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 - 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: 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 - Scopus: 121Natural and Synthetic Nanovectors for Cancer Therapy(Ivyspring International Publisher, 2023) Eftekhari, Aziz; Kryschi, Carola; Pamies, David; Ahmadian, Elham; Janas, Dawid; Davaran, Soodabeh; Khalilov, Rovshan; Güleç, ŞükrüNanomaterials have been extensively studied in cancer therapy as vectors that may improve drug delivery. Such vectors not only bring numerous advantages such as stability, biocompatibility, and cellular uptake but have also been shown to overcome some cancer-related resistances. Nanocarrier can deliver the drug more precisely to the specific organ while improving its pharmacokinetics, thereby avoiding secondary adverse effects on the not target tissue. Between these nanovectors, diverse material types can be discerned, such as liposomes, dendrimers, carbon nanostructures, nanoparticles, nanowires, etc., each of which offers different opportunities for cancer therapy. In this review, a broad spectrum of nanovectors is analyzed for application in multimodal cancer therapy and diagnostics in terms of mode of action and pharmacokinetics. Advantages and inconveniences of promising nanovectors, including gold nanostructures, SPIONs, semiconducting quantum dots, various nanostructures, phospholipid-based liposomes, dendrimers, polymeric micelles, extracellular and exome vesicles are summarized. The article is concluded with a future outlook on this promising field. © The author(s).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.Editorial Citation - Scopus: 1Lessons From a Ten-Year Journey: Building a Student-Driven Computational Biology Society Across Turkey(F1000 Research, 2022) Kaya, Yasin; Karakulak, Tülay; Saylan, Cemil Can; Gür, E. Ravza; Tatlıdil, Engin; Güleşen, Sevilay; Betül Dinçaslan, Fatma; Dönertaş, Handan MelikeThe Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology and bioinformatics fields by providing opportunities for improving their academic and technical skills in the field. Over the last ten years, we have built a well-known student-driven academic society in Turkey that organizes numerous events every year and continues to grow with over 650 current members. Celebrating the 10th anniversary of RSG-Turkey, in this communication, we share our experiences, five main lessons we learned, and the steps to establish a long-standing academic community: having a clear mission, building a robust structure, effective communication, turning challenges into opportunities, and building collaborations. We believe that our experiences can help students and academics establish long-standing communities in fast-developing areas like bioinformatics.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.Book Part Citation - Scopus: 444 Current Challenges in Mirnomics(Humana Press, 2022) Akgül, Bünyamin; Stadler, Peter F.; Hawkins, Liam J.; Hadj-Moussa, Hanane; Storey, Kenneth B.; Ergin, Kemal; Allmer, JensMature microRNAs (miRNAs) are short RNA sequences about 18–24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (mature miRNA) is incorporated into RISC (miRISC). The sequence of the incorporated miRNA provides the function of RNA target recognition via hybridization. Following binding of the target, the mRNA is either degraded or translation is inhibited, which ultimately leads to less protein production. Conversely, it has been shown that binding within the 5? UTR of the mRNA can lead to an increase in protein product. Regulation of homeostasis is very important for a cell; therefore, all steps in the miRNA-based regulation pathway, from transcription to the incorporation of the mature miRNA into RISC, are under tight control. While much research effort has been exerted in this area, the knowledgebase is not sufficient for accurately modelling miRNA regulation computationally. The computational prediction of miRNAs is, however, necessary because it is not feasible to investigate all possible pairs of a miRNA and its target, let alone miRNAs and their targets. We here point out open challenges important for computational modelling or for our general understanding of miRNA-based regulation and show how their investigation is beneficial. It is our hope that this collection of challenges will lead to their resolution in the near future. © 2022, Springer Science+Business Media, LLC, part of Springer Nature.Book Part Citation - Scopus: 15Stem Cell Culture Under Simulated Microgravity(Springer, 2020) Anıl İnevi, Müge; Sarıgil, Öykü; Kızılkaya, Melike; Meşe, Gülistan; Tekin, Hüseyin Cumhur; Özçivici, EnginChallenging environment of space causes several pivotal alterations in living systems, especially due to microgravity. The possibility of simulating microgravity by ground-based systems provides research opportunities that may lead to the understanding of in vitro biological effects of microgravity by eliminating the challenges inherent to spaceflight experiments. Stem cells are one of the most prominent cell types, due to their self-renewal and differentiation capabilities. Research on stem cells under simulated microgravity has generated many important findings, enlightening the impact of microgravity on molecular and cellular processes of stem cells with varying potencies. Simulation techniques including clinostat, random positioning machine, rotating wall vessel and magnetic levitation-based systems have improved our knowledge on the effects of microgravity on morphology, migration, proliferation and differentiation of stem cells. Clarification of the mechanisms underlying such changes offers exciting potential for various applications such as identification of putative therapeutic targets to modulate stem cell function and stem cell based regenerative medicine. © Springer Nature Switzerland AG 2020.Book Part Citation - WoS: 59Citation - Scopus: 68Stem Cell Therapy for Multiple Sclerosis(Springer, 2019) Genç, Bilgesu; Bozan, Hemdem Rodi; Genç, Şermin; Genç, KürşadMultiple sclerosis (MS) is a chronic inflammatory, autoimmune, and neurodegenerative disease of the central nervous system (CNS). It is characterized by demyelination and neuronal loss that is induced by attack of autoreactive T cells to the myelin sheath and endogenous remyelination failure, eventually leading to functional neurological disability. Although recent evidence suggests that MS relapses are induced by environmental and exogenous triggers such as viral infections in a genetic background, its very complex pathogenesis is not completely understood. Therefore, the efficiency of current immunosuppression-based therapies of MS is too low, and emerging disease-modifying immunomodulatory agents such as fingolimod and dimethyl fumarate cannot stop progressive neurodegenerative process. Thus, the cell replacement therapy approach that aims to overcome neuronal cell loss and remyelination failure and to increase endogenous myelin repair capacity is considered as an alternative treatment option. A wide variety of preclinical studies, using experimental autoimmune encephalomyelitis model of MS, have recently shown that grafted cells with different origins including mesenchymal stem cells (MSCs), neural precursor and stem cells, and induced-pluripotent stem cells have the ability to repair CNS lesions and to recover functional neurological deficits. The results of ongoing autologous hematopoietic stem cell therapy studies, with the advantage of peripheral administration to the patients, have suggested that cell replacement therapy is also a feasible option for immunomodulatory treatment of MS. In this chapter, we overview cell sources and applications of the stem cell therapy for treatment of MS. We also discuss challenges including those associated with administration route, immune responses to grafted cells, integration of these cells to existing neural circuits, and risk of tumor growth. Finally, future prospects of stem cell therapy for MS are addressed.
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