PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
Browse
16 results
Search Results
Article Unveiling the Therapeutic Role of 3D-Cultured Mesenchymal Stem Cells in Diabetic Foot Ulcers through Transcriptomic Integration and Fibroblast Modulation(Springer, 2026-03-31) Ozturk, Esengul; Bicer, MesudeBackground Diabetic foot ulcers (DFUs) are among the most severe complications of diabetes mellitus and remain difficult to manage due to chronic inflammation, defective angiogenesis, delayed tissue repair, which increase the risk of recurrence and limb amputation. Standard treatments, such as debridement, infection management, pressure off-loading and revascularization, are commonly used, however; these interventions often inadequate to fully restore effective wound repair. Mesenchymal stem cells (MSCs) have attracted remarkable interest due to their potential regenerative ability and paracrine activity. Nevertheless, the molecular interaction between MSCs and fibroblasts under hyperglycemic conditions has not been fully elucidated. Objective This study aimed to examine differentially expressed genes (DEGs) associated with DFUs and MSC-related regenerative mechanisms using transcriptomic datasets (such as GSE143735, GSE199939, and GSE217709). Methods and results Differentially expressed genes and protein-protein interaction (PPI) network analysis were performed to determine central regulatory genes. Four key genes including CXCL1, MMP9, THBS1, and POSTN were recognized as hub genes related to inflammatory response, extracellular matrix reorganization, and angiogenesis. For experimental validation, L929 murine fibroblasts were exposed to high-glucose conditions to set-up an in vitro diabetic model and subsequently treated with MSCs with/without a 3D platform. Hyperglycemic conditions significantly reduced fibroblast proliferation and migration downregulated the expression of the identified hub genes and enhanced apoptotic activity. MSC treatment partially increased cellular function, while MSCs embedded into 3D culture enhanced a more pronounced recovery in both gene expression patterns and functional assays. Conclusions These findings suggest that high glucose impair fibroblast functions for wound repair, while 3D-cultured MSCs enhance regenerative responses and may represent a promising strategy for diabetic wound healing.Article Deep-Learning Detection of Open-Apex Teeth on Panoramic Radiographs Using YOLO Models(Springer, 2025-12-23) Edik, Merve; Celebi, Fatma; Cukurluoglu, AykaganObjectivesThe use of deep learning in detecting teeth with open apices can prevent the need for additional radiographs for patients. The presented study aims to detect open-apex teeth using You Only Look Once (YOLO)-based deep learning models and compare these models.MethodsA total of 966 panoramic radiographs were included in the study. Open-apex teeth in panoramic radiographs were labeled. During the labeling process, they were divided into 6 classes in the maxilla and mandible, namely incisors, premolars, and molars. AI models YOLOv3, YOLOv4, and YOLOv5 were used. To evaluate the performance of the three detection models, both overall and separately for each class in the test dataset, precision, recall, average precision (mAP), and F1 score were calculated.ResultsYOLOv4 achieved the highest overall performance with a mean average precision (mAP) of 87.84% at IoU (Intersection over Union) 0.5 (mAP@0.5), followed by YOLOv5 with 85.6%, and YOLOv3 with 84.46%. Regarding recall, YOLOv4 also led with 90%, while both YOLOv3 and YOLOv5 reached 89%. Moreover, the F1 score was the highest for YOLOv4 (0.87), followed by YOLOv3 (0.86) and YOLOv5 (0.85).ConclusionsIn this study, YOLOv3, YOLOv4, and YOLOv5 were evaluated for the detection of open-apex teeth, and their mAP, recall, and F1 scores exceeded 84%. Deep learning-based systems can provide faster and more accurate results in the detection of open-apex teeth. This may help reduce the need for additional radiographs from patients and aid dentists by saving time.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.Review Aerial Swarms: Recent Applications and Challenges(Springer, 2021) Mohamed Abdelkader; Samet GülerPurpose of review: Currently, there is a large body of research on multi-agent systems addressing their different system theoretic aspects. Aerial swarms as one type of multi-agent robotic systems have recently gained huge interest due to their potential applications. However, aerial robot groups are complex multi-disciplinary systems and usually research works focus on specific system aspects for particular applications. The purpose of this review is to provide an overview of the main motivating applications that drive the majority of research works in this field, and summarize fundamental and common algorithmic components required for their development._x000D_ _x000D_ Recent findings: Most system demonstrations of current aerial swarms are based on simulations, some have shown