PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Vision Transformers-Based Deep Feature Generation Framework for Hydatid Cyst Classification in Computed Tomography Images(Springer, 2025) Sagik, Metin; Gumus, AbdurrahmanHydatid 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: 4Citation - Scopus: 4Novel Electrospun-Based Extractive Probes for Rapid Determination of Clinically Important Compounds in Human Plasma(Elsevier B.V., 2024) Temel,E.R.; Eroğlu,A.E.; Salih,B.; Boyaci,E.Background: Coated blade spray (CBS) represents an innovative approach that utilizes solid-phase microextraction principles for sampling and sample preparation. When combined with ambient mass spectrometry (MS), it can also serve as an electrospray ionization source. Therefore, it became a promising tool in analytical applications as it can significantly reduce the analysis time. However, the current CBS coatings are based on the immobilization of extractive particles in bulk polymeric glue, which constrains the diffusion of the analytes to reach the extractive phase; therefore, the full reward of the system cannot be taken at pre-equilibrium. This has sparked the notion of developing new CBS probes that exhibit enhanced kinetics. Results: With this aim, to generate a new extractive phase with improved extraction kinetics, poly(divinylbenzene) (PDVB) nanoparticles were synthesized by mini-emulsion polymerization and then immobilized into sub-micrometer (in diameter) sized polyacrylonitrile fibers which were obtained by electrospinning method. Following the optimization and characterization studies, the electrospun-coated blades were used to determine cholesterol, testosterone, and progesterone in plasma spots using the CBS-MS approach. For testosterone and progesterone, 10 ng mL−1 limits of quantification could be obtained, which was 200 ng mL−1 for cholesterol in spot-sized samples without including any pre-treatment steps to samples prior to extraction. Significance: The comparison of the initial kinetics for dip-coated and electrospun-coated CBS probes proved that the electrospinning process could enhance the extraction kinetics; therefore, it can be used for more sensitive analyses. The total analysis time with this method, from sample preparation to instrumental analysis, takes only 7 min, which suggests that the new probes are promising for fast diagnostic applications. © 2024 Elsevier B.V.Article Citation - Scopus: 5Risk Analysis for Groundwater Intakes Based on the Example of Neonicotinoids(Elsevier Ltd, 2024) Pietrzak,D.; Kania,J.; Kmiecik,E.; Baba,A.Neonicotinoids are a class of broad-spectrum insecticides that are dominant in the world market. They are widely distributed in the environment. Understanding the sources, distribution, and fate of these contaminants is critical to mitigating their effects and maintaining the health of aquatic ecosystems. Contamination of surface and groundwater by neonicotinoids has become a widespread problem worldwide, requiring comprehensive action to accurately determine the mechanisms behind the migration of these pesticides, their properties, and their adverse effects on the environment. A new approach to risk analysis for groundwater intake contamination with emerging contaminants was proposed. It was conducted on the example of four neonicotinoids (acetamiprid, clothianidin, thiamethoxam, and imidacloprid) in relation to groundwater accessed by a hypothetical groundwater intake, based on data obtained in laboratory tests using a dynamic method (column experiments). The results of the risk analysis conducted have shown that in this case study the use of acetamiprid and thiamethoxam for agricultural purposes poses an acceptable risk, and does not pose a risk to the quality of groundwater extracted from the intake for food purposes. Consequently, it does not pose a risk to the health and life of humans and other organisms depending on that water. The opposite situation is observed for clothianidin and imidacloprid, which pose a higher risk of groundwater contamination. For higher maximum concentration of neonicotinoids used in the risk analysis, the concentration of clothianidin and imidacloprid in the groundwater intake significantly (from several to several hundred thousand times) exceeds the maximum permissible levels for drinking water (<0.1 μg/L). This risk exists even if the insecticides containing these pesticides are used according to the information sheet provided by the manufacturer (lower maximum concentration), which results in exceeding the maximum permissible levels for drinking water from several to several hundred times. © 2024 Elsevier LtdArticle Citation - WoS: 10Citation - Scopus: 11Arabinoxylan-Based Psyllium Seed Hydrocolloid: Single-Step Aqueous Extraction and Use in Tissue Engineering(Elsevier B.V., 2024) Yildirim-Semerci,Ö.; Bilginer-Kartal,R.; Arslan-Yildiz,A.Biomacromolecules derived from natural sources offer superior biocompatibility, biodegradability, and water-holding capacity, which make them promising scaffolds for tissue engineering. Psyllium seed has gained attention in biomedical applications recently due to its gel-forming ability, which is provided by its polysaccharide-rich content