[{"oa_version":"Published Version","ec_funded":1,"_id":"19854","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"Asynchronous Boolean networks are a type of discrete dynamical system in which each variable can take one of two states, and a single variable state is updated in each time step according to pre-selected rules. Boolean networks are popular in systems biology due to their ability to model long-term biological phenotypes within a qualitative, predictive framework. Boolean networks model phenotypes as attractors, which are closely linked to minimal trap spaces (inescapable hypercubes in the system’s state space). In biological applications, attractors and minimal trap spaces are typically in one-to-one correspondence. However, this correspondence is not guaranteed: motif-avoidant attractors (MAAs) that lie outside minimal trap spaces are possible. MAAs are rare and poorly understood, despite recent efforts. In this contribution to the BMB & JMB Special Collection “Problems, Progress and Perspectives in Mathematical and Computational Biology”, we summarize the current state of knowledge regarding MAAs and present several novel observations regarding their response to node deletion reductions and linear extensions of edges. We conduct large-scale computational studies on an ensemble of 14 000 models derived from published Boolean models of biological systems, and more than 100 million Random Boolean Networks. Our findings quantify the rarity of MAAs; in particular, we only observed MAAs in biological models after applying standard simplification methods, highlighting the role of network reduction in introducing MAAs into the dynamics. We also show that MAAs are fragile to linear extensions: in sparse networks, even a single linear node can disrupt virtually all MAAs. Motivated by this observation, we improve the upper bound on the number of delays needed to disrupt a motif-avoidant attractor."}],"author":[{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel","orcid":"0000-0003-1993-0331","last_name":"Pastva","first_name":"Samuel"},{"full_name":"Park, Kyu Hyong","first_name":"Kyu Hyong","last_name":"Park"},{"full_name":"Huvar, Ondřej","first_name":"Ondřej","last_name":"Huvar"},{"full_name":"Rozum, Jordan C.","last_name":"Rozum","first_name":"Jordan C."},{"first_name":"Réka","last_name":"Albert","full_name":"Albert, Réka"}],"external_id":{"arxiv":["2410.03976"],"isi":["001507009300001"]},"department":[{"_id":"ToHe"}],"date_updated":"2025-09-30T13:36:46Z","file_date_updated":"2025-06-23T11:10:01Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"file_size":1243163,"date_updated":"2025-06-23T11:10:01Z","file_id":"19871","content_type":"application/pdf","relation":"main_file","file_name":"2025_JourMathBiology_Pastva.pdf","creator":"dernst","success":1,"date_created":"2025-06-23T11:10:01Z","checksum":"a385ef2662f1d0c3497ed3f2721fe594","access_level":"open_access"}],"publication_status":"published","volume":91,"year":"2025","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        91","article_number":"11","date_published":"2025-06-12T00:00:00Z","citation":{"short":"S. Pastva, K.H. Park, O. Huvar, J.C. Rozum, R. Albert, Journal of Mathematical Biology 91 (2025).","ista":"Pastva S, Park KH, Huvar O, Rozum JC, Albert R. 2025. An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? Journal of Mathematical Biology. 91, 11.","apa":"Pastva, S., Park, K. H., Huvar, O., Rozum, J. C., &#38; Albert, R. (2025). An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? <i>Journal of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00285-025-02235-8\">https://doi.org/10.1007/s00285-025-02235-8</a>","mla":"Pastva, Samuel, et al. “An Open Problem: Why Are Motif-Avoidant Attractors so Rare in Asynchronous Boolean Networks?” <i>Journal of Mathematical Biology</i>, vol. 91, 11, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00285-025-02235-8\">10.1007/s00285-025-02235-8</a>.","ama":"Pastva S, Park KH, Huvar O, Rozum JC, Albert R. An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? <i>Journal of Mathematical Biology</i>. 2025;91. doi:<a href=\"https://doi.org/10.1007/s00285-025-02235-8\">10.1007/s00285-025-02235-8</a>","ieee":"S. Pastva, K. H. Park, O. Huvar, J. C. Rozum, and R. Albert, “An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?,” <i>Journal of Mathematical Biology</i>, vol. 91. Springer Nature, 2025.","chicago":"Pastva, Samuel, Kyu Hyong Park, Ondřej Huvar, Jordan C. Rozum, and Réka Albert. “An Open Problem: Why Are Motif-Avoidant Attractors so Rare in Asynchronous Boolean Networks?” <i>Journal of Mathematical Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00285-025-02235-8\">https://doi.org/10.1007/s00285-025-02235-8</a>."},"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","publication":"Journal of Mathematical Biology","license":"https://creativecommons.org/licenses/by/4.0/","month":"06","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Springer Nature","OA_type":"hybrid","title":"An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?","ddc":["000"],"corr_author":"1","publication_identifier":{"issn":["0303-6812"],"eissn":["1432-1416"]},"scopus_import":"1","date_created":"2025-06-22T22:02:05Z","arxiv":1,"doi":"10.1007/s00285-025-02235-8","has_accepted_license":"1","status":"public","type":"journal_article","day":"12","acknowledgement":"Ondřej Huvar has been supported by the Czech Science Foundation grant No. GA22-10845S. Samuel Pastva received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. Kyu Hyong Park and Réka Albert have been supported by NSF grant MCB 1715826 and ARO grant 79961-SM-MUR. No funding bodies had any role in study design, analysis, decision to publish, or preparation of the manuscript."},{"file_date_updated":"2025-06-23T11:02:59Z","date_updated":"2025-09-30T13:34:20Z","publication_status":"published","volume":540,"year":"2025","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"file_name":"2025_MonthlyNoticesRAS_Gazagnes.pdf","file_size":3111567,"date_updated":"2025-06-23T11:02:59Z","content_type":"application/pdf","file_id":"19870","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_created":"2025-06-23T11:02:59Z","checksum":"f912c990a0474f1ddf9be6b8a89c7759"}],"oa":1,"page":"2331-2348","article_type":"original","oa_version":"Published Version","_id":"19855","department":[{"_id":"JoMa"}],"abstract":[{"text":"We present indirect constraints on the absolute escape fraction of ionizing photons (f_{\\rm esc}^{\\rm LyC}) of the system GN 42912 which comprises two luminous galaxies (M_{\\rm UV} magnitudes of -20.89 and -20.37) at z\\sim7.5, GN 42912-NE and GN 42912-SW, to determine their contribution to the ionizing photon budget of the Epoch of Reionization (EoR). The high-resolution James Webb Space Telescope NIRSpec and NIRCam observations reveal the two galaxies are separated by only ~0.1\" (0.5 kpc) on the sky and have a 358 km s^{-1} velocity separation. GN 42912-NE and GN 42912-SW are relatively massive for this redshift (log(M_\\ast/M_\\odot) \\sim 8.4 and 8.9, respectively), with gas-phase metallicities of 18 per cent and 23 per cent solar, O_{32} ratios of 5.3 and >5.8, and \\beta slopes of -1.92 and -1.51, respectively. We use the Mg II\\lambda\\lambda2796,2803 doublet to constrain f_{\\rm esc}^{\\rm LyC}. Mg II has an ionization potential close to that of neutral hydrogen and, in the optically thin regime, can be used as an indirect tracer of the LyC leakage. We establish realistic conservative upper limits on f_{\\rm esc}^{\\rm LyC} of 8.5 per cent for GN 42912-NE and 14 per cent for GN 42912-SW. These estimates align with f_{\\rm esc}^{\\rm LyC} trends observed with \\beta, O_{32}, and the H\\beta equivalent width at z<4. The small inferred ionized region sizes (<0.3 pMpc) around both galaxies indicate they have not ionized a significant fraction of the surrounding neutral gas. While these z>7 f_{\\rm esc}^{\\rm LyC} constraints do not decisively determine a specific reionization model, they support a minor contribution from these two relatively luminous galaxies to the EoR.","lang":"eng"}],"external_id":{"arxiv":["2410.03337"],"isi":["001506103600001"]},"author":[{"first_name":"S.","last_name":"Gazagnes","full_name":"Gazagnes, S."},{"first_name":"J.","last_name":"Chisholm","full_name":"Chisholm, J."},{"full_name":"Endsley, R.","last_name":"Endsley","first_name":"R."},{"full_name":"Berg, D. A.","last_name":"Berg","first_name":"D. A."},{"last_name":"Leclercq","first_name":"F.","full_name":"Leclercq, F."},{"full_name":"Jurlin, N.","last_name":"Jurlin","first_name":"N."},{"first_name":"A.","last_name":"Saldana-Lopez","full_name":"Saldana-Lopez, A."},{"full_name":"Finkelstein, S. L.","last_name":"Finkelstein","first_name":"S. L."},{"full_name":"Flury, S. R.","first_name":"S. R.","last_name":"Flury"},{"full_name":"Guseva, N. G.","first_name":"N. G.","last_name":"Guseva"},{"full_name":"Henry, A.","first_name":"A.","last_name":"Henry"},{"last_name":"Izotov","first_name":"Y. I.","full_name":"Izotov, Y. I."},{"last_name":"Jung","first_name":"I.","full_name":"Jung, I."},{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","last_name":"Matthee"},{"first_name":"D.","last_name":"Schaerer","full_name":"Schaerer, D."}],"scopus_import":"1","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"ddc":["520"],"issue":"3","title":"A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization","OA_type":"gold","day":"01","type":"journal_article","acknowledgement":"This work is based on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–03127 for JWST. These observations are associated with program #01871. Support for program #01871 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–03127. SG is grateful for the support enabled by the Harlan J. Smith McDonald fellowship. YI and NG acknowledge support from the Simons Foundation and the National Academy of Sciences of Ukraine (Project 0121U109612). ASL acknowledges support from Knut and Alice Wallenberg Foundation.","date_created":"2025-06-22T22:02:05Z","doi":"10.1093/mnras/staf768","arxiv":1,"has_accepted_license":"1","status":"public","citation":{"ieee":"S. Gazagnes <i>et al.</i>, “A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 540, no. 3. Oxford University Press, pp. 2331–2348, 2025.","chicago":"Gazagnes, S., J. Chisholm, R. Endsley, D. A. Berg, F. Leclercq, N. Jurlin, A. Saldana-Lopez, et al. “A Negligible Contribution of Two Luminous z ∼7.5 Galaxies to the Ionizing Photon Budget of Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/mnras/staf768\">https://doi.org/10.1093/mnras/staf768</a>.","ama":"Gazagnes S, Chisholm J, Endsley R, et al. A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. 2025;540(3):2331-2348. doi:<a href=\"https://doi.org/10.1093/mnras/staf768\">10.1093/mnras/staf768</a>","mla":"Gazagnes, S., et al. “A Negligible Contribution of Two Luminous z ∼7.5 Galaxies to the Ionizing Photon Budget of Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 540, no. 3, Oxford University Press, 2025, pp. 2331–48, doi:<a href=\"https://doi.org/10.1093/mnras/staf768\">10.1093/mnras/staf768</a>.","apa":"Gazagnes, S., Chisholm, J., Endsley, R., Berg, D. A., Leclercq, F., Jurlin, N., … Schaerer, D. (2025). A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staf768\">https://doi.org/10.1093/mnras/staf768</a>","ista":"Gazagnes S, Chisholm J, Endsley R, Berg DA, Leclercq F, Jurlin N, Saldana-Lopez A, Finkelstein SL, Flury SR, Guseva NG, Henry A, Izotov YI, Jung I, Matthee JJ, Schaerer D. 2025. A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization. Monthly Notices of the Royal Astronomical Society. 540(3), 2331–2348.","short":"S. Gazagnes, J. Chisholm, R. Endsley, D.A. Berg, F. Leclercq, N. Jurlin, A. Saldana-Lopez, S.L. Finkelstein, S.R. Flury, N.G. Guseva, A. Henry, Y.I. Izotov, I. Jung, J.J. Matthee, D. Schaerer, Monthly Notices of the Royal Astronomical Society 540 (2025) 2331–2348."},"date_published":"2025-07-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       540","month":"07","OA_place":"publisher","publisher":"Oxford University Press","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes","publication":"Monthly Notices of the Royal Astronomical Society"},{"publication":"Physical Review Letters","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"American Physical Society","month":"06","article_number":"238201","intvolume":"       134","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-06-13T00:00:00Z","citation":{"short":"M. Zu, A.A. Desai, C.P. Goodrich, Physical Review Letters 134 (2025).","apa":"Zu, M., Desai, A. A., &#38; Goodrich, C. P. (2025). Fully independent response in disordered solids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">https://doi.org/10.1103/PhysRevLett.134.238201</a>","ista":"Zu M, Desai AA, Goodrich CP. 2025. Fully independent response in disordered solids. Physical Review Letters. 134(23), 238201.","mla":"Zu, Mengjie, et al. “Fully Independent Response in Disordered Solids.” <i>Physical Review Letters</i>, vol. 134, no. 23, 238201, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">10.1103/PhysRevLett.134.238201</a>.","ama":"Zu M, Desai AA, Goodrich CP. Fully independent response in disordered solids. <i>Physical Review Letters</i>. 2025;134(23). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">10.1103/PhysRevLett.134.238201</a>","chicago":"Zu, Mengjie, Aayush A Desai, and Carl Peter Goodrich. “Fully Independent Response in Disordered Solids.