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.
Exploring inflammatory depression: associations of CRP and NLR with neuroanatomical alterations and symptom dimensions in hospitalized patients with major depressive disorder
(Elsevier BV, 2027) Sabitay, İmren Kurt; Eser, Hale Yapıcı; Ballı, Muhammed; Kırlıoğlu Balcıoğlu, S. S.; School of Medicine; Graduate School of Health Sciences; SCHOOL OF MEDICINE; GRADUATE SCHOOL OF HEALTH SCIENCES
Growing evidence indicates that immune dysfunction contributes to the heterogeneity of major depressive disorder, yet it remains unclear when inflammation is clinically relevant, how it manifests in symptomatology and brain structure, and for whom immune-related mechanisms may be most important. Clarifying these questions is essential for patient stratification and the development of immunomodulatory treatments. Methods Clinical, biochemical, and neuroimaging data from 176 hospitalized adults with DSM-5 major depressive disorder was involved. Peripheral inflammation was assessed using routinely available markers, including C-reactive protein (CRP) and the neutrophil-to-lymphocyte ratio (NLR), and a high-inflammation subgroup was defined using literature-based thresholds (CRP > 3.0 mg/L and/or NLR > 3.53). Depressive symptoms, functioning, and illness severity were evaluated from structured clinical records. Voxel-based morphometry analyses were conducted to investigate associations between inflammatory markers and gray matter volume. Results Approximately one-third of patients met criteria for an inflammation-associated subtype. In univariate analyses, CRP was nominally higher in patients with anhedonia and suicide attempt, though neither association survived FDR correction. After adjusting for age, sex, and BMI, CRP was independently associated with suicide attempt (OR = 1.221, p = 0.004) and suicidal plan (OR = 1.173, p = 0.021), while the anhedonia association was no longer significant. CRP correlated with higher CGI-S (ρ = 0.193, pFDR = 0.041) and predicted both GAF and CGI-S in covariate-adjusted models. NLR showed no significant associations with any symptom or clinical severity measure. The high-inflammation subgroup was characterized by older age, higher BMI, and later age at illness onset, without significant differences in symptoms, CGI-S, or GAF after covariate adjustment. Exploratory VBM analyses revealed CRP-related gray matter increases in the left middle and inferior temporal gyrus and decreases in occipital and inferior parietal regions, while NLR was associated with increased volume in the right thalamic nuclei and decreased volume in the right superior temporal gyrus; subgroup contrasts indicated greater occipital and cuneus volume in the low-inflammation group and greater temporal pole volume in the high-inflammation group, with all findings reported at uncorrected thresholds. Conclusions Our findings suggest that CRP, a routinely available inflammatory marker, is independently associated with suicidality and clinical severity in severely depressed inpatients, even after accounting for confounders. The divergent neuroanatomical correlates of CRP and NLR, though exploratory, point to distinct inflammatory pathways with regionally specific brain signatures. These findings support the potential utility of CRP in identifying a clinically relevant inflammatory dimension within severe depression. Prospective studies with larger samples are needed to replicate these associations, clarify the temporal dynamics of inflammation in depression, and evaluate whether inflammatory stratification can guide treatment selection.
Sok: a taxonomy of attacks and defenses in split Learning
(Springer, 2027) Küpçü, Alptekin; Kanpak, Halil; Shabbir, A.; Sav, S.; KUIS AI (Koç University & İş Bank Artificial Intelligence Center); Department of Computer Engineering; Graduate School of Sciences and Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING; College of Engineering; Research Center
Split Learning (SL) has emerged as a promising paradigm for distributed deep learning, allowing resource-constrained clients to offload portions of their model computation to servers while maintaining collaborative learning. However, recent research has demonstrated that SL remains vulnerable to a range of privacy and security threats, including information leakage, model inversion, and adversarial attacks. While various defense mechanisms have been proposed, a systematic understanding of the attack landscape and corresponding countermeasures is still lacking. In this study, we present a comprehensive taxonomy of attacks and defenses in SL, categorizing them along three key dimensions: employed strategies, constraints, and effectiveness. Furthermore, we identify key open challenges and research gaps in SL based on our systematization, highlighting potential future directions.
Thienothiophene-assisted hydrophobic carbon dots: photophysical properties and fluorescent ZIF-8 composites
(Elsevier BV, 2027) Jahangiri, Hadi; Isci, R.; İbiş, Ö.; Ünlü, F. Y.; Gökçe, H.; Ünlü, C.; Ozturk, T.; KUYTAM (Koç University Surface Science and Technology Center); Research Center
Despite extensive studies on heteroatom-containing carbon dots and CD/ZIF-8 composites, molecularly defined fused sulfur heteroarenes have received little attention as precursors for hydrophobic carbon dots. Consequently, the relationship between precursor-derived sulfur environments, excited-state dynamics, and subsequent integration into porous crystalline hosts remains poorly defined. Herein, thienothiophene (TT) was used as a molecular co-precursor in a matched solvothermal synthesis with toluene-derived carbon dots (To-CDs) serving as a control. TT-assisted synthesis produced quasi-spherical carbon dots with closer average interlayer packing and distinct sulfur-containing bond environments. FTIR difference analysis and high-resolution C 1 s and S 2p XPS identified TT-derived thiophene and CS signatures together with reduced C–S–C and oxidized‑sulfur environments. These structural changes shifted the emission from blue region toward green and produced fluorescence decay dynamics longer than those of molecular TT but shorter than those of To-CDs. Subsequent ZIF-8 crystallization in the presence of preformed TT-CDs generated a washed, green-emissive crystalline composite that retained the ZIF-8 diffraction pattern while showing a substantial decrease in N₂-accessible BET surface area. By separating TT-induced carbon-dot differentiation from porous-host formation, this precursor-to-host strategy establishes a direct connection between molecular precursor chemistry, carbon-dot photophysics, and integration into an emissive microporous solid.