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    Comparing the effectiveness of different vaccination regimens using Sinovac and BNT162b2 vaccines among hospitalised patients: A single-centre hospital-based retrospective cohort study
    (2025) Turan, Atakan; Öğüt, Hamdi; Varol, Aylin Ayyıldız; Koca, Nizameddin; Bozkurt, Hayri
    Objectives: This study aimed to assess the effectiveness of different vaccination regimens using two distinct SARS-CoV-2 vaccines against mortality risk and the need for intensive care unit (ICU) admission among hospitalised patients. Methods: The single-centre hospital-based retrospective cohort study was performed with adult COVID-19 patients in a tertiary-level hospital between March 2020 and September 2022. The associations between patients’ demographics and clinical features, vaccine status and regimens, in-hospital mortality, and need for ICU admission were evaluated using multivariable regression analyses. Results: During the study period, 2,373 patients were included. Mortality among unvaccinated patients was 85.0%, which was significantly lower in vaccinated groups (P<0.001), particularly with BNT162b2 than with Sinovac. Vaccination reduced mortality and ICU admission rates, with higher efficacy observed with increased vaccine doses and BNT162b2 regimens. Multivariable analyses confirmed age as a significant determinant and various vaccination schedules showed consistent reductions in mortality and ICU admissions. Conclusions: A two-dose initial plus one or more-dose booster BNT162b2 regimen effectively reduced mortality risks and ICU admission.
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    Comparing the Prediction Capabilities of Artificial Neural Network (ANN) and Nonlinear Regression Models in Pet-Poy Yarn Characteristics and Optimization of Yarn Production Conditions
    (Inda, 2017) Yıldırım, Kenan; Öğüt, Hamdi; Ulcay, Yusuf
    In the manufacture of yarn, predicting the effect of changing production conditions is vital to reducing defects in the end product. This study compares, for the first time, non-linear regression and artificial neural network (ANN) models in predicting 10 yarn properties shaped by the influence of winding speed, quenching air temperature and/or quenching air speed during production. A multilayer perceptron ANN model was created by training 81 patterns using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm. The hyperbolic tangent, or TanH, activation function and logistic activation functions were used for the hidden and output layers respectively. Results showed that the ANN approach exhibited a greater prediction capability over the non-linear regression method. ANN simultaneously predicted all of the 10 final properties of a yarn; tensile strength, tensile strain, draw force, crystallinity ratio, dye uptake based on the colour strengths (K/S), brightness, boiling shrinkage and yarn evenness, more accurately than the non-linear regression model (R-2 = 0.97 vs. R-2 = 0.92). These results lend support to the idea that the ANN analysis combined with optimization can be used successfully to prevent production defects by fine tuning the production environment.
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    Comparison of changes in blood group, hemogram and biochemical parameters in healthcare workers with and without COVID-19
    (2025) Turan, Atakan; Öğüt, Hamdi; Bozkurt, Hayri; Varol, Aylin Ayyıldız
    Objective: This study aimed to evaluate blood groups and some hematologic and biochemical parameters in healthcare workers with and without COVID-19. Methods: The sample consisted of 1232 healthcare workers who consented to participate in the study after being informed about its purpose and methodology. The study's case group consisted of 704 individuals who got COVID-19, whereas the control group consisted of 528 individuals who didn't get the virus. A survey conducted online was used to gather data. The study was conducted with adherence to ethical norms. Results: Participants in the case and control groups showed a significant difference in their vitamin D level variables, and those with low vitamin D levels were 1.9 times more likely to contract COVID-19 than those with normal levels. Blood glucose, lactate dehydrogenase (LDH), ferritin, troponin-I, D-dimer, C-reactive protein (CRP), anti- human immunodeficiency virüs (HIV), white blood cell, hemoglobulin, platelets, lymphocyte, and neutrophil averages were significantly different between the case and control groups when the biochemistry values of the participants were compared (P<0.05). Conclusions: Vitamin D level, blood glucose, LDH, ferritin, troponin I, D-dimer, CRP, and anti-HIV among the significant biochemistry parameters in our study; leukocyte, hemoglobin, platelets, lymphocyte, and neutrophil levels among hemogram parameters are in parallel with the literature data in predicting the diagnosis of COVID-19. The use of these parameters in the clinic will contribute to the early detection of the diagnosis, early isolation of patients, and early initiation of the treatment process.
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    Highly Transferable pAQU-Related Plasmids Encoding Multidrug Resistance Are Widespread in the Human and Fish Pathogen Photobacterium damselae subsp. damselae in Aquaculture Areas in the Black Sea
    (Springer, 2020) Vences, Ana; Abushattal, Saqr; Matanza, Xose M.; Dubert, Javier; Uzun, Ecren; Öğüt, Hamdi
    The marine bacterium Photobacterium damselae subsp. damselae is a pathogen that causes disease in diverse marine animals, and is also a serious opportunistic human pathogen that can cause fatal infections. Strains of this pathogen isolated from diseased European sea bass in aquaculture facilities in the Turkish coast of the Black Sea were found to exhibit reduced sensitivity to multiple antimicrobials. Selected representative strains were subjected to complete genome sequencing and plasmid characterization. It was found that multidrug resistant (MDR) isolates harboured large conjugative plasmids sharing part of their sequence backbone with pAQU-group plasmids, hitherto reported exclusively in China and Japan. Four new pAQU-group versions of plasmids were identified in the present study, containing distinct combinations of the resistance determinants tetB, floR, sul2, qnrVC, dfrA and strAB. Conjugative transfer of pPHDD2-OG2, a representative plasmid of 170,998 bp, occurred at high frequencies (2.2 x 10(-2) transconjugants per donor cell), to E. coli and to pathogenic P. damselae subsp. damselae and subsp. piscicida strains. Upon transfer, pPHDD2-OG2 conferred reduced susceptibility to a number of antimicrobials to the recipient strains. Comparative genomics analysis of host strains suggested that these MDR plasmids of the pAQU-group were acquired by different genetic lineages of Pdd. This study provides evidence that P. damselae subsp. damselae isolated from diseased fish constitute a reservoir for conjugative MDR pAQU-group plasmids in the Mediterranean basin, and have the potential to spread to diverse bacterial species.