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">https://doi.org/10.1103/PhysRevLett.134.238201</a>.","ieee":"M. Zu, A. A. Desai, and C. P. Goodrich, “Fully independent response in disordered solids,” <i>Physical Review Letters</i>, vol. 134, no. 23. American Physical Society, 2025."},"has_accepted_license":"1","status":"public","arxiv":1,"doi":"10.1103/PhysRevLett.134.238201","date_created":"2025-06-22T22:02:06Z","acknowledgement":"We gratefully acknowledge Edouard Hannezo for helpful comments on the manuscript. The work was funded by the Institute of Science and Technology Austria.","type":"journal_article","day":"13","OA_type":"hybrid","issue":"23","title":"Fully independent response in disordered solids","ddc":["530"],"corr_author":"1","scopus_import":"1","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"author":[{"first_name":"Mengjie","last_name":"Zu","full_name":"Zu, Mengjie","id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2"},{"last_name":"Desai","first_name":"Aayush A","id":"502cfd30-32c1-11ee-a9a4-d8dad5c6739e","full_name":"Desai, Aayush A"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter"}],"external_id":{"isi":["001509005900006"],"arxiv":["2412.05031"]},"abstract":[{"lang":"eng","text":"Unlike in crystals, it is difficult to trace emergent material properties of amorphous solids to their underlying structure. Nevertheless, one can tune features of a disordered spring network, ranging from bulk elastic constants to specific allosteric responses, through highly precise alterations of the structure. This has been understood through the notion of independent bond-level response—the observation that, in many cases, different springs have different effects on different properties. While this idea has motivated inverse design in numerous contexts, it has not been formalized and quantified in a general context that not just informs but enables and predicts inverse design. Here, we show how to quantify independent response by linearizing the simultaneous change in multiple emergent features, and introduce the much stronger notion of fully independent response. Remarkably, we find that the mechanical properties of disordered solids are always fully independent across a wide array of scenarios, regardless of the target features, tunable parameters, system size, dimensionality, and class of interactions. Furthermore, our formulation quantifies the susceptibility of features to parameter changes, which is correlated with the maximum linear tunability. We also demonstrate the implications for multifeature inverse design beyond the linear regime. These results formalize our understanding of a key fundamental difference between ordered and disordered solids while also creating a practical tool to both understand and perform inverse design."}],"department":[{"_id":"CaGo"},{"_id":"IlCa"}],"_id":"19856","oa_version":"Published Version","article_type":"original","oa":1,"file":[{"file_name":"2025_PhysReviewLetters_Zu.pdf","date_updated":"2025-06-23T11:41:08Z","file_size":1132625,"relation":"main_file","content_type":"application/pdf","file_id":"19874","access_level":"open_access","success":1,"creator":"dernst","checksum":"040b6779c91aac62c15a9b2cc417b360","date_created":"2025-06-23T11:41:08Z"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/infinite-diversity-in-infinite-combinations/","description":"News on ISTA website","relation":"press_release"}]},"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2025","volume":134,"publication_status":"published","date_updated":"2026-04-28T13:28:02Z","file_date_updated":"2025-06-23T11:41:08Z"},{"department":[{"_id":"CaGu"}],"abstract":[{"text":"Bacteria have evolved a wide range of defence strategies to protect themselves against bacterial viruses (phages). Most known bacterial antiphage defence systems target phages with DNA genomes, which raises the question of how bacteria defend against phages with RNA genomes. Bacterial toxin–antitoxin systems that cleave intracellular RNA could potentially protect bacteria against RNA phages, but this has not been explored experimentally. In this study, we investigated the role of a model toxin–antitoxin system, MazEF, in protecting Escherichia coli against two RNA phage species. When challenged with these phages, the native presence of mazEF moderately reduced population susceptibility and increased the survival of individual E. coli cells. Genomic analysis further revealed an underrepresentation of the MazF cleavage site in genomes of RNA phages infecting E. coli, indicating selection against cleavage. These results show that, in addition to other physiological roles, RNA-degrading toxin–antitoxin systems may also help defend against RNA phages.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"author":[{"last_name":"Nikolic","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"},{"orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet"}],"external_id":{"isi":["001505019800001"],"pmid":["40494395"]},"oa":1,"article_type":"original","oa_version":"Published Version","_id":"19857","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","call_identifier":"FWF","_id":"26956E74-B435-11E9-9278-68D0E5697425","grant_number":"V00738"}],"ec_funded":1,"publication_status":"published","volume":21,"year":"2025","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"access_level":"open_access","checksum":"016f644ed068f8609ded306ad26dbd3f","date_created":"2025-06-23T11:34:39Z","success":1,"creator":"dernst","file_name":"2025_BiologyLetters_Nikolic.pdf","relation":"main_file","file_id":"19873","content_type":"application/pdf","date_updated":"2025-06-23T11:34:39Z","file_size":1850797}],"file_date_updated":"2025-06-23T11:34:39Z","date_updated":"2025-09-30T13:38:08Z","pmid":1,"month":"06","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"The Royal Society","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication":"Biology Letters","date_published":"2025-06-11T00:00:00Z","citation":{"mla":"Nikolic, Nela, et al. “A Bacterial Toxin-Antitoxin System as a Native Defence Element against RNA Phages.” <i>Biology Letters</i>, vol. 21, no. 6, 20250080, The Royal Society, 2025, doi:<a href=\"https://doi.org/10.1098/rsbl.2025.0080\">10.1098/rsbl.2025.0080</a>.","chicago":"Nikolic, Nela, Maros Pleska, Tobias Bergmiller, and Calin C Guet. “A Bacterial Toxin-Antitoxin System as a Native Defence Element against RNA Phages.” <i>Biology Letters</i>. The Royal Society, 2025. <a href=\"https://doi.org/10.1098/rsbl.2025.0080\">https://doi.org/10.1098/rsbl.2025.0080</a>.","ieee":"N. Nikolic, M. Pleska, T. Bergmiller, and C. C. Guet, “A bacterial toxin-antitoxin system as a native defence element against RNA phages,” <i>Biology Letters</i>, vol. 21, no. 6. The Royal Society, 2025.","ama":"Nikolic N, Pleska M, Bergmiller T, Guet CC. A bacterial toxin-antitoxin system as a native defence element against RNA phages. <i>Biology Letters</i>. 2025;21(6). doi:<a href=\"https://doi.org/10.1098/rsbl.2025.0080\">10.1098/rsbl.2025.0080</a>","short":"N. Nikolic, M. Pleska, T. Bergmiller, C.C. Guet, Biology Letters 21 (2025).","ista":"Nikolic N, Pleska M, Bergmiller T, Guet CC. 2025. A bacterial toxin-antitoxin system as a native defence element against RNA phages. Biology Letters. 21(6), 20250080.","apa":"Nikolic, N., Pleska, M., Bergmiller, T., &#38; Guet, C. C. (2025). A bacterial toxin-antitoxin system as a native defence element against RNA phages. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2025.0080\">https://doi.org/10.1098/rsbl.2025.0080</a>"},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"20250080","intvolume":"        21","type":"journal_article","day":"11","acknowledgement":"This work was supported by ISTFELLOW (People Program – Marie Curie Actions of the European Union’s Seventh Framework Program FP7 under REA grant agreement 291734), the FWF (Austrian Science Fund) Elise Richter Program project number V 738 and the Wellcome Trust Institutional Strategic Support Award (WT105618MA), to N.N. M.P. was a Simons Foundation Fellow of the Life Sciences Research Foundation. We are grateful to Kathrin Tomasek, Lisa Butt, Chris Estell, Alys Jepson, Franklin Nobrega, Stefano Pagliara, Remy Chait, Steve West, Vicki Gold, Josh Eaton, Ivana Gudelj and Rob Beardmore for useful discussions and technical support, as well as to Robin Wright, Christian Fitch and Ben Temperton for sharing equipment. We thank Laurence Van Melderen for sharing the strains. We acknowledge the IST Austria Lab Support Facility, LSI Technical Services Team at the University of Exeter and the Translational Research Exchange @ Exeter (TREE) network. N.N. is grateful to Fabrice Gielen for his support.","date_created":"2025-06-22T22:02:06Z","doi":"10.1098/rsbl.2025.0080","status":"public","has_accepted_license":"1","corr_author":"1","ddc":["570"],"scopus_import":"1","publication_identifier":{"eissn":["1744-957X"],"issn":["1744-9561"]},"OA_type":"hybrid","issue":"6","title":"A bacterial toxin-antitoxin system as a native defence element against RNA phages"},{"department":[{"_id":"MoHe"}],"author":[{"first_name":"Antoine","last_name":"El-Hayek","full_name":"El-Hayek, Antoine","orcid":"0000-0003-4268-7368","id":"888a098e-fcac-11ee-aff7-d347be57b725"},{"full_name":"Hanauer, Kathrin","first_name":"Kathrin","last_name":"Hanauer"},{"last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"}],"external_id":{"arxiv":["2310.01149"],"isi":["001532136900004"]},"abstract":[{"text":"Given a graph G that undergoes a sequence of edge insertions and deletions, we study the Maximum k-Edge Coloring problem (MkEC): Having access to k different colors, color as many edges of G as possible such that no two adjacent edges share the same color. While this problem is different from simply maintaining a b-matching with b = k, the two problems are related. However, maximum b-matching can be solved efficiently in the static setting, whereas MkEC is NP-hard and even APX-hard for k ≥ 2. \r\nWe present new results on both problems: For b-matching, we show a new integrality gap result and we adapt Wajc’s matching sparsification scheme [David Wajc, 2020] for the case where b is a constant.\r\nUsing these as basis, we give three new algorithms for the dynamic MkEC problem: Our MatchO algorithm builds on the dynamic (2+ε)-approximation algorithm of Bhattacharya, Gupta, and Mohan [Sayan Bhattacharya et al., 2017] for b-matching and achieves a (2+ε)(k+1)/k-approximation in O(poly(log n, ε^-1)) update time against an oblivious adversary. Our MatchA algorithm builds on the dynamic (7+ε)-approximation algorithm by Bhattacharya, Henzinger, and Italiano [Sayan Bhattacharya et al., 2015] for fractional b-matching and achieves a (7+ε)(3k+3)/(3k-1)-approximation in O(poly(log n, ε^-1)) update time against an adaptive adversary. Moreover, our reductions use the dynamic b-matching algorithm as a black box, so any future improvement in the approximation ratio for dynamic b-matching will automatically translate into a better approximation ratio for our algorithms. Finally, we present a greedy algorithm with O(Δ+k) update time, which guarantees a 2.16 approximation factor.","lang":"eng"}],"oa":1,"project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer"}],"_id":"19858","ec_funded":1,"oa_version":"Published Version","volume":330,"year":"2025","publication_status":"published","file":[{"access_level":"open_access","date_created":"2025-06-23T11:23:29Z","checksum":"ad93a1e052adb29d7bfe8bd551bab193","creator":"dernst","success":1,"file_name":"2025_LIPIcs_ElHayek.pdf","content_type":"application/pdf","file_id":"19872","relation":"main_file","file_size":995666,"date_updated":"2025-06-23T11:23:29Z"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","alternative_title":["LIPIcs"],"file_date_updated":"2025-06-23T11:23:29Z","date_updated":"2025-09-30T13:37:28Z","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","month":"06","publication":"4th Symposium on Algorithmic Foundations of Dynamic Networks","article_processing_charge":"No","quality_controlled":"1","conference":{"name":"SAND: Symposium on Algorithmic Foundations of Dynamic Networks","end_date":"2025-06-11","start_date":"2025-06-09","location":"Liverpool, United Kingdom"},"date_published":"2025-06-02T00:00:00Z","citation":{"short":"A. El-Hayek, K. Hanauer, M. Henzinger, in:, 4th Symposium on Algorithmic Foundations of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025.","ista":"El-Hayek A, Hanauer K, Henzinger M. 2025. On b-matching and fully-dynamic maximum k-edge coloring. 4th Symposium on Algorithmic Foundations of Dynamic Networks. SAND: Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 330, 4.","apa":"El-Hayek, A., Hanauer, K., &#38; Henzinger, M. (2025). On b-matching and fully-dynamic maximum k-edge coloring. In <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i> (Vol. 330). Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">https://doi.org/10.4230/LIPIcs.SAND.2025.4</a>","mla":"El-Hayek, Antoine, et al. “On B-Matching and Fully-Dynamic Maximum k-Edge Coloring.” <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>, vol. 330, 4, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">10.4230/LIPIcs.SAND.2025.4</a>.","chicago":"El-Hayek, Antoine, Kathrin Hanauer, and Monika Henzinger. “On B-Matching and Fully-Dynamic Maximum k-Edge Coloring.” In <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>, Vol. 330. