WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14627/6
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Article Metabolic Responses to Benzoic Acid Stress and Glutamine Transport-Dependent Vulnerabilities in Escherichia Coli Revealed by NMR Metabolomics(Springer, 2026) Yuksektepe, Ecem; Elgin, Emine Sonay; Onat-Tasdelen, Kadriye Aslihan; Chae, Young Kee; Dogu, Eralp; Catav, Sukru Serter; Ozturkel-Kabakas, HaticeBenzoic acid (BA) is a widely used weak organic acid preservative with antimicrobial activity, yet the metabolic basis of its antibacterial action and the determinants of bacterial sensitivity remain incompletely understood. Here we combined growth assays with H-1 NMR metabolomics to characterize BA-induced metabolic responses in Escherichia coli BW25113 and to examine metabolic changes associated with impaired glutamine transport. Wild-type BW25113 and its BA-sensitive isogenic Delta glnP mutant, lacking the membrane-bound glutamine permease of the high-affinity GlnHPQ transport system, were exposed to sublethal BA concentrations. BA slowed growth and significantly altered the levels of 42 metabolites in the wild-type and 38 in Delta glnP, with the mutant showing stronger growth inhibition and reduced BA tolerance. Both strains exhibited metabolic changes consistent with cellular responses to oxidative and acid stress, including alterations in central carbon metabolism, lysine degradation, cysteine and methionine metabolism, pyrimidine metabolism, and one-carbon pool by folate. However, several metabolic responses differed between the two strains. In wild-type cells, BA exposure was associated with changes in glycerolipid metabolism, glycerophospholipid metabolism, nicotinate and nicotinamide metabolism, lysine biosynthesis, glycine, serine and threonine metabolism, and purine metabolism. In contrast, Delta glnP cells showed distinct alterations in D-amino acid metabolism, arginine biosynthesis, and other carbon fixation pathways. In addition, the mutant displayed substantial baseline differences relative to the wild-type, including altered nucleotide and amino acid pools. Together, these results indicate that both BA exposure and deletion of glnP induce broad metabolic adjustments in Escherichia coli. Loss of glnP is associated with distinct metabolic states and altered responses to BA stress, highlighting the importance of glutamine transport in adaptation to weak organic acid stress.Article Ibuprofen and Nimesulide Derivatives Selectively Induce Apoptosis in HER2-Positive Breast Cancer via Inhibition of the PLA2-COX-2-NF-κB Pathway(Springer, 2026) Bedir, Ipek; Cakirli, Egemen; Kucukguzel, S. Guniz; Yilmaz, Ozgur; Biliz, Yagmur; Telci, DilekBackground Chronic inflammation contributes to breast cancer development through the phospholipase A(2) (PLA(2))-cyclooxygenase-2 (COX-2)-nuclear factor kappa B (NF-kappa B) cascade, which regulates prostaglandin synthesis, oxidative stress, and transcription of pro-inflammatory and anti-apoptotic genes. This pathway is particularly active in HER2-positive breast cancer, promoting proliferation, invasion, and resistance to apoptosis. Non-steroidal anti-inflammatory drugs such as ibuprofen and nimesulide target COX enzymes and have shown potential in suppressing inflammation-driven tumorigenesis. In this study, we evaluated the anticancer and anti-inflammatory activity of newly synthesized, structurally modified ibuprofen and nimesulide derivatives designed to modulate PLA(2)-COX-2-NF-kappa B axis. Methods and Results Cytotoxicity was assessed in HER2-positive breast cancer cells (AU565 and SKBR3) and compared with normal dermal fibroblasts (HDF) and breast epithelial cells (MCF-12A), using WST-1 assays. Apoptosis, cell cycle distribution, caspase-3/7 activation, and ROS generation were analyzed by imaging-based assays, flow cytometry, and fluorescence methods. Gene expression of PLA2G2A and PTGS2 was quantified by qRT-PCR, and NF-kappa B translocation was analyzed by immunocytochemistry. Two ibuprofen triazole derivative (D1) and ibuprofen thioether derivative (D7) and one nimesulide derivative (D8) significantly reduced cell viability in a dose-dependent manner without affecting normal cells. These derivatives induced G(0)/G(1) arrest, caspase-3/7 activation, ROS reduction, and increased late apoptosis. Downregulation of PLA2G2A and PTGS2 expression and inhibition of NF-kappa B translocation confirmed disruption of the PLA(2)-COX-2-NF-kappa B cascade. Conclusion These findings demonstrate that structurally optimized ibuprofen and nimesulide derivatives exert dual anti-inflammatory and anticancer effects in HER2-positive breast cancer by suppressing PLA(2)-COX-2-NF-kappa B pathway and promoting apoptotic cell death.Article Determination of the Susceptibility of Onychomycosis Agents Isolated in Sakarya to Octenidine Dihydrochloride and Hypochlorous Acid(Springer, 2026) Köroğlu, Mehmet; Çiftci, Ihsan