WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Editorial Editors' Introduction: Fall 2025(Cambridge Univ Press, 2025-10-28) Dincer, Evren M.; Yukseker, Deniz; Kolluoglu, BirayConference Object Ceramide Is a Key Factor That Regulates the Crosstalk Between TGF-Β and Sonic Hedgehog Signaling at the Basal Cilia to Control Cell Migration and Tumor Metastasis(Federation Amer Soc Exp Biol, 2016-07) Gencer, Salih; Oleinik, Natalia; Dany, Mohammed; Ogretmen, BesimArticle 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 Effect of Different Pitch Ratios on the Flow Around Tandem Circular Cylinders with Spoilers(Elsevier Ltd, 2025-12) İlkentapar, M.; Akşit, S.; Öner, A.A.; Genç, M.S.This study experimentally investigates the unsteady aerodynamic characteristics of two tandem circular cylinders subjected to various pitch ratios and spoiler configurations in a controlled wind tunnel environment. The primary objective is to understand how the placement and presence of spoiler's influence flow separation, wake interference, surface pressure distributions, and overall aerodynamic performance. The experiments were conducted for three pitch ratios (2D, 4D, and 7D) and four spoiler configurations: NN (no spoilers on either cylinder), NS (spoiler on the downstream cylinder only), SN (spoiler on the upstream cylinder only), and SS (spoilers on both cylinders). Measurements included surface pressure, velocity distribution via hot-wire anemometry, and aerodynamic forces, while qualitative flow patterns were assessed using smoke-wire visualization. The results indicate that the usage of spoilers substantially alters the wake structure and pressure profiles, especially in closely spaced configurations. In the NN configuration, increasing the pitch ratio led to a progressive decoupling of the flow between the cylinders, transitioning from a merged wake to more isolated vortex shedding. In the SN and NS configurations, the asymmetrical placement of spoilers induced unsteady wake interactions and altered reattachment dynamics on the downstream body. The SS configuration exhibited the most disturbed flow regime at low pitch ratios, which gradually stabilized as the spacing increased. Violin plots derived from velocity measurements provided statistical insight into flow symmetry and turbulence intensity, while smoke visualizations captured coherent structures and transition zones across the configurations. The combined analysis demonstrates that both pitch ratio and spoiler configuration are critical parameters in controlling aerodynamic interference and unsteady wake behavior in tandem arrangements. These findings offer valuable implications for flow management and control strategies in offshore structures, cylindrical risers, and heat exchanger tube banks, where vortex-induced vibrations and flow separation play crucial roles. © 2025 Elsevier B.V., All rights reserved.Article Citation - WoS: 40Citation - Scopus: 49Spatio-Temporal Rich Model-Based Video Steganalysis on Cross Sections of Motion Vector Planes(Institute of Electrical and Electronics Engineers Inc., 2016-07) Taşdemir, K.; Kurugöllü, F.; Sakir Sezer, S.; Sezer, SakirA rich model-based motion vector (MV) steganalysis benefiting from both temporal and spatial correlations of MVs is proposed in this paper. The proposed steganalysis method has a substantially superior detection accuracy than the previous methods, even the targeted ones. The improvement in detection accuracy lies in several novel approaches introduced in this paper. First, it is shown that there is a strong correlation, not only spatially but also temporally, among neighbouring MVs for longer distances. Therefore, temporal MV dependency alongside the spatial dependency is utilized for rigorous MV steganalysis. Second, unlike the filters previously used, which were heuristically designed against a specific MV steganography, a diverse set of many filters, which can capture aberrations introduced by various MV steganography methods is used. The variety and also the number of the filter kernels are substantially more than that of used in the previous ones. Besides that, filters up to fifth order are employed whereas the previous methods use at most second order filters. As a result of these, the proposed system captures various decorrelations in a wide spatio-Temporal range and provides a better cover model. The proposed method is tested against the most prominent MV steganalysis and steganography methods. To the best knowledge of the authors, the experiments section has the most comprehensive tests in MV steganalysis field, including five stego and seven steganalysis methods. Test results show that the proposed method yields around 20% detection accuracy increase in low payloads and 5% in higher payloads. © 2016 Elsevier B.V., All rights reserved.Article Citation - WoS: 2Citation - Scopus: 2Route Choice to Inform Navigation System Design and Accessibility Analysis for Older Pedestrians: A Scoping Review(Elsevier Sci Ltd, 2025-10) Fulman, Nir; Huber, Johannes; Lloyd, Armagan Teke; Foshag, Kathrin; Grinblat, Yulia; Turk, Umut; Zipf, AlexanderIntroduction: Routing systems can support older adults by helping them overcome barriers to walking, promoting independence and well-being. The paths generated by these systems also inform urban accessibility metrics, such as those used in 15-min-city planning. Yet current systems rarely reflect the preferences or constraints of older