[{"license":"https://creativecommons.org/licenses/by-nc/4.0/","OA_place":"publisher","ec_funded":1,"day":"04","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"}],"author":[{"full_name":"Önal, Hüseyin C","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","id":"4659D740-F248-11E8-B48F-1D18A9856A87","last_name":"Önal"}],"file":[{"creator":"hoenal","file_size":25869143,"file_id":"19272","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-02-01T23:30:02Z","relation":"source_file","checksum":"c1a4d75a7471de9f954697b06cd18d28","embargo_to":"open_access","file_name":"Cihan_Onal_Thesis_Final.docx","date_created":"2025-02-28T13:57:01Z","access_level":"closed"},{"file_name":"Cihan_Onal_Thesis_Final_pdfa.pdf","date_created":"2025-02-28T13:57:04Z","access_level":"open_access","embargo":"2026-02-01","date_updated":"2026-02-01T23:30:02Z","relation":"main_file","checksum":"de4e62147ab9f04098dc8cd898c630da","file_id":"19273","content_type":"application/pdf","creator":"hoenal","file_size":12077596}],"supervisor":[{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19271","publication_status":"published","type":"dissertation","year":"2025","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9437"},{"id":"15084","status":"public","relation":"part_of_dissertation"}]},"date_published":"2025-03-04T00:00:00Z","oa":1,"date_created":"2025-02-28T14:15:53Z","oa_version":"Published Version","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"03","project":[{"grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"publication_identifier":{"eissn":["2663-337X"]},"abstract":[{"lang":"eng","text":"The medial habenula (MHb) is implicated in regulating emotional responses\r\nto aversive events. Studies in zebrafish have identified a remarkable morphological\r\nleft-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian\r\nMHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in\r\nmodulating fear responses. However, there is little evidence for structural or\r\nfunctional lateralization in the mammalian MHb-IPN pathway.\r\nHere, I investigated the synaptic properties of the left and right MHb\r\nafferents to the IPN in mice and addressed whether these synaptic connections\r\nselectively influence the expression of conditioned fear in mice. My findings reveal\r\nthat each individual IPN neuron receives inputs from both left and right MHb.\r\nElectrophysiological recordings from the same postsynaptic IPN neurons\r\ndemonstrate that the left MHb-originating synapses exhibit lower release\r\nprobability and higher 𝛾-aminobutyric acid type B receptor (GABABR)-mediated\r\npotentiation compared to the right MHb-originating synapses. Interestingly,\r\nchemogenetic inhibition of cholinergic neurons in the left but not the right MHb\r\nsignificantly attenuated cue-dependent fear recall. Furthermore, conditional\r\ndeletion of GABABR in the left MHb interfered with the recall of cued fear memory,\r\nwhereas that in the right MHb neurons spared fear memory expression.\r\nCollectively, I demonstrate a functional asymmetry of the MHb in mice,\r\nrevealing a predominant role for GABABR-mediated signaling in the left MHb-IPN\r\npathway in the modulation of fear memories. These findings suggest that\r\nlateralized pathways could represent a fundamental principle in the neural\r\nregulation of emotion across species."}],"citation":{"apa":"Önal, C. (2025). Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19271","mla":"Önal, Cihan. Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19271.","ama":"Önal C. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. 2025. doi:10.15479/AT-ISTA-19271","short":"C. Önal, Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula, Institute of Science and Technology Austria, 2025.","chicago":"Önal, Cihan. “Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19271.","ista":"Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria.","ieee":"C. Önal, “Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula,” Institute of Science and Technology Austria, 2025."},"file_date_updated":"2026-02-01T23:30:02Z","doi":"10.15479/AT-ISTA-19271","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"RySh"}],"has_accepted_license":"1","corr_author":"1","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","acknowledgement":"I would like to thank the European Research Council and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to Ryuichi Shigemoto and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), and the Austrian Neuroscience Association for providing financial support and opportunities, which were important in allowing me to present my work. I also wish to thank the\r\nPreclinical Facility, especially Michael Schunn, for always welcoming me from my earliest days as an intern. My gratitude goes as well to the Miba Machine Shop, in particular Todor Asenov, Astrit Arslani, and Thomas Menner, whose technical expertise often saved the day.","ddc":["570","571","573","599"],"date_updated":"2026-10-21T08:33:44Z","publisher":"Institute of Science and Technology Austria","_id":"19271","title":"Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula"},{"date_published":"2025-04-04T00:00:00Z","oa":1,"date_created":"2025-04-04T07:48:24Z","type":"dissertation","year":"2025","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"19421"},{"id":"13212","relation":"part_of_dissertation","status":"public"}]},"fulldoi":"https://doi.org/10.15479/AT-ISTA-19478","publication_status":"published","supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"}],"file":[{"file_id":"19526","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":16344814,"creator":"hchen","date_created":"2025-04-08T08:00:07Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_0403_Huihuang.docx","relation":"source_file","date_updated":"2026-10-08T22:30:02Z","checksum":"b154973663a1bba505683faab7ae5ead"},{"file_size":8482147,"creator":"hchen","file_id":"19527","content_type":"application/pdf","checksum":"0099565f024388830c125ec17375c1a0","date_updated":"2026-10-09T22:30:03Z","relation":"main_file","embargo":"2026-10-08","access_level":"open_access","date_created":"2025-04-08T08:00:06Z","file_name":"Thesis_0406_PDFA_Huihuang_1.pdf"}],"day":"04","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi_confirm":"1","author":[{"last_name":"Chen","id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","full_name":"Chen, Huihuang"}],"page":"118","OA_place":"publisher","ec_funded":1,"title":"The cAMP second messenger in auxin signalling","degree_awarded":"PhD","acknowledgement":"This project was funded by the European Research Council Advanced Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian Science Fund (FWF; P\r\n37051-B).","ddc":["580"],"date_updated":"2026-10-23T07:25:54Z","publisher":"Institute of Science and Technology Austria","_id":"19478","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"corr_author":"1","abstract":[{"lang":"eng","text":"Auxin is one of the most important phytohormones, playing a crucial role in plant growth and \r\ndevelopment. Genetic studies in Arabidopsis have identified core components of auxin \r\nsignalling and established the classical transcriptional regulation mechanism. This classical \r\nparadigm recognizes TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN \r\nSIGNALLING F-BOX (AFB) proteins as auxin receptors possessing E3 ubiquitin ligase \r\nactivity. Auxin functions as a \"molecular glue\" enhancing TIR1/AFB-Aux/IAA \r\n(AUXIN/INDOLE-3-ACETIC ACID) inhibitor interactions, leading to Aux/IAAs’ \r\nubiquitination and degradation. This process releases AUXIN RESPONSE FACTORs (ARFs) \r\nfrom repression, enabling transcriptional activation of auxin-responsive genes. Notably, the \r\ndiscovery of adenylate cyclase (AC) activity in TIR1/AFBs, catalysing cAMP production from \r\nATP, presents novel transcriptional regulatory possibilities, though cAMP's mechanistic role \r\nin auxin signalling remains unclear. Beyond transcriptional regulation (slow response) a non\r\ntranscriptional pathway (rapid response) mediated by AFB1 also exists, as auxin triggers rapid \r\nroot growth inhibition within 30 seconds. How TIR1 and AFB1, with their distinct subcellular \r\nlocalizations, differentially regulate transcriptional and non-transcriptional processes remains \r\nunclear. To address these two key questions, this study conducted the following investigations. \r\nTIR1 and AFB1 display distinct subcellular localization patterns, with AFB1 specifically \r\nmediating auxin-induced rapid root growth inhibition. To examine whether subcellular \r\nlocalization differences contribute to functional divergence between TIR1 and AFB1, we \r\nutilized microfluidic systems combined with genetic complementation assays. Nuclear export \r\nsignal-fused TIR1 failed to rescue the rapid response defects observed in afb1 mutants. In \r\ncontrast, nuclear localization signal-fused AFB1 exhibited dual functional deficiencies: it \r\nneither restored the rapid response impairment in afb1 mutants nor compensated for \r\ntranscriptional regulation defects in tir1 mutants which limitation stemmed from AFB1's \r\nintrinsic incapacity to assemble functional SCF complexes. These results collectively establish \r\nthat the functional specialization of TIR1 and AFB1 is governed by both their subcellular \r\ncompartmentalization and inherent biochemical characteristics. \r\nThe mechanism by which cAMP derived from the auxin receptor TIR1/AFB modulates \r\ntranscriptional regulation remains undefined. To address this, we genetically dissociated TIR1 \r\nAC activity from its E3 ubiquitin ligase function to investigate cAMP's signalling role. AC\r\ninactivating mutations preserved TIR1-mediated Aux/IAAs’ degradation but abolished ARF\r\ni \r\ndependent transcriptional activation. tir1afb2 mutants expressing AC-deficient TIR1 variants \r\nfailed to restore transcriptional responses. Crucially, compartmentalized cAMP accumulation \r\nwithin Aux/IAA - ARF complexes vicinity triggered auxin signalling independently of both \r\nauxin perception and Aux/IAAs’ degradation, confirming its secondary messenger identity. \r\nFurther mechanistic analysis demonstrated cAMP directly interact with ARF. cAMP \r\ndirectly promotes ARF dissociation from Aux/IAA repressors and enhances ARF \r\nhomodimerization. Genetic complementation assays revealed that ARF mutants lacking \r\nconserved cAMP-binding motifs exhibited partial functional recovery, providing direct \r\nevidence for cAMP-ARF physical interaction during signal propagation. \r\nThese findings collectively challenge the established model of auxin signalling and define \r\na novel TIR1-cAMP-ARF regulatory axis, substantially advancing our comprehension of \r\nauxin-mediated physiological regulation. "}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT-ISTA-19478","file_date_updated":"2026-10-09T22:30:03Z","citation":{"chicago":"Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19478.","short":"H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science and Technology Austria, 2025.","ama":"Chen H. The cAMP second messenger in auxin signalling. 