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">https://doi.org/10.4230/LIPIcs.SAND.2025.4</a>.","ieee":"A. El-Hayek, K. Hanauer, and M. Henzinger, “On b-matching and fully-dynamic maximum k-edge coloring,” in <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>, Liverpool, United Kingdom, 2025, vol. 330.","ama":"El-Hayek A, Hanauer K, Henzinger M. On b-matching and fully-dynamic maximum k-edge coloring. In: <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>. Vol 330. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">10.4230/LIPIcs.SAND.2025.4</a>"},"intvolume":"       330","article_number":"4","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024. This work was further supported by the Federal Ministry of Education and Research (BMBF) project, 6G-RIC: 6G Research and Innovation Cluster, grant 16KISK020K.","day":"02","type":"conference","status":"public","has_accepted_license":"1","doi":"10.4230/LIPIcs.SAND.2025.4","arxiv":1,"date_created":"2025-06-22T22:02:06Z","ddc":["000"],"corr_author":"1","scopus_import":"1","publication_identifier":{"isbn":["9783959773683"],"issn":["1868-8969"]},"OA_type":"gold","title":"On b-matching and fully-dynamic maximum k-edge coloring"},{"corr_author":"1","ddc":["510"],"scopus_import":"1","publication_identifier":{"eissn":["2644-9463"]},"OA_type":"gold","title":"Color-avoiding percolation on the Erdős–Rényi random graph","day":"01","type":"journal_article","DOAJ_listed":"1","acknowledgement":"We thank Dieter Mitsche for enlightening discussions, Balázs Ráth for a number of comments\r\nand corrections on a first version of this paper, and an anonymous referee for several useful remarks.","date_created":"2025-06-22T22:02:07Z","doi":"10.5802/ahl.228","arxiv":1,"status":"public","has_accepted_license":"1","date_published":"2025-06-01T00:00:00Z","citation":{"short":"L. Lichev, B. Schapira, Annales Henri Lebesgue 8 (2025) 35–65.","apa":"Lichev, L., &#38; Schapira, B. (2025). Color-avoiding percolation on the Erdős–Rényi random graph. <i>Annales Henri Lebesgue</i>. École normale supérieure de Rennes. <a href=\"https://doi.org/10.5802/ahl.228\">https://doi.org/10.5802/ahl.228</a>","ista":"Lichev L, Schapira B. 2025. Color-avoiding percolation on the Erdős–Rényi random graph. Annales Henri Lebesgue. 8, 35–65.","mla":"Lichev, Lyuben, and Bruno Schapira. “Color-Avoiding Percolation on the Erdős–Rényi Random Graph.” <i>Annales Henri Lebesgue</i>, vol. 8, École normale supérieure de Rennes, 2025, pp. 35–65, doi:<a href=\"https://doi.org/10.5802/ahl.228\">10.5802/ahl.228</a>.","ieee":"L. Lichev and B. Schapira, “Color-avoiding percolation on the Erdős–Rényi random graph,” <i>Annales Henri Lebesgue</i>, vol. 8. École normale supérieure de Rennes, pp. 35–65, 2025.","chicago":"Lichev, Lyuben, and Bruno Schapira. “Color-Avoiding Percolation on the Erdős–Rényi Random Graph.” <i>Annales Henri Lebesgue</i>. École normale supérieure de Rennes, 2025. <a href=\"https://doi.org/10.5802/ahl.228\">https://doi.org/10.5802/ahl.228</a>.","ama":"Lichev L, Schapira B. Color-avoiding percolation on the Erdős–Rényi random graph. <i>Annales Henri Lebesgue</i>. 2025;8:35-65. doi:<a href=\"https://doi.org/10.5802/ahl.228\">10.5802/ahl.228</a>"},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"         8","month":"06","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"École normale supérieure de Rennes","article_processing_charge":"Yes","quality_controlled":"1","publication":"Annales Henri Lebesgue","file_date_updated":"2025-06-23T11:59:22Z","date_updated":"2025-06-23T12:01:36Z","publication_status":"published","volume":8,"year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","success":1,"date_created":"2025-06-23T11:59:22Z","checksum":"cca22d171b7affa010d17f5e793b0045","access_level":"open_access","file_size":746588,"date_updated":"2025-06-23T11:59:22Z","file_id":"19875","content_type":"application/pdf","relation":"main_file","file_name":"2025_AnnalesHenriLebesgue_Lichev.pdf"}],"oa":1,"page":"35-65","article_type":"original","oa_version":"Published Version","_id":"19859","department":[{"_id":"MaKw"}],"abstract":[{"text":"We consider a recently introduced model of color-avoiding percolation (abbreviated CA-percolation) defined as follows. Every edge in a graph G is colored in some of k>=2 colors. Two vertices u and v in G are said to be CA-connected if u and v may be connected using any subset of k-1 colors. CA-connectivity defines an equivalence relation on the vertex set of G whose classes are called CA-components.\r\nWe study the component structure of a randomly colored Erdős–Rényi random graph of constant average degree. We distinguish three regimes for the size of the largest component: a supercritical regime, a so-called intermediate regime, and a subcritical regime, in which the largest CA-component has respectively linear, logarithmic, and bounded size. Interestingly, in the subcritical regime, the bound is deterministic and given by the number of colors.","lang":"eng"}],"author":[{"first_name":"Lyuben","last_name":"Lichev","full_name":"Lichev, Lyuben","id":"9aa8388e-d003-11ee-8458-c4c1d7447977"},{"full_name":"Schapira, Bruno","first_name":"Bruno","last_name":"Schapira"}],"external_id":{"arxiv":["2211.16086 "]}},{"publication":"Discrete & Computational Geometry","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"06","citation":{"ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. 2025. doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>","ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2025.","chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>.","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>.","apa":"Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2025). Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>","ista":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2025. Eight-partitioning points in 3D, and efficiently too. Discrete &#38; Computational Geometry.","short":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, Discrete &#38; Computational Geometry (2025)."},"date_published":"2025-06-12T00:00:00Z","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-025-00739-0"}],"arxiv":1,"date_created":"2025-06-22T22:02:07Z","doi":"10.1007/s00454-025-00739-0","acknowledgement":"BA and AB would like to thank William Steiger for insightful initial discussions of the problems addressed in this work. Open Access funding enabled and organized by CAUL and its Member Institutions.","type":"journal_article","day":"12","title":"Eight-partitioning points in 3D, and efficiently too","OA_type":"hybrid","scopus_import":"1","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"ddc":["500"],"external_id":{"arxiv":["2403.02627"],"isi":["001506904300001"]},"author":[{"full_name":"Aronov, Boris","last_name":"Aronov","first_name":"Boris"},{"full_name":"Basit, Abdul","last_name":"Basit","first_name":"Abdul"},{"full_name":"Ramesh, Indu","first_name":"Indu","last_name":"Ramesh"},{"id":"0433290C-AF8F-11E9-A4C7-F729E6697425","full_name":"Tasinato, Gianluca","last_name":"Tasinato","first_name":"Gianluca"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"abstract":[{"lang":"eng","text":"An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in R^3\r\n consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in R^3 admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument. We prove the following variant of this result: any mass distribution (or point set) in R^3 admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction. Moreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in R^3 (with prescribed normal direction of one of the planes) in time O(n^7/3). A preliminary version of this work appeared in SoCG’24 (Aronov et al., 40th International Symposium on Computational Geometry, 2024)."}],"department":[{"_id":"UlWa"}],"_id":"19860","oa_version":"Published Version","article_type":"original","oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s00454-025-00759-w"}],"record":[{"status":"public","relation":"earlier_version","id":"18917"},{"status":"public","relation":"dissertation_contains","id":"20339"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"year":"2025","publication_status":"epub_ahead","date_updated":"2026-06-18T18:18:28Z"},{"abstract":[{"lang":"eng","text":"Assortative mating and sexual selection are widespread in nature and can play an important role in speciation by facilitating the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified.\r\nHere, we consider a polygenic “magic” trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at\r\nindividual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early-generation hybrids. Our analysis clarifies how “tipping\r\npoints” (characterized by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene\r\nflow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI. "}],"acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","first_name":"Parvathy"},{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"}],"external_id":{"isi":["001490646300001"]},"department":[{"_id":"NiBa"}],"oa_version":"Published Version","_id":"19876","oa":1,"page":"1185-1198","article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","checksum":"288ca936cef794d68a55356e70671846","date_created":"2025-12-30T08:43:33Z","success":1,"creator":"dernst","file_name":"2025_Evolution_Surendranadh.pdf","relation":"main_file","content_type":"application/pdf","file_id":"20898","file_size":2784295,"date_updated":"2025-12-30T08:43:33Z"}],"related_material":{"record":[{"id":"18712","status":"public","relation":"research_data"}]},"publication_status":"published","year":"2025","volume":79,"date_updated":"2025-12-30T08:44:13Z","file_date_updated":"2025-12-30T08:43:33Z","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication":"Evolution","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"07","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Oxford University Press","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"intvolume":"        79","date_published":"2025-07-01T00:00:00Z","citation":{"mla":"Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” <i>Evolution</i>, vol. 79, no. 7, Oxford University Press, 2025, pp. 1185–98, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf047\">10.1093/evolut/qpaf047</a>.","ama":"Surendranadh P, Sachdeva H. Effect of assortative mating and sexual selection on polygenic barriers to gene flow. <i>Evolution</i>. 2025;79(7):1185-1198. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf047\">10.1093/evolut/qpaf047</a>","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf047\">https://doi.org/10.1093/evolut/qpaf047</a>.","ieee":"P. Surendranadh and H. Sachdeva, “Effect of assortative mating and sexual selection on polygenic barriers to gene flow,” <i>Evolution</i>, vol. 79, no. 7. Oxford University Press, pp. 1185–1198, 2025.","short":"P. Surendranadh, H. Sachdeva, Evolution 79 (2025) 1185–1198.","apa":"Surendranadh, P., &#38; Sachdeva, H. (2025). Effect of assortative mating and sexual selection on polygenic barriers to gene flow. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf047\">https://doi.org/10.1093/evolut/qpaf047</a>","ista":"Surendranadh P, Sachdeva H. 2025. Effect of assortative mating and sexual selection on polygenic barriers to gene flow. Evolution. 79(7), 1185–1198."},"date_created":"2025-06-23T13:51:00Z","doi":"10.1093/evolut/qpaf047","status":"public","has_accepted_license":"1","day":"01","type":"journal_article","acknowledgement":"We thank Nick Barton for useful comments on the manuscript. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by Scientific Computing (SciComp).","OA_type":"hybrid","title":"Effect of assortative mating and sexual selection on polygenic barriers to gene flow","issue":"7","corr_author":"1","ddc":["570"],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"scopus_import":"1"},{"author":[{"full_name":"Frantar, Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias","last_name":"Frantar"},{"full_name":"Castro, Roberto L.","last_name":"Castro","first_name":"Roberto L."},{"last_name":"Chen","first_name":"Jiale","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","full_name":"Chen, Jiale","orcid":"0000-0001-5337-5875"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"},{"last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"external_id":{"arxiv":["2408.11743"],"isi":["001437826500019"]},"abstract":[{"lang":"eng","text":"As inference on Large Language Models (LLMs) emerges as an important workload in machine learning applications, model weight quantization has become a standard technique for efficient GPU deployment. Quantization not only reduces model size, but has also been shown to yield substantial speedups for single-user inference, due to reduced memory movement, with low accuracy impact. Yet, it remains a key open question whether speedups are achievable also in batched settings with multiple parallel clients, which are highly relevant for practical serving. It is unclear whether GPU kernels can be designed to remain practically memory-bound, while supporting the substantially increased compute requirements of batched workloads.