PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Predicting Respiratory Infection and Symptoms Development Using Gene Set Enrichment Scores and Machine Learning(Elsevier Sci Ltd, 2026) Aydin, Zafer; Isik, Yunus EmreRecent advancements in precision medicine enable personalized predictions grounded in individual-level genetic data. However, relying solely on a single type of data can decrease prediction accuracy and limit the biological interpretability of the resulting models. Incorporating predefined genetic knowledge, such as derived gene sets, can improve performance and provide deeper biological insights for complex diseases, including respiratory infections. This study aimed to evaluate the usability of enrichment scores (ES), calculated using gene sets from the Molecular Signatures Database (MSigDB), as a feature representation for machine learning models to predict respiratory viral infections and symptom development. In addition, the proposed feature representation approach was extensively compared with the de facto gene-level expression representation. A total of 36,834 predefined gene sets were compiled from the MSigDB, and their ES values were calculated. Experiments used the GSE73072 dataset from Gene Expression Omnibus, containing gene expression profiles before and after virus exposure. Various machine learning and feature selection algorithms were applied to ES-based and probe-level feature sets. The results showed that both feature representation approaches achieved an area under the precision-recall curve (AUPRC) value greater than 0.90 for all tasks. Compared with the Respiratory Viral DREAM Challenge leaderboard phase, our models showed a 14.8% improvement in pre-exposure predictions (T0) and a 17.4% improvement in symptom classification. Using enrichment scores as a feature representation generally resulted in better performance than probe-level representation when predicting respiratory infections and symptom development. Identifying key gene sets through feature selection and comparing them with essential genes for respiratory viruses enabled a more comprehensive analysis, providing deeper insights into the pathways that contribute to these predictions.Article Electrospun PCL/PEG Nanofibers Incorporating Plantago Lanceolata Extract and Clove Oil for Dual-Function Wound Dressings(IOP Publishing Ltd, 2026) Teke, Selin Nur; Yuruk, Adile; Isoglu, Ismail AlperIn this study, we developed electrospun polycaprolactone/polyethylene glycol (PCL/PEG) nanofibers loaded with Plantago lanceolata (P. lanceolata) extract and clove oil to evaluate their combined potential for wound healing and antibacterial activity. PCL/PEG nanofibers were electrospun and post-loaded with P. lanceolata extract at 5%, 10%, and 15% (w/v), together with 1% (v/v) clove oil. Scanning electron microscope analysis showed a uniform, bead-free nanofibrous structure, with fiber diameters ranging from 768 +/- 140 nm to 892 +/- 206 nm and pore sizes from 3.93 +/- 0.97 & micro;m to 6.20 +/- 1.16 & micro;m. The nanofibers exhibited swelling ratios between 103.23 +/- 16.42% and 133.93 +/- 40.45% within 1 h and showed gradual degradation ranging from 25.92 +/- 2.84% to 57.76 +/- 0.92% over 21 d, with cumulative extract release approaching a plateau by day 28 under the experimental conditions. The incorporation of plant extract and essential oil initially increased the water contact angle from 15.97 +/- 1.07 degrees to 48.61 +/- 7.85 degrees, indicating that the nanofiber surface remained hydrophilic; at higher extract contents, the nanofibers transitioned to a superhydrophilic state. Antibacterial activity was primarily governed by clove oil, yielding up to 85.16 +/- 0.36% efficacy against E. coli (E. coli) and 79.90 +/- 0.29% against S. aureus (S. aureus). While P. lanceolata extract alone showed limited antibacterial activity, its presence within clove oil-loaded nanofibers consistently enhanced antibacterial performance at the composite level. In vitro scratch assays demonstrated pronounced wound closure at later time points (72-96 h), particularly for nanofibers containing higher extract concentrations, confirming the dominant contribution of P. lanceolata to the