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Article Citation - WoS: 4Citation - Scopus: 4Detection of spermatogonial stem/progenitor cells in prepubertal mouse testis with deep learning(Springer/plenum Publishers, 2023) Kahveci, Burak; Onen, Selin; Akal, Fuat; Korkusuz, PetekPurposeRapid and easy detection of spermatogonial stem/progenitor cells (SSPCs) is crucial for clinicians dealing with male infertility caused by prepubertal testicular damage. Deep learning (DL) methods may offer visual tools for tracking SSPCs on testicular strips of prepubertal animal models. The purpose of this study is to detect and count the seminiferous tubules and SSPCs in newborn mouse testis sections using a DL method.MethodsTesticular sections of the C57BL/6-type newborn mice were obtained and enumerated. Odd-numbered sections were stained with hematoxylin and eosin (H&E), and even-numbered sections were immune labeled (IL) with SSPC specific marker, SALL4. Seminiferous tubule and SSPC datasets were created using odd-numbered sections. SALL4-labeled sections were used as positive control. The YOLO object detection model based on DL was used to detect seminiferous tubules and stem cells.ResultsTest scores of the DL model in seminiferous tubules were obtained as 0.98 mAP, 0.93 precision, 0.96 recall, and 0.94 f1-score. The SSPC test scores were obtained as 0.88 mAP, 0.80 precision, 0.93 recall, and 0.82 f1-score.ConclusionSeminiferous tubules and SSPCs on prepubertal testicles were detected with a high sensitivity by preventing human-induced errors. Thus, the first step was taken for a system that automates the detection and counting process of these cells in the infertility clinic.Article Citation - Scopus: 2The Effects of Paddy Cultivation and Microbiota Members on Arsenic Accumulation in Rice Grain(Mdpi, 2023) Ersoy Omeroglu, Esra; Bayer, Asli; Sudagidan, Mert; Ozalp, Veli Cengiz; Yasa, IhsanAccess to safe food is one of the most important issues. In this context, rice plays a prominent role. Because high levels of arsenic in rice grain are a potential concern for human health, in this study, we determined the amounts of arsenic in water and soil used in the rice development stage, changes in the arsC and mcrA genes using qRT-PCR, and the abundance and diversity (with metabarcoding) of the dominant microbiota. When the rice grain and husk samples were evaluated in terms of arsenic accumulation, the highest values (1.62 ppm) were obtained from areas where groundwater was used as irrigation water, whereas the lowest values (0.21 ppm) occurred in samples from the stream. It was observed that the abundance of the Comamonadaceae family and Limnohabitans genus members was at the highest level in groundwater during grain formation. As rice development progressed, arsenic accumulated in the roots, shoots, and rice grain. Although the highest arsC values were reached in the field where groundwater was used, methane production increased in areas where surface water sources were used. In order to provide arsenic-free rice consumption, the preferred soil, water source, microbiota members, rice type, and anthropogenic inputs for use on agricultural land should be evaluated rigorously.Article Citation - WoS: 10Alkaline Hydrothermal Synthesis, Characterization, and Photocatalytic Activity of Tio2 Nanostructures: the Effect of Initial Tio2 Phase(Amer Scientific Publishers, 2019) Erdogan, Nursev; Park, Jongee; Choi, Woohyuk; Kim, Soo Young; Ozturk, AbdullahOne-dimensional (1D) titanate nanostructures were synthesized by hydrothermal route, using commercially available TiO2 (P25) and anatase powders as precursor materials and strong NaOH solution as catalyzer. The prepared titanates were calcined, followed by protonation to produce TiO2 nanostructures having enhanced photocatalytic and photovoltaic properties. The synthesized TiO2 1D nanostructures were characterized using field-emission scanning electron microscope, high-resolution electron microscope, X-ray diffraction analysis, and UV-Vis photospectroscopy to understand the effect of initial TiO2 phase on morphological and crystallographic features, and bandgap. Methylene blue degradation test was applied to evaluate the photoactivity of the products obtained after different stages of the process. The findings indicate that 1D TiO2 nanostructures form by different mechanisms from dissolved aggregates during hydrothermal process, depending on the crystal structure of the initial precursor used. Photocatalytic test results reveal that protonated titanates have considerable adsorption capability, while photocatalytic