PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Citation - WoS: 6Citation - Scopus: 7Sustainability Assessment of Denim Fabric Made of PET Fiber and Recycled Fiber From Postconsumer PET Bottles Using LCA and LCC Approach With the EDAS Method(Wiley, 2024-11-01) Fidan, Fatma Sener; Aydogan, Emel Kizilkaya; Uzal, NigmetThe textile industry is under pressure to adopt sustainable production methods because its contribution to global warming is expected to rise by 50% by 2030. One solution is to increase the use of recycled raw material. The use of recycled raw material must be considered holistically, including its environmental and economic impacts. This study examined eight scenarios for sustainable denim fabric made from recycled polyethylene terephthalate (PET) fiber, conventional PET fiber, and cotton fiber. The evaluation based on the distance from average solution (EDAS) multicriteria decision-making method was used to rank scenarios according to their environmental and economic impacts, which are assessed using life cycle assessment and life cycle costing. Allocation, a crucial part of evaluating the environmental impact of recycled products, was done using cut-off and waste value. Life cycle assessments reveal that recycled PET fiber has lower freshwater ecotoxicity and fewer eutrophication and acidification impacts. Cotton outperformed PET fibers in human toxicity. Only the cut-off method reduces potential global warming with recycled PET. These findings indicated that recycled raw-material life cycle assessment requires allocation. Life cycle cost analysis revealed that conventional PET is less economically damaging than cotton and recycled PET. The scenarios were ranked by environmental and economic impacts using EDAS. This ranking demonstrated that sustainable denim fabric production must consider both economic and environmental impacts. Integr Environ Assess Manag 2024;00:1-19. (c) 2024 The Author(s). Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).Article Citation - WoS: 25Citation - Scopus: 27Progression of Irradiated Mesenchymal Stromal Cells From Early to Late Senescence: Changes in SASP Composition and Anti-Tumour Properties(Wiley, 2023-03-22) Alessio, Nicola; Acar, Mustafa Burak; Squillaro, Tiziana; Aprile, Domenico; Ayaz-Guner, Serife; Di Bernardo, Giovanni; Galderisi, UmbertoGenotoxic injuries converge on senescence-executive program that promotes production of a senescence-specific secretome (SASP). The study of SASP is particularly intriguing, since through it a senescence process, triggered in a few cells, can spread to many other cells and produce either beneficial or negative consequences for health. We analysed the SASP of quiescent mesenchymal stromal cells (MSCs) following stress induced premature senescence (SIPS) by ionizing radiation exposure. We performed a proteome analysis of SASP content obtained from early and late senescent cells. The bioinformatics studies evidenced that early and late SASPs, besides some common ontologies and signalling pathways, contain specific factors. In spite of these differences, we evidenced that SASPs can block in vitro proliferation of cancer cells and promote senescence/apoptosis. It is possible to imagine that SASP always contains core components that have an anti-tumour activity, the progression from early to late senescence enriches the SASP of factors that may promote SASP tumorigenic activity only by interacting and instructing cells of the immune system. Our results on Caco-2 cancer cells incubated with late SASP in presence of peripheral white blood cells strongly support this hypothesis. We evidenced that quiescent MSCs following SIPS produced SASP that, while progressively changed its composition, preserved the capacity to block cancer growth by inducing senescence and/or apoptosis only in an autonomous manner.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, KimBackgroundAlthough 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: 29Citation - Scopus: 32Life Cycle Sustainability Assessment of a Light Rail Transit System: Integration of Environmental, Economic, and Social Impacts(Wiley, 2021-04-01) Gulcimen, Sedat; Aydogan, Emel K.; Uzal, NigmetThe transition toward sustainable urban transportation has gained importance in recent decades. However, urban transportation has not been addressed for all dimensions of sustainability. This study presents a life cycle sustainability assessment of a light rail transit system in Kayseri, Turkey, by integrating environmental, economic, and social aspects. The sustainability performance of the light rail transit system is evaluated using a cradle-to-grave approach to assess three aspects of sustainability. For the environmental evaluation, a life cycle assessment was applied using SimaPro 8.4.1 PhD version based on ISO 14040 and 14044. The method, which includes nine environmental impact categories, was employed to assess the environmental performance of the light rail transit system with a functional unit of 1 passenger-km. For the economic assessment, life cycle costing was utilized with the functional unit of USD for 1 