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: 13Role of Pretty Nanoflowers as Novel Versatile Analytical Tools for Sensing in Biomedical and Bioanalytical Applications(Wiley, 2024-02) Dadi, Seyma; Ocsoy, IsmailIn recent years, an encouraging breakthrough in the synthesis of immobilized enzymes in flower-shaped called "organic-inorganic hybrid nanoflowers (hNFs)" with greatly enhanced catalytic activity and stability were reported. Although, these hNFs were discovered by accident, the enzymes exhibited highly enhanced catalytic activities and stabilities in the hNFs compared with the free and conventionally immobilized enzymes. Herein, we rationally utilized the catalytic activity of the hNFs for analytical applications. In this comprehensive review, we covered the design and use of the hNFs as novel versatile sensors for electrochemical, colorimetric/optical and immunosensors-based detection strategies in analytical perspective. Formation of nanoflowers and their biosensor function in biomedical and bioanalytical applications. imageArticle 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 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 - Scopus: 1Image Processing Methodology for Patient-Specific Instrument Design(Wiley, 2020-09-12) Mohammad Sadeghi, Majid; Kececi, Emin FarukBackground Patient-specific instrumentation (PSI) improves accuracy of surgical operations. PSI needs software for preoperative planning and instrument design. In this study, we explain the methodology of developing a software tool for PSI guide design and preoperative planning in reverse shoulder arthroplasty (RSA). Methods Approaches used to prepare input data, transform them into meaningful features and use of those features to create special guide geometries are explained by describing different algorithms and libraries. Results The developed software is tested on three different patients' data. Preoperative planning is performed and guides designed by software and the patients' bones are manufactured and tested for RSA. The method of building a software is presented to do the preoperative planning and designing specific guides for each patient are shown to be properly functional. Conclusions This study proves processes in the development of the PSI software and the design of a specific guide for RSA.Article Citation - WoS: 13Citation - Scopus: 20IGPRED: Combination of Convolutional Neural and Graph Convolutional Networks for Protein Secondary Structure Prediction(Wiley, 2021-05-25) Gormez, Yasin; Sabzekar, Mostafa; Aydin, ZaferThere is a close relationship between the tertiary structure and the function of a protein. One of the important steps to determine the tertiary structure is protein secondary structure prediction (PSSP). For this reason, predicting secondary structure with higher accuracy will give valuable information about the tertiary structure. Recently, deep learning techniques have obtained promising improvements in several machine learning applications including PSSP. In this article, a novel deep learning model, based on convolutional neural network and graph convolutional network is proposed. PSIBLAST PSSM, HHMAKE PSSM, physico-chemical properties of amino acids are combined with structural profiles to generate a rich feature set. Furthermore, the hyper-parameters of the proposed network are optimized using Bayesian optimization. The proposed model IGPRED obtained 89.19%, 86.34%, 87.87%, 85.76%, and 86.54% Q3 accuracies for CullPDB, EVAset, CASP10, CASP11, and CASP12 datasets, respectively.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: 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: 5Citation - Scopus: 6Capturing B Type Acute Lymphoblastic Leukemia Cells Using Two Types of Antibodies(Wiley, 2018-11-20) Icoz, Kutay; Gercek, Tayyibe; Murat, Ayseguel; Ozcan, Servet; Unal, EkremOne way to monitor minimal residual disease (MRD) is to screen cells for multiple surface markers using flow cytometry. In order to develop an alternative microfluidic based method, isolation of B type acute lymphoblastic cells using two types of antibodies should be investigated. The immunomagnetic beads coated with various antibodies are used to capture the B type acute lymphoblastic cells. Single beads, two types of beads and surface immobilized antibody were used to measure the capture efficiency. Both micro and nanosize immunomagnetic beads can be used to capture B type acute lymphoblastic cells with a minimum efficiency of 94% and maximum efficiency of 98%. Development of a microfluidic based biochip incorporating immunomagnetic beads and surface immobilized antibodies for monitoring MRD can be an alternative to current cost and time inefficient laboratory methods. (c) 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2737, 2019