PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7645

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  • Article
    Relationships Between Light Exposure and Aspects of Cognitive Function in Everyday Life
    (Springer Nature, 2025) Didikoglu, Altug; Woelders, Tom; Bickerstaff, Lucien; Mohammadian, Navid; Johnson, Sheena; van Tongeren, Martie; Lucas, Robert J.
    Light exposure can modulate cognitive function, yet its effects outside of controlled laboratory settings remain insufficiently explored. To examine the relationship between real-world light exposure and cognitive performance, we assessed personal light exposure and measured subjective sleepiness, vigilance, working memory, and visual search performance over 7 days of daily life, in a convenience sample of UK adults (n = 58) without significant circadian challenge (shiftwork or jet-lag). A subset of participants (n = 41) attended an in-lab session comprising a battery of pupillometric and psychophysical tests aimed to quantify melanopsin-driven visual responses. We find significant associations between recent light exposure and subjective sleepiness. Recent light exposure was also associated with reaction times for both psychomotor vigilance and working memory tasks. In addition, higher daytime light exposure and an exposure pattern with reduced fragmentation were linked to improved cognitive performance across visual search, psychomotor vigilance, and working memory tasks. Higher daytime light exposure and earlier estimated bedtimes were associated with stronger relationships between recent light exposure and subjective sleepiness. These results provide real world support for the notion that intra- and inter-individual differences in light exposure meaningfully influence aspects of cognition, with beneficial effects of short-term bright light and of habitual light exposure patterns characterized by brighter daytimes, earlier rest phase, and greater intra- and inter-daily stability.
  • Article
    Interaction of Hazelnut-Derived Polyphenols With Biodegradable Film Matrix: Structural, Barrier, and Functional Properties
    (Multidisciplinary Digital Publishing Institute (MDPI), 2026) Hızır-Kadı, I.; Demircan, E.; Özçelik, B.
    The study presents a sustainable approach to valorizing hazelnut processing by-products, specifically skins and shells, through their conversion into bioactive polyphenol-rich extracts using pressurized hot water extraction (PHWE), an environmentally friendly green technology. PHWE yielded extracts with total phenolic contents of 25.4 mg GAE/g dw (shell) and 83.7 mg GAE/g dw (skin), which were incorporated into biodegradable poly(vinyl alcohol)/carboxymethyl cellulose (PVA/CMC) films at concentrations of 1–3% (w/v). The resulting composites were comprehensively characterized in terms of structural, mechanical, thermal, and barrier properties. FTIR, DSC, and XRD analyses demonstrated strong hydrogen bonding, increased thermal stability, and reduced crystallinity due to polyphenol–polymer interactions. Phenolic incorporation enhanced UV-blocking capability, increased antioxidant activity by up to five-fold, and reduced oxygen permeability from 0.048 to 0.015 (cm3·mm·m−2·day−1·atm−1) (69% reduction, p < 0.05), compared to neat PVA while maintaining desirable transparency (>70%). Optimal formulations (HSkE-II) exhibited a 39% increase in elongation at break and improved flexibility without compromising film integrity. Application tests using fresh-cut apples, watermelon, and chicken revealed significant reductions in microbial growth (up to ~1.2 log CFU/g), lipid oxidation, and weight loss during storage, confirming the films’ potential for active food packaging. This work highlights an efficient valorization strategy for nut industry by-products and demonstrates their functional integration into sustainable biodegradable packaging systems. © 2025 by the authors.
  • Article
    Efficacy of Fermented Foods for the Prevention and Treatment of Bacterial Vaginosis and Vulvovaginal Candidiasis
    (Frontiers Media SA, 2025) Akpinar, A.; Markiewicz, L.H.; Harsa, H.S.; Paveljšek, D.; Domínguez-Soberanes, J.; Agirbasli, Z.; Karakaş-Budak, B.