2025. doi:10.15479/AT-ISTA-19478","ieee":"H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science and Technology Austria, 2025.","ista":"Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria.","mla":"Chen, Huihuang. The CAMP Second Messenger in Auxin Signalling. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19478.","apa":"Chen, H. (2025). The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19478"},"article_processing_charge":"No","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"},{"_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681"}],"month":"04","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version"},{"fulldoi":"https://doi.org/10.15479/AT-ISTA-20467","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","year":"2025","related_material":{"record":[{"status":"public","id":"19566","relation":"part_of_dissertation"}]},"type":"dissertation","date_created":"2025-10-14T10:24:41Z","date_published":"2025-10-14T00:00:00Z","oa":1,"OA_place":"publisher","page":"99","license":"https://creativecommons.org/licenses/by/4.0/","doi_confirm":"1","author":[{"last_name":"Miteva","id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Miteva, Florianne E","first_name":"Florianne E"}],"day":"14","acknowledged_ssus":[{"_id":"Bio"},{"_id":"SSU"},{"_id":"PreCl"},{"_id":"LifeSc"}],"file":[{"checksum":"03537697be8c688d3a05cf948288e48f","relation":"main_file","date_updated":"2026-10-14T22:30:02Z","embargo":"2026-10-14","access_level":"open_access","date_created":"2025-10-17T11:09:11Z","file_name":"2025_Miteva_Florianne_thesis.pdf","file_size":13668588,"creator":"fschootu","content_type":"application/pdf","file_id":"20484"},{"file_size":28991918,"creator":"fschootu","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20525","date_updated":"2026-10-14T22:30:02Z","relation":"source_file","checksum":"df4930d7211cf9cfe1254b77204dc1d3","date_created":"2025-10-23T11:33:06Z","access_level":"closed","embargo_to":"open_access","file_name":"2025_Miteva_florianne_thesis.docx"}],"supervisor":[{"full_name":"Siegert, Sandra","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Prostaglandins play a central role in the inflammatory response. Prostaglandins are synthesized \r\nin a rate-limiting manner by the enzyme cyclooxygenase (Cox), which exists in two isoforms: \r\nthe Cox-2 and Cox-1 isoforms. Traditionally, Cox-1 is thought to mediate homeostatic \r\nfunctions due to its constitutive expression due to its constitutive expression, whereas Cox-2 is \r\ntemporary induced in response to inflammatory stimuli and is associated with the inflammatory \r\nresponse. Interestingly, in the central nervous system, Cox-1 is predominantly expressed in \r\nmicroglia. As the resident immune cells of the brain, microglia play a key role in inflammation. \r\nCox-1 expressing microglia are increased in neurodegenerative diseases, and both global \r\nknockout of Cox-1 and selective Cox-1 inhibition has been shown to ameliorate inflammatory \r\neffects in neurodegenerative diseases. However, direct evidence elucidating how microglial \r\nCox-1 expression influences their response to insults remains limited and warrants further \r\ninvestigation. \r\nFirst, I utilize the optic nerve crush (ONC) model to study the microglial response to injury and \r\ninflammation, confirming a reactive microglial response in both the crushed and uninjured \r\ncontralateral retina using CD68 expression and morphological analysis. While previous studies \r\nreported retinal ganglion cell (RGC) loss in the contralateral eye, I did not observe this, \r\nsuggesting that unilateral ONC induces microglial activation in the contralateral eye without \r\nRGC degeneration. To explore the role of Cox-1 in this response, I generated a mouse model \r\nwith microglia-specific deletion of Cox-1. After ONC, these mice exhibited an attenuated \r\nmicroglial response in both the ipsilateral and contralateral retinas, as well as in visual \r\nprocessing areas of the brain. Notably, Cox-2 does not show any expression after ONC in both \r\nwild-type and Cox-1 knockout mice Additionally, Cox-1KO mice show a reduction in \r\nphagocytic cups and a reduction in microglia proliferation after ONC. However, due to \r\nreproducibility problems of the observed phenotype, even after the generation of two new \r\nmouse models, I cannot draw any definitive conclusions based on the data. \r\nNext, due to the ambiguity of the mouse model, I explored an alternative route to investigate \r\nfunctional consequences of Cox-1 in microglia. I generated a COX1 knock-out human induced \r\npluripotent cell (hIPSC) line using CRISPR/Cas9. These cells are were differentiated in \r\nmicroglia-like cells and integrated in dissociated retinal organoids according to protocols \r\ndeveloped in our lab. In response to LPS and POLY(I:C) stimulation, the release and expression \r\nof cytokines and chemokines was decreased in COX1 knockout cells. However, the \r\nprostaglandin PGE2 was not increased in microglia-like cells in both control and COX1 \r\nknockout cells. \r\nOverall, the results from the COX1 knock-out microglia-like cells suggests that COX1 \r\nexpression in microglia play a role in neuroinflammation by affecting the release of \r\ninflammatory cytokines and chemokines. Hereby further challenging that the dogma of the \r\nCox-1 isoform involved in housekeeping functions and the Cox-2 isoform involved in \r\ninflammation applies for the central nervous system. "}],"citation":{"ista":"Miteva FE. 2025. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. Institute of Science and Technology Austria.","ieee":"F. E. Miteva, “The role of cyclooxygenase 1 on microglial response to inflammatory stressors,” Institute of Science and Technology Austria, 2025.","ama":"Miteva FE. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. 2025. doi:10.15479/AT-ISTA-20467","chicago":"Miteva, Florianne E. “The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20467.","short":"F.E. Miteva, The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors, Institute of Science and Technology Austria, 2025.","apa":"Miteva, F. E. (2025). The role of cyclooxygenase 1 on microglial response to inflammatory stressors. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20467","mla":"Miteva, Florianne E. The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20467."},"doi":"10.15479/AT-ISTA-20467","file_date_updated":"2026-10-14T22:30:02Z","corr_author":"1","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"has_accepted_license":"1","date_updated":"2026-10-23T08:01:12Z","ddc":["570"],"publisher":"Institute of Science and Technology Austria","_id":"20467","degree_awarded":"PhD","acknowledgement":"The work presented in this Thesis was carried out at the Institute of Science and Technology\r\nAustria (ISTA), and was supported by the Austrian Science Fund (FWF) [10.55776/P37131].\r\nI would like to thank the Scientific Service Units (SSU) of ISTA for the provided resources,\r\nspecifically the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the\r\nPre-Clinical Facility (PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael\r\nSchunn, for mouse colony management and support. ","title":"The role of cyclooxygenase 1 on microglial response to inflammatory stressors","oa_version":"Published Version","month":"10","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"project":[{"name":"Dissecting the morpho-functional relationship of microglia","_id":"7be82147-9f16-11ee-852c-f44682d73140","grant_number":"P37131"}]},{"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"Well-defined powder precursors are important for the rational design of crystalline inorganic \r\nmaterials with controlled defects and functional properties. Such powders can be prepared from \r\ndried nanoparticles synthesized using a surfactant-assisted/colloidal method that provides \r\nprecise control over size, shape, composition, and surface chemistry of nanoparticles. These \r\ntailored nanoparticles further act as building blocks for three-dimensional assemblies, \r\nexhibiting collective nanoscale properties and enabling tailored microstructures of crystalline \r\ninorganic materials. However, the programmable engineering of such materials using \r\nnanoparticle-based precursors remains limited, due to a lack of fundamental understanding of \r\nboth the synthesis of nanoparticles and their conversion into macroscopic solids. Furthermore, \r\nthe formation of three-dimensional assemblies often requires multi-step post-synthetic \r\ntreatments, which can limit reproducibility and the production of the bulk inorganic materials. \r\nIn this thesis, I demonstrate a key synthetic parameter governing the formation of desired \r\nnanostructures, especially metal/semiconductor core–shell nanoparticles which are potential \r\nprecursors for engineering composition, crystal structure, and defects of final materials. Then, \r\nI investigate their transformative pathways to unveil structural and chemical changes that occur \r\nduring heat treatment of the nanoparticle-based precursors. Building on understanding of \r\natomic-scale interactions during nanoparticle-based precursor formation, I further demonstrate \r\nthe possibility of synthesizing the nanoparticle assembly directly in the nanoparticle synthesis \r\nreaction and rationalize the process of in situ self-assembly of nanoparticles. Finally, the impact \r\nof NP-based precursors on the formation and properties of crystalline inorganic materials is \r\nevaluated, demonstrating the potential of employing NP-based precursors for the rational \r\ndesign of functional inorganic materials. ","lang":"eng"}],"file_date_updated":"2026-10-03T22:30:02Z","citation":{"ama":"Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:10.15479/AT-ISTA-20415","short":"S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025.","chicago":"Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20415.","ista":"Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria.","ieee":"S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic solids,” Institute of Science and Technology Austria, 2025.","apa":"Lee, S. (2025). Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20415","mla":"Lee, Seungho. Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20415."},"doi":"10.15479/AT-ISTA-20415","corr_author":"1","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"has_accepted_license":"1","ddc":["540"],"date_updated":"2026-10-23T08:16:15Z","_id":"20415","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","title":"Nanoparticle-based precursors toward advanced crystalline inorganic solids","oa_version":"Published Version","language":[{"iso":"eng"}],"month":"10","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20415","publication_status":"published","status":"public","year":"2025","related_material":{"record":[{"relation":"part_of_dissertation","id":"12237","status":"public"},{"id":"15357","status":"public","relation":"part_of_dissertation"}]},"type":"dissertation","date_created":"2025-10-01T09:04:00Z","date_published":"2025-10-01T00:00:00Z","oa":1,"OA_place":"publisher","page":"144","author":[{"last_name":"Lee","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho","first_name":"Seungho"}],"doi_confirm":"1","day":"01","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"file":[{"file_size":88706648,"creator":"slee","file_id":"20420","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-10-03T22:30:02Z","relation":"source_file","checksum":"fa6d5946feb37b678ee1c6dffb4fa167","date_created":"2025-10-03T12:29:43Z","access_level":"closed","embargo_to":"open_access","file_name":"2025_Lee_Seungho_Thesis.docx"},{"embargo":"2026-10-03","checksum":"c5ba6d464113ad0c5812a9d24b539b86","relation":"main_file","date_updated":"2026-10-03T22:30:02Z","file_name":"2025_Lee_Seungho_Thesis__.pdf","access_level":"open_access","date_created":"2025-10-03T12:29:25Z","creator":"slee","file_size":14587276,"file_id":"20421","content_type":"application/pdf"}],"supervisor":[{"first_name":"Maria","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"},{"last_name":"Protesescu","first_name":"Loredana","full_name":"Protesescu, Loredana"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"}]},{"title":"Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders","external_id":{"pmid":["37951597"]},"publisher":"Oxford University Press","_id":"14543","ddc":["570"],"date_updated":"2024-07-16T08:23:24Z","has_accepted_license":"1","department":[{"_id":"GradSch"}],"keyword":["Neurology (clinical)"],"citation":{"mla":"Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, vol. 147, no. 4, Oxford University Press, 2024, pp. 1436–56, doi:10.1093/brain/awad380.","apa":"Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2024). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380","ieee":"R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain, vol. 147, no. 4. Oxford University Press, pp. 1436–1456, 2024.","ista":"Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2024. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 147(4), 1436–1456.","chicago":"Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2024. https://doi.org/10.1093/brain/awad380.","short":"R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain 147 (2024) 1436–1456.","ama":"Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2024;147(4):1436-1456. doi:10.1093/brain/awad380"},"doi":"10.1093/brain/awad380","file_date_updated":"2024-07-16T08:22:13Z","abstract":[{"text":"The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.","lang":"eng"}],"publication_identifier":{"eissn":["1460-2156"],"issn":["0006-8950"]},"article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"month":"04","oa_version":"Submitted Version","oa":1,"date_published":"2024-04-01T00:00:00Z","date_created":"2023-11-16T12:36:51Z","issue":"4","type":"journal_article","intvolume":" 147","year":"2024","extern":"1","status":"public","publication":"Brain","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","fulldoi":"https://doi.org/10.1093/brain/awad380","volume":147,"quality_controlled":"1","file":[{"creator":"dernst","file_size":2641456,"success":1,"file_id":"17254","content_type":"application/pdf","date_updated":"2024-07-16T08:22:13Z","relation":"main_file","checksum":"0ee7a8ab9300225d60968f7a3e3cfa0d","file_name":"2024_Brain_Kaiyrzhanov.pdf","date_created":"2024-07-16T08:22:13Z","access_level":"open_access"}],"article_type":"original","pmid":1,"day":"01","author":[{"last_name":"Kaiyrzhanov","first_name":"Rauan","full_name":"Kaiyrzhanov, Rauan"},{"last_name":"Rad","full_name":"Rad, Aboulfazl","first_name":"Aboulfazl"},{"last_name":"Lin","full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia"},{"last_name":"Bertoli-Avella","full_name":"Bertoli-Avella, Aida","first_name":"Aida"},{"full_name":"Kallemeijn, Wouter W","first_name":"Wouter W","last_name":"Kallemeijn"},{"first_name":"Annie","full_name":"Godwin, Annie","last_name":"Godwin"},{"last_name":"Zaki","first_name":"Maha S","full_name":"Zaki, Maha S"},{"last_name":"Huang","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin","first_name":"Kevin"},{"first_name":"Tracy","full_name":"Lau, Tracy","last_name":"Lau"},{"last_name":"Petree","first_name":"Cassidy","full_name":"Petree, Cassidy"},{"first_name":"Stephanie","full_name":"Efthymiou, Stephanie","last_name":"Efthymiou"},{"first_name":"Ehsan","full_name":"Ghayoor Karimiani, Ehsan","last_name":"Ghayoor Karimiani"},{"last_name":"Hempel","full_name":"Hempel, Maja","first_name":"Maja"},{"last_name":"Normand","first_name":"Elizabeth A","full_name":"Normand, Elizabeth A"},{"last_name":"Rudnik-Schöneborn","first_name":"Sabine","full_name":"Rudnik-Schöneborn, Sabine"},{"first_name":"Ulrich A","full_name":"Schatz, Ulrich A","last_name":"Schatz"},{"last_name":"Baggelaar","full_name":"Baggelaar, Marc P","first_name":"Marc P"},{"first_name":"Muhammad","full_name":"Ilyas, Muhammad","last_name":"Ilyas"},{"last_name":"Sultan","full_name":"Sultan, Tipu","first_name":"Tipu"},{"last_name":"Alvi","full_name":"Alvi, Javeria Raza","first_name":"Javeria Raza"},{"full_name":"Ganieva, Manizha","first_name":"Manizha","last_name":"Ganieva"},{"last_name":"Fowler","full_name":"Fowler, Ben","first_name":"Ben"},{"last_name":"Aanicai","full_name":"Aanicai, Ruxandra","first_name":"Ruxandra"},{"last_name":"Akay Tayfun","full_name":"Akay Tayfun, Gulsen","first_name":"Gulsen"},{"first_name":"Abdulaziz","full_name":"Al Saman, Abdulaziz","last_name":"Al Saman"},{"last_name":"Alswaid","first_name":"Abdulrahman","full_name":"Alswaid, Abdulrahman"},{"full_name":"Amiri, Nafise","first_name":"Nafise","last_name":"Amiri"},{"last_name":"Asilova","full_name":"Asilova, Nilufar","first_name":"Nilufar"},{"last_name":"Shotelersuk","full_name":"Shotelersuk, Vorasuk","first_name":"Vorasuk"},{"last_name":"Yeetong","full_name":"Yeetong, Patra","first_name":"Patra"},{"last_name":"Azam","full_name":"Azam, Matloob","first_name":"Matloob"},{"last_name":"Babaei","first_name":"Meisam","full_name":"Babaei, Meisam"},{"last_name":"Bahrami Monajemi","first_name":"Gholamreza","full_name":"Bahrami Monajemi, Gholamreza"},{"full_name":"Mohammadi, Pouria","first_name":"Pouria","last_name":"Mohammadi"},{"first_name":"Saeed","full_name":"Samie, Saeed","last_name":"Samie"},{"full_name":"Banu, Selina Husna","first_name":"Selina Husna","last_name":"Banu"},{"last_name":"Basto","full_name":"Basto, Jorge Pinto","first_name":"Jorge Pinto"},{"last_name":"Kortüm","first_name":"Fanny","full_name":"Kortüm, Fanny"},{"full_name":"Bauer, Mislen","first_name":"Mislen","last_name":"Bauer"},{"full_name":"Bauer, Peter","first_name":"Peter","last_name":"Bauer"},{"full_name":"Beetz, Christian","first_name":"Christian","last_name":"Beetz"},{"first_name":"Masoud","full_name":"Garshasbi, Masoud","last_name":"Garshasbi"},{"first_name":"Awatif","full_name":"Hameed Issa, Awatif","last_name":"Hameed Issa"},{"last_name":"Eyaid","first_name":"Wafaa","full_name":"Eyaid, Wafaa"},{"last_name":"Ahmed","first_name":"Hind","full_name":"Ahmed, Hind"},{"full_name":"Hashemi, Narges","first_name":"Narges","last_name":"Hashemi"},{"last_name":"Hassanpour","first_name":"Kazem","full_name":"Hassanpour, Kazem"},{"last_name":"Herman","full_name":"Herman, Isabella","first_name":"Isabella"},{"last_name":"Ibrohimov","first_name":"Sherozjon","full_name":"Ibrohimov, Sherozjon"},{"full_name":"Abdul-Majeed, Ban A","first_name":"Ban A","last_name":"Abdul-Majeed"},{"last_name":"Imdad","first_name":"Maria","full_name":"Imdad, Maria"},{"full_name":"Isrofilov, Maksudjon","first_name":"Maksudjon","last_name":"Isrofilov"},{"last_name":"Kaiyal","first_name":"Qassem","full_name":"Kaiyal, Qassem"},{"full_name":"Khan, Suliman","first_name":"Suliman","last_name":"Khan"},{"first_name":"Brian","full_name":"Kirmse, Brian","last_name":"Kirmse"},{"last_name":"Koster","first_name":"Janet","full_name":"Koster, Janet"},{"first_name":"Charles Marques","full_name":"Lourenço, Charles Marques","last_name":"Lourenço"},{"first_name":"Tadahiro","full_name":"Mitani, Tadahiro","last_name":"Mitani"},{"full_name":"Moldovan, Oana","first_name":"Oana","last_name":"Moldovan"},{"first_name":"David","full_name":"Murphy, David","last_name":"Murphy"},{"full_name":"Najafi, Maryam","first_name":"Maryam","last_name":"Najafi"},{"last_name":"Pehlivan","full_name":"Pehlivan, Davut","first_name":"Davut"},{"first_name":"Maria Eugenia","full_name":"Rocha, Maria Eugenia","last_name":"Rocha"},{"last_name":"Salpietro","first_name":"Vincenzo","full_name":"Salpietro, Vincenzo"},{"last_name":"Schmidts","first_name":"Miriam","full_name":"Schmidts, Miriam"},{"last_name":"Shalata","full_name":"Shalata, Adel","first_name":"Adel"},{"last_name":"Mahroum","first_name":"Mohammad","full_name":"Mahroum, Mohammad"},{"last_name":"Talbeya","first_name":"Jawabreh Kassem","full_name":"Talbeya, Jawabreh Kassem"},{"last_name":"Taylor","first_name":"Robert W","full_name":"Taylor, Robert