WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Citation - WoS: 1Two-Local Modifications of Sachdev-Ye Model With Quantum Chaos(American Physical Society, 2026-01-27) Hanada, M.; Van Leuven, S.; Oktay, O.; Tezuka, M.The Sachdev-Ye-Kitaev (SYK) model may provide us with a good starting point for the experimental study of quantum chaos and holography in the laboratory. Still, the four-local interaction of fermions makes quantum simulation challenging, and it would be good to search for simpler models that keep the essence. In this paper, we argue that the four-local interaction may not be important by introducing a few models that have two-local interactions. The first model is a generalization of the spin-SYK model, which is obtained by replacing the spin variables with SU(d) generators. Simulations of this class of models might be straightforward on qudit-based quantum devices. We study the case of d=3,4,5,6 numerically and observe quantum chaos already for two-local interactions in a wide energy range. We also introduce modifications of spin-SYK and SYK models that have similar structures as the SU(d) model (e.g., H=∑p,qJpqχpχp+1χqχq+1 instead of the original SYK Hamiltonian H=∑p,q,r,sJpqrsχpχqχrχs), which shows strongly chaotic features although the interaction is essentially two-local. These models may be a good starting point for the quantum simulation of the original SYK model. ©2026 American Physical Society.Article Disorder-Engineered Hybrid Plasmonic Cavities for Emission Control of Defects in HBN(American Chemical Society, 2026-02-07) Genc, Sinan; Yucel, Oguzhan; Aglarci, Furkan; Rodriguez-Fernandez, Carlos; Yilmaz, Alpay; Caglayan, Humeyra; Bek, AlpanDefect-based quantum emitters in hexagonal boron nitride (hBN) are promising building blocks for scalable quantum photonics due to their stable single-photon emission at room temperature. However, enhancing their emission intensity and controlling the decay dynamics remain significant challenges. This study demonstrates a low-cost, scalable fabrication approach to integrate plasmonic nanocavities with defect-based quantum emitters in hBN nanoflakes. Using the thermal dewetting process, we realize two distinct configurations: stochastic Ag nanoparticles (AgNPs) on hBN flakes and hybrid plasmonic nanocavities formed by AgNPs on top of hBN flakes supported on gold/silicon dioxide (Au/SiO2) substrates. While AgNPs on bare hBN yield up to a 2-fold photoluminescence (PL) enhancement with reduced emitter lifetimes, the hybrid nanocavity architecture provides a dramatic, up to 100-fold PL enhancement and improved uniformity across multiple emitters, all without requiring deterministic positioning. Finite-difference time-domain (FDTD) simulations and time-resolved PL measurements confirm size-dependent control over decay dynamics and cavity-emitter interactions. Our versatile solution overcomes key quantum photonic device development challenges, including material integration, emission intensity optimization, and spectral multiplexity.Article Measuring Disaster Resilience in MENA Countries and Its Impact on Disaster Losses(Nature Portfolio, 2025-12-08) Demir, Abdullah; Dincer, Ali Ersin; Dincer, Nazire NergizDisaster resilience is a protective feature aimed at reducing the effects of natural disaster events and losses resulting from these events. This study develops a Disaster Resilience Index (DRI) for MENA countries to assess resilience across ten dimensions, including economic, social, institutional, infrastructural, and environmental factors. Unlike most prior studies, which focus on individual countries or use narrower sets of indicators, this study provides a multi-country, region-specific framework tailored to MENA's socio-economic and environmental heterogeneity. The index integrates geospatial data on disaster risk from geographic information systems (GIS) and a natural hazard risk dimension. Validation using disaster-related fatalities, supported by a dual PCA-based sensitivity analysis, confirms the robustness of the DRI and reveals that countries with stronger governance, higher human capital, and robust infrastructure tend to exhibit greater resilience, while fragile states and resource-dependent economies are more vulnerable. Notably, the DRI calculated using both dimension-specific and all-indicator PCA produces closely aligned values, indicating the choice of conducting PCA at the dimension level does not significantly alter the overall assessment of disaster resilience. These insights provide a foundation for targeted disaster risk reduction strategies and highlight areas where international cooperation and policy interventions can strengthen resilience in the region.Article Vim-Polyp: Multimodal Colon Polyp Dataset with Video, Histopathology, and Protein Expression(Nature Portfolio, 2025-12-03) Dogan, Refika Sultan; Akay, Ebru; Dogan, Serkan; Yilmaz, BulentThe dataset in this study includes 