    Vaginal function in healthy women is closely associated with a lactobacilli-dominated microbiome. Among the most common conditions arising from dysbiosis are bacterial vaginosis (BV) and vulvovaginal candidiasis (VVC). While the efficacy of oral probiotics for the treatment of BV and VVC is well documented, the role of consuming fermented foods remains underexplored. This systematic review aims to present a systematic evaluation of the potential role of fermented foods in the prevention and treatment of BV and VVC and establish the extant research gap between the realm of the clinical sciences and the field of food science and technology. For this purpose, under the guidance of COST Action CA20128—Promoting Innovation of Fermented Foods (PIMENTO), a systematic literature review was conducted in two phases. PubMed, Scopus, and Cochrane databases were used for Phase I to analyze articles on human trials and observational studies where the intervention/exposure involved oral consumption of fermented food. In Phase II, a two-step search strategy was employed: (i) identifying microorganisms with demonstrated clinical efficacy in managing BV and VVC, and (ii) reviewing food science literature where these strains are utilized for fermentation. It was observed that 87% of the food starter applications exploited only two of the 54 efficacious strains identified through clinical studies, namely Lactobacillus rhamnosus GG and Lactobacillus acidophilus LA-5. Findings underscore the potential of fermented foods as carriers for beneficial microorganisms and their relevance in supporting vaginal health. This review contributes to a deeper understanding of the interplay between nutritional consumption of viable probiotic strains and their importance in immunomodulation, highlighting the need for more integrated research efforts across disciplines. Future research aimed at filling this gap will enable informed clinical decisions and dietary recommendations. © © 2025 Akpınar, Markiewicz, Harsa, Paveljšek, Domínguez-Soberanes, Agirbasli, Naziri, El Jalil, Bouchaud, Salminen, Savary-Auzeloux, Humblot, Chassard, Pracer, Vergères and Karakaş-Budak.
  • Article
    Chemosensitizing Effect of Apigenin on T-ALL Cell Therapy
    (Frontiers Media SA, 2025) Huseynova, N.; Baran, Z.; Khalilov, R.; Mammadova, A.; Baran, Y.
    T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with limited therapeutic options and frequent treatment-associated toxicities. L-asparaginase, a cornerstone in T-ALL therapy, is often restricted by hypersensitivity reactions and systemic side effects, highlighting the need for safer strategies to enhance its efficacy. This study investigated the potential of apigenin, a naturally occurring flavonoid with antioxidant and pro-apoptotic properties, to act as a chemosensitizer for L-asparaginase in MOLT-4 T-ALL cells. Cytotoxicity was assessed using the MTT assay, apoptosis by Annexin V/PI staining, cell cycle distribution by flow cytometry, and mitochondrial membrane potential by JC-1 staining. Both apigenin and L-asparaginase produced dose- and time-dependent cytotoxicity, with combination treatment resulting in reduced IC<inf>50</inf> values. Apoptotic analysis showed significantly higher apoptosis in the combination-treated groups than in single-agent groups. Cell cycle analysis revealed that apigenin induced S-phase arrest and L-asparaginase induced G1-phase arrest, while the combination disrupted cell cycle progression at multiple checkpoints. JC-1 assay further demonstrated enhanced mitochondrial depolarization, with up to a 29.2-fold increase in cytoplasmic-to-mitochondrial fluorescence ratio in combination therapy compared to L-asparaginase alone. These findings indicate that apigenin potentiates L-asparaginase-induced cytotoxicity through mitochondrial dysfunction and intrinsic apoptotic signaling. The combined use of apigenin and L-asparaginase may provide a novel strategy to improve therapeutic efficacy in T-ALL while potentially reducing the toxicity associated with high-dose L-asparaginase monotherapy. © © 2025 Huseynova, Baran, Khalilov, Mammadova and Baran.
  • Article
    Impact of Yogurt Consumption on Bone Health Markers in Adults with or without Osteoporosis: A Systematic Review and Meta-Analysis
    (Frontiers Media SA, 2025) Mayo, B.; Malagón-Rojas, J.; Agahi, F.; Frias, J.; Künili, İ.E.; Kütt, M.-L.; Tamang, J.P.
    Yogurt is a fermented dairy product widely recognized for its nutritional value and potential health benefits, particularly due to its high content of calcium, phosphorus, vitamins, and other bioactive compounds. Its purported role in promoting bone health has attracted increasing attention, especially among adults at risk of osteoporosis. However, the specific impact of yogurt consumption on bone health remains controversial, as current evidence is limited and often inconclusive. This systematic review and meta-analysis sought to evaluate the exclusive effects of yogurt consumption on bone health in adults with and without osteoporosis. Employing rigorous inclusion and exclusion criteria and standardized methodologies, the study reviewed data from both observational and clinical studies to assess the effect of yogurt consumption on bone mineral density (BMD), fracture risk, and other bone health markers. In addition, yogurt characteristics were documented in accordance with EFSA guidelines, the possible bioactive components listed, and their potential mechanism of action in relation to bone health discussed. Studies fitting the inclusion and exclusion criteria (n = 12) were all observational, limiting the ability to infer causality. The meta-analysis of cohort studies (n = 6) found no significant association between yogurt consumption and hip fracture risk (HR = 1.01, 95% CI: 0.96–1.07), while the observed positive effect on BMD was minimal and clinically irrelevant (SMD = 0.009). Although some studies reported modest improvements in BMD and bone biomarkers, the overall evidence remains inconclusive, hindered by the heterogeneity in study designs and inconsistent yogurt intake. In conclusion, current evidence does not support a significant role of yogurt consumption in preventing fractures or improving BMD in adults. Well-designed randomized controlled studies are needed to clarify its effects, particularly in adults at risk of or with osteoporosis or osteopenia. In conclusion, the effectiveness of yogurt as a primary strategy for enhancing bone health is not fully substantiated by current data, though its inclusion within a balanced diet may still offer benefits for bone health. Systematic review registration: https://osf.io/, 10.17605/OSF.IO/ES2PM © 2025 Elsevier B.V., All rights reserved.