W"},{"last_name":"Vazquez","first_name":"Dayana","full_name":"Vazquez, Dayana"},{"last_name":"Vetro","full_name":"Vetro, Annalisa","first_name":"Annalisa"},{"full_name":"Waterham, Hans R","first_name":"Hans R","last_name":"Waterham"},{"last_name":"Zaman","full_name":"Zaman, Mashaya","first_name":"Mashaya"},{"last_name":"Schrader","first_name":"Tina A","full_name":"Schrader, Tina A"},{"last_name":"Chung","first_name":"Wendy K","full_name":"Chung, Wendy K"},{"last_name":"Guerrini","first_name":"Renzo","full_name":"Guerrini, Renzo"},{"last_name":"Lupski","first_name":"James R","full_name":"Lupski, James R"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph"},{"first_name":"Mohnish","full_name":"Suri, Mohnish","last_name":"Suri"},{"last_name":"Jamshidi","full_name":"Jamshidi, Yalda","first_name":"Yalda"},{"first_name":"Kailash P","full_name":"Bhatia, Kailash P","last_name":"Bhatia"},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"first_name":"Michael","full_name":"Schrader, Michael","last_name":"Schrader"},{"first_name":"Mariasavina","full_name":"Severino, Mariasavina","last_name":"Severino"},{"last_name":"Guille","full_name":"Guille, Matthew","first_name":"Matthew"},{"first_name":"Edward W","full_name":"Tate, Edward W","last_name":"Tate"},{"first_name":"Gaurav K","full_name":"Varshney, Gaurav K","last_name":"Varshney"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"}],"page":"1436-1456"},{"OA_place":"publisher","page":"12080-12099","author":[{"first_name":"Ondrej","full_name":"Draganov, Ondrej","orcid":"0000-0003-0464-3823","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov"},{"last_name":"Skiena","full_name":"Skiena, Steven","first_name":"Steven"}],"day":"01","OA_type":"gold","quality_controlled":"1","file":[{"file_name":"2024_EMNLP_Draganov.pdf","date_created":"2025-02-10T08:20:34Z","access_level":"open_access","date_updated":"2025-02-10T08:20:34Z","relation":"main_file","checksum":"f4416a5962194f0181ab0dc7f9ef93c0","success":1,"content_type":"application/pdf","file_id":"19016","creator":"dernst","file_size":1312638}],"publication_status":"published","arxiv":1,"fulldoi":"https://doi.org/10.18653/v1/2024.findings-emnlp.705","publication":"Findings of the Association for Computational Linguistics: EMNLP 2024","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"conference":{"start_date":"2024-11-12","name":"EMNLP: Conference on Empirical Methods in Natural Language Processing","end_date":"2024-11-16","location":"Miami, FL, United States"},"status":"public","year":"2024","type":"conference","date_created":"2025-02-04T16:19:28Z","oa":1,"date_published":"2024-11-01T00:00:00Z","oa_version":"Published Version","month":"11","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","doi":"10.18653/v1/2024.findings-emnlp.705","citation":{"apa":"Draganov, O., & Skiena, S. (2024). The shape of word embeddings: Quantifying non-isometry with topological data analysis. In Findings of the Association for Computational Linguistics: EMNLP 2024 (pp. 12080–12099). Miami, FL, United States: Association for Computational Linguistics. https://doi.org/10.18653/v1/2024.findings-emnlp.705","mla":"Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” Findings of the Association for Computational Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp. 12080–99, doi:10.18653/v1/2024.findings-emnlp.705.","ama":"Draganov O, Skiena S. The shape of word embeddings: Quantifying non-isometry with topological data analysis. In: Findings of the Association for Computational Linguistics: EMNLP 2024. Association for Computational Linguistics; 2024:12080-12099. doi:10.18653/v1/2024.findings-emnlp.705","chicago":"Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” In Findings of the Association for Computational Linguistics: EMNLP 2024, 12080–99. Association for Computational Linguistics, 2024. https://doi.org/10.18653/v1/2024.findings-emnlp.705.","short":"O. Draganov, S. Skiena, in:, Findings of the Association for Computational Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp. 12080–12099.","ista":"Draganov O, Skiena S. 2024. The shape of word embeddings: Quantifying non-isometry with topological data analysis. Findings of the Association for Computational Linguistics: EMNLP 2024. EMNLP: Conference on Empirical Methods in Natural Language Processing, 12080–12099.","ieee":"O. Draganov and S. Skiena, “The shape of word embeddings: Quantifying non-isometry with topological data analysis,” in Findings of the Association for Computational Linguistics: EMNLP 2024, Miami, FL, United States, 2024, pp. 12080–12099."},"file_date_updated":"2025-02-10T08:20:34Z","abstract":[{"text":"Word embeddings represent language vocabularies as clouds of d-dimensional points. We investigate how information is conveyed by the general shape of these clouds, instead of representing the semantic meaning of each token. Specifically, we use the notion of persistent homology from topological data analysis (TDA) to measure the distances between language pairs from the shape of their unlabeled embeddings. These distances quantify the degree of non-isometry of the embeddings. To distinguish whether these differences are random training errors or capture real information about the languages, we use the computed distance matrices to construct language phylogenetic trees over 81 Indo-European languages. Careful evaluation shows that our reconstructed trees exhibit strong and statistically-significant similarities to the reference.","lang":"eng"}],"corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publisher":"Association for Computational Linguistics","_id":"18998","ddc":["500"],"date_updated":"2025-02-10T08:21:37Z","external_id":{"arxiv":["2404.00500"]},"title":"The shape of word embeddings: Quantifying non-isometry with topological data analysis"},{"author":[{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano"},{"orcid":"0000-0003-0464-3823","last_name":"Draganov","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","full_name":"Draganov, Ondrej","first_name":"Ondrej"},{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Saghafian, Morteza","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","last_name":"Saghafian"}],"day":"06","OA_place":"repository","OA_type":"green","fulldoi":"https://doi.org/10.48550/ARXIV.2406.04102","publication_status":"submitted","arxiv":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"arXiv","date_created":"2025-02-04T16:21:21Z","date_published":"2024-06-06T00:00:00Z","oa":1,"year":"2024","status":"public","type":"preprint","month":"06","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2406.04102"}],"oa_version":"Preprint","article_number":"2406.04102","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"has_accepted_license":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Exploring the shape of point configurations has been a key driver in the evolution of TDA (short for topological data analysis) since its infancy. This survey illustrates the recent efforts to broaden these ideas to model spatial interactions among multiple configurations, each distinguished by a color. It describes advances in this area and prepares the ground for further exploration by mentioning unresolved questions and promising research avenues while focusing on the overlap with discrete geometry."}],"doi":"10.48550/ARXIV.2406.04102","citation":{"ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic topological data analysis. arXiv, 2406.04102.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic topological data analysis,” arXiv. .","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic topological data analysis. arXiv. doi:10.48550/ARXIV.2406.04102","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Topological Data Analysis.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2406.04102.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic topological data analysis. arXiv. https://doi.org/10.48550/ARXIV.2406.04102","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Topological Data Analysis.” ArXiv, 2406.04102, doi:10.48550/ARXIV.2406.04102."},"title":"Chromatic topological data analysis","ddc":["510"],"date_updated":"2025-02-10T08:14:27Z","_id":"18999","external_id":{"arxiv":["2406.04102"]}},{"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT:ISTA:17344","abstract":[{"lang":"eng","text":"This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. "}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/AT:ISTA:17344","citation":{"ama":"Surendranadh P, Sachdeva H. Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2024. doi:10.15479/AT:ISTA:17344","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17344.","short":"P. Surendranadh, H. Sachdeva, (2024).","ista":"Surendranadh P, Sachdeva H. 2024. Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17344.","ieee":"P. Surendranadh and H. Sachdeva, “Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2024.","apa":"Surendranadh, P., & Sachdeva, H. (2024). Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344","mla":"Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17344."