passenger-km. A social life cycle assessment was applied to assess the social performance of the light rail transit system based on guidelines published by the United Nations Environment Programme in collaboration with the Society of Environmental Toxicology and Chemistry. For the determination of social impacts, 11 subcategories and 18 social indicators were selected. The results showed that the global warming potential and abiotic depletion potential of the light rail system per passenger-km were 2.4E - 02 kg CO2 eq. and 2.7E - 01 MJ, respectively, with a service life of 50 years. The total life cycle cost of the light rail system was calculated as 0.046 USD for 1 passenger-km. The results also revealed that the main contributor to the total life cycle cost was energy cost, with 92% (2.88E + 08 USD) of the total cost. In the social performance evaluation, it is found that the industry performs well for society, the local community, and workers but has a weaker social performance for the consumer due to a weak feedback mechanism. Integr Environ Assess Manag 2021;00:1-13. (c) 2021 SETACArticle Citation - WoS: 33Citation - Scopus: 37In Silico Evaluation of Food-Derived Carotenoids Against SARS-CoV Drug Targets: Crocin Is a Promising Dietary Supplement Candidate for COVID-19(Wiley, 2022-05-11) Mujwar, Somdutt; Sun, Lei; Fidan, OzkanThe current COVID-19 pandemic is severely threatening public healthcare systems around the globe. Some supporting therapies such as remdesivir, favipiravir, and ivermectin are still under the process of a clinical trial, it is thus urgent to find alternative treatment and prevention options for SARS-CoV-2. In this regard, although many natural products have been tested and/or suggested for the treatment and prophylaxis of COVID-19, carotenoids as an important class of natural products were underexplored. The dietary supplementation of some carotenoids was already suggested to be potentially effective in the treatment of COVID-19 due to their strong antioxidant properties. In this study, we performed an in silico screening of common food-derived carotenoids against druggable target proteins of SARS-CoV-2 including main protease, helicase, replication complex, spike protein and its mutants for the recent variants of concern, and ADP-ribose phosphatase. Molecular docking results revealed that some of the carotenoids had low binding energies toward multiple receptors. Particularly, crocin had the strongest binding affinity (-10.5 kcal/mol) toward the replication complex of SARS-CoV-2 and indeed possessed quite low binding energy scores for other targets as well. The stability of crocin in the corresponding receptors was confirmed by molecular dynamics simulations. Our study, therefore, suggests that carotenoids, especially crocin, can be considered an effective alternative therapeutics and a dietary supplement candidate for the prophylaxis and treatment of SARS-CoV-2. Practical applications In this study, food-derived carotenoids as dietary supplements have the potential to be used for the prophylaxis and/or treatment of SARS-CoV-2. Using in silico techniques, we aimed at discovering food-derived carotenoids with inhibitory effects against multiple druggable sites of SARS-CoV-2. Molecular docking experiments against main protease, helicase, replication complex, spike protein and its mutants for the recent variants of concern, and ADP-ribose phosphatase resulted in a few carotenoids with multitarget inhibitory effects. Particularly, crocin as one of the main components of saffron exhibited strong binding affinities to the multiple drug targets including main protease, helicase, replication complex, mutant spike protein of lineage B.1.351, and ADP-ribose phosphatase. The stability of the crocin complexed with these drug targets was further confirmed through molecular dynamics simulations. Overall, our study provides the preliminary data for the potential use of food-derived carotenoids, particularly crocin, as dietary supplements in the prevention and treatment of COVID-19.Article Citation - WoS: 17Citation - Scopus: 21Finite Element Analysis of the Stress Distribution Associated With Different Implant Designs for Different Bone Densities(Wiley, 2022-06-06) Kurtulus, Ikbal Leblebicioglu; Kilic, Kerem; Bal, Burak; Kilavuz, Ahmet; Leblebicioğlu Kurtuluş, IkbalPurpose The main objective of this study was to investigate the influence of implant design, bone type, and abutment angulation on stress distribution around dental implants. Materials and methods Two implant designs with different thread designs, but with the same length and brand were used. The three-dimensional geometry of the bone was simulated with four different bone types, for two different abutment angulations. A 30 degrees oblique load of 200 N was applied to the implant abutments. Maximum principal stress and minimum principal stresses were obtained for bone and Von misses stresses were obtained for dental implants. Results The distribution of the load was concentrated at the coronal portion of the bone and implants. The stress distributions to the D4 type bone were higher