experiments using few 10 s of robots in controlled indoor environment, and limited number of works have reported outdoor experiments with small number of autonomous aerial vehicles. This indicates scalability issues of current swarm systems in real world environments. This is mainly due to the limited confidence on the individual robot's localization, swarm-level relative localization, and the rate of exchanged information between the robots that is required for planning safe coordinated motions._x000D_ _x000D_ Summary: This paper summarizes the main motivating aerial swarm applications and the associated research works. In addition, the main research findings of the core elements of any aerial swarm system, state estimation and mission planning, are also presented. Finally, this paper presents a proposed abstraction of an aerial swarm system architecture that can help developers understand the main required modules of such systems.Article Citation - WoS: 3Citation - Scopus: 3Theoretical Investigation of Substituent Effects on the Relative Stabilities and Electronic Structure of [BnXn]2- Clusters(Springer, 2021-11-29) Tahaoglu, Duygu; Alkan, Fahri; Durandurdu, MuratIn this study, we provide a theoretical evaluation of relative stabilities and electronic structure for [BnXn](2-) clusters (n = 10, 12, 13, 14, 15, 16). Structural and electronic characteristics of [BnXn](2-) clusters are examined by comparison with the [B12X12](2-) counterparts with a focus on the substituent effects (X = H, F, Cl, Br, CN, BO, OH, NH2) on the electronic structure, electron detachment energies, formation enthalpies, and charge distributions. For the electronic structure and electron detachment energies, substituent effects on boron clusters are shown to follow a very similar trend to the mesomeric and inductive effects (+/- M and +/- I) of pi-conjugated systems, and the most stable derivatives in terms of HOMO/LUMO and electron detachment energies are calculated for CN and BO substituents due to strong -M effects. In the case of formation enthalpies for larger boron clusters (n >= 13), the icosahedral barrier is shown to increase with the halogen and CN substitution, whereas it is possible to reduce the icosahedral barrier for the cases of X = OH and NH2. It is shown that this reduction results from destabilizing the [B12X12](2-) cluster with electronic (+ M) and symmetry effects induced by OH and NH2 ligands.Article Citation - WoS: 5Citation - Scopus: 7Rational Design of EDTA-Incorporated Nanoflowers as Novel and Effective Endodontic Disinfection Against Biofilms(Springer, 2023-10-03) Aslan, Tugrul; Dadi, Seyma; Kafdag, Ozgur; Temur, Nimet; Ildiz, Nilay; Ocsoy, Ismail; Ustun, YakupThe ethylenediaminetetradiacetic acid (EDTA) is one of the most commonly used irrigation solutions. Although EDTA has a very low antimicrobial property, it is used to remove inorganic part of smear layer in areas of root canal system. Herein, we developed EDTA-incorporated nanoflowers (EDTA NFs), for the first time, as novel and effective irrigation solution with quite high antimicrobial property to provide complete disinfection in root canal system. We both systematically elucidated the formation of the EDTA NFs with various techniques, and their catalytic and antimicrobial activities in the presence of hydrogen peroxide (H2O2) were documented through intrinsic EDTA property and peroxidase-like activities.Article Citation - WoS: 3Citation - Scopus: 4Rapamycin and Niacin Combination Induces Apoptosis and Cell Cycle Arrest Through Autophagy Activation on Acute Myeloid Leukemia Cells(Springer, 2024-12-23) Subay, Lale Beril; Akcok, Emel Basak Gencer; Akcok, Ismail; Gencer Akçok, Emel BaşakBackgroundAcute myeloid leukemia (AML) is a heterogeneous hematological malignancy caused by disorders in stem cell differentiation and excessive proliferation resulting in clonal expansion of dysfunctional cells called myeloid blasts. The combination of chemotherapeutic agents with natural product-based molecules is promising in the treatment of AML. In this study, we aim to investigate the anti-cancer effect of Rapamycin and Niacin combination on THP-1 and NB4 AML cell lines.Methods and ResultsThe anti-proliferative effects of Rapamycin and Niacin were determined by MTT cell viability assay in a dose- and time-dependent manner. The combination indexes were calculated by isobologram analysis. Furthermore, apoptosis was investigated by Annexin-V/Propidium Iodide(PI) double staining and cell cycle distribution was measured by PI staining. The expression levels of autophagy-related proteins were detected by western blotting. The combination of Rapamycin and Niacin synergistically decreased cell viability of AML cell lines. The combination treatment induced the apoptotic cell population of THP-1 and NB4 by 4.9-fold and 7.3-fold, respectively. In THP-1 cells, the cell cycle was arrested at the G2/M phase by 10% whereas the NB4 cells were accumulated at the G0/G1 phase. The combination