pedestrians. Empirical studies of route choice can help close this gap by revealing how people trade off different route attributes in real settings. Methods: We conducted a scoping review, following PRISMA-ScR guidelines, of empirical studies analyzing pedestrian route choice among adults. The goal was to identify findings that could inform the design of more age-inclusive routing tools. Results: Eleven studies met the inclusion criteria, eight of which focused exclusively on older adults. Despite varied contexts, three consistent themes emerged: (i) sidewalk quality and manageable gradients; (ii) aesthetic and sensory comfort, including greenery, low noise, and good lighting; and (iii) access to benches, transit, and everyday amenities. However, most studies relied on qualitative methods, limiting direct integration into routing algorithms. Conclusions: Future work should prioritize hybrid qualitative-quantitative designs, large-scale sampling of routes, and fine-grained mapping of micro-barriers. Analyses should account for age, gender, and functional ability, and consider circular leisure walks as a distinct travel pattern. These directions can enhance the usability and equity of routing systems and urban planning frameworks.Article Citation - WoS: 4Citation - Scopus: 4Bright Green and Blue Solid-State Emitting Carbon Dots With Optimized Photoluminescence Characteristics for Fabrication of High-Performance Light Emitting Diodes(Elsevier Sci Ltd, 2025-09) Havasi, Nasrin; Sahraei, Reza; Soheyli, Ehsan; Lan, Yu; Lou, Qing; Houshmand, Fatemeh; Shan, Chong-XinLuminescent carbon dots (CDs) possess a range of fundamental and technological advantages, including low-cost, and scalable preparation methods, high emission efficiency, tunable electronic properties, and adaptable surface characteristics. However, aggregation-caused quench in solid-state emission of CDs has constrained their applications in luminescent solar-concentrators, and light-emitting devices. This study introduces a rapid and straightforward microwave method for producing bright blue-and green-emissive CDs, with emission peaks at 440 nm and 520 nm, respectively. Blue-CDs showed excitation-dependent feature with a biexponential decay profile and average lifetime of 6.3 ns, while the green one signified an excitation-independent photoluminescence profile with longer average lifetime of 9 ns through biexponential fitting of decay plot. Upon optimization of experimental parameters, reproducible green emission with a high efficiency of 78 % was achieved in dimethyl sulfoxide (DMSO). The critical role of biurea as a nitrogen precursor was elucidated through experimental and computational investigations. Furthermore, owing to the bright solid-state emission of the synthesized CDs, they were utilized as color-converting layers in the fabrication of durable monochrome LEDs, yielding blue and yellowish-green emissions with Commission Internationale de L'E<acute accent>clairage (CIE) coordinates of (0.16, 0.10) and (0.35, 0.57), respectively. This study highlights the potential of CDs for applications in light-emitting panels.Article Achieving Extreme Solubility and Green Solvent-Processed Organic Field-Effect Transistors: A Viable Asymmetric Functionalization of [1]Benzothieno[3,2-B][1]Benzothiophenes(American Chemical Society, 2025-08-22) Yıldız, T.A.; Deneme, İ.; Usta, H.Novel structural engineering strategies for solubilizing high-mobility semiconductors are critical, which enables green solvent processing for eco-friendly, sustainable device fabrication, and unique molecular properties. Here, we introduce a viable asymmetric functionalization approach, synthesizing monocarbonyl [1]benzothieno[3,2-b][1]benzothiophene molecules on a gram scale in two transition-metal-free steps. An unprecedented solubility of up to 176.0 mg·mL–1(at room temperature) is achieved, which is the highest reported to date for a high-performance organic semiconductor. The single-crystal structural analysis reveals a herringbone motif with multiple edge-to-face interactions and nonclassical hydrogen bonds involving the carbonyl unit. The asymmetric backbones adopt an antiparallel arrangement, enabling face-to-face π-π interactions. The mono(alkyl-aryl)carbonyl-BTBT compound, m-C<inf>6</inf>PhCO-BTBT enables formulations in varied green solvents, including acetone and ethanol, all achieving p-channel top-contact/bottom-gate OFETs in ambient conditions. Charge carrier mobilities of up to 1.87 cm2/V·s (μ<inf>eff</inf>≈ 0.4 cm2/V·s; I<inf>on</inf>/I<inf>off</inf>≈ 107–108) were achieved. To the best of our knowledge, this is one of the highest OFET performances achieved using a green solvent. Hansen solubility parameters (HSP) analysis, combined with Scatchard–Hildebrand regular solution theory and single-crystal packing analysis, elucidates this exceptional solubility and reveals unique relationships between molecular structure, interaction energy densities, cohesive energetics, and solute–solvent distances (R<inf>a</inf>). An optimal solute–green solvent interaction distance in HSP space proves critical for green solvent-processed thin-film properties. This asymmetric functionalization approach, with demonstrated unique solubility insights, provides a foundation for designing green solvent-processable π-conjugated systems, potentially advancing innovation in sustainable (opto)electronics and bioelectronics. © 2025 Elsevier B.V., All rights reserved.