Hakkı; Gül, Merve; Yağmur, Ahmet Can; Aydemir, Özlem; Kılbaş, İmdat; Erman, GülayThe aim of this study was to investigate the susceptibility of onychomycosis agents to octenidine dihydrochloride (OCT-D) and hypochlorous acid (HOCl) antiseptics using agar dilution, tube dilution, and flow cytometry methods. In this study, onychomycosis agents including dermatophytes (Trichophyton spp., Microsporum spp., Candida spp.) and secondary agents such as Aspergillus niger and Fusarium solani were cultured on Sabouraud dextrose agar (SDA). Species identification was confirmed using MALDI-TOF MS. The minimum inhibitory concentration (MIC) values of OCT-D, HOCl, and terbinafine for dermatophytes grown on culture plates were determined using the agar dilution method and the broth microdilution (tube dilution) method in accordance with the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Following MIC determination, the minimum fungicidal concentration (MFC) was assessed. Based on the MFC results, flow cytometry analysis was performed using SYTO 9 and propidium iodide (PI) dyes to investigate the fungicidal effects of OCT-D, HOCl, and terbinafine.As a result of antifungal susceptibility testing of onychomycosis agents, approximate MIC values obtained by the agar dilution method were 250 mg/L for OCT-D, 128 mg/L for HOCl, and 0.064 mg/L for terbinafine. Using the tube dilution method, approximate MIC values were 62.5 mg/L, 64 mg/L, and 0.032 mg/L for OCT-D, HOCl, and terbinafine, respectively. Flow cytometry-based viability analyses showed that the results obtained using the tube dilution method were more consistent. Since OCT-D and HOCl demonstrated MIC values far below their commercially available concentrations and exhibited high fungicidal activity, further studies suggest that these agents may be strong alternatives for topical treatment.Article The Relationship Between Spiritual Well-Being, Resilience, and Adherence Among Patients Receiving Hemodialysis Treatment in Türkiye(Springer, 2026) Bulbul, Elif; Sukut, Ozge; Dikec, GulThis study examined the relationship between spiritual well-being, resilience, and adherence of hemodialysis patients and the factors affecting them. The data were collected from 182 hemodialysis patients receiving treatment in a dialysis center who met the inclusion criteria by purposive sampling method in Istanbul. The data were collected with the patient description questionnaire, which measures patient sociodemographic characteristics and characteristics related to the medical diagnosis, the Spiritual Well-Being Scale, the Brief Resilience Scale, and the End-Stage Renal Failure-Adherence Questionnaire. Gender, educational status, employment status, and mean age of patients were found to be correlated with psychological resilience. Marital status, employment status, cohabitants, and mean age of patients were found to be correlated with spiritual well-being. Gender, number of weekly dialysis sessions, and dialysis competencies were found to be correlated with hemodialysis patients' adherence to their treatment. Hemodialysis patients' adherence was positively correlated with both the faith subscale of spiritual well-being and psychological resilience. According to regression analysis, gender and resilience explained 12.8% of the total variance of adherence. This study determined that resilience is an essential factor in increasing the adherence of hemodialysis patients.Article Advances and Strategies in Biosensor-Based Diagnostics for Parasitic Infections: A Comprehensive Scoping Review(Springer, 2026) Aminizadeh, Selva; Alizadeh, Gita; Alizadeh, Zahra; Khalilzadeh, Balal; Abidin, Zurina Zainal; Marzi, Mahdi; Rafiei-Sefiddashti, RahelehParasitic diseases are among the most widespread infections worldwide, causing millions of deaths and illnesses each year. So rapid and accurate diagnosis is essential, requiring highly sensitive and specific tests. Biosensors can provide significant advantages over traditional diagnostic methods because of their specificity, sensitivity, speed, simplicity, ease of use, repeatability, and capacity for early-stage disease detection. Recent advances in modern diagnostic tools for detecting parasitic infections use nanomaterials such as gold nanoparticles, carbon nanofibers, and carbon nanotubes. These developments have significantly lowered detection limits to the picogram and femtogram levels. This review will cover recent advancements in biosensor-based diagnostic techniques in parasitology.Article Citation - WoS: 2Citation - Scopus: 1Comprehensive Bibliometric Analysis of Characteristics, Patterns, and Causes of Retractions in Pediatric Literature(Springer, 2025) Abo-Elnour, Dina Essam; Helal, Mohamed Mohsen; Albalasy, Abdulrahman Ahmed; Abdul-Hafez, Hamza A.; Abdelkader, Ahmed; El-Sherbini, Eman Raafat; Amer, Samar A.This study aimed to systematically identify the key characteristics of retracted articles