},"file_date_updated":"2024-07-29T13:51:11Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"has_accepted_license":"1","status":"public","date_updated":"2025-01-14T13:02:59Z","year":"2024","ddc":["576"],"publisher":"Institute of Science and Technology Austria","_id":"17344","type":"research_data","date_created":"2024-07-29T14:01:43Z","date_published":"2024-07-01T00:00:00Z","title":"Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","oa":1,"oa_version":"Published Version","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Surendranadh, Parvathy","first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6395-386X"},{"last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"success":1,"file_id":"17345","content_type":"application/octet-stream","creator":"psurendr","file_size":726132,"file_name":"Submission.nb","date_created":"2024-07-29T13:51:11Z","access_level":"open_access","date_updated":"2024-07-29T13:51:11Z","relation":"main_file","checksum":"75bdbc7ad7cc6afe4459bc4a8824a302"}]},{"keyword":["Farkas lemma","linear programming","extended reals","calculus of inductive constructions"],"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"article_processing_charge":"No","abstract":[{"text":"Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take \"infinite values\".","lang":"eng"}],"citation":{"ieee":"M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally verified,” arXiv. .","ista":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. arXiv, 2409.08119.","short":"M. Dvorak, V. Kolmogorov, ArXiv (n.d.).","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.08119.","ama":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. arXiv. doi:10.48550/arXiv.2409.08119","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” ArXiv, 2409.08119, doi:10.48550/arXiv.2409.08119.","apa":"Dvorak, M., & Kolmogorov, V. (n.d.). Duality theory in linear optimization and its extensions -- formally verified. arXiv. https://doi.org/10.48550/arXiv.2409.08119"},"doi":"10.48550/arXiv.2409.08119","title":"Duality theory in linear optimization and its extensions -- formally verified","date_updated":"2026-07-29T12:56:51Z","_id":"20071","external_id":{"arxiv":["2409.08119"]},"acknowledgement":"We would like to thank David Bartl and Jasmin Blanchette for frequent consultations. We would also like to express gratitude to Andrew Yang for the proof of Finset.univ sum of zero when not and to Henrik B¨oving for a help with generalization from extended rationals to extended linearly ordered fields. We would also like to acknowledge Antoine Chambert-Loir, Apurva Nakade, Ya¨el Dillies, Richard Copley, Edward van de Meent, Markus Himmel, Mario Carneiro, and Kevin Buzzard.","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"09","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2409.08119","open_access":"1"}],"oa_version":"Preprint","article_number":"2409.08119","fulldoi":"https://doi.org/10.48550/arXiv.2409.08119","arxiv":1,"publication_status":"draft","publication":"arXiv","date_created":"2025-07-23T11:21:52Z","date_published":"2024-09-12T00:00:00Z","oa":1,"year":"2024","status":"public","related_material":{"record":[{"id":"22607","relation":"later_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"21393"}],"link":[{"description":"full version of all definitions, statement, and proofs","relation":"software","url":"https://github.com/madvorak/duality/tree/v3.2"}]},"type":"preprint","author":[{"first_name":"Martin","full_name":"Dvorak, Martin","last_name":"Dvorak","orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"day":"12","OA_place":"repository","OA_type":"green"},{"author":[{"id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","last_name":"Wang","first_name":"Xiaoyu","full_name":"Wang, Xiaoyu"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"}],"isi":1,"day":"14","das_tickbox":"1","volume":161,"supplementarymaterial":"no","article_type":"original","pmid":1,"quality_controlled":"1","publication_status":"published","arxiv":1,"fulldoi":"https://doi.org/10.1063/5.0217232","publication":"Journal of Chemical Physics","date_created":"2024-07-21T22:01:00Z","oa":1,"date_published":"2024-07-14T00:00:00Z","intvolume":" 161","related_material":{"link":[{"url":"https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0","relation":"software"}]},"year":"2024","status":"public","researchdata_availability":"no","issue":"3","type":"journal_article","month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.02216","open_access":"1"}],"oa_version":"Preprint","article_number":"034111","dataavailabilitystatement":"All simulation setups, analysis scripts, and raw data in the study are available in the SI repository https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0.","corr_author":"1","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"article_processing_charge":"No","citation":{"apa":"Wang, X., & Cheng, B. (2024). Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0217232","mla":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal of Chemical Physics, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:10.1063/5.0217232.","ama":"Wang X, Cheng B. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 2024;161(3). doi:10.1063/5.0217232","chicago":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0217232.","short":"X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).","ista":"Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 161(3), 034111.","ieee":"X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures,” Journal of Chemical Physics, vol. 161, no. 3. AIP Publishing, 2024."},"doi":"10.1063/5.0217232","abstract":[{"lang":"eng","text":"An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult due to the complexities and convergence problems of Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes, or lack thereof, in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes and reveal that they tend to form when the mixture components have similar boiling points and strong interactions."}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"title":"Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures","publisher":"AIP Publishing","_id":"17278","date_updated":"2026-08-07T10:38:59Z","acknowledgement":"B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No. EP/P020259/1).","external_id":{"isi":["001281819100016"],"pmid":["39007379"],"arxiv":["2405.02216"]}},{"date_created":"2025-02-20T10:13:42Z","oa":1,"date_published":"2024-03-01T00:00:00Z","related_material":{"link":[{"url":" https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed","relation":"software"}]},"status":"public","year":"2024","type":"preprint","arxiv":1,"publication_status":"submitted","fulldoi":"https://doi.org/10.48550/arXiv.2403.06833","publication":"arXiv","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"green","file":[{"file_name":"2403.06833v3.pdf","date_created":"2025-02-20T10:11:45Z","access_level":"open_access","relation":"main_file","date_updated":"2025-02-20T10:11:45Z","checksum":"35eb43968684b87be59144603ef10af0","success":1,"content_type":"application/pdf","file_id":"19064","creator":"ezverev","file_size":530972}],"author":[{"first_name":"Egor","full_name":"Zverev, Egor","id":"05162b19-1340-11ed-8f02-fa94e0e8c3bc","last_name":"Zverev"},{"full_name":"Abdelnabi, Sahar","first_name":"Sahar","last_name":"Abdelnabi"},{"orcid":"0009-0003-4119-6281","last_name":"Tabesh","id":"06000900-6068-11ef-8d61-c2472ef2e752","first_name":"Soroush","full_name":"Tabesh, Soroush"},{"full_name":"Fritz, Mario","first_name":"Mario","last_name":"Fritz"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"day":"01","OA_place":"repository","title":"Can LLMs separate instructions from data? And what do we even mean by that?","_id":"19063","ddc":["000"],"date_updated":"2026-08-13T07:26:54Z","acknowledgement":"The authors would like to sincerely thank Juan Rocamonde for valuable feedback to our manuscript. We acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We thank Dan Alistarh for providing us with computational resources. This work was partially funded by the German Federal Ministry of Education and Research (BMBF) under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and Safe AI funded by the European Union under grant agreement No. 101070617. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or European Commission. Neither the European Union nor the European Commission can be held responsible for them.","external_id":{"arxiv":["2403.06833"]},"corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"article_processing_charge":"No","file_date_updated":"2025-02-20T10:11:45Z","citation":{"apa":"Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., & Lampert, C. (n.d.). Can LLMs separate instructions from data? And what do we even mean by that? arXiv. https://doi.org/10.48550/arXiv.2403.06833","mla":"Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” ArXiv, 2403.06833, doi:10.48550/arXiv.2403.06833.","ista":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv, 2403.06833.","ieee":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate instructions from data? And what do we even mean by that?,” arXiv. .","ama":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv. doi:10.48550/arXiv.2403.06833","chicago":"Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.06833.","short":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.)."},"doi":"10.48550/arXiv.2403.06833","abstract":[{"text":"Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n","lang":"eng"}],"article_number":"2403.06833","language":[{"iso":"eng"}],"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"day":"05","author":[{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","file":[{"success":1,"file_id":"17394","content_type":"text/plain","creator":"melkrewi","file_size":2465,"file_name":"README.txt","access_level":"open_access","date_created":"2024-08-05T22:24:18Z","checksum":"26b5d41b3103f4284dd97d56e370a5b6","date_updated":"2024-08-05T22:24:18Z","relation":"main_file"},{"file_name":"Data_artemia_single_nucleus_atlas.zip","access_level":"open_access","date_created":"2024-08-05T23:28:52Z","checksum":"95adab5e36148015da313505e3910707","date_updated":"2024-08-05T23:28:52Z","relation":"main_file","success":1,"file_id":"17395","content_type":"application/x-zip-compressed","creator":"melkrewi","file_size":2526735400}],"project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"citation":{"ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17362.","ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:10.15479/AT:ISTA:17362","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17362.","short":"M.N. Elkrewi, B. Vicoso, (2024).","apa":"Elkrewi, M. N., & Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17362","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17362."