","day":"04","external_id":{"arxiv":["2310.18034"]},"acknowledgement":"This   project   has   received   funding   from   the   Euro-pean  Research  Council  (ERC)  under  the  EuropeanUnion’s  Horizon  2020  research  and  innovation  programme  (Grant  agreement  No.   101019564  “The  De-sign  of  Modern  Fully  Dynamic  Data  Structures  (Mo-DynStruct)”  and  the  Austrian  Science  Fund  (FWF)project Z 422-N, project “Static and Dynamic Hierar-chical  Graph  Decompositions”,  I  5982-N,  and  project“Fast  Algorithms  for  a  Reactive  Network  Layer  (Re-actNet)”, P 33775-N, with additional funding from thenetidee SCIENCE Stiftung, 2020–2024.D.  Sauplic  has  received  funding  from  the  Euro-pean  Union’s  Horizon  2020  research  and  innovation programme under the Marie Sklodowska-Curie    grant    agreementNo 101034413.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.18034"}],"publication_status":"published","date_created":"2024-01-09T16:22:47Z","project":[{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"conference":{"name":"ALENEX: Workshop on Algorithm Engineering and Experiments","end_date":"2024-01-08","start_date":"2024-01-07","location":"Alexandria, VA, United States"},"date_updated":"2025-07-15T12:51:52Z","_id":"14769","department":[{"_id":"MoHe"}],"citation":{"ieee":"M. H. Henzinger, D. Saulpic, and L. Sidl, “Experimental evaluation of fully dynamic k-means via coresets,” in <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>, Alexandria, VA, United States, 2024, pp. 220–233.","mla":"Henzinger, Monika H., et al. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>, Society for Industrial &#38; Applied Mathematics, 2024, pp. 220–33, doi:<a href=\"https://doi.org/10.1137/1.9781611977929.17\">10.1137/1.9781611977929.17</a>.","ama":"Henzinger MH, Saulpic D, Sidl L. Experimental evaluation of fully dynamic k-means via coresets. In: <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>. Society for Industrial &#38; Applied Mathematics; 2024:220-233. doi:<a href=\"https://doi.org/10.1137/1.9781611977929.17\">10.1137/1.9781611977929.17</a>","chicago":"Henzinger, Monika H, David Saulpic, and Leonhard Sidl. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” In <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i>, 220–33. Society for Industrial &#38; Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/1.9781611977929.17\">https://doi.org/10.1137/1.9781611977929.17</a>.","ista":"Henzinger MH, Saulpic D, Sidl L. 2024. Experimental evaluation of fully dynamic k-means via coresets. 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. ALENEX: Workshop on Algorithm Engineering and Experiments, 220–233.","apa":"Henzinger, M. H., Saulpic, D., &#38; Sidl, L. (2024). Experimental evaluation of fully dynamic k-means via coresets. In <i>2024 Proceedings of the Symposium on Algorithm Engineering and Experiments</i> (pp. 220–233). Alexandria, VA, United States: Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977929.17\">https://doi.org/10.1137/1.9781611977929.17</a>","short":"M.H. Henzinger, D. Saulpic, L. Sidl, in:, 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial &#38; Applied Mathematics, 2024, pp. 220–233."},"month":"01","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"first_name":"David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","last_name":"Saulpic","full_name":"Saulpic, David"},{"last_name":"Sidl","full_name":"Sidl, Leonhard","first_name":"Leonhard","id":"8b563fd0-b441-11ee-9101-a3891c61efa6"}],"scopus_import":"1","article_processing_charge":"No","quality_controlled":"1","status":"public","abstract":[{"lang":"eng","text":"For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution."}],"date_published":"2024-01-04T00:00:00Z","publisher":"Society for Industrial & Applied Mathematics","oa":1,"type":"conference","publication_identifier":{"eisbn":["9781611977929"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"220-233","doi":"10.1137/1.9781611977929.17","language":[{"iso":"eng"}],"ec_funded":1,"arxiv":1,"publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","oa_version":"Preprint"}]