\r\nIn this paper, we resolve this question positively by introducing a new design for Mixed-precision Auto-Regressive LINear kernels, called MARLIN. Concretely, given a model whose weights are compressed via quantization to, e.g., 4 bits per element, MARLIN shows that batchsizes up to 16-32 can be practically supported with close to maximum (4×) quantization speedup, and larger batchsizes up to 64-128 with gradually decreasing, but still significant, acceleration. MARLIN accomplishes this via a combination of techniques, such as asynchronous memory access, complex task scheduling and pipelining, and bespoke quantization support. Our experiments show that MARLIN's near-optimal performance on individual LLM layers across different scenarios can also lead to significant end-to-end LLM inference speedups (of up to 2.8×) when integrated with the popular vLLM open-source serving engine. Finally, we show that MARLIN is extensible to further compression techniques, like NVIDIA 2:4 sparsity, leading to additional speedups."}],"department":[{"_id":"DaAl"}],"_id":"19877","oa_version":"Published Version","page":"239-251","oa":1,"file":[{"access_level":"open_access","creator":"dernst","success":1,"date_created":"2025-06-24T06:04:17Z","checksum":"a0566ea3c168e8273501a5eb7d767cf8","file_name":"2025_PPoPP_Frantar.pdf","file_size":1330044,"date_updated":"2025-06-24T06:04:17Z","content_type":"application/pdf","file_id":"19883","relation":"main_file"}],"related_material":{"record":[{"id":"19884","status":"public","relation":"software"}]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2025","publication_status":"published","date_updated":"2025-09-30T13:41:57Z","file_date_updated":"2025-06-24T06:04:17Z","publication":"Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","OA_place":"publisher","month":"02","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"conference":{"end_date":"2025-03-05","name":"PPoPP: Symposium on Principles and Practice of Parallel Programming","location":"Las Vegas, NV, United States","start_date":"2025-03-01"},"date_published":"2025-02-28T00:00:00Z","citation":{"ama":"Frantar E, Castro RL, Chen J, Hoefler T, Alistarh D-A. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. In: <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2025:239-251. doi:<a href=\"https://doi.org/10.1145/3710848.3710871\">10.1145/3710848.3710871</a>","ieee":"E. Frantar, R. L. Castro, J. Chen, T. Hoefler, and D.-A. Alistarh, “MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models,” in <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>, Las Vegas, NV, United States, 2025, pp. 239–251.","chicago":"Frantar, Elias, Roberto L. Castro, Jiale Chen, Torsten Hoefler, and Dan-Adrian Alistarh. “MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models.” In <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>, 239–51. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3710848.3710871\">https://doi.org/10.1145/3710848.3710871</a>.","mla":"Frantar, Elias, et al. “MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models.” <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2025, pp. 239–51, doi:<a href=\"https://doi.org/10.1145/3710848.3710871\">10.1145/3710848.3710871</a>.","apa":"Frantar, E., Castro, R. L., Chen, J., Hoefler, T., &#38; Alistarh, D.-A. (2025). MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. In <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i> (pp. 239–251). Las Vegas, NV, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3710848.3710871\">https://doi.org/10.1145/3710848.3710871</a>","ista":"Frantar E, Castro RL, Chen J, Hoefler T, Alistarh D-A. 2025. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming. PPoPP: Symposium on Principles and Practice of Parallel Programming, 239–251.","short":"E. Frantar, R.L. Castro, J. Chen, T. Hoefler, D.-A. Alistarh, in:, Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2025, pp. 239–251."},"status":"public","has_accepted_license":"1","arxiv":1,"date_created":"2025-06-23T13:51:58Z","doi":"10.1145/3710848.3710871","acknowledgement":"The authors would like to thank the Neural Magic team, in particular Michael Goin, Alexander Matveev, and Rob Shaw, for support with the vLLM integration. This research was supported in part by generous grants from NVIDIA and Google.","day":"28","type":"conference","OA_type":"hybrid","title":"MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models","corr_author":"1","ddc":["000"],"publication_identifier":{"isbn":["9798400714436"]},"scopus_import":"1"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       130","article_number":"e2025JF008360","date_published":"2025-06-15T00:00:00Z","citation":{"mla":"Melo Velasco, Juan Vicente, et al. “Method Dependence in Thermal Conductivity and Aerodynamic Roughness Length Estimates on a Debris‐covered Glacier.” <i>Journal of Geophysical Research: Earth Surface</i>, vol. 130, no. 6, e2025JF008360, Wiley, 2025, doi:<a href=\"https://doi.org/10.1029/2025jf008360\">10.1029/2025jf008360</a>.","ieee":"J. V. Melo Velasco <i>et al.</i>, “Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier,” <i>Journal of Geophysical Research: Earth Surface</i>, vol. 130, no. 6. Wiley, 2025.","chicago":"Melo Velasco, Juan Vicente, Evan Miles, Michael McCarthy, Thomas Shaw, Catriona Louise Fyffe, Adrià Fontrodona-Bach, and Francesca Pellicciotti. “Method Dependence in Thermal Conductivity and Aerodynamic Roughness Length Estimates on a Debris‐covered Glacier.” <i>Journal of Geophysical Research: Earth Surface</i>. Wiley, 2025. <a href=\"https://doi.org/10.1029/2025jf008360\">https://doi.org/10.1029/2025jf008360</a>.","ama":"Melo Velasco JV, Miles E, McCarthy M, et al. Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier. <i>Journal of Geophysical Research: Earth Surface</i>. 2025;130(6). doi:<a href=\"https://doi.org/10.1029/2025jf008360\">10.1029/2025jf008360</a>","short":"J.V. Melo Velasco, E. Miles, M. McCarthy, T. Shaw, C.L. Fyffe, A. Fontrodona-Bach, F. Pellicciotti, Journal of Geophysical Research: Earth Surface 130 (2025).","apa":"Melo Velasco, J. V., Miles, E., McCarthy, M., Shaw, T., Fyffe, C. L., Fontrodona-Bach, A., &#38; Pellicciotti, F. (2025). Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier. <i>Journal of Geophysical Research: Earth Surface</i>. Wiley. <a href=\"https://doi.org/10.1029/2025jf008360\">https://doi.org/10.1029/2025jf008360</a>","ista":"Melo Velasco JV, Miles E, McCarthy M, Shaw T, Fyffe CL, Fontrodona-Bach A, Pellicciotti F. 2025. Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier. Journal of Geophysical Research: Earth Surface. 130(6), e2025JF008360."},"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication":"Journal of Geophysical Research: Earth Surface","month":"06","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Wiley","OA_type":"hybrid","issue":"6","title":"Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier","ddc":["550"],"corr_author":"1","publication_identifier":{"issn":["2169-9003"],"eissn":["2169-9011"]},"scopus_import":"1","doi":"10.1029/2025jf008360","date_created":"2025-06-23T13:54:01Z","has_accepted_license":"1","status":"public","type":"journal_article","day":"15","acknowledgement":"This project received funding from the Swiss National Science Foundation (Grant 204322, project “REsolving the thickNess Of debris on Earth's glacIers and its Rate of change,” RENOIR). We thank Lars Groeneveld, Diego Hernández, Alonso Mejías, Gabriela Reyes and Gabriela Tala for their support during fieldwork. Open access funding provided by Institute of Science and Technology Austria/KEMÖ.","oa_version":"Published Version","_id":"19878","oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"Rock debris partially covers glaciers worldwide, with varying extents and distributions, and controls sub‐debris melt rates by modifying energy transfer from the atmosphere to the ice. Two key physical properties controlling this energy exchange are thermal conductivity (k) and aerodynamic roughness length (z0). Accurate representation of these properties in energy‐balance models is critical for understanding climate‐glacier interactions and predicting the behavior of debris‐covered glaciers. However, k and z0 have been derived at very few sites from limited local measurements, using different approaches, and most model applications rely on values reported from these few sites and studies. We derive k and z0 using established and modified approaches from data at three locations on Pirámide Glacier in the central Chilean Andes. By comparing methods and evaluating melt simulated with an energy‐balance model, we reveal substantial differences between approaches. These lead to discrepancies between ice melt from energy‐balance simulations and observed data, and highlight the impact of method choice on calculated ice melt. Optimizing k against measured melt appears a viable approach to constrain melt simulations. Determining z0 seems less critical, as it has a smaller impact on total melt. Profile aerodynamic method measurements for estimating z0, despite higher costs, are independent of ice melt calculations. The large, unexpected differences between methods indicate a substantial knowledge gap. The fact that field‐derived k and z0 fail to work well in energy‐balance models, suggests that model values represent bulk properties distinct from theoretical field measurements. Addressing this gap is essential for improving glacier melt predictions."}],"author":[{"first_name":"Juan Vicente","last_name":"Melo Velasco","full_name":"Melo Velasco, Juan Vicente","id":"2611dec0-b9c6-11ed-9bea-a81c2b17a549"},{"full_name":"Miles, Evan","first_name":"Evan","last_name":"Miles"},{"id":"22a2674a-61ce-11ee-94b5-d18813baf16f","full_name":"McCarthy, Michael","last_name":"McCarthy","first_name":"Michael"},{"last_name":"Shaw","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas"},{"first_name":"Catriona Louise","last_name":"Fyffe","full_name":"Fyffe, Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228"},{"last_name":"Fontrodona-Bach","first_name":"Adrià","id":"f06891fd-9f42-11ee-8632-a20971c43046","full_name":"Fontrodona-Bach, Adrià"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca"}],"external_id":{"isi":["001508794200001"]},"department":[{"_id":"FrPe"}],"date_updated":"2025-09-30T13:42:28Z","file_date_updated":"2025-06-24T06:27:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"access_level":"open_access","creator":"dernst","success":1,"date_created":"2025-06-24T06:27:34Z","checksum":"ca91541516c71d240321630ca42b4dc4","file_name":"2025_JGREarthSurface_MeloVelasco.pdf","date_updated":"2025-06-24T06:27:34Z","file_size":3949928,"content_type":"application/pdf","file_id":"19886","relation":"main_file"}],"publication_status":"published","volume":130,"year":"2025"},{"OA_type":"hybrid","title":"Precoloring extension in planar near-Eulerian-triangulations","ddc":["510"],"corr_author":"1","publication_identifier":{"issn":["0195-6698"]},"scopus_import":"1","status":"public","has_accepted_license":"1","doi":"10.1016/j.ejc.2025.104138","date_created":"2025-06-23T13:54:46Z","arxiv":1,"acknowledgement":"Supported by project 22-17398S (Flows and cycles in graphs on surfaces) of Czech Science Foundation. An extended abstract appeared in Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications (EUROCOMB’23)","type":"journal_article","day":"01","article_number":"104138","intvolume":"       127","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-06-01T00:00:00Z","citation":{"apa":"Dvořák, Z., Moore, B., Seifrtová, M., &#38; Šámal, R. (2025). Precoloring extension in planar near-Eulerian-triangulations. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">https://doi.org/10.1016/j.ejc.2025.104138</a>","ista":"Dvořák Z, Moore B, Seifrtová M, Šámal R. 2025. Precoloring extension in planar near-Eulerian-triangulations. European Journal of Combinatorics. 127, 104138.","short":"Z. Dvořák, B. Moore, M. Seifrtová, R. Šámal, European Journal of Combinatorics 127 (2025).","ieee":"Z. Dvořák, B. Moore, M. Seifrtová, and R. Šámal, “Precoloring extension in planar near-Eulerian-triangulations,” <i>European Journal of Combinatorics</i>, vol. 127. Elsevier, 2025.","chicago":"Dvořák, Zdeněk, Benjamin Moore, Michaela Seifrtová, and Robert Šámal. “Precoloring Extension in Planar Near-Eulerian-Triangulations.” <i>European Journal of Combinatorics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">https://doi.org/10.1016/j.ejc.2025.104138</a>.","ama":"Dvořák Z, Moore B, Seifrtová M, Šámal R. Precoloring extension in planar near-Eulerian-triangulations. <i>European Journal of Combinatorics</i>. 2025;127. doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">10.1016/j.ejc.2025.104138</a>","mla":"Dvořák, Zdeněk, et al. “Precoloring Extension in Planar Near-Eulerian-Triangulations.” <i>European Journal of Combinatorics</i>, vol. 127, 104138, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">10.1016/j.ejc.2025.104138</a>."