consisting mostly of arabinoxylan. This study focuses on the extraction and gelation of Psyllium seed hydrocolloid (PSH) in a single-step water-based protocol, and scaffold fabrication using freeze-drying method. After characterization of the scaffold, including morphological, mechanical, swelling, and protein adsorption analyses, 3D cell culture studies were done using NIH-3 T3 fibroblast cells on PSH scaffold, and cell viability was assessed using Live/Dead and Alamar Blue assays. Starting from day 1, high cell viability was obtained, and it reached 90 % at the end of 15-day culture period. Cellular morphology on PSH scaffold was monitored via SEM analysis; cellular aggregates then spheroid formation were observed throughout the study. Collagen Type-I and F-actin expressions were followed by immunostaining revealing a 9- and 10-fold increase during long-term culture. Overall, a single-step and non-toxic protocol was developed for extraction and gelation of PSH. Obtained results unveiled that PSH scaffold provided a favorable 3D microenvironment for cells, holding promise for further tissue engineering applications. © 2024 Elsevier B.V.Article Citation - WoS: 9Citation - Scopus: 11Experimental 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.Review Citation - WoS: 7Gangliosides as Therapeutic Targets for Neurodegenerative Diseases(Hindawi Ltd, 2024) Inci, Orhan Kerim; Basirli, Hande; Can, Melike; Yanbul, Selman; Seyrantepe, VolkanGangliosides, sialic acid-containing glycosphingolipids, are abundant in cell membranes and primarily involved in controlling cell signaling and cell communication. The altered ganglioside pattern has been demonstrated in several neurodegenerative diseases, characterized during early-onset or infancy, emphasizing the significance of gangliosides in the brain. Enzymes required for the biosynthesis of gangliosides are linked to several devastating neurological disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), hereditary spastic paraplegia (HSP). In this review, we summarized not only the critical roles of biosynthetic enzymes and their inhibitors in ganglioside metabolism but also the efficacy of treatment strategies of ganglioside to address their significance in those diseases.Article Assessment of Undergraduate Health Students' Perception and Satisfaction on Training and Participation in Community Health Outreach(Springer, 2023) Adegbore, Abidemi Kafayat; Adedokun, Amudatu Ambali; Adegoke, Juliet Ifeoluwa; Lawal, Maruf Ayobami; Oke, MuseAimThe need to improve training of health professionals has increased in recent years due to increasing frequencies of public health events. Consequently, a descriptive cross-sectional survey was carried out to determine the level of satisfaction and knowledge acquired by undergraduate students in the health sciences during a community health outreach program.Subject and methodsStudents were invited to complete an online-administered questionnaire (consisting of both open- and closed-ended questions) to assess their perceptions and experiences on the community health outreach program. Additionally, the survey was carried out to assess the quality of training provided and obtain suggestions for further improvements. Responses were collected and analysed using Microsoft Excel.ResultsMost respondents (>83%) reported satisfaction with the community diagnosis and community intervention briefing and training sessions. All respondents reported familiarity with standard community health outreach instruments and were capable of identifying environmental health risk factors that may contribute to the spread of communicable diseases. Interestingly, respondents reported greater appreciation of health challenges faced by rural communities. However, respondents expressed dissatisfaction with the duration of the outreach program (24%) and funding (15%).ConclusionAlthough respondents reported overall satisfaction with the organization and execution of the health outreach program, certain aspects of the program were deemed unsatisfactory. Despite the shortcomings, we believe that our student-centred learning strategy is readily adaptable for training future healthcare professionals and improving health literacy of rural communities, particularly in sub-Saharan Africa.Data Paper Citation - WoS: 15Citation - Scopus: 20Database Covering the Prayer Movements Which Were Not Available Previously(Nature Publishing Group, 2023) Mihçin, Şenay; Şahin, Ahmet Mert; Yılmaz, Mehmet; Alpkaya, Alican Tuncay; Tuna, Merve; Akdeniz, Sevinç; Can, Nuray Korkmaz; Tosun, Aliye; Şahin, SerapLower body implants are designed according to the boundary conditions of gait data and tested against. However, due to diversity in cultural backgrounds, religious rituals might cause different ranges of motion and different loading patterns. Especially in the Eastern part of the world, diverse Activities of Daily Living (ADL) consist of salat, yoga rituals, and different style sitting postures. A database covering these diverse activities of the Eastern world is non-existent. This study focuses on data collection protocol and the creation of an online database of previously excluded ADL activities, targeting 200 healthy subjects