202 videos with a total of 422 minutes, reaching Kayseri City Hospital's gastroenterology department as colonoscopy videos and 1903 microscopy images between 2019 and 2021. It includes 399 colonoscopy, microscopy images, and pathological diagnoses of polyps, as well as immunohistochemical staining results for proteins that play an important role in the assessment of cancerous cells, such as staining results for p53 (clone: bp53-11), Ki-67 (clone: 30-9), CD34 (clone: QBend/10), PD-L1 (clone: SP142), BRAF (clone: V600E) and VEGF (clone: SP125). By sharing the data openly, we aim to facilitate benchmarking, exploratory analysis and transfer-learning studies on colorectal polyps and cancer. In combination with external datasets or pretrained models, the resource can help advance data-driven detection and characterisation work. The diverse range of polyps assigned to cancer stages from 201 patients makes this tool valuable for researchers and clinicians in furthering diagnosis and treatment.Article Development and Characterization of Starch-Fatty Acid Complexes Produced with Buckwheat Starch and Capric/Stearic Acid Using Different Reaction Conditions(Elsevier, 2025-12) Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent Yurdaer; Kahraman, KevserThe aim of present study was to investigate the impact of reaction parameters on the complex formation between buckwheat starch and capric acid (B-Capric) or stearic acid (B-Stearic). The most effective parameters on complex formation indicator (Complex index (CI) value) were found as reaction temperature (60-90 degrees C) and pH (5-8). Additionally, the effect of these parameters on physicochemical, pasting, and in-vitro digestibility properties of complex samples were evaluated. XRD and FTIR was also used in characterize the complex samples. In general, increasing pH increased the CI values of B-Stearic samples while decreasing those of B-Capric samples. Syneresis of buckwheat starch increased after complexation while paste clarity and swelling power diminished. The pasting properties of native starch significantly changed after complex formation. The FTIR results showed that starch structure changed with complex formation. XRD revealed that buckwheat starch, having an A-type pattern, converted to V-type pattern after complexation. Complex formation of buckwheat starch with capric and stearic acid significantly increased the RS content of buckwheat starch (19.01 %) by up to 36.25 % and 30.60 %, respectively. These results highlight the possibility of using buckwheat starch-capric acid/stearic acid complexes in food formulation to enhance the RS content.Article Citation - Scopus: 1Labyrinthine Microstructures With a High Dipole Moment Boron Complex for Molecular Physically Unclonable Functions(American Chemical Society, 2025-10-29) Yıldız, T.A.; Kiremitler, N.B.; Kayacı, N.; Kalay, M.; Özcan, E.; Deneme, I.; Usta, H.The design and development of novel molecular-physically unclonable functions (PUFs) with advanced encoding characteristics and ease of fabrication have recently attracted attention in cryptography, secure authentication, and anticounterfeiting. Here, we report the development of a new high dipole-moment small molecule, InIm-BF<inf>2</inf>, a difluoroborate complex of an indolyl-imine ligand, and the fabrication of unique labyrinthine patterns through a facile two-step thin film process under ambient conditions. The new molecule has a dipolar, coplanar π-backbone and arranges in the solid state with antisymmetric cofacial π-stackings (3.86 Å). These properties, along with short C–H···π contacts (2.74–2.88 Å) and nonclassical C–H···F hydrogen bonds (2.47–2.51 Å) (23.4% and 11.5% of the Hirshfeld surfaces, respectively), drive the formation of amorphous molecular PUF patterns with disordered, short-range interactions. Spin-coating followed by thermal annealing at a moderate temperature produces nanoscopic molecular thin films with intricate labyrinthine patterns. These patterns, characterized by interconnected, irregularly shaped, micron-sized (≈50–100 μm) features, exhibit excellent PUF characteristics, verified through advanced image analysis and computational algorithms. Unlike randomly positioned isolated features in classical binarized keys, the interconnected labyrinthine patterns possess rich entropy and complex features, directly authenticated via deep-learning methodologies. Our work not only demonstrates a facile, promising approach to fabricating unique high-entropy PUF patterns but also provides critical insights into designing advanced molecular materials for next-generation security applications. © 2025 The Authors. Published by American Chemical SocietyArticle Citation - WoS: 1Citation - Scopus: 1Effect of Yttrium/Lanthanum-Doped Ultrasonically Assisted Nano-Hydroxyapatite on Remineralization and Bracket Bond Strength in Artificial Enamel Lesions(BMC, 2025-09-29) Ozturk, Taner; Mammadov, Elshan; Bulduk