},"publication":"European Journal of Combinatorics","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Elsevier","month":"06","date_updated":"2025-09-30T13:42:59Z","file_date_updated":"2025-06-24T06:33:30Z","file":[{"date_created":"2025-06-24T06:33:30Z","checksum":"8b3585df45b25091fba9bee9854b7d01","creator":"dernst","success":1,"access_level":"open_access","content_type":"application/pdf","file_id":"19887","relation":"main_file","file_size":564203,"date_updated":"2025-06-24T06:33:30Z","file_name":"2025_EuropJournCombinatorics_Dvorak.pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"volume":127,"year":"2025","publication_status":"published","_id":"19879","oa_version":"Published Version","article_type":"original","oa":1,"author":[{"full_name":"Dvořák, Zdeněk","last_name":"Dvořák","first_name":"Zdeněk"},{"first_name":"Benjamin","last_name":"Moore","full_name":"Moore, Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6"},{"full_name":"Seifrtová, Michaela","last_name":"Seifrtová","first_name":"Michaela"},{"full_name":"Šámal, Robert","last_name":"Šámal","first_name":"Robert"}],"external_id":{"arxiv":["2312.13061"],"isi":["001443061400001"]},"abstract":[{"text":"We consider the 4-precoloring extension problem in planar near-Eulerian- triangulations, i.e., plane graphs where all faces except possibly for the outer one have length three, all vertices not incident with the outer face have even degree, and exactly the vertices incident with the outer face are precolored. We give a necessary topological condition for the precoloring to extend, and give a complete characterization when the outer face has length at most five and when all vertices of the outer face have odd degree and are colored using only three colors.","lang":"eng"}],"department":[{"_id":"MaKw"}]},{"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"scopus_import":"1","ddc":["530"],"corr_author":"1","title":"Quantum transport in the presence of a chiral molecular potential","issue":"23","OA_type":"hybrid","type":"journal_article","day":"21","acknowledgement":"We thank Artem Volosniev, Narcis Avarvari, Georgios Koutentakis, Sandro Wimberger, and Binghai Yan for useful discussions. R.A. received funding from the Austrian Academy of Science ÖWA, Grant No. PR1029OEAW03. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862-NeqMolRot.","arxiv":1,"doi":"10.1063/5.0271155","date_created":"2025-06-23T13:55:28Z","status":"public","has_accepted_license":"1","citation":{"ista":"Al Hyder R, Lemeshko M, Cappellaro A. 2025. Quantum transport in the presence of a chiral molecular potential. The Journal of Chemical Physics. 162(23), 234106.","apa":"Al Hyder, R., Lemeshko, M., &#38; Cappellaro, A. (2025). Quantum transport in the presence of a chiral molecular potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0271155\">https://doi.org/10.1063/5.0271155</a>","short":"R. Al Hyder, M. Lemeshko, A. Cappellaro, The Journal of Chemical Physics 162 (2025).","ama":"Al Hyder R, Lemeshko M, Cappellaro A. Quantum transport in the presence of a chiral molecular potential. <i>The Journal of Chemical Physics</i>. 2025;162(23). doi:<a href=\"https://doi.org/10.1063/5.0271155\">10.1063/5.0271155</a>","ieee":"R. Al Hyder, M. Lemeshko, and A. Cappellaro, “Quantum transport in the presence of a chiral molecular potential,” <i>The Journal of Chemical Physics</i>, vol. 162, no. 23. AIP Publishing, 2025.","chicago":"Al Hyder, Ragheed, Mikhail Lemeshko, and Alberto Cappellaro. “Quantum Transport in the Presence of a Chiral Molecular Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0271155\">https://doi.org/10.1063/5.0271155</a>.","mla":"Al Hyder, Ragheed, et al. “Quantum Transport in the Presence of a Chiral Molecular Potential.” <i>The Journal of Chemical Physics</i>, vol. 162, no. 23, 234106, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0271155\">10.1063/5.0271155</a>."},"date_published":"2025-06-21T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"234106","intvolume":"       162","pmid":1,"month":"06","OA_place":"publisher","publisher":"AIP Publishing","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publication":"The Journal of Chemical Physics","file_date_updated":"2025-06-23T14:03:30Z","date_updated":"2025-09-30T13:40:55Z","publication_status":"published","year":"2025","volume":162,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"file_name":"2025_JourChemicalPhysics_AlHyder.pdf","file_id":"19881","content_type":"application/pdf","relation":"main_file","file_size":7202681,"date_updated":"2025-06-23T14:03:30Z","access_level":"open_access","date_created":"2025-06-23T14:03:30Z","checksum":"e278631d949657baa9d5309dad5f4b77","creator":"dernst","success":1}],"oa":1,"article_type":"original","oa_version":"Published Version","_id":"19880","project":[{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"},{"name":"Non-Equilibrium Field Theory of Molecular Rotations","grant_number":"101062862","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"grant_number":"12078","_id":"8fa7db46-16d5-11f0-9cad-917600954daf","name":"Polarons in Lead Halide Perovskites"}],"ec_funded":1,"department":[{"_id":"MiLe"}],"abstract":[{"text":"We investigate quantum transport in a two-dimensional electron system coupled to a chiral molecular potential, demonstrating how molecular chirality and orientation affect charge and spin transport properties. We propose a minimal model for realizing true chiral symmetry breaking on a magnetized surface, with a crucial role played by the tilt angle of the molecular dipole with respect to the surface. For non-zero tilting, we show that the Hall response exhibits clear signatures of chirality-induced effects, in both charge- and spin-resolved observables. Concerning the former, tilted enantiomers produce asymmetric Hall conductances and, even more remarkably, the persistence of this feature in the absence of spin–orbit coupling (SOC) signals how the enantiospecific charge response results from electron scattering off the molecular potential. Concerning spin-resolved observables where SOC plays a relevant role, we reveal that chiral symmetry breaking is crucial in enabling spin-flipping processes.","lang":"eng"}],"external_id":{"pmid":["40526561"],"isi":["001512872900010"],"arxiv":["2503.14124"]},"author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder","first_name":"Ragheed"},{"last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Alberto","last_name":"Cappellaro","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"}]},{"year":"2025","acknowledgement":"The authors would like to thank Barnaby van Straaten, Jonas Schuff, Daniel Jirovec and Hanifa Tidjani for fruitful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. G.K. acknowledges support from the NOMIS Foundation, the HORIZON-RIA (project no. 101069515) and the FWF Projects (DOIs: 10.55776/F86 and 10.55776/I5060). N.A. acknowledges support from the European Research Council (grant agreement 948932), and the Royal Society (grant no. URF/R1/191150). This project received support from the US Army Research Office (ARO) under Award No. W911NF-24-2-0043. C.C. acknowledges support from the UKRI Doctoral Training Partnership related to EP/W524311/1 (project ref. 2887634).","type":"research_data","day":"01","status":"public","has_accepted_license":"1","file":[{"creator":"jsaezmol","success":1,"date_created":"2025-06-24T15:14:13Z","checksum":"eff1ae9e46599fdfab8da00a2ca3c289","access_level":"open_access","date_updated":"2025-06-24T15:14:13Z","file_size":3404814792,"content_type":"application/x-zip-compressed","file_id":"19893","relation":"main_file","file_name":"DatasetsPaper.zip"},{"access_level":"open_access","success":1,"creator":"jsaezmol","checksum":"21840ceac04d677a799b8e5bd919804f","date_created":"2025-06-25T07:11:52Z","file_name":"README.txt","file_size":622,"date_updated":"2025-06-25T07:11:52Z","relation":"main_file","content_type":"text/plain","file_id":"19899"}],"doi":"10.15479/AT:ISTA:19885","date_created":"2025-06-24T06:56:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","file_date_updated":"2025-06-25T07:11:52Z","ddc":["530"],"date_updated":"2025-07-01T07:19:26Z","title":"Automated All-RF Tuning for Spin Qubit Readout and Control","publisher":"Institute of Science and Technology Austria","month":"06","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"author":[{"id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","first_name":"Jaime"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"text":"This .zip file contains the data to reproduce the figures and supplementary figures of \"Automated All-RF Tuning for Spin Qubit Readout and Control\" by Cornelius Carlsson and Jaime Saez-Mollejo et al.","lang":"eng"}],"article_processing_charge":"No","oa":1,"citation":{"mla":"Saez Mollejo, Jaime. <i>Automated All-RF Tuning for Spin Qubit Readout and Control</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19885\">10.15479/AT:ISTA:19885</a>.","ieee":"J. Saez Mollejo, “Automated All-RF Tuning for Spin Qubit Readout and Control.” Institute of Science and Technology Austria, 2025.","chicago":"Saez Mollejo, Jaime. “Automated All-RF Tuning for Spin Qubit Readout and Control.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:19885\">https://doi.org/10.15479/AT:ISTA:19885</a>.","ama":"Saez Mollejo J. Automated All-RF Tuning for Spin Qubit Readout and Control. 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19885\">10.15479/AT:ISTA:19885</a>","short":"J. Saez Mollejo, (2025).","apa":"Saez Mollejo, J. (2025). Automated All-RF Tuning for Spin Qubit Readout and Control. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:19885\">https://doi.org/10.15479/AT:ISTA:19885</a>","ista":"Saez Mollejo J. 2025. 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The extent to which humans cooperate with each other is also an essential feature that differentiates them from other animals. Cooperation occurs even in the absence of altruistic motivations, when it is selfishly incentivised by the expectation of a future reward. For example, many economic interactions are well described that way. This kind of cooperation requires that people exhibit reciprocal behaviour that acts as a mechanism that rewards cooperation.\r\nWith game-theoretic models, it is possible to formally study potential such mechanisms and under what conditions they can exist. This thesis contributes to this effort by analysing recently introduced models of cooperation that advance on previous work by taking into account the potential for pre-existing inequality among cooperating individuals as well as the different forms that reciprocity can take.\r\nIndividuals may differ both intrinsically, in their abilities, as well as extrinsically, in the amount of resources they have available. Allowing for such differences in a model of cooperation helps to understand how inequality affects the potential for, and outcomes of, cooperation among unequals. In this thesis, it is shown that in the presence of intrinsic inequality, a similar unequal distribution of resources can increase the potential for cooperation. This effect is stronger the smaller the group is in which cooperation takes place. It is also shown that under particular assumptions, if the unequal members of a group vary the size of their contributions to a cooperative effort over time, they can thereby increase their efficiency and improve the collective outcome.\r\nCooperative behaviour in a two-person interaction can be rewarded either by direct reciprocation whenever the same two people interact again, or indirectly by a third party who observed the interaction. In the latter case of indirect reciprocity, individuals are proximally rewarded by a good reputation, which ultimately translates to being rewarded with cooperative behaviour by others. This mechanism can enable selfishly motivated cooperation even in circumstances where individuals are unlikely to meet again, akin to how money facilitates trade. While these two forms of reciprocity have mostly been studied in isolation, this thesis analyses both direct and indirect reciprocity in a general model in order to compare their relative effectiveness under different circumstances. The contribution of this thesis is an extension of previous work regarding a specific kind of interaction, whose parameters allow for convenient mathematical analysis, to the most general set of possible interactions."}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_updated":"2026-04-07T12:30:57Z","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"}],"file_date_updated":"2025-07-09T13:37:00Z","degree_awarded":"PhD","file":[{"file_name":"Thesis Valentin Hübner source.tar.xz","file_size":6192760,"date_updated":"2025-06-25T13:38:07Z","content_type":"application/x-xz","file_id":"19905","relation":"source_file","access_level":"closed","creator":"vhuebner","date_created":"2025-06-25T13:38:07Z","checksum":"794c02f8c82ca59ba6dda3bd7eed871a"},{"file_name":"Thesis Valentin Hübner.pdf","relation":"main_file","content_type":"application/pdf","file_id":"19976","date_updated":"2025-07-09T13:37:00Z","file_size":4837864,"access_level":"open_access","checksum":"ac56063d81c81e40322b6ff5a8c4912e","date_created":"2025-07-09T13:37:00Z","creator":"vhuebner"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"19843"},{"id":"15083","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"19074"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2025","publication_status":"published","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"date_published":"2025-06-25T00:00:00Z","citation":{"short":"V. Hübner, Reciprocity and Inequality in Social Dilemmas, Institute of Science and Technology Austria, 2025.","ista":"Hübner V. 2025. Reciprocity and inequality in social dilemmas. Institute of Science and Technology Austria.","apa":"Hübner, V. (2025). <i>Reciprocity and inequality in social dilemmas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>","mla":"Hübner, Valentin. <i>Reciprocity and Inequality in Social Dilemmas</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>.","ieee":"V. Hübner, “Reciprocity and inequality in social dilemmas,” Institute of Science and Technology Austria, 2025.","chicago":"Hübner, Valentin. “Reciprocity and Inequality in Social Dilemmas.