PubMed İndeksli Yayınlar Koleksiyonu

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

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  • Article
    Tooth Decay Promotes Senescence in Dental Pulp Stem Cells, Modifying Their Biological and Proteomic Profiles
    (Wiley, 2026) Durukan, Sebahat Melike; Tez, Banu Cicek; Ozcan, Servet; Simsek, Ahmet; Al-Sammarrie, Sura Hilal Ahmed; Gunaydin, Zeynep; Acar, Mustafa Burak
    Dental caries is a prevalent oral health problem that significantly reduces an individual's quality of life; although, it can be effectively managed through restorative treatments. Even in cases where the caries does not reach the pulp, released microbial products from the lesion can still penetrate the pulp chamber, potentially inducing stress on pulp cells. In this study, we conducted a comparative analysis of the biological and proteomic profiles of dental pulp stem cells (DPSCs) isolated from clinically asymptomatic teeth with dentinal caries that had not reached the pulp and isolated from healthy teeth. Following biological evaluations, we examined proteomes of these DPSCs by conducting a shotgun proteomics approach. Our findings show that DPSCs from decayed teeth exhibit a significantly higher proportion of senescent cells. Proteomic profiling revealed upregulation of inflammatory signaling, extracellular matrix remodeling, and senescence-associated secretory phenotype (SASP) related proteins. Additionally, we observed an upregulation in the expression of proteins associated with extracellular matrix (ECM) remodeling and components of the SASP, which are hallmarks of the senescence process. The study reveals that DPSCs can be affected by stress from carious lesions, even when the pulp appears clinically intact. Senescence and inflammatory response in these affected cells may have deleterious effects on other tissues within the organism. Consequently, restorative treatments should consider targeting not only the decayed tissue but also the senescent cells within the pulp that may have been affected by the stress induced by caries.
  • Article
    A Small Indole Derivative Isolated From Caper (Capparis Ovata) as an Inducer of P53-Mediated Apoptosis in Prostate Cancer: Comprehensive In Vitro and In Silico Studies
    (Wiley, 2025-12-31) Acar, Ozden Ozgun; Gazioglu, Isil; Oruc, Hatice; Kale, Elif; Senol, Halil; Topcu, Gulacti; Sen, Alaattin
    Natural products with stunning chemical diversity have been extensively researched for their anticancer potential for more than fifty years. This study aimed to determine the effect of indole derivative 1H-indole-2-hydroxy-3-carboxylic acid (IHCA), isolated as a novel alkaloid from Capparis ovata, on selected tumor suppressor, apoptotic, and cell cycle regulatory genes, which are known to be important in cancer pathophysiology, on Caco-2 and LNCaP cells in comparison with Taxol. The molecular mechanism of IHCA's anticancer activity is essentially undefined. Different concentrations of IHCA increased the expression levels of apoptosis-related genes, including BCL-2 and TNF-alpha. In addition, the tumor suppressor genes PTEN, P53, and RB were increased in LNCaP and Caco-2 cells. KRAS, an oncogenic gene, was significantly downregulated by IHCA in LNCaP cells. Western blot results showed that the protein expression levels of P53 and PTEN in LNCaP cells were increased when treated with IHCA, whereas CDK4 and TNF-alpha were decreased. Finally, IHCA and doxorubicin significantly increased P53-driven luciferase activity compared to the control. The results strongly suggest that the novel natural compound IHCA has an anticancer effect involving the regulation of the P53 gene and its networks in vitro. The molecular docking and MD simulation analyses reveal that IHCA exhibits superior binding potential to the MDM2 protein compared to Nutlin-3a. MD simulations further confirm that IHCA maintains a more stable and consistent interaction with MDM2, as indicated by lower RMSD values and reduced ligand fluctuation. These results highlight IHCA's potential as a more effective MDM2 inhibitor, suggesting its promise as a lead compound for anticancer drug development.Clinical Trial Registration: Not applicable.
  • Article
    Patient Experiences of Behavioural Therapy for Bipolar Depression: A33 Qualitative Study
    (Wiley, 2024-12-10) Yilmaz, Sakir; Hancox, Anna; Price, Molly; Regan, Jemma; Dunn, Barney; O'Mahen, Heather; Wright, Kim
    BackgroundAlthough multiple qualitative studies have explored participants' experiences of behavioural activation (BA) for unipolar depression, none have investigated the experiences of BA in people with bipolar depression. This is of particular interest because qualitative studies concerning the experience of receiving therapy can help inform the theory of change underpinning the intervention.AimThe purpose of this study was to explore the experiences and perspectives of individuals with bipolar disorder who received a course of one-to-one BA for bipolar depression. We sought to explore participants' experience of the effects of BA therapy, both proximally and distally.MethodSemi-structured interviews were conducted with nine individuals meeting research diagnostic criteria for bipolar I or II disorder who had received up to 20 sessions of BA adapted for bipolar depression. Thematic analysis using a framework approach was used to explore and describe the experiences of participants.ResultsParticipants' perspectives on the impact of therapy were categorized under four subthemes: client behaviour inside and outside sessions, changes in clients' perspectives, the impact on symptoms and impact on life and functioning.ConclusionsParticipants' accounts of the impact of therapy were broadly consistent with the theory underpinning a behavioural approach. Participants described a central role for perspective change, and particularly increased acceptance of the self and mood states, as facilitating behavioural changes and more distal benefits. Process evaluations embedded in future trials may include quantitative measures of key processes described by our participants, as well as those clearly implied by the behavioural theory of depression.