},"doi":"10.15479/AT:ISTA:17362","file_date_updated":"2024-08-05T23:28:52Z","abstract":[{"text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.","lang":"eng"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.15479/AT:ISTA:17362","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"corr_author":"1","type":"research_data","_id":"17362","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"17890","relation":"used_in_publication"}]},"year":"2024","status":"public","date_updated":"2026-09-24T11:17:37Z","ddc":["576"],"oa":1,"title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","date_published":"2024-08-05T00:00:00Z","date_created":"2024-08-02T07:27:45Z"},{"author":[{"first_name":"Vage","full_name":"Egiazarian, Vage","last_name":"Egiazarian"},{"first_name":"Andrei","full_name":"Panferov, Andrei","id":"2c18daae-4dbe-11ef-8491-98ce2d960f09","last_name":"Panferov"},{"last_name":"Kuznedelev","full_name":"Kuznedelev, Denis","first_name":"Denis"},{"full_name":"Frantar, Elias","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar"},{"first_name":"Artem","full_name":"Babenko, Artem","last_name":"Babenko"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"day":"01","page":"12284-12303","das_tickbox":"0","supplementarymaterial":"no","volume":235,"quality_controlled":"1","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27","start_date":"2024-07-21","location":"Vienna, Austria"},"arxiv":1,"publication_status":"published","publication":"Proceedings of the 41st International Conference on Machine Learning","date_created":"2024-09-22T22:01:43Z","date_published":"2024-09-01T00:00:00Z","oa":1,"status":"public","researchdata_availability":"no","year":"2024","intvolume":" 235","type":"conference","language":[{"iso":"eng"}],"month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2401.06118"}],"oa_version":"Preprint","corr_author":"1","alternative_title":["PMLR"],"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"article_processing_charge":"No","abstract":[{"text":"The emergence of accurate open large language models (LLMs) has led to a race towards performant quantization techniques which can enable their execution on end-user devices. In this paper, we revisit the problem of “extreme” LLM compression—defined as targeting extremely low bit counts, such as 2 to 3 bits per parameter—from the point of view of classic methods in Multi-Codebook Quantization (MCQ). Our algorithm, called AQLM, generalizes the classic Additive Quantization (AQ) approach for information retrieval to advance the state-of-the-art in LLM compression, via two innovations: 1) learned additive quantization of weight matrices in input-adaptive fashion, and 2) joint optimization of codebook parameters across each transformer blocks. Broadly, AQLM is the first scheme that is Pareto optimal in terms of accuracy-vs-model-size when compressing to less than 3 bits per parameter, and significantly improves upon all known schemes in the extreme compression (2bit) regime. In addition, AQLM is practical: we provide fast GPU and CPU implementations of AQLM for token generation, which enable us to match or outperform optimized FP16 implementations for speed, while executing in a much smaller memory footprint.","lang":"eng"}],"publication_identifier":{"eissn":["2640-3498"]},"citation":{"mla":"Egiazarian, Vage, et al. “Extreme Compression of Large Language Models via Additive Quantization.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 12284–303.","apa":"Egiazarian, V., Panferov, A., Kuznedelev, D., Frantar, E., Babenko, A., & Alistarh, D.-A. (2024). Extreme compression of large language models via additive quantization. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 12284–12303). Vienna, Austria: ML Research Press.","ieee":"V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, and D.-A. Alistarh, “Extreme compression of large language models via additive quantization,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 12284–12303.","ista":"Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A. 2024. Extreme compression of large language models via additive quantization. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 12284–12303.","short":"V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 12284–12303.","chicago":"Egiazarian, Vage, Andrei Panferov, Denis Kuznedelev, Elias Frantar, Artem Babenko, and Dan-Adrian Alistarh. “Extreme Compression of Large Language Models via Additive Quantization.” In Proceedings of the 41st International Conference on Machine Learning, 235:12284–303. ML Research Press, 2024.","ama":"Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A. Extreme compression of large language models via additive quantization. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:12284-12303."},"title":"Extreme compression of large language models via additive quantization","date_updated":"2026-10-01T09:34:19Z","_id":"18113","publisher":"ML Research Press","external_id":{"arxiv":["2401.06118"]},"acknowledgement":"Authors would like to thank Ruslan Svirschevski for his help in solving technical issues with AQLM and baselines. We also thank Tim Dettmers for helpful discussions on the structure of weights in modern LLMs and size-accuracy trade-offs. The authors would also like to thank Daniil Pavlov for his assistance with CPU benchmarking. Finally, authors would like to thank the communities of ML enthusiasts known as LocalLLaMA5 and Petals community on discord6\r\nfor the crowd wisdom about running LLMs on consumer devices. Egiazarian Vage and Denis Kuznedelev and Andrei Panferov were supported by the grant for research centers in the field of AI provided by the Analytical Center for the Government of the Russian Federation (ACRF) in\r\naccordance with the agreement on the provision of subsidies (identifier of the agreement 000000D730321P5Q0002) and the agreement with HSE University No. 70-2021-00139."},{"scopus_import":"1","language":[{"iso":"eng"}],"month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2401.04679"}],"title":"RoSA: Accurate parameter-efficient fine-tuning via robust adaptation","acknowledgement":"The authors would like to thank Eldar Kurtic for experimental support and useful suggestions throughout the project","external_id":{"arxiv":["2401.04679"]},"_id":"18117","publisher":"ML Research Press","date_updated":"2026-10-01T09:34:36Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"corr_author":"1","citation":{"mla":"Nikdan, Mahdi, et al. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 38187–206.","apa":"Nikdan, M., Tabesh, S., Crncevic, E., & Alistarh, D.-A. (2024). RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 38187–38206). Vienna, Austria: ML Research Press.","chicago":"Nikdan, Mahdi, Soroush Tabesh, Elvir Crncevic, and Dan-Adrian Alistarh. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” In Proceedings of the 41st International Conference on Machine Learning, 235:38187–206. ML Research Press, 2024.","short":"M. Nikdan, S. Tabesh, E. Crncevic, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 38187–38206.","ama":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:38187-38206.","ieee":"M. Nikdan, S. Tabesh, E. Crncevic, and D.-A. Alistarh, “RoSA: Accurate parameter-efficient fine-tuning via robust adaptation,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 38187–38206.","ista":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. 2024. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 235, 38187–38206."},"publication_identifier":{"eissn":["2640-3498"]},"abstract":[{"text":"We investigate parameter-efficient fine-tuning (PEFT) methods that can provide good accuracy under limited computational and memory budgets in the context of large language models (LLMs). We present a new PEFT method called Robust Adaptation (RoSA) inspired by robust principal component analysis that jointly trains low-rank\r\n and highly-sparse components on top of a set of fixed pretrained weights to efficiently approximate the performance of a full-fine-tuning (FFT) solution. Across a series of challenging generative tasks such as grade-school math and SQL query generation, which require fine-tuning for good performance, we show that RoSA outperforms LoRA, pure sparse fine-tuning, and alternative hybrid methods at the same parameter budget, and can even recover the performance of FFT on some tasks. We provide system support for RoSA to complement the training algorithm, specifically in the form of sparse GPU kernels which enable memory- and computationally-efficient training, and show that it is also compatible with low-precision base weights, resulting in the first joint representation combining quantization, low-rank and sparse approximations. Our code is available at https://github.com/IST-DASLab/RoSA.","lang":"eng"}],"article_processing_charge":"No","volume":235,"supplementarymaterial":"no","quality_controlled":"1","day":"01","author":[{"last_name":"Nikdan","id":"66374281-f394-11eb-9cf6-869147deecc0","first_name":"Mahdi","full_name":"Nikdan, Mahdi"},{"first_name":"Soroush","full_name":"Tabesh, Soroush","last_name":"Tabesh","orcid":"0009-0003-4119-6281","id":"06000900-6068-11ef-8d61-c2472ef2e752"},{"last_name":"Crncevic","id":"41888001-440d-11ef-8299-d0e838b8185e","first_name":"Elvir","full_name":"Crncevic, Elvir"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"das_tickbox":"0","page":"38187-38206","oa":1,"date_published":"2024-09-01T00:00:00Z","date_created":"2024-09-22T22:01:44Z","type":"conference","intvolume":" 235","related_material":{"link":[{"url":"https://github.com/IST-DASLab/RoSA","relation":"software"}]},"status":"public","researchdata_availability":"yes","year":"2024","conference":{"end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21","location":"Vienna, Austria"},"publication":"Proceedings of the 41st International Conference on Machine Learning","publication_status":"published","arxiv":1},{"supplementarymaterial":"no","das_tickbox":"0","day":"11","author":[{"full_name":"Arkhipov, Pavel","first_name":"Pavel","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","last_name":"Arkhipov"}],"type":"preprint","year":"2024","status":"public","researchdata_availability":"yes","oa":1,"date_published":"2024-06-11T00:00:00Z","date_created":"2024-06-12T07:01:52Z","publication":"arXiv","publication_status":"submitted","arxiv":1,"fulldoi":"https://doi.org/10.48550/arXiv.2406.07026","article_number":"2406.07026","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2406.07026"}],"language":[{"iso":"eng"}],"month":"06","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"I am grateful to Matthew Kwan for setting the problem, providing useful literature,\r\nfruitful discussions, text review, mentorship, general encouragement and support.","external_id":{"arxiv":["2406.07026"]},"_id":"17136","date_updated":"2026-10-02T11:06:38Z","title":"Majority dynamics and internal partitions of random regular graphs: Experimental results","doi":"10.48550/arXiv.2406.07026","citation":{"ieee":"P. Arkhipov, “Majority dynamics and internal partitions of random regular graphs: Experimental results,” arXiv. .","ista":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. arXiv, 2406.07026.","short":"P. Arkhipov, ArXiv (n.d.).","chicago":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2406.07026.","ama":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. arXiv. doi:10.48550/arXiv.2406.07026","mla":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” ArXiv, 2406.07026, doi:10.48550/arXiv.2406.07026.","apa":"Arkhipov, P. (n.d.). Majority dynamics and internal partitions of random regular graphs: Experimental results. arXiv. https://doi.org/10.48550/arXiv.2406.07026"},"abstract":[{"text":"This paper focuses on Majority Dynamics in sparse graphs, in particular, as a\r\ntool to study internal cuts. It is known that, in Majority Dynamics on a finite\r\ngraph, each vertex eventually either comes to a fixed state, or oscillates with\r\nperiod two. The empirical evidence acquired by simulations suggests that for\r\nrandom odd-regular graphs, approximately half of the vertices end up\r\noscillating with high probability. We notice a local symmetry between\r\noscillating and non-oscillating vertices, that potentially can explain why the\r\nfraction of the oscillating vertices is concentrated around $\\frac{1}{2}$. In\r\nour simulations, we observe that the parts of random odd-regular graph under\r\nMajority Dynamics with high probability do not contain $\\lceil \\frac{d}{2}\r\n\\rceil$-cores at any timestep, and thus, one cannot use Majority Dynamics to\r\nprove that internal cuts exist in odd-regular graphs almost surely. However, we\r\nsuggest a modification of Majority Dynamics, that yields parts with desired\r\ncores with high probability.","lang":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"}]},{"article_number":"124503 ","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"09","acknowledgement":"The computational results presented here were enabled via a generous share of CPU time, offered by the Vienna Scientific Cluster (VSC) under Project No. 71263. The authors thank Ms. Katrin Muck for her guidance related to the use of HPC. A.J.A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1.","external_id":{"isi":["001325268300004"],"arxiv":["2409.06447"],"pmid":["39344889"]},"_id":"18174","publisher":"AIP Publishing","ddc":["530"],"date_updated":"2026-10-02T11:10:03Z","title":"Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system","doi":"10.1063/5.0226954","citation":{"mla":"Wassermair, Michael, et al. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” The Journal of Chemical Physics, vol. 161, no. 12, 124503, AIP Publishing, 2024, doi:10.1063/5.0226954.","apa":"Wassermair, M., Kahl, G., Roth, R., & Archer, A. J. (2024). Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0226954","short":"M. Wassermair, G. Kahl, R. Roth, A.J. Archer, The Journal of Chemical Physics 161 (2024).","chicago":"Wassermair, Michael, Gerhard Kahl, Roland Roth, and Andrew J. Archer. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” The Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0226954.","ama":"Wassermair M, Kahl G, Roth R, Archer AJ. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of chemical physics. 2024;161(12). doi:10.1063/5.0226954","ieee":"M. Wassermair, G. Kahl, R. Roth, and A. J. Archer, “Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system,” The Journal of chemical physics, vol. 161, no. 12. AIP Publishing, 2024.","ista":"Wassermair M, Kahl G, Roth R, Archer AJ. 2024. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of chemical physics. 161(12), 124503."},"file_date_updated":"2024-10-07T11:25:00Z","abstract":[{"text":"We investigate the phase ordering (pattern formation) of systems of two-dimensional core–shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases. In DFT, the hard core part of the potential is treated using either fundamental measure theory or a simple local density approximation, whereas the soft shoulder is treated using the random phase approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities and shortcomings. We find that having the liquid state static structure factor S(k) for wavenumber k is sufficient to identify the Fourier modes governing both the liquid and solid phases. This allows us to identify from easier-to-obtain liquid state data the wavenumbers relevant to the periodic phases and to predict roughly where in the phase diagram these patterned phases arise.","lang":"eng"}],"publication_identifier":{"eissn":["1089-7690"]},"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","department":[{"_id":"GradSch"}],"corr_author":"1","quality_controlled":"1","file":[{"access_level":"open_access","date_created":"2024-10-07T11:25:00Z","file_name":"2024_JourChemicalPhysics_Wassermair.pdf","checksum":"f3874e64ef94e94b2376f00a1fee24c3","date_updated":"2024-10-07T11:25:00Z","relation":"main_file","content_type":"application/pdf","file_id":"18185","success":1,"file_size":15009000,"creator":"dernst"}],"article_type":"original","pmid":1,"volume":161,"supplementarymaterial":"yes","das_tickbox":"1","day":"28","author":[{"orcid":"0009-0003-6339-4051","last_name":"Wassermair","id":"23d132c4-4e98-11ef-b275-9e8d4cd8c917","full_name":"Wassermair, Michael","first_name":"Michael"},{"full_name":"Kahl, Gerhard","first_name":"Gerhard","last_name":"Kahl"},{"last_name":"Roth","first_name":"Roland","full_name":"Roth, Roland"},{"last_name":"Archer","first_name":"Andrew J.","full_name":"Archer, Andrew J."}],"isi":1,"issue":"12","type":"journal_article","intvolume":" 161","researchdata_availability":"upon request","status":"public","year":"2024","oa":1,"date_published":"2024-09-28T00:00:00Z","date_created":"2024-10-06T22:01:12Z","publication":"The Journal of chemical physics","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","arxiv":1,"fulldoi":"https://doi.org/10.1063/5.0226954"},{"article_number":"117168","dataavailabilitystatement":"Data will be made available on request.","oa_version":"Published Version","scopus_import":"1","month":"01","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","external_id":{"isi":["001125054400001"]},"publisher":"Elsevier","_id":"14653","ddc":["540"],"date_updated":"2026-10-02T11:07:09Z","title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)","doi":"10.1016/j.ijms.2023.117168","citation":{"ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 2024;495. doi:10.1016/j.ijms.2023.117168","chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier, 2024. https://doi.org/10.1016/j.ijms.2023.117168.","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2024).","ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2024. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” International Journal of Mass Spectrometry, vol. 495. Elsevier, 2024.","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller, T. (2024). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168","mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry, vol. 495, 117168, Elsevier, 2024, doi:10.1016/j.ijms.2023.117168."},"file_date_updated":"2024-07-16T08:27:34Z","publication_identifier":{"issn":["1387-3806"]},"abstract":[{"lang":"eng","text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data."}],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","department":[{"_id":"GradSch"}],"quality_controlled":"1","file":[{"success":1,"content_type":"application/pdf","file_id":"17256","creator":"dernst","file_size":3003139,"file_name":"2024_IJMS_Kluibenschedl.pdf","access_level":"open_access","date_created":"2024-07-16T08:27:34Z","checksum":"6c5eb6dc07af70a59251d2c6fed38894","date_updated":"2024-07-16T08:27:34Z","relation":"main_file"}],"article_type":"original","volume":495,"supplementarymaterial":"yes","das_tickbox":"1","day":"01","author":[{"first_name":"Florian","full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl","orcid":"0000-0003-4695-5526","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9"},{"last_name":"Ploner","first_name":"Anna","full_name":"Ploner, Anna"},{"first_name":"Christina","full_name":"Meisenbichler, Christina","last_name":"Meisenbichler"},{"last_name":"Konrat","first_name":"Robert","full_name":"Konrat, Robert"},{"last_name":"Müller","full_name":"Müller, Thomas","first_name":"Thomas"}],"isi":1,"type":"journal_article","intvolume":" 495","researchdata_availability":"upon request","year":"2024","status":"public","oa":1,"date_published":"2024-01-01T00:00:00Z","date_created":"2023-12-10T23:00:57Z","publication":"International Journal of Mass Spectrometry","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","fulldoi":"https://doi.org/10.1016/j.ijms.2023.117168"},{"article_number":"020327","scopus_import":"1","month":"05","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","title":"Quantum-informed recursive optimization algorithms","external_id":{"arxiv":["2308.13607"]},"acknowledgement":"J.R.F. and A.K. thank Libor Caha and Alexander Kliesch for insightful discussions. The authors thank Lilly Palackal, Maximilian Passek, Carlos Riofrío, and Gili Rosenberg for thorough reviews of the manuscript, and the Amazon Braket, BMW, and QuEra teams for their support. C.M. thanks the Munich Quantum Valley initiative, which is supported by the Bavarian State Government with funds from the Hightech Agenda Bayern Plus. H.G.K. would like to thank Am Platzl 1A for providing the necessary environment for creative thinking. An open-source implementation of QIRO is available online [60].","date_updated":"2026-10-02T11:07:49Z","ddc":["530"],"publisher":"American Physical Society","_id":"15407","department":[{"_id":"GradSch"}],"has_accepted_license":"1","corr_author":"1","abstract":[{"text":"We propose and implement a family of quantum-informed recursive optimization (QIRO) algorithms for combinatorial optimization problems. Our approach leverages quantum resources to obtain information that is used in problem-specific classical reduction steps that recursively simplify the problem. These reduction steps address the limitations of the quantum component (e.g., locality) and ensure solution feasibility in constrained optimization problems. Additionally, we use backtracking techniques to further improve the performance of the algorithm without increasing the requirements on the quantum hardware. We showcase the capabilities of our approach by informing QIRO with correlations from classical simulations of shallow circuits of the quantum approximate optimization algorithm, solving instances of maximum independent set and maximum satisfiability problems with hundreds of variables. We also demonstrate how QIRO can be deployed on a neutral atom quantum processor to find large independent sets of graphs. In summary, our scheme achieves results comparable to classical heuristics even with relatively weak quantum resources. Furthermore, enhancing the quality of these quantum resources improves the performance of the algorithms. Notably, the modular nature of QIRO offers various avenues for modifications, positioning our work as a template for a broader class of hybrid quantum-classical algorithms for combinatorial optimization.","lang":"eng"}],"publication_identifier":{"eissn":["2691-3399"]},"citation":{"apa":"Finžgar, J. R., Kerschbaumer, A., Schuetz, M. J. A., Mendl, C. B., & Katzgraber, H. G. (2024). Quantum-informed recursive optimization algorithms. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.5.020327","mla":"Finžgar, Jernej Rudi, et al. “Quantum-Informed Recursive Optimization Algorithms.” PRX Quantum, vol. 5, no. 2, 020327, American Physical Society, 2024, doi:10.1103/PRXQuantum.5.020327.","ista":"Finžgar JR, Kerschbaumer A, Schuetz MJA, Mendl CB, Katzgraber HG. 2024. Quantum-informed recursive optimization algorithms. PRX Quantum. 5(2), 020327.","ieee":"J. R. Finžgar, A. Kerschbaumer, M. J. A. Schuetz, C. B. Mendl, and H. G. Katzgraber, “Quantum-informed recursive optimization algorithms,” PRX Quantum, vol. 5, no. 2. American Physical Society, 2024.","ama":"Finžgar JR, Kerschbaumer A, Schuetz MJA, Mendl CB, Katzgraber HG. Quantum-informed recursive optimization algorithms. PRX Quantum. 2024;5(2). doi:10.1103/PRXQuantum.5.020327","chicago":"Finžgar, Jernej Rudi, Aron Kerschbaumer, Martin J.A. Schuetz, Christian B. Mendl, and Helmut G. Katzgraber. “Quantum-Informed Recursive Optimization Algorithms.” PRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/PRXQuantum.5.020327.","short":"J.R. Finžgar, A. Kerschbaumer, M.J.A. Schuetz, C.B. Mendl, H.G. Katzgraber, PRX Quantum 5 (2024)."},"doi":"10.1103/PRXQuantum.5.020327","file_date_updated":"2024-05-21T09:35:14Z","DOAJ_listed":"1","article_processing_charge":"Yes","supplementarymaterial":"yes","volume":5,"file":[{"file_size":2016085,"creator":"dernst","file_id":"15409","content_type":"application/pdf","success":1,"checksum":"76bdf0b4dc06d59d073a57bd6957a96c","date_updated":"2024-05-21T09:35:14Z","relation":"main_file","access_level":"open_access","date_created":"2024-05-21T09:35:14Z","file_name":"2024_PRXQuantum_Finzgar.pdf"}],"quality_controlled":"1","article_type":"original","OA_type":"gold","day":"01","author":[{"last_name":"Finžgar","first_name":"Jernej Rudi","full_name":"Finžgar, Jernej Rudi"},{"first_name":"Aron","full_name":"Kerschbaumer, Aron","orcid":"0009-0002-2370-8661","last_name":"Kerschbaumer","id":"ade85a9c-3200-11ee-973b-91c1eb240410"},{"last_name":"Schuetz","full_name":"Schuetz, Martin J.A.","first_name":"Martin J.A."},{"first_name":"Christian B.","full_name":"Mendl, Christian B.","last_name":"Mendl"},{"first_name":"Helmut G.","full_name":"Katzgraber, Helmut G.","last_name":"Katzgraber"}],"das_tickbox":"0","OA_place":"publisher","date_published":"2024-05-01T00:00:00Z","oa":1,"date_created":"2024-05-19T22:01:13Z","type":"journal_article","issue":"2","researchdata_availability":"no","status":"public","year":"2024","intvolume":" 5","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"PRX Quantum","fulldoi":"https://doi.org/10.1103/PRXQuantum.5.020327","arxiv":1,"publication_status":"published"},{"article_number":"044050","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"04","language":[{"iso":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.18126","open_access":"1"}],"title":"Floquet analysis of a superradiant many-qutrit refrigerator","external_id":{"isi":["001226579400001"],"arxiv":["2310.18126"]},"acknowledgement":"Financial support by the DFG (project ID 278162697 – SFB 1242) is gratefully acknowledged.\r\n","date_updated":"2026-10-02T11:07:26Z","_id":"15360","publisher":"American Physical Society","department":[{"_id":"GradSch"}],"publication_identifier":{"eissn":["2331-7019"]},"abstract":[{"text":"We investigate superradiant enhancements in the refrigeration performance of a set of N three-level systems that are collectively coupled to a hot and a cold thermal reservoir and are additionally subject to collective periodic (circular) driving. Assuming the system-reservoir coupling to be weak, we explore the regime of stronger periodic driving strengths by comparing collective weak driving, Floquet-Lindblad, and Floquet-Redfield master equations. We identify regimes where the power injected by the periodic driving is used to pump heat from the cold to the hot reservoir and derive analytic sufficient conditions for them based on a cycle analysis of the Floquet-Lindblad master equation. In those regimes, we also argue for which parameters collective enhancements like a quadratic scaling of the cooling current with N can be expected and support our arguments by numerical simulations.","lang":"eng"}],"doi":"10.1103/PhysRevApplied.21.044050","citation":{"ieee":"D. Kolisnyk, F. Queißer, G. Schaller, and R. Schützhold, “Floquet analysis of a superradiant many-qutrit refrigerator,” Physical Review Applied, vol. 21, no. 4. American Physical Society, 2024.","ista":"Kolisnyk D, Queißer F, Schaller G, Schützhold R. 2024. Floquet analysis of a superradiant many-qutrit refrigerator. Physical Review Applied. 21(4), 044050.","chicago":"Kolisnyk, Dmytro, Friedemann Queißer, Gernot Schaller, and Ralf Schützhold. “Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.” Physical Review Applied. American Physical Society, 2024. https://doi.org/10.1103/PhysRevApplied.21.044050.","short":"D. Kolisnyk, F. Queißer, G. Schaller, R. Schützhold, Physical Review Applied 21 (2024).","ama":"Kolisnyk D, Queißer F, Schaller G, Schützhold R. Floquet analysis of a superradiant many-qutrit refrigerator. Physical Review Applied. 2024;21(4). doi:10.1103/PhysRevApplied.21.044050","mla":"Kolisnyk, Dmytro, et al. “Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.” Physical Review Applied, vol. 21, no. 4, 044050, American Physical Society, 2024, doi:10.1103/PhysRevApplied.21.044050.","apa":"Kolisnyk, D., Queißer, F., Schaller, G., & Schützhold, R. (2024). Floquet analysis of a superradiant many-qutrit refrigerator. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.21.044050"},"article_processing_charge":"No","supplementarymaterial":"yes","volume":21,"quality_controlled":"1","article_type":"original","day":"26","isi":1,"author":[{"full_name":"Kolisnyk, Dmytro","first_name":"Dmytro","last_name":"Kolisnyk","orcid":"0000-0002-8612-8202","id":"530a7320-5355-11ee-ae5a-82a46997aaa7"},{"last_name":"Queißer","first_name":"Friedemann","full_name":"Queißer, Friedemann"},{"last_name":"Schaller","full_name":"Schaller, Gernot","first_name":"Gernot"},{"last_name":"Schützhold","first_name":"Ralf","full_name":"Schützhold, Ralf"}],"das_tickbox":"0","date_published":"2024-04-26T00:00:00Z","oa":1,"date_created":"2024-05-05T22:01:04Z","type":"journal_article","issue":"4","researchdata_availability":"no","status":"public","year":"2024","intvolume":" 21","publication":"Physical Review Applied","fulldoi":"https://doi.org/10.1103/PhysRevApplied.21.044050","publication_status":"published","arxiv":1},{"doi":"10.1134/S0005117924060031","citation":{"mla":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” Automation and Remote Control, vol. 85, no. 6, Springer Nature, 2024, pp. 522–32, doi:10.1134/S0005117924060031.","apa":"Arkhipov, P. (2024). An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. Springer Nature. https://doi.org/10.1134/S0005117924060031","ieee":"P. Arkhipov, “An algorithm for finding the generalized Chebyshev center of sets defined via their support functions,” Automation and Remote Control, vol. 85, no. 6. Springer Nature, pp. 522–532, 2024.","ista":"Arkhipov P. 2024. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 85(6), 522–532.","short":"P. Arkhipov, Automation and Remote Control 85 (2024) 522–532.","chicago":"Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” Automation and Remote Control. Springer Nature, 2024. https://doi.org/10.1134/S0005117924060031.","ama":"Arkhipov P. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 2024;85(6):522-532. doi:10.1134/S0005117924060031"},"abstract":[{"text":"This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a shift to a vector x0 ∈ \r\nRn. The goal is to find t0 and x0. In the special case of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev center and the Chebyshev radius of A. This paper focuses on the case in which A and B are defined with their black-box support functions. An algorithm for solving such problems efficiently is suggested. The algorithm has a superlinear convergence rate, and it can solve hundred-dimensional test problems in a reasonable time, but some additional conditions on A and B are required to guarantee the presence of convergence. Additionally, the behavior of the algorithm for a simple special case is investigated, which leads to a number of theoretical results. Perturbations of this special case are also studied.","lang":"eng"}],"publication_identifier":{"issn":["0005-1179"],"eissn":["1608-3032"]},"article_processing_charge":"No","department":[{"_id":"GradSch"}],"corr_author":"1","acknowledgement":"The author is grateful to Maxim Balashov for setting the problem, providing useful literature, important discussions and text review. Also, I thank Dmitry Tsarev and Kseniia Petukhova for meaningful talks and support.","external_id":{"isi":["001338721700007"]},"_id":"18482","publisher":"Springer Nature","date_updated":"2026-10-02T11:10:45Z","title":"An algorithm for finding the generalized Chebyshev center of sets defined via their support functions","oa_version":"None","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"06","publication":"Automation and Remote Control","publication_status":"published","fulldoi":"https://doi.org/10.1134/S0005117924060031","issue":"6","type":"journal_article","intvolume":" 85","researchdata_availability":"no","year":"2024","status":"public","date_published":"2024-06-01T00:00:00Z","date_created":"2024-10-27T23:01:45Z","das_tickbox":"0","page":"522-532","day":"01","author":[{"id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","last_name":"Arkhipov","full_name":"Arkhipov, Pavel","first_name":"Pavel"}],"isi":1,"quality_controlled":"1","article_type":"original","OA_type":"closed access","volume":85,"supplementarymaterial":"no"}]