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>.","ama":"Hübner V. Reciprocity and inequality in social dilemmas. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>"},"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"06","title":"Reciprocity and inequality in social dilemmas","corr_author":"1","ddc":["519"],"publication_identifier":{"issn":["2663-337X"]},"status":"public","has_accepted_license":"1","doi":"10.15479/AT-ISTA-19903","date_created":"2025-06-25T13:50:10Z","acknowledgement":"The research for this thesis was supported by the European Research Council\r\n(grant agreements No. 863818 and No. 850529), the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie grant agreement No. 754411),\r\nthe Austrian Science Fund (grant DOI 10.55776/COE12), the French Agence Nationale\r\nde la Recherche under the Programme d’investissements d’avenir (project reference 17-\r\nEURE-0010) and the Australian Government through the Australian Research Council\r\n(grant No. SR200100005, “Securing Antarctica’s Environmental Future”).","day":"25","type":"dissertation"},{"citation":{"ama":"Springstein BL. Files for “Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19915\">10.15479/AT:ISTA:19915</a>","chicago":"Springstein, Benjamin L. “Files for ‘Evolutionary Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cyanobacterial Cell Shape.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:19915\">https://doi.org/10.15479/AT:ISTA:19915</a>.","ieee":"B. L. Springstein, “Files for ‘Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape.’” Institute of Science and Technology Austria, 2025.","mla":"Springstein, Benjamin L. <i>Files for “Evolutionary Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cyanobacterial Cell Shape.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19915\">10.15479/AT:ISTA:19915</a>.","apa":"Springstein, B. L. (2025). Files for “Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:19915\">https://doi.org/10.15479/AT:ISTA:19915</a>","ista":"Springstein BL. 2025. Files for ‘Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:19915\">10.15479/AT:ISTA:19915</a>.","short":"B.L. Springstein, (2025)."},"oa":1,"date_published":"2025-06-27T00:00:00Z","oa_version":"Published Version","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"contributor":[{"first_name":"Benjamin L","last_name":"Springstein","contributor_type":"project_leader","orcid":"0000-0002-3461-5391","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083"},{"last_name":"Javoor","contributor_type":"researcher","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Daniela","contributor_type":"researcher","last_name":"Megrian"},{"last_name":"Hajdu","contributor_type":"researcher","first_name":"Roman","id":"ffab949d-133f-11ed-8f02-94de21ace503"},{"first_name":"Dustin M","last_name":"Hanke","contributor_type":"researcher"},{"last_name":"Schur","contributor_type":"researcher","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"first_name":"Martin","contributor_type":"supervisor","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"_id":"19915","ec_funded":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"grant_number":"101076260","_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","name":"A molecular atlas of Actin filament IDentities in the cell motility machinery"}],"month":"06","department":[{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"orcid":"0000-0002-3461-5391","full_name":"Springstein, Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","first_name":"Benjamin L","last_name":"Springstein"}],"file_date_updated":"2025-07-02T08:10:21Z","corr_author":"1","title":"Files for \"Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape\"","date_updated":"2026-06-10T08:05:45Z","type":"research_data","day":"27","year":"2025","acknowledgement":"We thank all members of the Martin Loose lab at ISTA for helpful discussions and Marko Kojic for critical reading of the manuscript. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF), the Scientific Computing (SciComp) and the Electron Microscopy Facility (EMF), as well as the Lab Support Facility (LSF). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No.101034413 awarded to BLS as well as an ERC grant (ActinID, 101076260) from the European Union awarded to FKMS. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.\r\n\r\nWe are grateful for Antonia Herrero (Sevilla University) for sharing her extensive BACTH plasmid library and other plasmids as well as cyanobacterial strains. Likewise, we would like to thank Tal Dagan and Fabian Nies (both Kiel University) for sharing cyanobacterial strains and plasmids and for valuable discussions.\r\n\r\nWe would further like to express our gratitude to Nicolas Sapay and Alexis Michon for providing the Amphipaseek code, which enabled us to perform our large-scale amphipathic helix screen of cyanobacterial CorR proteins. Finally, we also want to thank Jesse Hansen for advice in cryo-EM data processing","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","doi":"10.15479/AT:ISTA:19915","date_created":"2025-06-27T07:34:52Z","has_accepted_license":"1","status":"public","file":[{"relation":"main_file","content_type":"video/x-msvideo","file_id":"19916","file_size":2003892,"date_updated":"2025-06-27T07:35:29Z","file_name":"Supplementary Movie 1) in vivo time lapse microscopy of mNG-CorM.avi","checksum":"5b85c299bdd46cbde000e3449da835e0","date_created":"2025-06-27T07:35:29Z","success":1,"creator":"bsprings","access_level":"open_access"},{"creator":"bsprings","success":1,"date_created":"2025-06-27T07:35:28Z","checksum":"a05c19dad5ac10bc05f349c3507a70a7","access_level":"open_access","date_updated":"2025-06-27T07:35:28Z","file_size":126618,"content_type":"video/x-msvideo","file_id":"19917","relation":"main_file","file_name":"Supplementary Movie 2) mNG-CorM single 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Florian","first_name":"Florian","last_name":"Deckert"},{"first_name":"Anastasiya","last_name":"Hladik","full_name":"Hladik, Anastasiya"},{"last_name":"Steinbichl","first_name":"Linda","full_name":"Steinbichl, Linda"},{"last_name":"Cimatti","first_name":"Laura","full_name":"Cimatti, Laura"},{"first_name":"Katarina","last_name":"Milanovic","full_name":"Milanovic, Katarina"},{"full_name":"Jain, Mamta","first_name":"Mamta","last_name":"Jain"},{"full_name":"Torgasheva, Natalya","last_name":"Torgasheva","first_name":"Natalya"},{"last_name":"Tanzer","first_name":"Andrea","full_name":"Tanzer, Andrea"},{"full_name":"De Paepe, Kim","last_name":"De Paepe","first_name":"Kim"},{"last_name":"Van De Wiele","first_name":"Tom","full_name":"Van De Wiele, Tom"},{"last_name":"Hausmann","first_name":"Bela","full_name":"Hausmann, Bela"},{"last_name":"Lang","first_name":"Michaela","full_name":"Lang, Michaela"},{"last_name":"Pechhacker","first_name":"Martin","full_name":"Pechhacker, Martin"},{"first_name":"Nahla","last_name":"Ibrahim","full_name":"Ibrahim, Nahla"},{"last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"full_name":"Brostjan, Christine","first_name":"Christine","last_name":"Brostjan"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Christoph","last_name":"Gasche","full_name":"Gasche, Christoph"},{"full_name":"Boon, Louis","last_name":"Boon","first_name":"Louis"},{"first_name":"David","last_name":"Berry","full_name":"Berry, David"},{"last_name":"Jantsch","first_name":"Michael F.","full_name":"Jantsch, Michael F."},{"full_name":"Pereira, Fatima C.","last_name":"Pereira","first_name":"Fatima C."},{"first_name":"Cornelia","last_name":"Vesely","full_name":"Vesely, Cornelia"}],"external_id":{"isi":["001502896900001"],"pmid":["40471139"]},"abstract":[{"lang":"eng","text":"Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation."}],"department":[{"_id":"MiSi"}],"OA_type":"hybrid","title":"Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis","issue":"9","ddc":["570"],"publication_identifier":{"issn":["0022-1007"],"eissn":["1540-9538"]},"scopus_import":"1","status":"public","has_accepted_license":"1","doi":"10.1084/jem.20240109","date_created":"2025-06-29T22:01:15Z","acknowledgement":"Sequencing was performed by the Vienna BioCenter Core Facilities (Medical University of Vienna Core Facility) and the Biomedical Sequencing Facility at CeMM, Vienna. Cell sorting and flow cytometry were performed at the Core Facility Flow Cytometry and Imaging (Medical University of Vienna). We thank Jasmin Schwarz, Gudrun Kohl, Petra Pjevac, and Joana Seneca Silva from the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna for assisting with amplicon and metagenomic sequencing, as well as repositing of sequencing data. We thank Sophia Derdak and Michael Schuster for initial data analysis, Robert Vilvoi and Stephan Hemm for animal handling, Marcel Kertesz for mouse genotyping, and Salwan Roumaia for next generation sequencing sample preparation. Treatment schemes and graphical abstracts were created with https://BioRender.com.\r\n\r\nThis work was supported by the Austrian Science Fund, grant number ZK 57-B28 to C. Vesely, R. Gawish, and F.C. Pereira; grant number V 1025-B to R. Gawish; grant number DOC32-B28 to R. Varada and M.F. Jantsch; and F8007 and P32678 to M.F. Jantsch. Open Access funding provided by Medical University of Vienna.","day":"01","type":"journal_article","intvolume":"       222","article_number":"e20240109","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-09-01T00:00:00Z","citation":{"short":"R. Gawish, R. Varada, F. Deckert, A. Hladik, L. Steinbichl, L. Cimatti, K. Milanovic, M. Jain, N. Torgasheva, A. Tanzer, K. De Paepe, T. Van De Wiele, B. Hausmann, M. Lang, M. Pechhacker, N. Ibrahim, I. de Vries, C. Brostjan, M.K. Sixt, C. Gasche, L. Boon, D. Berry, M.F. Jantsch, F.C. Pereira, C. Vesely, Journal of Experimental Medicine 222 (2025).","apa":"Gawish, R., Varada, R., Deckert, F., Hladik, A., Steinbichl, L., Cimatti, L., … Vesely, C. (2025). Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis. <i>Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20240109\">https://doi.org/10.1084/jem.20240109</a>","ista":"Gawish R, Varada R, Deckert F, Hladik A, Steinbichl L, Cimatti L, Milanovic K, Jain M, Torgasheva N, Tanzer A, De Paepe K, Van De Wiele T, Hausmann B, Lang M, Pechhacker M, Ibrahim N, de Vries I, Brostjan C, Sixt MK, Gasche C, Boon L, Berry D, Jantsch MF, Pereira FC, Vesely C. 2025. Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis. Journal of Experimental Medicine. 222(9), e20240109.","mla":"Gawish, Riem, et al. “Filamin A Editing in Myeloid Cells Reduces Intestinal Inflammation and Protects from Colitis.” <i>Journal of Experimental Medicine</i>, vol. 222, no. 9, e20240109, Rockefeller University Press, 2025, doi:<a href=\"https://doi.org/10.1084/jem.20240109\">10.1084/jem.20240109</a>.","ama":"Gawish R, Varada R, Deckert F, et al. Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis. <i>Journal of Experimental Medicine</i>. 2025;222(9). doi:<a href=\"https://doi.org/10.1084/jem.20240109\">10.1084/jem.20240109</a>","chicago":"Gawish, Riem, Rajagopal Varada, Florian Deckert, Anastasiya Hladik, Linda Steinbichl, Laura Cimatti, Katarina Milanovic, et al. “Filamin A Editing in Myeloid Cells Reduces Intestinal Inflammation and Protects from Colitis.” <i>Journal of Experimental Medicine</i>. Rockefeller University Press, 2025. <a href=\"https://doi.org/10.1084/jem.20240109\">https://doi.org/10.1084/jem.20240109</a>.","ieee":"R. Gawish <i>et al.</i>, “Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis,” <i>Journal of Experimental Medicine</i>, vol. 222, no. 9. Rockefeller University Press, 2025."},"publication":"Journal of Experimental Medicine","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Rockefeller University Press","OA_place":"publisher","pmid":1,"month":"09"},{"file":[{"file_size":5758102,"date_updated":"2025-06-30T08:28:40Z","relation":"main_file","file_id":"19933","content_type":"application/pdf","file_name":"2025_AstronomyAstrophysics_GurungLopez.pdf","success":1,"creator":"dernst","checksum":"a50a817b72f03534c6a867035b51e433","date_created":"2025-06-30T08:28:40Z","access_level":"open_access"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":698,"year":"2025","publication_status":"published","date_updated":"2026-02-16T12:11:56Z","file_date_updated":"2025-06-30T08:28:40Z","author":[{"full_name":"Gurung-López, Siddhartha","first_name":"Siddhartha","last_name":"Gurung-López"},{"first_name":"Chris","last_name":"Byrohl","full_name":"Byrohl, Chris"},{"full_name":"Gronke, Max","last_name":"Gronke","first_name":"Max"},{"last_name":"Spinoso","first_name":"Daniele","full_name":"Spinoso, Daniele"},{"last_name":"Torralba Torregrosa","first_name":"Alberto","id":"018f0249-0e87-11f0-b167-cbce08fbd541","full_name":"Torralba Torregrosa, Alberto","orcid":"0000-0001-5586-6950"},{"full_name":"Fernández-Soto, Alberto","first_name":"Alberto","last_name":"Fernández-Soto"},{"full_name":"Arnalte-Mur, Pablo","first_name":"Pablo","last_name":"Arnalte-Mur"},{"last_name":"Martínez","first_name":"Vicent J.","full_name":"Martínez, Vicent J."}],"external_id":{"arxiv":["2501.04077"],"isi":["001507317300003"]},"abstract":[{"text":"Context. The observed Lyman-alpha (Lyα) line profile is a convolution of the complex Lyα radiative transfer taking place in the interstellar, circumgalactic, and intergalactic media (ISM, CGM, and IGM, respectively). Discerning the different components of the Lyα line is crucial in order to use it as a probe of galaxy formation or the evolution of the IGM.