treatment decreased Akt and p-Akt expression. Besides, the ATG7 expression was reduced by combination treatment on THP-1 cells. Similarly, the ATG5 level was downregulated in NB4 cells. The level of LC3B-II/LC3B-I, which is an indicator of autophagy flux, was upregulated in THP-1 and NB4 cells.ConclusionAlthough further studies are required, the combination of Rapamycin and Niacin combats cell proliferation by inducing cellular apoptosis, cell cycle arrest and autophagy activation.Article Citation - WoS: 2Citation - Scopus: 2Possible Boron-Rich Amorphous Silicon Borides From Ab Initio Simulations(Springer, 2023-03-10) Karacaoglan, Aysegul Ozlem Cetin; Durandurdu, MuratContextBy means of ab initio molecular dynamics simulations, possible boron-rich amorphous silicon borides (BnSi1-n, 0.5 <= n <= 0.95) are generated and their microstructure, electrical properties and mechanical characters are scrutinized in details. As expected, the mean coordination number of each species increases progressively and more closed packed structures form with increasing B concentration. In all amorphous models, pentagonal pyramid-like configurations are observed and some of which lead to the development of B-12 and B11Si icosahedrons. It should be noted that the B11Si icosahedron does not form in any crystalline silicon borides. Due to the affinity of B atoms to form cage-like clusters, phase separations (Si:B) are perceived in the most models. All simulated amorphous configurations are a semiconducting material on the basis of GGA+U calculations. The bulk modulus of the computer-generated amorphous compounds is in the range of 90 GPa to 182 GPa. As predictable, the Vickers hardness increases with increasing B content and reaches values of 25-33 GPa at 95% B concentration. Due to their electrical and mechanical properties, these materials might offer some practical applications in semiconductor technologies.MethodThe density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations were used to generate B-rich amorphous configurations.Article Citation - WoS: 16Citation - Scopus: 18Microfluidic Chip Based Direct Triple Antibody Immunoassay for Monitoring Patient Comparative Response to Leukemia Treatment(Springer, 2020-07-13) Icoz, Kutay; Akar, Unal; Unal, EkremWe report a time and cost-efficient microfluidic chip for screening the leukemia cells having three specific antigens. In this method, the target blast cells are double sorted with immunomagnetic beads and captured by the 3rd antibody immobilized on the gold surface in a microfluidic chip. The captured blast cells in the chip were imaged using a bright-field optical microscope and images were analyzed to quantify the cells. First sorting was performed with nano size immunomagnetic beads and followed by 2nd sorting where micron size immunomagnetic beads were used. The low-cost microfluidic platform is made of PMMA and glass including micro size gold pads. The developed microfluidic platform was optimized with cultured B type lymphoblast cells and tested with the samples of leukemia patients. The 8 bone marrow samples of 4 leukemia patients on the initial diagnosis and on the 15th day after the start of the chemotherapy treatment were tested both with the developed microfluidic platform and the flow cytometry. A 99% statistical agreement between the two methods shows that the microfluidic chip is able to monitor the decrease in the number of blast cells due to the chemotherapy. The experiments with the patient samples demonstrate that the developed system can perform relative measurements and have a potential to monitor the patient response to the applied therapy and to enable personalized dose adjustment.Article Identification of Nonsense Variants in the ATM Gene Mimicking SCID Phenotype: A Brief Report(Springer, 2025-05-16) Firtina, Sinem; Saritas, Merve; Ng, Yuk Yin; Nepesov, Serdar; Kiykim, Ayca; Bozkurt, Selcen; Sayitoglu, MugeSevere combined immunodeficiency (SCID) represents a life-threatening inborn error of immunity, necessitating rapid diagnosis and intervention to prevent fatal outcomes. While SCID is characterized by profound T-cell lymphopenia, it may overlap with other conditions like ataxia-telangiectasia (AT), which also presents with T-cell deficiencies. This study examines two cases of suspected SCID in infants, later identified as AT due to pathogenic variants in the ATM gene. Despite initial negative results from SCID-targeted gene panels, further genetic testing revealed nonsense mutations (p.Y2036X and p.E1996X) in the FAT domain of the ATM gene, confirmed by Sanger sequencing. The patients exhibited significant T-cell lymphopenia and reduced ATM protein activity, indicative of AT. These findings highlight the importance of comprehensive genetic screening beyond common SCID-associated genes, especially in patients with atypical presentations. Early and accurate diagnosis can prevent mismanagement and guide appropriate therapies, improving patient outcomes.