  • Article
    Vision Transformers-Based Deep Feature Generation Framework for Hydatid Cyst Classification in Computed Tomography Images
    (Springer, 2025) Sagik, Metin; Gumus, Abdurrahman
    Hydatid cysts, caused by Echinococcus granulosus, form progressively enlarging fluid-filled cysts in organs like the liver and lungs, posing significant public health risks through severe complications or death. This study presents a novel deep feature generation framework utilizing vision transformer models (ViT-DFG) to enhance the classification accuracy of hydatid cyst types. The proposed framework consists of four phases: image preprocessing, feature extraction using vision transformer models, feature selection through iterative neighborhood component analysis, and classification, where the performance of the ViT-DFG model was evaluated and compared across different classifiers such as k-nearest neighbor and multi-layer perceptron (MLP). Both methods were evaluated independently to assess classification performance from different approaches. The dataset, comprising five cyst types, was analyzed for both five-class and three-class classification by grouping the cyst types into active, transition, and inactive categories. Experimental results showed that the proposed VIT-DFG method achieves higher accuracy than existing methods. Specifically, the ViT-DFG framework attained an overall classification accuracy of 98.10% for the three-class and 95.12% for the five-class classifications using 5-fold cross-validation. Statistical analysis through one-way analysis of variance (ANOVA), conducted to evaluate significant differences between models, confirmed significant differences between the proposed framework and individual vision transformer models (p<0.05\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p < 0.05$$\end{document}). These results highlight the effectiveness of combining multiple vision transformer architectures with advanced feature selection techniques in improving classification performance. The findings underscore the ViT-DFG framework's potential to advance medical image analysis, particularly in hydatid cyst classification, while offering clinical promise through automated diagnostics and improved decision-making.
  • Article
    Citation - WoS: 9
    Citation - Scopus: 11
    Experimental Investigation of Spray Characteristics of Ethyl Esters in a Constant Volume Chamber
    (Springer, 2024) Ulu, A.; Yildiz, G.; Özkol, Ü.; Rodriguez, A.D.
    Abstract: Biodiesels are mainly produced via the utilization of methanol in transesterification, which is the widespread biodiesel production process. The majority of this methanol is currently obtained from fossil resources, i.e. coal and natural gas. However, in contrast with methanol, biomass-based ethanol can also be used to produce biodiesels; this could allow the production line to become fully renewable. This study aimed to investigate the spray characteristics of various ethyl ester type biodiesels derived from sunflower and corn oils in comparison to methyl esters based on the same feedstocks and reference petroleum-based diesel. Spray penetration length (SPL) and spray cone angle (SCA) were experimentally evaluated in a constant volume chamber allowing optical access, under chamber pressures of 0, 5, 10 and 15 bar and injection pressures of 600 and 800 bar. Sauter mean diameter (SMD) values were estimated by using an analytical correlation. Consequently, ethyl esters performed longer SPL (2.8–20%) and narrower SCA (5.1–19%) than diesel under ambient pressures of 5 and 10 bar. Although the SMD values of ethyl esters were 48% higher than diesel on average, their macroscopic spray characteristics were very similar to those of diesel under 15 bar chamber pressure. Moreover, ethyl esters were found to be very similar to methyl esters in terms of spray characteristics. The differences in SPL, SCA and SMD values for both types of biodiesels were lower than 4%. When considering the uncertainty (± 0.84%) and repeatability (±5%) ratios, the difference between the spray characteristics of methyl and ethyl esters was not major. Graphical abstract: [Figure not available: see fulltext.] © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
  • Article
    Citation - WoS: 61
    Citation - Scopus: 60
    Performance of Structures in İzmir After the Samos Island Earthquake
    (Springer, 2022) Yakut, A.; Sucuoǧlu, H.; Binici, B.; Canbay, E.; Dönmez, C.; Ilki, A.; Ay, B.Ö.