healing response. Overall, the electrospun PCL/PEG nanofibers represent a dual-function wound dressing, with clove oil contributing antibacterial protection and P. lanceolata extract supporting wound healing.Article Effects of Group Aerobic Exercise on Health and Social Adaptation in Earthquake Survivors: A Qualitative Study(Lippincott Williams and Wilkins, 2026) Yardimci, Fatma Betul; Kaya, M. Siyabend; Anaforoglu, Bahar; Altay Ili, Hafize; Apak, HidirArticle Dissecting the Strain and Sex Specific Connectome Signatures of Unanesthetized C57BL/6J and DBA/2J Mice Using Magnetic Resonance Imaging(Wiley, 2026) Neuberger, Thomas; Kamens, Helen M.; Zhang, Nanyin; Ünsal, Hayreddin Said; Arefin, Tanzil M.Mouse models are an essential tool for understanding behavior and disease states in neuroscience research. While genetic and sex-specific effects have been reported in many neurodegenerative and psychiatric illnesses, these factors may also alter baseline neuroanatomical features of mice. This raises the question of whether the observed changes are related to the disease being studied (i.e., pathological differences) or if there are baseline strain or sex differences that may predispose animals to different responses. Over the past decade, tremendous effort has been made to map neural architecture at various scales; however, the complex relationships, including identifying genetic and sex-specific differences in brain structure and function, remain understudied. To bridge this gap, we used C57BL/6J and DBA/2J mice, two of the most widely used inbred mouse strains in neuroscience research, to investigate strain and sex-specific features of the brain connectome in awake animals using magnetic resonance imaging (MRI). By combining resting-state functional MRI and diffusion MRI, we found that the motor, sensory, limbic, and salience networks exhibit significant differences in both functional and structural domains between C57BL/6J and DBA/2J mice. Further, functional and structural properties of the brain were significantly correlated in both strains. Our results underscore the importance of considering these baseline differences when interpreting brain-behavior interactions in mouse models of human disorders.Article Three-Dimensional Culture Enhances the Antimicrobial Activity of Mesenchymal Stem Cells against Shiga Toxin-Producing Escherichia Coli O157:H7 in Vitro(Oxford Univ Press, 2026) Fidan, Özkan; Türkyılmaz, Süheyla; Bicer, Mesude; Öztürk, Esengül; Sener, FatmaAims This study examines the in vitro antibacterial activity of palatal adipose tissue-derived mesenchymal stem cells (PAT-MSCs) and the expression of antimicrobial peptide LL-37, with a particular focus on the effect of three-dimensional (3D) nanofibrillar cellulose-based hydrogel against Shiga toxin-producing Escherichia coli (STEC) harboring stx1 and/or stx2 genes isolated from mastitis milk in Turkey.Methods and results The antibacterial activity of conventionally cultured PAT-MSCs and 3D-cultured PAT-MSCs (PAT-MSCs-3D) was evaluated against STEC isolates and Escherichia coli ATCC 35150 using quantitative colony-forming unit (CFU) assay. The expression levels of antimicrobial peptide (AMP)-encoding genes were evaluated by quantitative real-time PCR, and AMP production was further validated by immunocytochemical staining. The results indicated that PAT-MSCs-3D exhibited significantly enhanced antibacterial efficacy, resulting in marked bacterial inhibition of all tested STEC strains, with bacterial reductions reaching up to 6-7 log under specific experimental conditions. Molecular and immunocytochemical analyses demonstrated increased expression of the antimicrobial peptide LL-37 in PAT-MSCs-3D compared to 2D cultures.Conclusions Our results show that culturing PAT-MSCs in 3D conditions leads to a significant enhancement in their antimicrobial properties, which could be linked to the upregulation of LL-37.Article Functional Characterization of Loss of RNF43 Reveals Neuronal Defects in a Caenorhabditis Elegans Model(MDPI, 2026) Kazan, Hasan Huseyin; Turkyilmaz, Zafer; Ekim, Burcu; Kaya, Cem; Ergun, Mehmet Ali; Sonmez, Kaan; Güzel, SinemRing finger protein 43 (RNF43) encodes a transmembrane E3 