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.
For more information or inquiries please contact openaccess@ku.edu.tr
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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.
GLP-1 receptor agonists in kidney transplant recipients with type 2 diabetes mellitus: a systematic review and meta-analysis on mortality and major adverse kidney events
(Springer, 2026) Aliyeva, Türkan; Natche, Julia; Jiakponna, Enyinnaya Calistus; Ahmad, Feras; Eze, Belinda; Nawaz, Usama Hassan; El-Amri, Imane; Shrestha, Sheelu; KUH (Koç University Hospital); KUH (KOÇ UNIVERSITY HOSPITAL)
Background Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) are increasingly used in patients with type 2 diabetes mellitus and chronic kidney disease. However, their safety and efficacy in kidney transplant recipients remain uncertain. This study aims to evaluate the impact of GLP-1 RAs on all-cause mortality, major adverse cardiovascular events (MACE), and major adverse kidney events (MAKE) in adult kidney transplant recipients. Methods We conducted a systematic review and meta-analysis of retrospective cohort studies reporting outcomes in adult kidney transplant recipients treated with GLP-1 RAs. A comprehensive search of PubMed, Embase and Cochrane Library was performed up to July 2025. Studies were included if they reported on at least one of the following outcomes: all-cause mortality, MACE, or MAKE. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated using a random-effects model. Results A total of four retrospective cohort studies involving 27,153 were included. A total of 5,479 (20.2%) patients received GLP-1 RAs. The median follow-up period across studies ranged from 1.38 to 3.1 years. GLP-1 RAs treatment was associated with a significant reduction in all-cause mortality, with an aHR of 0.52 (95% CI: 0.32-0.85, I-2 = 86%; p = 0.009). Similarly, a significant reduction in MAKEs was observed, with a pooled aHR of 0.62 (95% CI, 0.53-0.73; I-2 = 15%; p < 0.00001). Conclusions In kidney transplant recipients with type 2 DM, GLP-1 RAs appear to be associated with reduced risks of all-cause mortality and MAKEs. However, given the high heterogeneity across studies and the influence of a single large cohort, these findings should be interpreted with caution and considered exploratory. Prospective studies are needed to confirm the long-term safety and efficacy of GLP-1 RAs in this population.
Neuromodulation via Krotov-Hopfield improves accuracy and robustness of restricted Boltzmann machines
(American Physical Society, 2026) Kabakçıoğlu, Alkan; Tambaş B.; Subaşı A.L.; Department of Physics; College of Sciences
In biological systems, neuromodulation tunes synaptic plasticity based on the internal state of the organism, complementing stimulus-driven Hebbian learning. The algorithm recently proposed by Krotov and Hopfield (KH) [D. Krotov and J. J. Hopfield, Proc. Natl. Acad. Sci. USA116, 7723 (2026) 0027-8424 10.1073/pnas.1820458116] can be utilized to mirror this process in artificial neural networks, where its built-in intralayer competition and selective inhibition of synaptic updates offer a cost-effective remedy for the lack of lateral connections through a simplified attention mechanism. We demonstrate that KH-modulated restricted Boltzmann machines (RBMs) outperform standard (shallow) RBMs in both reconstruction and classification tasks, offering a superior trade-off between generalization performance and model size, with the additional benefit of robustness to weight initialization as well as to overfitting during training.
When polarization meets backsliding: affective polarization and support for undemocratic practices in Turkey
(Taylor and Francis, 2026) Irmak, Seda; Aytaç, Selim Erdem; Karakoç, Büşra Söylemez; Department of International Relations; College of Administrative Sciences and Economics
While the corrosive effect of affective polarization on democratic norms is a major concern, existing research has largely overlooked its dynamics outside established democracies. This study addresses this gap by examining Turkey, a paradigmatic, highly polarized hybrid regime where democratic norms are actively contested. Drawing on original, nationally representative survey data from spring 2024, we investigate how affective polarization shapes citizens’ willingness to endorse concrete violations of electoral fairness and civil liberties, moving beyond abstract measures of democratic support. We find that higher levels of affective polarization are strongly associated with greater endorsement of undemocratic practices motivated by both out-party discrimination and in-party favouritism, though the association is somewhat stronger for the latter. This relationship holds among both government and opposition supporters, challenging the assumption that tolerance for such practices is unique to incumbent partisans. Contrary to recent evidence from Western democracies, we find no curvilinear relationship: affective polarization in Turkey consistently predicts greater tolerance of democratic violations. By analysing a case of sustained democratic backsliding, we extend debates on affective polarization beyond consolidated democracies, showing how it can create a permissive environment for illiberal practices and undermine citizen commitment to democratic norms.