degradation depends on TiO2 transformation.Article Citation - WoS: 7Citation - Scopus: 7Surface Plasmon Resonance Aptasensor for Soluble Icam-1 Protein in Blood Samples(Royal Soc Chemistry, 2022) Dursun, Ali Dogan; Dogan, Soner; Kavruk, Murat; Tasbasi, B. Busra; Sudagidan, Mert; Yilmaz, M. Deniz; Tuna, Bilge G.Intercellular Adhesion Molecule-1 (ICAM-1) is considered to be a cancer biomarker in the assessment of metastatic potential in patients and an early indicator of atherosclerosis. A labelless biosensor based on the surface plasmon resonance (SPR) signal from the specific affinity interaction of an aptamer and a soluble ICAM-1 protein was developed for blood samples. The developed aptasensor provided real-time information on the concentration of the ICAM-1 protein in blood when integrated to a purification step based on a magnetic pull-down separation. The SPR aptasensor was highly specific with a limit of detection of 1.4/0.2 ng ml(-1), which was achieved through aptamer-functionalized silica-coated magnetic nanoparticles.Article Citation - WoS: 6Effectiveness of Proprioceptive Neuromuscular Facilitation and Myofascial Release Techniques in Patients With Subacromial Impingement Syndrome(Taylor & Francis Ltd, 2022) Celik, Merve Sinem; Sonmezer, Emel; Acar, ManolyaPurpose To compare the effectiveness of proprioceptive neuromuscular facilitation and myofascial release technique in patients with subacromial impingement syndrome on pain, range of motion, muscle strength, quality of life, functionality and disability. Methods Thirty patients were randomly divided into two groups: proprioceptive neuromuscular facilitation group (n = 15) and proprioceptive neuromuscular facilitation combined with myofascial release technique group (n = 15). Both treatment methods were performed 3 times a week for 4 weeks. Pain severity was assessed by Visuel Analog Scale, range of motion by a goniometer, muscle strength by digital hand dynamometer, quality of life by Nottingham health profile, functionality by arm, shoulder and hand problems questionnaire, disability by shoulder pain and disability index. All measurements were used before and after treatments. Pain severity, range of motion and muscle strength were also evaluated after the first session. Results After the treatment, shoulder pain, range of motion, muscle strength, functionality and disability were improved in two groups (p < 0.05). Proprioceptive neuromuscular facilitation showed improvement in pain, whereas myofascial release technique improved pain, physical activity, emotional state, sleep and total dimensions of life quality (p < 0.05). Proprioceptive neuromuscular facilitation was more effective in reducing activity pain, whereas myofascial release technique was more effective in increasing flexion, external and internal rotation range of motion, flexion and abduction muscle strength after the first session (p < 0.05). Conclusions The combined application of proprioceptive neuromuscular facilitation and myofascial release technique has a more acute and cumulative positive effect on pain, range of motion, muscle strength, functionality, disability and quality of life in patients with subacromial impingement syndrome.Article Citation - WoS: 6Citation - Scopus: 6Quantitative Lipidomic Analysis of Takotsubo Syndrome Patients' Serum(Frontiers Media Sa, 2022) Karnati, Srikanth; Guntas, Gulcan; Rajendran, Ranjithkumar; Shityakov, Sergey; Hoering, Marcus; Liebisch, Gerhard; Foerster, Carola Y.Takotsubo syndrome (TTS), also known as the transient left ventricular apical ballooning syndrome, is in contemporary times known as novel acute cardiac syndrome. It is characterized by transient left ventricular apical akinesis and hyperkinesis of the basal left ventricular portions. Although the precise etiology of TTS is unknown, events like the sudden release of stress hormones, such as the catecholamines and the increased inflammatory status might be plausible causes leading to the cardiovascular pathologies. Recent studies have highlighted that an imbalance in lipid accumulation might promote a deviant immune response as observed in TTS. However, there is no information on comprehensive profiling of serum lipids of TTS patients. Therefore, we investigated a detailed quantitative lipid analysis of TTS patients using ES-MSI. Our results showed significant differences in the majority of lipid species composition in the TTS patients compared to the control group. Furthermore, the computational analyses presented was able to link the altered lipids to the pro-inflammatory cytokines and disseminate