ubiquitin ligase that negatively regulates canonical Wnt signaling and is classically associated with serrated polyposis syndrome and colorectal cancer. In this study, regarding a homozygous truncating RNF43 variant (NM_001305545.1:c.1906C>T; p.Gln636Ter) in a patient segregating with a severe neurodevelopmental phenotype characterized by developmental delay, neonatal hypotonia, recurrent seizures, progressive microcephaly, and bilateral optic atrophy, the loss of polarity defective 1 (plr-1), an ortholog of RNF43, was modeled in Caenorhabditis elegans and the phenotype was primarily characterized. The results demonstrated that loss of the plr-1 disrupted gamma aminobutyric acid (GABA)ergic axon organization, reduced locomotor speed calculated from 60 s recordings, and altered developmental growth. These findings expand the phenotypic spectrum of RNF43 and support a dosage-dependent developmental role.Article Comparison of Rapamycin and 3-Methyladenine in Cisplatin-Induced Experimental Cardiotoxicity(Wiley, 2026) Kaymak, Emin; Karabulut, Derya; Yalcin, Betul; Guner, Serife Ayaz; Ozturk, Emel; Findik, Fatma; Boyvat, DuduIn this study, we evaluated how cisplatin cardiotoxicity affects the histological and endocrine functions of the heart and autophagy while using Rapamycin(Rapa) and 3-methyladenine(3-MA) as autophagy activators and inhibitors. Control, Cisplatin (Cis), 3-methyladenine + Cisplatin (3-MA + Cis) and Rapamycin + Cisplatin (Rapa + Cis). Rapa and 3-MA were administered for 15 days, while a single dose of cisplatin was administered on the 7th day. Natriuretic peptide receptor-A(NPR-A), receptor-B(NPR-B) and biochemically atrial natriuretic peptide(ANP) and brain natriuretic peptide(BNP) levels were evaluated in heart tissue. Cis caused a statistically significant increase in NPR-A and NPR-B expression, as well as ANP and BNP levels. However, the levels of Beclin-1 and LC3B were not statistically significant. Rapa was more effective than 3-MA + Cis on NPR-A and NPR-B expressions, but did not show the same effect on ANP and NT-proBNP levels. Cis caused an increase in Beclin-1 and LC3B levels, while a decrease was observed in both 3-MA + Cis and Rapa + Cis groups. Our results revealed that Cis cardiotoxicity disrupts autophagy and endocrine function of the heart. It was concluded that by continuing the activator and inhibitor substances after Cis application, more effective results can be obtained in Beclin-1 expression than LC3B expression and that they can be effective in eliminating the toxicity of Cis.Article Cellulose-Based Hydrogel Matrix Enhances Antimicrobial and Biofilm-Inhibitory Responses of Palatal Mesenchymal Stem Cells(Springer Heidelberg, 2026) Fidan, Özkan; Bicer, Mesude; Öztürk, Esengül; Sener, FatmaMesenchymal stem cells (MSCs) have emerged as promising alternatives to fight drug-resistant bacterial infections. This study investigates the antibacterial activity of palatal adipose tissue-derived MSCs (PMSCs), particularly when cultured within a 3D nanofibrillar cellulose hydrogel, against four clinically relevant pathogens: Pseudomonas aeruginosa K6, Staphylococcus aureus ATCC 25,923, Bacillus cereus K9 and Escherichia coli O157:H7. This study showed that both PMSCs alone and PMSCs in 3D cellulose-based hydrogel effectively inhibited the growth of bacterial burden. Notably, PMSCs cultured in the 3D system demonstrated an excellent effect, reducing bacterial burden by up to 14 log in E. coli and 12 log in P. aeruginosa K6 at a 120 & micro;L inoculum after 2 h of incubation. RT-PCR and immunocytochemical analyses found out a remarkable upregulation of the Cathelicidin (LL-37) in PMSCs 3D cultures compared to PMSCs. Furthermore, 3D cellulose-based hydrogel exhibited a significant biofilm-inhibitory effect, reaching a 57.65% reduction. The results demonstrated the importance of 3D cellulose-based hydrogel for treating antibiotic-resistant infections. PMSC therapy based on 3D hydrogel may therefore be offered as more effective antimicrobial agent to overcome drug-resistant bacterial infections.Article The Effect of Video Modeling on Gymnastics-Based Motor Skills in Children with Autism Spectrum Disorder(MDPI, 2026) Bozdag, Berkan; Sonmez, Huseyin