PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

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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) Yıldız, T.A.; Deneme, İ.; Usta, H.; 01. Abdullah Gül University; 10. Rektörlük; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
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-C6PhCO-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 (μeff≈ 0.4 cm2/V·s; Ion/Ioff≈ 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 (Ra). 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.
Antifungal Efficacy of 3D-Cultured Palatal Mesenchymal Stem Cells and Their Secreted Factors Against Candida albicans
(American Chemical Society, 2025) Bicer, M.; Öztürk, E.; Sener, F.; Hakki, S.S.; Fidan, O.; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik; 01. Abdullah Gül University
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.
Burg-Aided 2D MIMO Array Extrapolation for Improved Spatial Resolution
(MDPI, 2025) Bekar, Muge; Bekar, Ali; Pirkani, Anum; Baker, Christopher John; Gashinova, Marina; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik Mühendisliği
In this paper, the extrapolation of a 2D multiple-input multiple-output (MIMO) array is proposed using the Burg algorithm to achieve higher angular resolution beyond that of the corresponding 2D MIMO virtual array. The main advantage of such an approach is that it allows us to dramatically decrease both the physical size and the number of antenna elements of the MIMO array. The performance and limitations of the Burg algorithm are examined through both simulation and experimentation at 77 GHz. The experimental methodology used to acquire 3D data of range, azimuth and elevation information with the 1D MIMO off-the-shelf radar is described. Using this method, the performance of the proposed array can be tested experimentally, especially at frequencies where it is desired to assess the antenna response prior to fabricating the antenna.
Correction: Engineering Novel Features for Diabetes Complication Prediction Using Synthetic Electronic Health Records
(Frontiers Media S.A., 2025) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, Malik; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Developing a Label Propagation Approach for Cancer Subtype Classification Problem
(Tubitak Scientific & Technological Research Council Turkey, 2022) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, Mustafa; 02. 04. Bilgisayar Mühendisliği; 01. Abdullah Gül University; 02. Mühendislik Fakültesi
Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches.
Effect of Yttrium/Lanthanum-Doped Ultrasonically Assisted Nano-Hydroxyapatite on Remineralization and Bracket Bond Strength in Artificial Enamel Lesions
(BMC, 2025) Ozturk, Taner; Mammadov, Elshan; Bulduk Karakaya, Humeyra; Yagci, Filiz; Dayan, Serkan; Yagci, Ahmet; 01. Abdullah Gül University
Background 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.
Labyrinthine Microstructures with a High Dipole Moment Boron Complex for Molecular Physically Unclonable Functions
(Amer Chemical Soc, 2025) Yildiz, Tevhide Ayca; Kiremitler, N. Burak; Kayaci, Nilgun; Kalay, Mustafa; Ozcan, Emrah; Deneme, Ibrahim; Usta, Hakan; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 10. Rektörlük
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-BF2, 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 pi-backbone and arranges in the solid state with antisymmetric cofacial pi-stackings (3.86 & Aring;). These properties, along with short C-Hpi contacts (2.74-2.88 & Aring;) and nonclassical C-HF hydrogen bonds (2.47-2.51 & Aring;) (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 (approximate to 50-100 mu m) 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.
Measuring Eudaimonic and Hedonic Wellbeing: Development and Validation of the Holistic Wellbeing Measure
(Routledge Journals, Taylor & Francis Ltd, 2025) Arslan, Gokmen; Coskun, Muhammet; 01. Abdullah Gül University
The primary goal of this study was to develop a concise, theoretically grounded tool -the Holistic Wellbeing Measure (HWM)- that captures both hedonic and eudaimonic facets of wellbeing. Items for the HWM were generated through a careful review of existing wellbeing scales and literature, followed by expert consultation, pilot testing, and iterative refinement to ensure conceptual coverage, clarity, and face validity. Data were collected from three distinct samples: adolescents (n = 453), young adults (n = 361), and adults (n = 358). Exploratory and confirmatory factor analyses supported a two-factor structure, with 12 items reflecting independent but related hedonic and eudaimonic wellbeing dimensions. The measure demonstrated strong internal reliability and evidence of convergent, discriminant, and concurrent validity across all age groups. Regression analyses further indicated that the HWM contributed unique variance to the prediction of general health indicators (physical, social, and mental health) and psychological problems (depression, anxiety, and somatization), above the effects of gender, age, and psychological wellbeing. These results suggest that the HWM is a valid and reliable measure for assessing both aspects of wellbeing across age groups and can support strategies aimed at promoting overall mental health.