\r\n\r\nAims. We aim to present the second version of zELDA (redshift Estimator for Line profiles of Distant Lyman-Alpha emitters), an open-source Python module focused on modelling and fitting observed Lyα line profiles. This new version of zELDA focuses on disentangling the galactic from the IGM effects.\r\n\r\nMethods. We built realistic Lyα line profiles that include the ISM and IGM contributions by combining the Monte Carlo radiative-transfer simulations for the so-called shell model (ISM) and IGM transmission curves generated from TNG100. We used these mock line profiles to train different artificial neural networks. These use the observed spectrum as input and the outflow parameters of the best fitting ‘shell model’ as output along with the redshift and Lyα emission IGM escape fraction of the source.\r\n\r\nResults. We measured the accuracy of zELDA on mock Lyα line profiles. We find that zELDA is capable of reconstructing the ISM emerging Lyα line profile with high levels of accuracy (Kolmogórov-Smirnov<0.1) for 95% of the cases for HST/COS-like observations and 80% for MUSE-WIDE-like observations. zELDA is able to measure the IGM transmission with typical uncertainties below 10% for HST/COS and MUSE-WIDE data.\r\n\r\nConclusions. This work represents a step forward in the high-precision reconstruction of IGM-attenuated Lyα line profiles. zELDA allows the disentanglement of the galactic and IGM contribution shaping the Lyα line shape and thus allows us to use Lyα as a tool to study galaxy and ISM evolution.","lang":"eng"}],"department":[{"_id":"JoMa"}],"_id":"19929","oa_version":"Published Version","article_type":"original","oa":1,"status":"public","has_accepted_license":"1","arxiv":1,"date_created":"2025-06-29T22:01:15Z","doi":"10.1051/0004-6361/202453547","acknowledgement":"The authors acknowledge the financial support from the MICIU with funding from the European Union NextGenerationEU and Generalitat Valenciana in the call Programa de Planes Complementarios de I+D+i (PRTR 2022) Project (VAL-JPAS), reference ASFAE/2022/025. This work is part of the research Project PID2023-149420NB-I00 funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU. This work is also supported by the project of excellence PROMETEO CIPROM/2023/21 of the Conselleria de Educación, Universidades y Empleo (Generalitat Valenciana). MG thanks the Max Planck Society for support through the Max Planck Research Group. DS acknowledges the support by the Tsinghua Shui Mu Scholarship, funding of the National Key R&D Program of China (grant no. 2023YFA1605600), the science research grants from the China Manned Space Project with no. CMS-CSST2021-A05, and the Tsinghua University Initiative Scientific Research Program (no. 20223080023). This research made use of matplotlib, a Python library for publication quality graphics (Hunter 2007), NumPy (Harris et al. 2020) and SciPy (Virtanen et al. 2020).","day":"01","type":"journal_article","OA_type":"diamond","title":"zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks","ddc":["520"],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"scopus_import":"1","publication":"Astronomy & Astrophysics","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"EDP Sciences","month":"06","article_number":"A139","intvolume":"       698","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-06-01T00:00:00Z","citation":{"ista":"Gurung-López S, Byrohl C, Gronke M, Spinoso D, Torralba Torregrosa A, Fernández-Soto A, Arnalte-Mur P, Martínez VJ. 2025. zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks. Astronomy &#38; Astrophysics. 698, A139.","apa":"Gurung-López, S., Byrohl, C., Gronke, M., Spinoso, D., Torralba Torregrosa, A., Fernández-Soto, A., … Martínez, V. J. (2025). zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202453547\">https://doi.org/10.1051/0004-6361/202453547</a>","short":"S. Gurung-López, C. Byrohl, M. Gronke, D. Spinoso, A. Torralba Torregrosa, A. Fernández-Soto, P. Arnalte-Mur, V.J. Martínez, Astronomy &#38; Astrophysics 698 (2025).","ama":"Gurung-López S, Byrohl C, Gronke M, et al. zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks. <i>Astronomy &#38; Astrophysics</i>. 2025;698. doi:<a href=\"https://doi.org/10.1051/0004-6361/202453547\">10.1051/0004-6361/202453547</a>","chicago":"Gurung-López, Siddhartha, Chris Byrohl, Max Gronke, Daniele Spinoso, Alberto Torralba Torregrosa, Alberto Fernández-Soto, Pablo Arnalte-Mur, and Vicent J. Martínez. “ZELDA II: Reconstruction of Galactic Lyman-Alpha Spectra Attenuated by the Intergalactic Medium Using Neural Networks.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202453547\">https://doi.org/10.1051/0004-6361/202453547</a>.","ieee":"S. Gurung-López <i>et al.</i>, “zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks,” <i>Astronomy &#38; Astrophysics</i>, vol. 698. EDP Sciences, 2025.","mla":"Gurung-López, Siddhartha, et al. “ZELDA II: Reconstruction of Galactic Lyman-Alpha Spectra Attenuated by the Intergalactic Medium Using Neural Networks.” <i>Astronomy &#38; Astrophysics</i>, vol. 698, A139, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202453547\">10.1051/0004-6361/202453547</a>."}},{"ddc":["520"],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"scopus_import":"1","OA_type":"diamond","title":"Evolution of the UV slope of galaxies at cosmic morning (z > 4): The properties of extremely blue galaxies","day":"01","type":"journal_article","acknowledgement":"We acknowledges support from the INAF Large Grant for Extragalactic Surveys with JWST and from the PRIN 2022 MUR project 2022CB3PJ3 – First Light And Galaxy aSsembly (FLAGS) funded by the European Union – Next Generation EU. PS acknowledges INAF Mini Grant 2022 “The evolution of passive galaxies through cosmic time”. Part of the research activities described in this paper were carried out with the contribution of the Next Generation EU funds within the National Recovery and Resilience Plan (PNRR), Mission 4 – Education and Research, Component 2 – From Research to Business (M4C2), Investment Line 3.1 – Strengthening and creation of Research Infrastructures, Project IR0000034 – “STILES – Strengthening the Italian Leadership in ELT and SKA”. RA acknowledges support of Grant project PID2023-147386NB-I00 funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU, and the Severo Ochoa grant CEX2021-001131-S funded by MCIN/AEI/10.13039/50110001103.","doi":"10.1051/0004-6361/202453267","arxiv":1,"date_created":"2025-06-29T22:01:15Z","status":"public","has_accepted_license":"1","date_published":"2025-06-01T00:00:00Z","citation":{"mla":"Dottorini, D., et al. “Evolution of the UV Slope of Galaxies at Cosmic Morning (z &#62; 4): The Properties of Extremely Blue Galaxies.” <i>Astronomy &#38; Astrophysics</i>, vol. 698, A234, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202453267\">10.1051/0004-6361/202453267</a>.","ieee":"D. Dottorini <i>et al.</i>, “Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies,” <i>Astronomy &#38; Astrophysics</i>, vol. 698. EDP Sciences, 2025.","chicago":"Dottorini, D., A. Calabrò, L. Pentericci, Sara Mascia, M. Llerena, L. Napolitano, P. Santini, et al. “Evolution of the UV Slope of Galaxies at Cosmic Morning (z &#62; 4): The Properties of Extremely Blue Galaxies.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202453267\">https://doi.org/10.1051/0004-6361/202453267</a>.","ama":"Dottorini D, Calabrò A, Pentericci L, et al. Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies. <i>Astronomy &#38; Astrophysics</i>. 2025;698. doi:<a href=\"https://doi.org/10.1051/0004-6361/202453267\">10.1051/0004-6361/202453267</a>","short":"D. Dottorini, A. Calabrò, L. Pentericci, S. Mascia, M. Llerena, L. Napolitano, P. Santini, G. Roberts-Borsani, M. Castellano, R. Amorin, M. Dickinson, A. Fontana, N. Hathi, M. Hirschmann, A.M. Koekemoer, R.A. Lucas, E. Merlin, A. Morales, F. Pacucci, S. Wilkins, P. Arrabal Haro, M. Bagley, S.L. Finkelstein, J. Kartaltepe, C. Papovich, N. Pirzkal, Astronomy &#38; Astrophysics 698 (2025).","ista":"Dottorini D, Calabrò A, Pentericci L, Mascia S, Llerena M, Napolitano L, Santini P, Roberts-Borsani G, Castellano M, Amorin R, Dickinson M, Fontana A, Hathi N, Hirschmann M, Koekemoer AM, Lucas RA, Merlin E, Morales A, Pacucci F, Wilkins S, Arrabal Haro P, Bagley M, Finkelstein SL, Kartaltepe J, Papovich C, Pirzkal N. 2025. Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies. Astronomy &#38; Astrophysics. 698, A234.","apa":"Dottorini, D., Calabrò, A., Pentericci, L., Mascia, S., Llerena, M., Napolitano, L., … Pirzkal, N. (2025). Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202453267\">https://doi.org/10.1051/0004-6361/202453267</a>"},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"A234","intvolume":"       698","month":"06","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"EDP Sciences","article_processing_charge":"No","quality_controlled":"1","publication":"Astronomy & Astrophysics","file_date_updated":"2025-06-30T08:22:08Z","date_updated":"2026-02-16T12:11:39Z","publication_status":"published","volume":698,"year":"2025","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","success":1,"date_created":"2025-06-30T08:22:08Z","checksum":"100f897d468de9d0113277c870035b62","access_level":"open_access","file_size":2442076,"date_updated":"2025-06-30T08:22:08Z","file_id":"19932","content_type":"application/pdf","relation":"main_file","file_name":"2025_AstronomyAstrophysics_Dottorini.pdf"}],"oa":1,"article_type":"original","oa_version":"Published Version","_id":"19930","department":[{"_id":"JoMa"}],"abstract":[{"lang":"eng","text":"We present an analysis of the UV continuum slope, β, using a sample of 726 galaxies with z > 4, selected from a mixture of JWST ERS, GTO, and GO observational programs. We considered only spectroscopic data obtained with the low-resolution (R ∼ 30 − 300) PRISM/CLEAR NIRSpec configuration. Studying the correlation between β and MUV, we find an overall decreasing trend, described by β = ( − 0.055 ± 0.017)MUV + ( − 2.98 ± 0.34). This is consistent with previous studies, where brighter galaxies show redder β values. However, when analyzing the trend in separate redshift bins, we find that at high redshift the relation becomes much flatter and is consistent with a flat slope within 1σ. Furthermore, we find that β tends to decrease with redshift, following β = ( − 0.075 ± 0.010)z + ( − 1.496 ± 0.056). This is consistent with most recent results showing a steepening of the spectra at higher z. We selected a sample of galaxies with extremely blue slopes (i.e., β < −2.6). Such slopes are steeper than predicted by stellar evolution models – even for dust-free, young, metal-poor populations – when the contribution of nebular emission is included. We selected 44 extremely blue galaxies (XBGs) and investigated the possible physical origin of their steep slopes by comparing them to a subsample of redder galaxies (matched in Δz = ±0.5 and ΔMUV = ±0.2). We find that XBGs have younger stellar populations, stronger ionization fields, lower dust attenuation, and lower but not pristine metallicity (∼10% Z⊙) compared to red galaxies. However, these properties alone cannot explain the extreme β values. Using indirect inference of Lyman continuum escape with the most recent models, we estimated the escape fraction fesc > 10% in at least 25% of the XBGs, whereas all the red sources exhibit much lower fesc values. A reduced nebular continuum contribution – resulting from either a high escape fraction or a bursty star formation history – is likely the origin of the extremely blue slopes."}],"author":[{"full_name":"Dottorini, D.","first_name":"D.","last_name":"Dottorini"},{"first_name":"A.","last_name":"Calabrò","full_name":"Calabrò, A."},{"full_name":"Pentericci, L.","last_name":"Pentericci","first_name":"L."},{"full_name":"Mascia, Sara","id":"edaf889c-c7cd-11ef-ab1b-bb28c431bd29","first_name":"Sara","last_name":"Mascia"},{"full_name":"Llerena, M.","last_name":"Llerena","first_name":"M."},{"first_name":"L.","last_name":"Napolitano","full_name":"Napolitano, L."},{"full_name":"Santini, P.","last_name":"Santini","first_name":"P."},{"last_name":"Roberts-Borsani","first_name":"G.","full_name":"Roberts-Borsani, G."},{"first_name":"M.","last_name":"Castellano","full_name":"Castellano, M."},{"full_name":"Amorin, R.","first_name":"R.","last_name":"Amorin"},{"last_name":"Dickinson","first_name":"M.","full_name":"Dickinson, M."},{"full_name":"Fontana, A.","first_name":"A.","last_name":"Fontana"},{"full_name":"Hathi, N.","first_name":"N.","last_name":"Hathi"},{"last_name":"Hirschmann","first_name":"M.","full_name":"Hirschmann, M."},{"last_name":"Koekemoer","first_name":"A. M.","full_name":"Koekemoer, A. M."},{"full_name":"Lucas, R. A.","first_name":"R. A.","last_name":"Lucas"},{"first_name":"E.","last_name":"Merlin","full_name":"Merlin, E."},{"full_name":"Morales, A.","last_name":"Morales","first_name":"A."},{"first_name":"F.","last_name":"Pacucci","full_name":"Pacucci, F."},{"last_name":"Wilkins","first_name":"S.","full_name":"Wilkins, S."},{"last_name":"Arrabal Haro","first_name":"P.","full_name":"Arrabal Haro, P."},{"first_name":"M.","last_name":"Bagley","full_name":"Bagley, M."},{"first_name":"S. L.","last_name":"Finkelstein","full_name":"Finkelstein, S. L."},{"last_name":"Kartaltepe","first_name":"J.","full_name":"Kartaltepe, J."},{"first_name":"C.","last_name":"Papovich","full_name":"Papovich, C."