Welcome to the Koç University Institutional Academic Repository
The Koç University Institutional Academic Repository (KUHub Research) is a state-of-the-art academic repository that consolidates all academic outputs—such as articles, conference proceedings, theses, research data, and more—produced by the university since its establishment in 1993.
KUHub Research adheres to the principles of Open Access and FAIR (Findable, Accessible, Interoperable, Reusable), providing access to the bibliographic records, research data, and full texts of research outputs. Equipped with innovative features such as Author Profile pages and enhanced tools, KUHub Research aims to enhance the visibility of researchers both nationally and internationally. KUHub Research aims to preserve and maintain Koç University's valuable academic legacy for future generations while also serving the needs of today’s researchers.
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Recent Submissions
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2028-01-01) Chretien, Anaïs; Ertem Kuzucu, Fatma Betul; Summers, Jacob; Wranik, Maximilian; 0000-0001-8480-1443; 0000-0002-2144-989x; 0000-0003-3113-0353; 0000-0002-2482-0164
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2027-01-01) Summers, Jacob; Sanctis, Daniele; Vlahakis, Niko; Knight, Victoria; Ertem Kuzucu, Fatma Betul; Chretien, Anaïs; Nurizzo, Didier; 0000-0003-3113-0353; 0000-0003-0391-8290; 0000-0002-5092-0265; 0000-0002-2144-989x; 0000-0001-8480-1443; 0000-0002-7367-5098
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Effect of late-onset on multiple sclerosis phenotype and outcome: evidence from a multi-national registry
(Springer Science and Business Media LLC, 2026-02-01) Altıntaş, Ayşe; Souissi, Amira; Patti, Francesco; Spelman, Tim; Chisari, Clara; Gargouri, Amina; John, Nevin; Kermode, Allan G.; Kalincik, Tomas; Butzkueven, Helmut; Sajedi, Seyed Aidin; Lechner-Scott, Jeannette; Roos, Izanne; Laureys, Guy; Taylor, Bruce; Alroughani, Raed; Khoury, Samia J.; Macdonell, Richard; Weinstock-Guttman, Bianca; Havrdova, Eva Kubala; Maimone, Davide; Reddel, Stephen; Fabis-Pedrini, Marzena; Willekens, Barbara; Moghadasi, Abdorreza Naser; Lalive, Patrice; Lugaresi, Alessandra; Ozakbas, Serkan; Solaro, Claudio; Cárdenas-Robledo, Simón; Shaygannejad, Vahid; Etemadifar, Masoud; Boz, Cavit; Eichau, Sara; Tomassini, Valentina; Terzi, Murat; Prat, Alexandre; Habek, Mario; Blanco, Yolanda; Gerlach, Oliver; Turkoglu, Recai; Buzzard, Katherine; Skibina, Olga; Soysal, Aysun; van der Walt, Anneke; Hughes, Stella; van Pesch, Vincent; Foschi, Matteo; Surcinelli, Andrea; Prevost, Julie; Ramo-Tello, Cristina; McGuigan, Chris; Sa, Maria Jose; Kuhle, Jens; Spitaleri, Daniele; Singhal, Bhim; Ampapa, Radek; de Gans, Koen; Petersen, Thor; Simu, Mihaela; Lapointe, Emmanuelle; Sanchez-Menoyo, Jose Luis; Gray, Orla; Garber, Justin; Aguera-Morales, Eduardo; Gross-Paju, Katrin; Castillo-Triviño, Tamara; Al-Asmi, Abdullah; Grigoriadis, Nikolaos; Inshasi, Jihad; Al-Harbi, Talal; Hardy, Todd A.; Ramanathan, Sudarshini; Cambron, Melissa; Shuey, Neil; sempere, Angel Perez; Csepany, Tunde; Treviño-Frenk, Irene; Rozsa, Csilla; Cauchi, Marija; Karabudak, Rana; Mrabet, Saloua; Gouider, Riadh; to be filled manually; Yes; School of Medicine; KUTTAM (Koç University Research Center for Translational Medicine); to be filled manually
Multiple Sclerosis (MS) severity is influenced by several factors. Understanding the impact of age at disease onset may help to better characterize clinical and disease features across age groups. This study aimed to characterize the clinical features and disability outcomes of late-onset MS (LOMS) and very late-onset MS (vLOMS), compared to adult-onset MS (AOMS).We conducted an observational study using data from the MSBase registry and categorized patients based on age at MS onset: AOMS (18-39 years), transition onset (40-49 years), LOMS (50-59 years), and vLOMS (≥ 60 years). Disease progression was assessed using the 24 week confirmed disability progression, EDSS4 and 6 milestones, conversion to secondary progressive MS(SPMS), and the first progression independent of relapse activity (PIRA) event. Cox proportional hazard regression models were used to determine unadjusted hazard ratios(HR), and propensity score inverse probability of treatment weighting(PS-IPTW) balanced covariate distributions.Among 81,236 patients, 5.2% had LOMS and 1% had vLOMS. Primary progressive MS was more frequent in LOMS and vLOMS (21.7 and 24%, respectively). Patients with LOMS and vLOMS had a significantly increased risk of 24 week confirmed disability progression (HR:LOMS = 1.39, vLOMS = 1.80), EDSS 4 (HR:LOMS = 2.14, vLOMS = 2.95), EDSS 6 (HR:LOMS = 2.33, vLOMS = 6.33), SPMS (HR:LOMS = 1.62, vLOMS = 2.38), and first PIRA event (HR:LOMS = 2.12, vLOMS = 2.93).LOMS and vLOMS exhibited a more progressive disease onset and higher disability milestones compared with AOMS.