via Qualisys and IMU motion capture systems, and force plates, from West and Middle East Asian populations with a special focus on the lower body joints. The current version of the database covers 50 volunteers for 13 different activities. The tasks are defined and listed in a table to create a database to search based on age, gender, BMI, type of activity, and motion capture system. The collected data is to be used for designing implants to allow these sorts of activities to be performed.Article Citation - WoS: 8Citation - Scopus: 8Surface Microbiota and Associated Staphylococci of Houseflies (musca Domestica) Collected From Different Environmental Sources(Elsevier, 2022) Sudağıdan, Mert; Özalp, Veli Cengiz; Can, Özge; Eligül, Hakan; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Kavruk, Murat; Koçak, OnerHouseflies (Musca domestica) are important mechanical vectors for the transmission of pathogenic microorganisms. In this study, 129 houseflies (69 males and 60 females) were collected from 10 different environmental sources and a laboratory population was used. The surface microbiota of houseflies was identified by Next-Generation Sequencing. Staphylococci from the surfaces of houseflies were selectively isolated and their virulence genes, antibiotic susceptibilities, biofilm formation, and clonal relatedness were determined. Metagenomic analysis results demonstrated that Staphylococcus, Bacillus, and Enterococcus were mostly present on the surface of houseflies at the genus level. Additionally, the isolated 32 staphylococcal strains were identified as Staphylococcus sciuri (n = 11), S. saprophyticus (n = 9), S. arlettae (n = 6), S. xylosus (n = 4), S. epidermidis (n = 1) and S. gallinarum (n = 1). tetK, tetM, tetL, ermC, msrAB, and aad6 genes were found to carry by some of the staphylococcal strains. The strains were mostly resistant to oxacillin, penicillin, and erythromycin and three strains were multi-drug resistant. There was a statistical difference between housefly collection places and antibiotic resistance of isolated staphylococci to penicillin G, gentamicin, and erythromycin (p < 0.05). Biofilm test showed that 17 strains were strong biofilm formers, and it plays important role in the transmission of these bacteria on the surface of houseflies. Staphylococcal strains showed extracellular proteolytic and lipolytic activity in 31 and 12 strains, respectively. Closely related species were found in PFGE analysis from different environmental sources. By this study, surface microbiota and carriage of pathogenic staphylococci on the surfaces of houseflies and their virulence properties were elucidated.Article Citation - WoS: 139Granulocytic Sarcoma: a Systematic Review(e-Century Publishing Corporation, 2013) Yılmaz, Asu Fergün; Saydam, Güray; Şahin, Fahri; Baran, YusufGranulocytic sarcoma also called myeloid sarcoma is an extramedullary tumor of immature granulocytic cells. It is a rare entity, and mostly accompanied by acute myeloid leukemia. It is observed during the course of myeloproliferative disorders especially in chronic myeloid leukemia and myelodysplastic syndromes. In some rare circumstances, it is detected before clinical signs of leukemia or other diseases. When the bone marrow biopsy reveals no other hematologic malignancies, the granulocytic sarcoma is described as nonleukemic, primary or isolated. It is observed at any part of the body but the most common locations are soft tissues, bone, peritoneum and lymph nodes. Presenting signs or symptoms are mainly due to mass effect of the tumor and dysfunction of the organ, or the tissue that is affected. The diagnosis is performed by biopsy of the tumor. The tumor consists of immature granulocytic cells, which could be documented by H&E, immunohistochemistry, and flow cytometric methods. Fluorescence in-situ hybridization and molecular analysis are also performed. The optimal time and type of treatment is not clear. Surgery could be an option especially for tumors, which cause organ dysfunction and/or obstruction. Systemic treatment should be considered in all patients because without systemic treatment, relapses and progression to acute myeloid leukemia is the ultimate fate of the disease in many cases. Cytarabine-containing remission-induction chemotherapies have been the most applied therapeutic strategies, but it is not clear whether the consolidation therapies are required or not, and what kind of regimens are appropriate. The role of hematopoietic stem cell transplantation (HSC) as a consolidation regimen is not clear, but, after the relapse of the disease with or without bone marrow involvement, HSC transplantation should be considered in suitable patients after the reinduction performed by AML chemotherapies. There is only limited data about the role of radiotherapy in these patients. It could be used in patients with relapsed disease, organ dysfunction which should be quickly relieved and inadequate response to chemotherapy. The effect of radiotherapy on overall survival is not known. New prospective studies and clinical trials are needed to generate guidelines for the treatment of primary granulocytic sarcomas.
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