Citation - WoS: 25
Citation - Scopus: 30
miRcorrNet: Machine Learning-Based Integration of miRNA and mRNA Expression Profiles, Combined with Feature Grouping and Ranking
(PeerJ Inc., 2021) Yousef, M.; Göy, G.; Mitra, R.; Eischen, C.M.; Jabeer, A.; Bakir-Güngör, B.; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high throughput technologies allowed to generate mRNA and microRNA (miRNA) expression profiles; and the integrative analysis of these profiles allowed to uncover the functional effects of RNA expression in complex diseases, such as cancer. Several researches attempt to integrate miRNA and mRNA expression profiles using statistical methods such as Pearson correlation, and then combine it with enrichment analysis. In this study, we developed a novel tool called miRcorrNet, which performs machine learning-based integration to analyze miRNA and mRNA gene expression profiles. miRcorrNet groups mRNAs based on their correlation to miRNA expression levels and hence it generates groups of target genes associated with each miRNA. Then, these groups are subject to a rank function for classification. We have evaluated our tool using miRNA and mRNA expression profiling data downloaded from The Cancer Genome Atlas (TCGA), and performed comparative evaluation with existing tools. In our experiments we show that miRcorrNet performs as good as other tools in terms of accuracy (reaching more than 95% AUC value). Additionally, miRcorrNet includes ranking steps to separate two classes, namely case and control, which is not available in other tools. We have also evaluated the performance of miRcorrNet using a completely independent dataset. Moreover, we conducted a comprehensive literature search to explore the biological functions of the identified miRNAs. We have validated our significantly identified miRNA groups against known databases, which yielded about 90% accuracy. Our results suggest that miRcorrNet is able to accurately prioritize pan-cancer regulating high-confidence miRNAs. miRcorrNet tool and all other supplementary files are available at https://github.com/ malikyousef/miRcorrNet. © 2021 Elsevier B.V., All rights reserved.
Pangenome 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) Yetiman, Ahmet E.; Horzum, Mehmet; Kanbur, Ertan; Cadir, Mehmet; Bahar, Dilek; Gurbuz, Serife; Akbulut, Mikail; 01. Abdullah Gül University
This 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.
Citation - WoS: 39
Citation - Scopus: 49
Spatio-Temporal Rich Model-Based Video Steganalysis on Cross Sections of Motion Vector Planes
(Institute of Electrical and Electronics Engineers Inc., 2016) Taşdemir, K.; Kurugöllü, F.; Sakir Sezer, S.; 01. Abdullah Gül University
A 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.
Synthesis, Characterization, and Comprehensive in Vitro and in Silico Evaluation of the Anti-Inflammatory Potential of Novel 1,2,3-Triazole–Arylidenehydrazide/Thiazolidinone Hybrids
(Wiley-VCH verlag GmbH, 2025) Pepe, Nihan Aktas; Cakir, Furkan; Atalay, Tugba; Acar, Busra; Turgut, Gurbet Celik; Sen, Alaattin; Senol, Halil; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve Genetik
Five novel 1,2,3-triazole/arylidenehydrazide/thiazolidinone hybrid compounds (7-11) were synthesized and characterized using NMR, HRMS, IR, and HPLC purity analysis. The cytotoxicity of these compounds was evaluated on fibroblasts and THP-1 cells, showing that all compounds were nontoxic at the tested concentrations. The wound healing assay revealed that compounds 7, 9, and 10 significantly enhanced wound closure, with a 7.74%-32.69% improvement in treated cells. Compounds 8 and 11 showed moderate effects. Anti-inflammatory activity was assessed through qRT-PCR, demonstrating that compound 10 led to the most significant reduction in proinflammatory cytokines TNF-alpha, IL-1 beta, and NF-kappa B1. In addition, the expression of Iba1 protein in THP-1 cells confirmed that compound 8 showed the strongest anti-inflammatory effect, surpassing that of aspirin. Compound 10 showed the highest inhibition of NF-kappa B signaling and iNOS activity. Molecular docking studies revealed that compounds 10 and 11 had strong binding affinities to TNF-alpha and iNOS, with compound 11 showing the most stable interactions. Molecular dynamics simulations supported these findings, indicating that compound 11 demonstrated more stable binding to both targets. Overall, the results suggest that compounds 10 and 11 are promising anti-inflammatory candidates with potential for further development in therapeutic applications for inflammatory diseases.

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