Karakaya, Humeyra; Yagci, Filiz; Dayan, Serkan; Yagci, AhmetBackground This in vitro study aimed to evaluate the remineralization efficacy of ultrasonically assisted yttrium fluoride-doped (Ult-YF3-nHAP) and lanthanum fluoride-doped (Ult-LaF3-nHAP) nano-hydroxyapatite (nHAP) on artificially induced enamel lesions (aWSLs), and to compare their performance with acidulated phosphate fluoride (APF) gel, fluoride varnish, casein phosphopeptide-amorphous calcium phosphate (CPP-ACP), and resin infiltrant (ICON). Methods This in vitro study followed a four-phase design: enamel lesion creation, application of remineralization agents, a 14-day treatment protocol, and post-treatment analyses using QLF, Micro-CT, SEM-EDX, and SBS testing. This study included 168 extracted human premolars, divided into eight experimental groups (n = 21 per group): (1) Demineralized control (no remineralization treatment), (2) Acidulated phosphate fluoride (APF) gel, (3) Fluoride varnish, (4) Casein phosphopeptide-amorphous calcium phosphate (CPP-ACP), (5) Ultrasonically assisted nHAP (Control nHAP), (6) Ult-YF3-nHAP, (7) Ult-LaF3-nHAP, and (8) Resin infiltrant (ICON). The aWSLs were created under laboratory conditions. Brackets were bonded to the teeth with composite material, and aWSLs were created under laboratory conditions. After lesion formation and at the end of the experimental process, micro-computed tomography (Micro-CT) and laser-assisted quantitative light fluorescence (QLF) analysis were performed to assess lesion progression and remineralization. Additionally, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) and shear bond strength (SBS) tests were conducted at the end of the study. Statistical analysis was performed using one-way ANOVA, Kruskal-Wallis, and Mann-Whitney U tests, with a significance level of p < 0.05. Results The bracket bond strength test data showed no significant differences between the groups (p = 0.156). Significant differences were found among groups for QLF fluorescence recovery (Delta F, p < 0.001), with the Ult-YF3-nHAP group showing the greatest increase (median: +0.5, IQR: -1.4 to + 0.7), while the control group showed the greatest decrease (median: -12.1, IQR: -12.4 to -10.2). Micro-CT analysis also revealed significant differences between groups (p = 0.008). The APF Gel group showed values comparable to those of all other experimental groups. The highest remineralization values were recorded in the Ult-YF3-nHAP group (6.87 +/- 3.03 mm(3)), whereas the lowest values were found in the Varnish group. The demineralized control group had significantly higher values than the Varnish group, but lower than the Ult-LaF3-nHAP group. SEM-EDX analysis revealed that fluoride weight was significantly lower in the Tooth Mousse and Varnish groups compared to the other experimental groups (p < 0.001). Ca/P ratio was significantly lower in the demineralized control, Varnish, and Ult-YF3-nHAP groups than in other experimental groups (p = 0.002). Conclusion Ult-YF3-nHAP showed higher efficacy in remineralization of aWSLs compared to fluoride-based treatments, CPP-ACP, and resin infiltrant. The highest remineralization was detected in the Ult-YF3-nHAP group by micro-CT and QLF analysis, while fluoride varnish gave the lowest result.Article Citation - WoS: 2Citation - Scopus: 2Pangenome Analysis and Genome-Guided Probiotic Evaluation of Cyclic Dipeptides Producing Levilactobacillus Brevis DY55bre Strain From a Lactic Acid Fermented Shalgam to Assess Its Metabolic, Probiotic Potentials, and Cytotoxic Effects on Colorectal Cancer Cells(Springer, 2025-10-01) Yetiman, Ahmet E.; Horzum, Mehmet; Kanbur, Ertan; Cadir, Mehmet; Bahar, Dilek; Gurbuz, Serife; Akbulut, MikailThis study investigates the genetic, metabolic, and probiotic characteristics of Levilactobacillus brevis DY55bre, a strain isolated from the traditional Turkish fermented beverage, shalgam. Whole-genome sequencing revealed a circular genome of 2.485 Mb with a GC content of 45.72%, predicted 2791 genes, and multiple CRISPR-Cas systems. Pangenome analysis demonstrated an open structure, with 18.9% core genes and 103 strain-specific genes, highlighting its genetic diversity. The DY55bre exhibits heterofermentative carbohydrate metabolism due to the presence of the araBAD operon and the lack of 1-phosphofructokinase (pfK) and fructose-1,6-bisphosphate aldolase enzymes. Probiotic evaluation revealed firm survival under simulated gastrointestinal conditions, including resistance to acidic pH (as low as 3.0) and bile salts (up to 1%), along with significant adhesion to intestinal epithelial cell lines (HT29;59.3%, Caco-2;87%, and DLD-1;60.8%). The strain exhibited high auto-aggregation (84.55%) and cell surface hydrophobicity (56.69%), essential for gut colonization. Safety assessments confirmed its non-hemolytic nature and absence of horizontally acquired antibiotic resistance genes. Notably, GC-MS analysis