for implant models. Increased bone density and increased cortical bone thickness cause less stress on bone and implants. All implants showed a good distribution of forces for non-axial loads, with higher stresses concentrated at the crestal region of the bone-implant interface. In implant types using straight abutments there was a decrease in stress as the bone density decreased. The change in the abutment angle also caused an increase in stress. Conclusions The use of different implant threads and angled abutments affects the stress on the surrounding bone and implant. In addition, it was observed that a decrease in density in trabecular bone and a decrease in cortical bone thickness increased stress.Article Citation - WoS: 7Citation - Scopus: 7Diagnosis 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, GoekmenBackgroundOne 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: 15Citation - Scopus: 16Computational Fluid Dynamics (CFD) Analysis of Bioprinting(Wiley, 2024-05-02) Fareez, Umar Naseef Mohamed; Naqvi, Syed Ali Arsal; Mahmud, Makame; Temirel, MikailRegenerative medicine has evolved with the rise of tissue engineering due to advancements in healthcare and technology. In recent years, bioprinting has been an upcoming approach to traditional tissue engineering practices, through the fabrication of functional tissue by its layer-by-layer deposition process. This overcomes challenges such as irregular cell distribution and limited cell density, and it can potentially address organ shortages, increasing transplant options. Bioprinting fully functional organs is a long stretch but the advancement is rapidly growing due to its precision and compatibility with complex geometries. Computational Fluid Dynamics (CFD), a carestone of computer-aided engineering, has been instrumental in assisting bioprinting research and development by cutting costs and saving time. CFD optimizes bioprinting by testing parameters such as shear stress, diffusivity, and cell viability, reducing repetitive experiments and aiding in material selection and bioprinter nozzle design. This review discusses the current application of CFD in bioprinting and its potential to enhance the technology that can contribute to the evolution of regenerative medicine. Using computational fluid dynamics (CFD) allows the optimization of bioprinting by analyzing flow velocity, shear stress, and pressure distribution, which enhances the printability, nozzle design, and bioink formulations for tissue construction. CFD enhances bioink deposition and cell viability while reducing the need for repetitive experiments, curbing cost and time. Moreover, it enhances vascularization designs to mimic physiological conditions, thereby facilitating tissue development. imageArticle Citation - WoS: 3Citation - Scopus: 3Biochemical, Pharmacological, and Toxicological Attributes of Caper (Capparis Ovata) Flowering Buds and Berries Pickles(Wiley, 2022-07-30) Ozgun-Acar, Ozden; Celik-Turgut, Gurbet; Guner, Huseyin; Sezer, Serdar; Sen, AlaattinCapparis ovata is a natural plant that grows widely in Turkey and its flowering buds and berry pickle are used in traditional medicine. Thus, the current study was expanded to evaluate the biochemical, pharmacological, and toxicological aspects of the Capparis ovata water extract (COWE). To determine the biochemical properties of COWE, mineral and fatty acid content, elemental analysis, flavonoid/phenolic content, radical-scavenging capacity, and pesticide analysis were performed. Furthermore, to find out whether it had anti-inflammatory properties, reverse transcription-polymerase chain reaction (RT-PCR) and nuclear factor kappa B (NF-kappa B) luciferase activity tests were conducted. Whole-genome transcriptomic profiling was carried out at a dose level of 500 mg/kg COWE to understand its pharmacological effect. Transaminases in serum were tested, and quantitative polymerase chain reaction (qPCR) was done using a custom design array that included the stress and molecular toxicology pathway to establish its toxicological qualities. As a result of the evaluations, it was observed that COWE has a high mineral and unsaturated fatty acid content, flavonoid/phenolic content, and radical-scavenging ability. It significantly inhibited NF-kappa B transcriptional activity as well as inflammatory cytokine expression in T-lymphoblast cells. Whole-genome transcriptomic profiling depicted that COWE modulates immune responses by upregulating natural killer cell activation, cellular response to type I interferon, B-cell proliferation and differentiation, and Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathways. Molecular Toxicology Pathfinder RT2 Profiler PCR array analysis revealed that COWE at or lower dose of 500 mg/kg/day did not cause a comparatively adverse effect. According to the findings, COWE is a rich source of nutrients and can be used as an adjunct therapy for various inflammatory diseases.Article Citation - WoS: 4Citation - Scopus: 2Biochemical 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, OzkanPseudomonas 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.