Gazi; Turan, Ebru; Aldhahi, Monira I.; Kilinc, Omer; Ergin, Murat; Kocak, Calik VeliBackground and Objectives: While the effectiveness of video modeling (VM) in teaching academic, daily living, and social skills to individuals with Autism Spectrum Disorder (ASD) is frequently investigated, studies examining the use of VM in teaching gymnastics-based motor skills are limited. This study aimed to examine the effects of VM on the acquisition and maintenance of a gymnastics-based motor skills in preschool children with ASD. Methods: The study employed a multiple-probe method across participants in a single-subject research design. Three preschool children diagnosed with mild ASD participated in this study. Baseline, intervention, and follow-up data were systematically collected and analyzed. Social validity data were obtained through semi-structured interviews with parents and special education teachers. Results: The percentage of correct responses increased throughout the VM intervention sessions, and all participants reached the proficiency criterion. Follow-up data collected after the intervention showed that the acquired skill was maintained, and the percentages of correct responses ranged from 80% to 100%. Social validity findings revealed that both teachers and parents perceived VM as an effective and feasible teaching approach for teaching motor skills to children with ASD. Conclusions: The research findings demonstrate that VM is an effective and socially valid teaching method for teaching and maintaining gymnastics-based motor skills in preschool children with ASD. These results contribute to the existing literature by demonstrating the applicability of video modeling in the context of gymnastics-based training.Article Citation - WoS: 5Citation - Scopus: 5Targeting Cholinergic Dysfunction and Neuroinflammation through Rationally Designed Thieno[3,2-d]Pyrimidine Hybrids(Academic Press Inc Elsevier Science, 2026-07) Acar, Ozden Ozgun; Acar, Busra; Senol, Halil; Tokali, Feyzi Sinan; Sen, Alaattin; Demir, Yeliz; Cakir, FurkanNeurodegenerative diseases involve the convergence of cholinergic dysfunction, neuronal loss, and sustained neuroinflammatory responses, necessitating the development of multifunctional therapeutic agents. In this study, a series of novel thieno[3,2-d]pyrimidine-phenolic Mannich base hybrids were rationally designed, synthesized, and evaluated as dual cholinesterase inhibitors with neuroprotective and anti-neuroinflammatory potential. The synthesized compounds exhibited potent inhibition against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), with inhibition constants in the low nanomolar range. Among them, compounds 5 and 9 emerged as the most active derivatives, displaying Ki values of 8.79 and 14.11 nM for AChE and 7.04 and 11.75 nM for BChE, surpassing the reference inhibitors tacrine and donepezil. Molecular docking and molecular dynamics simulations supported the experimental findings, and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) binding free energy calculations further confirmed their superior binding affinities compared with donepezil. Cytotoxicity profiling in SH-SY5Y neuronal cells and RAW 264.7 and THP-1 immune cells identified a narrow sub-cytotoxic concentration window (EC05-EC10 = 1.2-2.1 mu M), ensuring biological effects independent of nonspecific cell damage. Within this range, both compounds exerted pronounced antineuroinflammatory activity. Notably, compound 9 significantly downregulated pro-inflammatory mediators, reducing IL-1 beta, IL-6, and NF-kappa B1 gene expression by up to 2.78-, 3.37-, and 4.84-fold, respectively. Consistently, it suppressed nitric oxide production in LPS-stimulated macrophages to levels comparable with ascorbic acid and markedly decreased Iba1 expression in activated THP-1 cells. This integrated enzymatic, computational, and cellular investigation identifies compounds 5 and 9 as promising multifunctional lead combining dual cholinesterase inhibition with robust anti-neuroinflammatory activity. The results provide a strong foundation for future in vivo studies and further optimization toward disease-modifying agents for neurodegenerative disorders.