identified bioactive cyclic dipeptides, Cyclo(D-Phe-L-Pro) and Cyclo(L-Leu-L-Pro), which demonstrated cytotoxic effects against colorectal cancer cell lines, with IC50 values of 7.71 mg/mL for HT29 and 3.19 mg/mL for DLD-1. The cell-free supernatant exhibited antimicrobial activity against pathogens, likely due to the synergistic effects of cyclic dipeptides, organic acids, and other metabolites. Antioxidant assays revealed significant ABTS+ (76.63%) and DPPH (34.25%) radical scavenging activities, while cholesterol assimilation tests showed a 27.29% reduction. These findings position the DY55bre as a promising candidate for functional foods, nutraceuticals, and therapeutic applications, warranting further in vivo validation.Article Citation - WoS: 2Citation - Scopus: 2Antifungal Efficacy of 3D-Cultured Palatal Mesenchymal Stem Cells and Their Secreted Factors Against Candida albicans(American Chemical Society, 2025-09-19) Bicer, M.; Öztürk, E.; Sener, F.; Hakki, S.S.; Fidan, O.Candida albicans is among the life-threatening fungal species and the primary contributor to hospital-acquired systemic infections, accounting for nearly 70% of all fungal infections worldwide. The current treatment primarily relies on azoles, pyrimidine analogs, polyenes, and echinocandins. However, growing antifungal resistance highlights the urgent need for the development of alternative treatments against C. albicans. Mesenchymal stem cells (MSCs) offer huge therapeutic potential for the treatment of C. albicans-associated diseases. In this study, palatal adipose tissue-derived MSCs (PAT-MSCs) and PAT-MSCs cultured in 3D biomaterial using nanofibrillar cellulose were tested against C. albicans strains ATCC 10231 and ATCC MYA 2876 using an in vitro antifungal activity assay. In addition, the conditioned medium from both PAT-MSCs and PAT-MSCs cultured in 3D hydrogel biomaterial (CM-PAT-MSCs-3D) were evaluated for their antifungal activities. The combined effect of PAT-MSCs and their secreted factors was also investigated. The expression of five antimicrobial peptide (AMP)-encoding genes was analyzed by quantitative real-time PCR. The expression of antimicrobial peptides was further confirmed via immunocytochemical staining. PAT-MSCs significantly inhibited the growth of C. albicans strains at varying inoculum concentrations (500 and 2000 CFU). Similarly, a comparable antifungal effect was observed when Candida strains were treated with PAT-MSC secreted factors alone. Statistical analysis revealed significant differences between the antifungal activities of PAT-MSCs and CM-PAT-MSCs. Lastly, the combination of PAT-MSCs and CM-PAT-MSC-3D led to a marked reduction in fungal growth, with inhibition rates of 99.75% and 99.91% for C. albicans ATCC 10231 and ATCC MYA-2876, respectively, at 500 CFU inocula. At 2000 CFU inocula, inhibition rates were 99.54% and 99.91%, respectively (****P ≤ 0.0001). These antifungal activities were further confirmed by using RT-PCR and immunocytochemical analysis. Our findings underscore a perspective on the potent antifungal activity of secreted factors from PAT-MSCs cultured within a 3D hydrogel matrix, specifically against various strains of C. albicans. Particularly, the combination of PAT-MSCs with their secreted factors represents a promising therapeutic platform, potentially offering a safer and more effective alternative to conventional antifungal treatments. © 2025 Elsevier B.V., All rights reserved.Article Citation - WoS: 8Citation - Scopus: 8Writing Chemical Patterns Using Electrospun Fibers as Nanoscale Inkpots for Directed Assembly of Colloidal Nanocrystals(Royal Soc Chemistry, 2020) Kiremitler, N. Burak; Torun, Ilker; Altintas, Yemliha; Patarroyo, Javier; Demir, Hilmi Volkan; Puntes, Victor F.; Onses, M. SerdarApplications that range from electronics to biotechnology will greatly benefit from low-cost, scalable and multiplex fabrication of spatially defined arrays of colloidal inorganic nanocrystals. In this work, we present a novel additive patterning approach based on the use of electrospun nanofibers (NFs) as inkpots for end-functional polymers. The localized grafting of end-functional polymers from spatially defined nanofibers results in covalently bound chemical patterns. The main factors that determine the width of the nanopatterns are the diameter of the NF and the extent of spreading during the thermal annealing process. Lowering the surface energy of the substrates via silanization and a proper choice of the grafting conditions enable the fabrication of nanoscale patterns over centimeter length scales. The fabricated patterns of end-grafted polymers serve as the templates for spatially defined assembly of colloidal metal and metal oxide nanocrystals of varying sizes (15 to 100 nm), shapes (spherical, cube, rod), and compositions (Au, Ag, Pt, TiO2), as well as semiconductor quantum dots, including the assembly of semiconductor nanoplatelets.