in pediatric literature and explore the patterns and reasons of pediatric retraction from 1995 to 2024. We searched PubMed and Retraction Watch databases to identify all retracted publications in the field of pediatrics. After the screening process, data were extracted into Excel. Statistical analysis was conducted using Jamovi and Excel. A correlation matrix was used for the important retraction-related factors. After screening, 590 unique retracted pediatric articles were included, with most of them, 572 (96.9%), having retraction notices available; 516 (87.5%) published as open access; 433 (73.4%) from Asia-mostly China; 348 (59%) retracted by the publisher; 301 (51.0%) published by Hindawi; 275 (46.6%) observational studies; and 221 (37.5%) retracted due to misconduct. Articles with four authors showed the highest retraction rate, and the retraction rate generally decreased as the number of authors increased. Most retractions occurred in 2023. The most common pediatric age group included in the retracted papers was children. The median H-index of authors of retracted papers was 8 for first authors and 10 for senior authors. The median time from submission to acceptance of retracted papers was 50 days and that from publication to retraction was 15 months. Additionally, time to retraction was positively correlated with the journal's impact factor (r = 0.106, p = 0.015) and the citation count (r = 0.213, p < 0.001) but showed no significant correlation with time to acceptance (r = - 0.019, p = 0.675). Conclusion: The increasing number of retracted pediatric papers reflects a growing concern with a complex pattern and various determinants. Researchers and publishers should adopt strong regulations and guidelines to improve the integrity of scientific research, especially pediatric research.Article Unraveling the Persistent Renal Impact of Intrauterine Growth Restriction and Catch-Up Growth: Integrating Morphological Insights with Metabolomic Profiling(Springer, 2025) Esrefoglu, Mukaddes; Koktasoglu, Fatmanur; Bayindir, Nihan; Cimen, Fatma Bedia Karakaya; Kirmizikan, Seda; Hekimoglu, Emine Rumeysa; Selek, SahabettinThe study aimed to investigate the long-term effects of IUGR and consequent catch-up growth on metabolic health by using a comprehensive approach that included histopathological, immunohistochemical, biochemical, and metabolomics analyses. Sprague-Dawley pregnant rats either undergo bilateral uterine artery ligation or a sham surgery on the 19th day of gestation. The offspring reached catch-up growth, kidney samples were collected at postnatal weeks 2, 4, and 8 for analysis. IUGR rats exhibited a spectrum of changes including reduced glomeruli number, proliferating cell number, altered oxidative stress markers, various enzymes involved in Krebs cycle, mitochondrial dynamics, and energy metabolism. Examination of the 8-week-old cohort identified a broader spectrum of metabolic alterations, notably in the biosynthesis of phenylalanine, tyrosine, and tryptophan, phenylalanine, tyrosine, glyoxylate, dicarboxylate, pyruvate, alanine, aspartate, and glutamate metabolism, glycolysis/gluconeogenesis and citrate (TCA) cycle. Our metabolomics analysis provides insights into the potential disease susceptibility of individuals born with IUGR, including obesity, diabetes, hypertriglyceridemia, cardiovascular diseases, and mental retardation. These findings underscore the intricate interplay between intrauterine conditions and long-term metabolic health outcomes, highlighting the need for further investigation into preventive and therapeutic strategies to mitigate the risk of metabolic diseases in individuals with a history of IUGR.Article Citation - WoS: 2Citation - Scopus: 2Best Practice Recommendations for Dysphagia Management in Intensive Care Unit (icu): a Delphi Study From Multidisciplinary Experts in Turkey(Springer, 2024) Umay, Ebru; Eyigor, Sibel; Demirag, Kubilay; Kaymak Karatas, Gulcin; Gundogdu, Ibrahim; Giray, Esra; Adiguzel, EmreThere is no study about all aspects of oropharyngoesophageal (OPE) dysphagia from diagnosis to follow-up in a multidisciplinary manner in the world. In order to close this gap, we aimed to create a recommendation study that can be used in clinical practice, addressing all aspects of dysphagia in the ICU in detail with the opinion of experienced multidisciplinary experts. This recommendation paper was generated by a multidisciplinary team, using the seven-step process and a three-modified Delphi round via e-mail. Firstly, 15 open-ended questions were created, and then detailed recommendations including general principles, management, diagnosis, rehabilitation, and follow-up were created with the answers from these questions, Each recommendation item was voted on by the experts as overall consensus (strong recommendation), approaching consensus (weak recommendation), and divergent consensus (not recommended).In the first