    The October 30, 2020 Earthquake caused unexpectedly significant damage in İzmir considering its distance to the city. This paper evaluates the recorded ground motions, summarizes the performance of structures affected from the earthquake with emphasis on the reasons of damage. A detailed damage assessment was carried out by the Earthquake Engineering Research Center of Middle East Technical University to compile data on the damage of RC and masonry buildings. It was observed that majority of the damage was concentrated in the Bayraklı district due to its peculiar soil properties where many 7–10 story mid-rise RC buildings suffered heavy damage and collapse. The level of amplified ground motions combined with deficiencies of apparently non-code compliant buildings exacerbated the damage. The main reasons of damage were mainly attributed to the presence of soft stories, lack of proper detailing, poor construction quality, presence of heavy overhangs, and hence significant lack of code-compliance in essence. The influence of infill walls on seismic performance of deficient and inadequate buildings was clearly seen in this earthquake. This paper also discusses seismic code requirements in effect and their influence on the observed building performance. The recorded ground motions were compared with the code spectra to evaluate the performance of the buildings. The code response spectra were found to be well above the recorded ground motion spectra at the sites where significant damage was observed. © 2021, The Author(s), under exclusive licence to Springer Nature B.V.
  • Article
    Citation - WoS: 34
    Citation - Scopus: 32
    Lymphedema After Sentinel Lymph Node Biopsy: Who Is at Risk
    (Mary Ann Liebert, Inc., 2022) Isik, A.; Soran, A.; Grasi, A.; Barry, N.; Sezgin, E.
    Background: Sentinel lymph node biopsy (SLNB) is the accepted approach to stage the clinically negative axilla. The incidence of lymphedema (LE) after SLNB is about 5%. We hypothesize that patients undergoing axillary excision of >5 lymph nodes (LNs) are at increased risk of developing LE. Methods and Results: A single institution prospective breast cancer database was retrospectively reviewed from January 2013 to December 2017, to identify patients who underwent SLNB and were diagnosed with LE. Inclusion criteria was (1) de novo breast cancer, (2) SLNB in clinically node negative patients, and (3) no preoperative diagnosis LE of an extremity. Exclusion criteria was history of axillary lymph node dissection. Age, body mass index, tumor-node-metastasis status, surgery type, neoadjuvant or adjuvant chemotherapy, radiotherapy, and hormone therapy were analyzed. Of the 3325 patients identified, 2940 patients met the inclusion criteria and were included in the final analysis. Median follow-up time was 24 months. Forty-seven (2%) patients were diagnosed with LE, and nine patients (19%) had >5 LNs excised. LE was diagnosed in 3.7% of patients who had >5 LNs excised versus 1.4% of patients with ≤5 LNs excised. Incidence of LE was higher in patients with >5 LNs excision (p = 0.006). Conclusion: Our study showed that patients have a higher likelihood of developing LE when >5 LNs are excised. © Copyright 2022, Mary Ann Liebert, Inc., publishers 2022.
  • Correction
    Citation - WoS: 1
    Erratum: Bioactive Snail Mucus-Slime Extract Loaded Chitosan Scaffolds for Hard Tissue Regeneration: the Effect of Mucoadhesive and Antibacterial Extracts on Physical Characteristics and Bioactivity of Chitosan Matrix (Biomedical Materials (Bristol) (2021) 16 (065008) Doi: 10.1088/1748-605x
    (IOP Publishing, 2023) Perpelek, M.; Tamburaci, S.; Aydemi̇r, S.; Tıhmınlıoğlu, F.; Baykara, B.; Karakaşli, A.; Havitçioǧlu, H.
    The authors regret that some errors were identified in 'figures 12 and 13' on pages 14 and 15, in the published manuscript concerning fluorescence microscopy images of Saos-2 and SW1353 cells on scaffolds for 1 and 3 d of incubation. The fluorescence images in figures 12 and 13 were mistakenly used as duplicated due to the inadvertently mislabeling during the processing of files and integrating them into the final figures. Intensity data regarding corrected fluorescence images were also measured and corrected. The revised figures (figures 12 and 13) and their captions appear below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. (Figure Presented). © 2023 IOP Publishing Ltd.