Budget inference attacks and countermeasures in locally differentially private data collection
(Association for Computing Machinery, 2026) Balioğlu, Berkay Kemal; Balioğlu, Berkay Kemal; Gürsoy, Mehmet Emre; Yes; Department of Computer Engineering
Local differential privacy (LDP) has recently become a popular notion for privacy-preserving data collection from user devices. It has been applied in numerous contexts related to the Internet of Things (IoT) and cyber-physical systems to enable privacy-preserving edge data analytics. The strength of privacy protection in LDP deployments depends on the privacy budget ɛ, and there are several scenarios in which it is desirable for the value of ɛ to remain hidden from untrusted third parties, or the inference of ɛ by an untrusted third party may constitute a privacy leakage. In this article, we propose a new class of attacks called budget inference attacks (BIAs), which enable an adversary to infer the ɛ budget value from the outputs of an LDP protocol. We develop BIAs for two types of adversaries: informed adversaries who have knowledge of the statistical data distribution, and uninformed adversaries who do not. We apply our BIAs on five popular LDP protocols and experimentally evaluate them using multiple datasets, varying ɛ budgets, population sizes, and attack settings and parameters. Results show that our BIAs are highly effective, as they enable the adversary to infer the ɛ value with low errors. We also propose three potential countermeasures against our BIAs. Analyses show that while our countermeasures can be effective in reducing BIA accuracy, they also increase utility loss; therefore, the tradeoff between BIA accuracy and utility loss needs to be carefully considered. © 2026 Copyright held by the owner/author(s).
Bi-allelic intermediate ATXN2 repeat expansions are associated with slow progressing, leg-onset familial ALS
(BMJ, 2026) Başak, Ayşe Nazlı; Demaegd, Koen Cedric; Koole, Wouter; van Vugt, Joke J. F. A.; Dankbaar, Jan Willem; Hendrikse, Jeroen; de Carvalho, Mamede; Corcia, Philippe; Codron, Philippe; Bernard, Emilien; Guissart, Claire; Couratier, Philippe; Povedano Panades, Monica; van Doorn, Pieter A.; Warrenburg, Bart P.; Cooper-Knock, Johnathan; Pasterkamp, R. Jeroen; van Rheenen, Wouter; van Damme, Philip; van den Berg, Leonard H.; Veldink, Jan Herman; van Es, Michael A.; NDAL (Neurodegeneration Research Laboratory); KUTTAM (Koç University Research Center for Translational Medicine); School of Medicine
Objectives The identification of bi-allelic intermediate ATXN2 repeat expansions in a pedigree with amyotrophic lateral sclerosis (ALS) through clinical testing prompted us to investigate its relevance in the wider ALS population.Methods ATXN2 repeat size was assessed in a large international cohort of ALS patients (n=6653 from Project MinE) and in neurologically intact control populations (n=13 515 controls from Project MinE and gnomad). For bi-allelic cases, we retrieved medical records, family history and MRI imaging. For familial cases, we obtained DNA samples from relatives for segregation analyses.Results In total, we identified bi-allelic intermediate ATXN2 repeat expansions in five familial cases from three different pedigrees and five apparently sporadic cases. There is a relatively homogeneous phenotype characterised by lower limb onset and long survival (median 6 years) without significant cerebellar atrophy. Bi-allelic expansions were absent in controls (0 out of 13 515).Discussion Here we report an apparently novel autosomal recessive form of familial ALS caused by bi-allelic intermediate ATXN2 repeat expansions, which is characterised by high penetrance, lower limb onset and slow progression. Although rare, testing for ATXN2 expansions should be performed in the clinical setting given its relevance to prognosis and genetic counselling.