Delphi round, a questionnaire consisting of 413 items evaluated with a scale of 0-10 was prepared from the opinions and suggestions given to 15 open-ended questions. In the second Delphi round, 55.4% were accepted and revised suggestions were created. At the end of the third Delphi round, the revised suggestion form was approved again and the final proposals containing 133 items were created. This study includes comprehensive and detailed recommendations, including a broad perspective from diagnosis to treatment and follow-up, as detailed as possible, for management of dysphagia in patients with both oropharyngeal- and esophageal-dysphagia in ICU.Article Citation - WoS: 11Citation - Scopus: 12Synchronous and Asynchronous Telerehabilitation Methods Produce Similar Benefits in Individuals With Non-Specific Neck Pain(Springer, 2024) Timurtas, Eren; Selcuk, Halit; Canoz, Ekin Ugur; Inceer, Mehmet; Batar, Suat; Demirbuken, Ilksan; Polat, Mine Gulden; Uğur Canöz, EkinIntroduction Evidence exists on clinical benefits of synchronous and asynchronous telerehabilitation for patients with non-specific neck pain (NSNP); however, limited studies are comparing synchronous and asynchronous telerehabilitation (TR) programs in this population. The aim of this study was to estimate the relative effectiveness of an 8-week synchronous or asynchronous TR in improving pain, functional disability, kinesiophobia, and mobility in patients with NSNP.Materials and methods This was a randomized, controlled clinical trial carried out on 60 individuals with NSNP. Participants were randomly assigned to synchronous TR group (n = 30) or asynchronous TR group (n = 30) that received the same exercise program for 8 weeks. Pain measured by Numeric Pain Rating Scale (NPRS), disability measured by Neck Disability Index (NDI), kinesiophobia measured by Tampa Scale of Kinesiophobia (TSK), and cervical range of motion were used as outcome measures. Assessments were performed at baseline, 4th week, 8th week, and 16th week.Results The analysis showed a significant effect of time and significant interaction between group and time in NPRS, NDI, TSK, and cervical mobility scores (p < 0.05), yet the group effect was not significant (p > 0.05). There were no significant differences between the groups at all time points (p > 0.05) except for cervical right lateral flexion at 8th week (p = 0.036).Conclusion Telerehabilitation technologies are expanding at a rapid rate, and it is essential to understand the outcomes produced using these technologies in health conditions. This study showed that synchronous and asynchronous telerehabilitation produces similar results in patients with NSNP, supporting that either method can be used interchangeably.Article Citation - WoS: 4Citation - Scopus: 6Mapping the Vascular and Muscular Topography of the Glabellar Region: Implication for Improving Safety and Efficacy of the Glabellar Injections(Springer, 2024) Ismailoglu, Abdul Veli; Ismailoglu, Pelin; Aktekin, MustafaBackground Botulinum neurotoxin (BoNT) and filler injections into the highly vascularized glabellar region for aesthetical purposes are extremely common. Injections into the glabellar region without precise anatomical knowledge of its vascular and muscular topography may pose the risk of severe complications.Objectives We aimed to improve the safety and efficacy of the glabellar injections by mapping the regional muscles and vasculature in relation to the medial canthus and the defined reference lines.Methods Meticulous dissection was performed to reveal glabellar region muscles and arteries under surgical microscope, in 16 hemifaces of whom arteries are injected with red-dyed latex. Location of the angular artery (AA) along with its branches was noted in relation to glabellar muscles.Results The AA was always located superficial to the levator labii superioris alaeque nasi muscle (LLSAN) and then coursed toward the medial canthus to anastomose with the supratrochlear artery deep to the origin of the depressor supercilii (DS). The AA gave subcutaneously located central and paracentral branches coursing close to the mid-face line in 14 out of 16 hemifaces. Variable muscular connections were also present between the LLSAN, the DS and the procerus (P) muscles. No arteries were detected at the base of the medial eyebrow to which the DS, the P, and the frontalis (F) inserted.Conclusions This study provides a detailed map of muscular and vascular anatomy of the glabellar region to facilitate safe and efficient filler and BoNT injections without complications.No Level Assigned This journal requires that authors assign a level of evidence to each submission to which Evidence-Based Medicine rankings are applicable. This excludes Review Articles, Book Reviews, and manuscripts that concern Basic Science, Animal Studies, Cadaver Studies, and Experimental Studies. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.