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    Natural calcium phosphates from fish bones and their potential biomedical applications
    (Elsevier Science Bv, 2018) Terzioğlu, Pınar; Öğüt, Hamdi; Kalemtaş, Ayşe
    The treatment and recovery of bio-wastes have raised considerable attention both from the environmental and economic point of view. Every year, a remarkable amount of fish processing by-products are generated and dumped as waste from all over the world. Fish bones can serve as a raw material for the production of high value-added compounds that can be used in various sectors including agrochemical, biomedical, food and pharmaceutical industries. The calcination of fish bones results in a single phase (hydroxyapatite) or bi-phasic (hydroxyapatite-tricalcium phosphate) bioceramics depending on the processing conditions as well as the content of the fish bones. This review summarizes the literature on the production of hydroxyapatite from fish bones and discusses their potential applications in biomedical field. The effect of processing conditions on the properties of final products including Ca/P ratio, crystal structure, particle shape, particle size and biological properties are presented in the light of X-ray diffraction, scanning electron microscopy, transmission electron microscopy, thermogravimetric-differential thermal analysis, bioactivity and biocompatibility investigations.
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    Photobacterium damselae subsp damselae, an Emerging Fish Pathogen in the Black Sea: Evidence of a Multiclonal Origin
    (Amer Soc Microbiology, 2016) Terceti, Mateus S.; Öğüt, Hamdi; Osorio, Carlos R.
    Photobacterium damselae subsp. damselae is considered to be an emerging pathogen of marine fish of importance in aquaculture, with a notable increase in its geographical distribution during the last several years. In this study, we carried out for the first time to our knowledge a genetic and pathobiological characterization of 14 strains isolated from sea bass (Dicentrarchus labrax) reared in the Southeastern Black Sea, where high mortalities were observed at two aquaculture farms during the summer and autumn of 2011. Heterogeneity was evidenced among strains in phenotypical traits, such as sucrose fermentation, motility, and hemolysis. Although 11 of 14 isolates were hemolytic, we found that all of the isolates lacked the pPHDD1 virulence plasmid that encodes the phospholipase-D damselysin (Dly) and the pore-forming toxin PhlyP, two hemolysins previously reported to constitute major virulence factors for turbot. Subsequent PCR and sequencing analyses demonstrated that the 11 hemolytic isolates harbored a complete hlyA(ch) gene, a chromosome I-borne gene that encodes HlyA(ch) hemolysin, whereas the three nonhemolytic isolates contained hlyA(ch) pseudogenes caused by insertion sequence elements. Virulence challenges with two representative strains revealed that, albeit less virulent than the pPHDD1-harboring strain RM-71, the plasmidless hlyA(ch)-positive and hlyA(ch)-negative Black Sea isolates were pathogenic for sea bass. A phylogenetic analysis based on the toxR gene sequence uncovered a greater diversity in the isolates, indicating that the presence of this pathogen in the Black Sea was not caused by the introduction and spread of a single virulent clone but by the proliferation of different clones.
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    Production, characterization, and cytotoxicity of calcium phosphate ceramics derived from the bone of meagre fish,Argyrosomus regius
    (Springer, 2021) Aydin, Gulsum; Terzioğlu, Pınar; Öğüt, Hamdi; Kalemtaş, Ayşe
    Hydroxyapatite ceramics derived from organic materials have similar physical properties and chemical content to stoichiometric hydroxyapatite ceramics produced via synthetic routes. The focus of the current study is to produce hydroxyapatite ceramics from meagre fish bones via calcination method. To the knowledge of the authors, this is the first report in which the meagre fish bones are used to produce hydroxyapatite. The effect of calcination temperature on the phase content, chemical composition, microstructure, and cytotoxic properties of hydroxyapatite ceramics produced from the bones of meagre fish,Argyrosomus regius, was investigated. Thermogravimetric-differential thermal analysis of the raw fish bones was performed over a temperature range of 20-1100 degrees C under air atmosphere with a heating rate of 10 degrees C/min. The total mass loss at this temperature range was about 59% for the fish bone. Thermal analysis of the sample exhibited a three major weight change stage. Calcination was performed in an air atmosphere at different calcination temperatures ranging from 800 to 1100 degrees C for 1 h. XRD analyses of the calcined fish bones revealed that the hydroxyapatite and whitlockite phases were formed at all calcination temperatures. Significantly marked alterations were observed at the microstructure of the samples depending on the calcination temperature. Scanning electron microscopy investigations revealed that nanocrystalline hydroxyapatite particles were achieved at 800 degrees C. As the calcination temperature was increased, particle size of the calcium phosphate phase was also increased and reached to approximately 1 mu m for the sample calcined at 1100 degrees C. Cytotoxicity evaluation of the hydroxyapatite carried out using XTT assay demonstrated that the materials are non-cytotoxic at concentrations up to 100 mg/ml.