  • Article
    Citation - WoS: 7
    Citation - Scopus: 7
    Diagnosis Melanoma With Artificial Intelligence Systems: A Meta-Analysis Study and Systematic Review
    (Wiley, 2025-06-06) Erturk Zararsiz, Gozde; Yerlitas Tastan, Serra Ilayda; Celik Gurbulak, Elif; Erakcaoglu, Aleyna; Yilmaz Isikhan, Selen; Demirbas, Abdullah; Zararsiz, Goekmen
    BackgroundOne of the most promising and rapidly advancing research areas in recent years is using dermoscopic images for automatic diagnosis with artificial intelligence and machine learning methods.ObjectiveThis study aimed to synthesize the existing studies for the clinical use of applications made with artificial intelligence methods and to summarize the predictive performance of deep learning and hybrid models-based algorithms in all these studies with a large-scale meta-analysis.MethodThe literature review was conducted between January 2006 and May 2024, and meta-analysis data were created by scanning the Web of Science (WOS), Scopus and MEDLINE databases. This study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist.ResultsA total of 2722 articles were evaluated. Data from 78 diagnostic tests from 39 primary studies meeting the inclusion and exclusion criteria were assessed. The pooled SROC overall model AUC was 0.96 [95% CI: 0.94-0.98], sensitivity was 0.89 [95% CI: 0.85-0.91] and specificity was 0.92 [95% CI: 0.90-0.94]. In the subgroup analyses, the pooled AUC was 0.98 [95% CI: 0.96-0.99] for HYBRID models.ConclusionRecent studies have suggested that artificial intelligence algorithms and machine learning methods should be used extensively in medicine to assist physicians, especially in diagnosing melanoma. The ability of HYBRID model algorithms to predict diseases is promising. In particular, the performance of HYBRID models was found to be high. This information can assist clinicians in interpreting the most appropriate algorithms for diagnosing melanoma.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    ConVarT: Search Engine for Missense Variants Between Humans and Other Organisms
    (Wiley, 2022-11) Pir, Mustafa S.; Cevik, Sebiha; Kaplan, Oktay I.
    ConVarT (https://convart.org/) is a search engine for searching for conjugate variants between humans and other species. The search engine is based on matching conjugate variants called MatchVars between species. Matching equivalent variants requires correct alignment of orthologous proteins with the use of multiple sequence alignments (MSA). Indeed, the ConVarT pipeline has performed over a million MSAs and integrated variants and variant-specific annotations (pathogenicity, phenotypic variants; etc.) into the corresponding positions on MSAs. When a clinically relevant variant is discovered whose functional relevance is unknown, ConVarT offers clinician scientists the possibility to search for a MatchVar in other species and to look for functional data on that variant. Fortunately, ConVarT enables users to paste a protein sequence in FASTA format to search for human orthologous proteins. A pairwise sequence alignment (PSA) is then performed between the provided protein sequence and the human orthologous protein, allowing users to visualize human variants on the PSA. Here, we describe the step-by-step usage of ConVarT.
  • Article
    Citation - WoS: 4
    Citation - Scopus: 2
    Biochemical Characterization and Genome Analysis of Pseudomonas Loganensis Sp. Nov., a Novel Endophytic Bacterium
    (Wiley, 2025-08) Karaman, Melisa Z.; Yetiman, Ahmet E.; Zhan, Jixun; Fidan, Ozkan
    Pseudomonas species are highly adaptable, thriving in diverse environments and exhibiting remarkable genetic and metabolic diversity. While some strains are pathogenic, others have significant ecological and industrial applications. Bioinformatics and biochemical analyses, including antibiotic sensitivity testing, revealed that Pseudomonas loganensis sp. nov. can tolerate NaCl concentrations up to 5% and pH ranges between 5 and 9. Antibiogram results corroborated genome data, demonstrating resistance to vancomycin, ampicillin, methicillin, oxacillin, and penicillin G. Phylogenetic analysis based on 16S rRNA, rpoB, rpoD, and gyrB genes, combined with average nucleotide identity (ANI) comparisons, confirmed P. loganensis sp. nov. as a novel species within the Pseudomonas genus. Genome analysis further revealed the presence of turnerbactin and carotenoid gene clusters. Turnerbactin, known to contribute to nitrogen fixation in plants, highlights the strain's potential as a biofertilizer. Additionally, the carotenoid gene cluster suggests potential applications in industrial carotenoid production. The discovery of a trehalose synthase (treS) gene indicates the capability for one-step conversion of maltose into trehalose, underscoring its potential utility in trehalose production.