},{"first_name":"N.","last_name":"Pirzkal","full_name":"Pirzkal, N."}],"external_id":{"arxiv":["2412.01623"],"isi":["001510826300019"]}},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       698","article_number":"A227","date_published":"2025-06-01T00:00:00Z","citation":{"apa":"Furtak, L. J., Secunda, A. R., Greene, J. E., Zitrin, A., Labbé, I., Golubchik, M., … Whitaker, K. E. (2025). Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202554110\">https://doi.org/10.1051/0004-6361/202554110</a>","ista":"Furtak LJ, Secunda AR, Greene JE, Zitrin A, Labbé I, Golubchik M, Bezanson R, Kokorev V, Atek H, Brammer GB, Chemerynska I, Cutler SE, Dayal P, Feldmann R, Fujimoto S, Glazebrook K, Leja J, Ma Y, Matthee JJ, Naidu RP, Nelson EJ, Oesch PA, Pan R, Price SH, Suess KA, Wang B, Weaver JR, Whitaker KE. 2025. Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1. Astronomy &#38; Astrophysics. 698, A227.","short":"L.J. Furtak, A.R. Secunda, J.E. Greene, A. Zitrin, I. Labbé, M. Golubchik, R. Bezanson, V. Kokorev, H. Atek, G.B. Brammer, I. Chemerynska, S.E. Cutler, P. Dayal, R. Feldmann, S. Fujimoto, K. Glazebrook, J. Leja, Y. Ma, J.J. Matthee, R.P. Naidu, E.J. Nelson, P.A. Oesch, R. Pan, S.H. Price, K.A. Suess, B. Wang, J.R. Weaver, K.E. Whitaker, Astronomy &#38; Astrophysics 698 (2025).","ama":"Furtak LJ, Secunda AR, Greene JE, et al. Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1. <i>Astronomy &#38; Astrophysics</i>. 2025;698. doi:<a href=\"https://doi.org/10.1051/0004-6361/202554110\">10.1051/0004-6361/202554110</a>","chicago":"Furtak, Lukas J., Amy R. Secunda, Jenny E. Greene, Adi Zitrin, Ivo Labbé, Miriam Golubchik, Rachel Bezanson, et al. “Investigating Photometric and Spectroscopic Variability in the Multiply Imaged Little Red Dot A2744-QSO1.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202554110\">https://doi.org/10.1051/0004-6361/202554110</a>.","ieee":"L. J. Furtak <i>et al.</i>, “Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1,” <i>Astronomy &#38; Astrophysics</i>, vol. 698. EDP Sciences, 2025.","mla":"Furtak, Lukas J., et al. “Investigating Photometric and Spectroscopic Variability in the Multiply Imaged Little Red Dot A2744-QSO1.” <i>Astronomy &#38; Astrophysics</i>, vol. 698, A227, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202554110\">10.1051/0004-6361/202554110</a>."},"article_processing_charge":"No","quality_controlled":"1","publication":"Astronomy & Astrophysics","month":"06","language":[{"iso":"eng"}],"publisher":"EDP Sciences","OA_place":"publisher","OA_type":"diamond","title":"Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1","ddc":["520"],"scopus_import":"1","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"doi":"10.1051/0004-6361/202554110","arxiv":1,"date_created":"2025-06-29T22:01:16Z","status":"public","has_accepted_license":"1","day":"01","type":"journal_article","acknowledgement":"We would like to thank Xihan Ji, Hannah Übler, and Roberto Maiolino, for cordial and useful discussions. The BGU lensing group acknowledges support by grant No. 2020750 from the United States-Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Israel Science Foundation Grant No. 864/23. P.D. warmly thanks the European Commission’s and University of Groningen’s CO-FUND Rosalind Franklin program. This work is based on observations obtained with the NASA/ESA/CSA JWST, namely programs GO-2756, -2561, -2883, -3538, -4111, and -3516, retrieved from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute (STScI). STScI is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS 5-26555. The spectroscopy products presented herein, from JWST program GO-2561, were retrieved from the Dawn JWST Archive (DJA). DJA is an initiative of the Cosmic Dawn Center (DAWN), which is funded by the Danish National Research Foundation under grant DNRF140. The data used in this work may be retrieved from the MAST archive at: http://dx.doi.org/10.17909/p7t7-te67. This work also makes use of the Center for Computational Astrophysics at the Flatiron Institute which is supported by the Simons Foundation. Support for JWST programs GO-2561, -4111, and -3516 was provided by NASA through grants from STScI. This research made use of Astropy, (http://www.astropy.org) a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018) and Photutils, an Astropy package for detection and photometry of astronomical sources (Bradley et al. 2024), as well as the packages NumPy (van der Walt et al. 2011), SciPy (Virtanen et al. 2020), Matplotlib (Hunter 2007), and the MAAT Astronomy and Astrophysics tools for MATLAB (Ofek 2014).","oa_version":"Published Version","_id":"19931","oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"JWST observations have uncovered a new population of red, compact objects at high redshifts dubbed “little red dots” (LRDs), which typically show broad emission lines and are thought to be dusty active galactic nuclei (AGNs). Some of their other features, however, challenge the AGN explanation, such as prominent Balmer breaks and extremely faint or even missing metal high-ionization lines, X-ray, or radio emission, including in deep stacks. Time variability is another robust test of AGN activity. Here, we exploit the z = 7.045 multiply imaged LRD A2744-QSO1, which offers a particularly unique test of variability due to lensing-induced time delays between the three images spanning 22 yr (2.7 yr in the rest-frame), to investigate its photometric and spectroscopic variability. We find the equivalent widths (EWs) of the broad Hα and Hβ lines, which are independent of magnification and other systematics, to exhibit significant variations, of up to 18 ± 3% for Hα and up to 22 ± 8% in Hβ, on a timescale of 875 d (2.4 yr) in the rest-frame. This suggests that A2744-QSO1 is indeed an AGN. We find no significant photometric variability beyond the limiting systematic uncertainties, so it currently cannot be determined whether the EW variations are due to line-flux or continuum variability. These results are consistent with a typical damped random walk variability model for an AGN such as A2744-QSO1 (MBH = 4 × 107 M⊙) given the sparse sampling of the light curve with the available data. Our results therefore support the AGN interpretation of this LRD, and highlight the need for further photometric and spectroscopic monitoring in order to build a detailed and reliable light curve."}],"author":[{"full_name":"Furtak, Lukas J.","last_name":"Furtak","first_name":"Lukas J."},{"first_name":"Amy R.","last_name":"Secunda","full_name":"Secunda, Amy R."},{"last_name":"Greene","first_name":"Jenny E.","full_name":"Greene, Jenny E."},{"last_name":"Zitrin","first_name":"Adi","full_name":"Zitrin, Adi"},{"last_name":"Labbé","first_name":"Ivo","full_name":"Labbé, Ivo"},{"full_name":"Golubchik, Miriam","last_name":"Golubchik","first_name":"Miriam"},{"full_name":"Bezanson, Rachel","first_name":"Rachel","last_name":"Bezanson"},{"first_name":"Vasily","last_name":"Kokorev","full_name":"Kokorev, Vasily"},{"first_name":"Hakim","last_name":"Atek","full_name":"Atek, Hakim"},{"full_name":"Brammer, Gabriel B.","first_name":"Gabriel B.","last_name":"Brammer"},{"first_name":"Iryna","last_name":"Chemerynska","full_name":"Chemerynska, Iryna"},{"full_name":"Cutler, Sam E.","last_name":"Cutler","first_name":"Sam E."},{"last_name":"Dayal","first_name":"Pratika","full_name":"Dayal, Pratika"},{"full_name":"Feldmann, Robert","last_name":"Feldmann","first_name":"Robert"},{"last_name":"Fujimoto","first_name":"Seiji","full_name":"Fujimoto, Seiji"},{"full_name":"Glazebrook, Karl","last_name":"Glazebrook","first_name":"Karl"},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"last_name":"Ma","first_name":"Yilun","full_name":"Ma, Yilun"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"first_name":"Erica J.","last_name":"Nelson","full_name":"Nelson, Erica J."},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"first_name":"Richard","last_name":"Pan","full_name":"Pan, Richard"},{"full_name":"Price, Sedona H.","first_name":"Sedona H.","last_name":"Price"},{"full_name":"Suess, Katherine A.","last_name":"Suess","first_name":"Katherine A."},{"first_name":"Bingjie","last_name":"Wang","full_name":"Wang, Bingjie"},{"last_name":"Weaver","first_name":"John R.","full_name":"Weaver, John R."},{"last_name":"Whitaker","first_name":"Katherine E.","full_name":"Whitaker, Katherine E."}],"external_id":{"arxiv":["2502.07875"],"isi":["001510826300017"]},"department":[{"_id":"JoMa"}],"date_updated":"2026-02-16T12:11:22Z","file_date_updated":"2025-06-30T08:44:24Z","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2025-06-30T08:44:24Z","checksum":"567fa02a9791d489355ec75d02bb1cb9","creator":"dernst","success":1,"access_level":"open_access","file_id":"19934","content_type":"application/pdf","relation":"main_file","date_updated":"2025-06-30T08:44:24Z","file_size":1835865,"file_name":"2025_AstronomyAstrophysics_Furtak.pdf"}],"publication_status":"published","volume":698,"year":"2025"},{"status":"public","has_accepted_license":"1","doi":"10.1145/3729284","date_created":"2025-06-30T08:47:31Z","acknowledgement":"We would like to thank the anonymous reviewers for their helpful feedback and Alex Summers\r\nfor insightful discussions. This work was funded in part by a Google PhD Fellowship for the first\r\nauthor.","type":"journal_article","day":"01","issue":"PLDI","title":"Destabilizing Iris","OA_type":"hybrid","scopus_import":"1","publication_identifier":{"eissn":["2475-1421"]},"corr_author":"1","ddc":["000"],"publication":"Proceedings of the ACM on Programming Languages","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"month":"06","intvolume":"         9","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Spies, Simon, et al. “Destabilizing Iris.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 9, no. PLDI, Association for Computing Machinery, 2025, pp. 848–73, doi:<a href=\"https://doi.org/10.1145/3729284\">10.1145/3729284</a>.","ama":"Spies S, Mück N, Zeng H, et al. Destabilizing Iris. <i>Proceedings of the ACM on Programming Languages</i>. 2025;9(PLDI):848-873. doi:<a href=\"https://doi.org/10.1145/3729284\">10.1145/3729284</a>","chicago":"Spies, Simon, Niklas Mück, Haoyi Zeng, Michael Joachim Sammler, Andrea Lattuada, Peter Müller, and Derek Dreyer. “Destabilizing Iris.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3729284\">https://doi.org/10.1145/3729284</a>.","ieee":"S. Spies <i>et al.</i>, “Destabilizing Iris,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 9, no. PLDI. Association for Computing Machinery, pp. 848–873, 2025.","short":"S. Spies, N. Mück, H. Zeng, M.J. Sammler, A. Lattuada, P. Müller, D. Dreyer, Proceedings of the ACM on Programming Languages 9 (2025) 848–873.","ista":"Spies S, Mück N, Zeng H, Sammler MJ, Lattuada A, Müller P, Dreyer D. 2025. Destabilizing Iris. Proceedings of the ACM on Programming Languages. 9(PLDI), 848–873.","apa":"Spies, S., Mück, N., Zeng, H., Sammler, M. J., Lattuada, A., Müller, P., &#38; Dreyer, D. (2025). Destabilizing Iris. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3729284\">https://doi.org/10.1145/3729284</a>"},"date_published":"2025-06-01T00:00:00Z","file":[{"date_created":"2025-06-30T09:01:08Z","checksum":"6b72d84c10a10ba7cd1646e2c36dc1ff","creator":"dernst","success":1,"access_level":"open_access","file_id":"19938","content_type":"application/pdf","relation":"main_file","date_updated":"2025-06-30T09:01:08Z","file_size":843343,"file_name":"2025_ProcACMProg_Spies.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":9,"year":"2025","publication_status":"published","date_updated":"2025-06-30T09:10:11Z","file_date_updated":"2025-06-30T09:01:08Z","author":[{"full_name":"Spies, Simon","first_name":"Simon","last_name":"Spies"},{"full_name":"Mück, Niklas","last_name":"Mück","first_name":"Niklas"},{"full_name":"Zeng, Haoyi","first_name":"Haoyi","last_name":"Zeng"},{"last_name":"Sammler","first_name":"Michael Joachim","id":"510d3901-2a03-11ee-914d-d9ae9011f0a7","full_name":"Sammler, Michael Joachim"},{"full_name":"Lattuada, Andrea","first_name":"Andrea","last_name":"Lattuada"},{"last_name":"Müller","first_name":"Peter","full_name":"Müller, Peter"},{"first_name":"Derek","last_name":"Dreyer","full_name":"Dreyer, Derek"}],"abstract":[{"text":"The separation logic framework Iris has been built on the premise that all assertions are stable, meaning they unconditionally enjoy the famous frame rule. This gives Iris—and the numerous program logics that build on it—very modular reasoning principles. But stability also comes at a cost. It excludes a core feature of the Viper verifier family, heap-dependent expression assertions, which lift program expressions to the assertion level in order to reduce redundancy between code and specifications and better facilitate SMT-based automation.\r\nIn this paper, we bring heap-dependent expression assertions to Iris with Daenerys. To do so, we must first revisit the very core of Iris, extending it with a new form of unstable resources (and adapting the frame rule accordingly). On top, we then build a program logic with heap-dependent expression assertions and lay the foundations for connecting Iris to SMT solvers. We apply Daenerys to several case studies, including some that go beyond what Viper and Iris can do individually and others that benefit from the connection to SMT.","lang":"eng"}],"department":[{"_id":"MiSa"}],"_id":"19935","oa_version":"Published Version","page":"848-873","article_type":"original","oa":1}]