possible mechanistic pathways involving TNF alpha and IL-6. Taken together, our study provides an extensive quantitative lipidome of TTS patients, which may provide a valuable Pre-diagnostic tool. This would facilitate the elucidation of the underlying mechanisms of the disease and to prevent the development of TTS in the future.Article Selection of DNA Aptamers Against Parathyroid Hormone for Electrochemical Impedimetric Biosensor System Development(John Wiley and Sons Inc, 2025) Didarian, Reza; Bargh, Saharnaz; Gulerman, Almina; Ozalp, Veli Cengiz; Erel, Ozcan; Yildirim-Tirgil, NimetThis work presents the pioneering development of an aptamer-based electrochemical biosensor for real-time monitoring of parathyroid hormone (PTH) levels, with a focus on intraoperative assessment during parathyroid surgery. It introduces, for the first time, the selection and characterization of aptamers targeting distinct segments of the PTH peptide. The study demonstrates the feasibility and efficacy of the biosensing platform through a precisely designed experimental framework, including SELEX-based aptamer selection, aptamer-peptide interaction analysis, and biosensor fabrication. The SELEX process yields aptamers with notable binding affinities to different fragments of PTH, with the PTH (53-84) aptamer showing particularly sensitive binding to the hormone's C terminus, allowing for precise PTH analysis. Electrochemical characterization reveals significant changes in electrochemical impedance spectroscopy (EIS) signals upon exposure to varying PTH concentrations, highlighting the sensor's sensitivity and selectivity. The increase in charge transfer resistance (Rct) values with rising PTH concentrations underscores the biosensor's capability to detect PTH-induced structural changes, validating its potential for accurate measurement. The biosensor shows remarkable selectivity in the presence of common interferents in serum samples, ensuring precise PTH detection. Stability assessments over a 45-day storage period demonstrate the biosensor's robustness and long-term reliability, affirming its practical suitability. In summary, the developed aptamer-based biosensor represents a promising tool for sensitive and selective PTH detection, with potential applications in biomedical research and clinical diagnostics, particularly for intraoperative PTH analysis during parathyroidectomy. Continued research and optimization efforts hold promise for enhancing its performance and expanding its utility in diverse healthcare settings.Article Citation - WoS: 3Citation - Scopus: 3How Do Implant Threads and Diameters Affect the All-On Success? a 3d Finite Element Analysis Study(IOS Press BV, 2022) Zor,Z.F.; Klllnç,Y.; Erkmen,E.; Kurt,A.BACKGROUND: The effect of different thread designs and diameters on the all-on-four concept is unclear. OBJECTIVE: The aim of the study was to clarify the differences in stress distribution of dental implants with various thread designs and diameters based on the all-on-four concept with three dimensional (3D) finite element analysis (FEA). METHODS: A 3D model of a totally edentulous mandible was used to perform the FEA. Four different models (M1, M2, M3, and M4) including 3.5 and 4.3 mm diameter dental implants with active and passive threaded designs were generated. The dental implants were positioned according to the all-on-four concept. The Von Mises stresses on dental implants and maximum and minimum principal stresses (Pmax and Pmin) on bony structures were calculated under vertical, oblique and horizontal loads. RESULTS: For Von Mises stresses, the highest stress values were detected on the distal implants for all models. Distal implants had also the highest stress values for vertical loading. The Von Mises stresses were found to be concentrated around the implant's neck. In all models the highest Pmax and Pmin stresses occurred in the bone surrounding the distal implant. It was noted that the active threaded implants showed the highest Pmax and Pmin stress values. CONCLUSION: The implant thread design and diameter might have a strong influence on the stress values in the all-on-four concept. © 2022 - IOS Press. All rights reserved.Article Bacterial Profiling of Brined Grapevine Leaves Collected From Different Local Markets in Türkiye(John Wiley and Sons Inc, 2025) Ucak, S.; Yegin, Z.; Yurt, M.N.Z.; Sudagidan, M.; Altunbas, O.; Ozalp, V.C.Microorganisms linked to the grapevine, Vitis vinifera, can impact crop quality, plant growth, and human and plant health. This study examined the bacterial community structures of brined grapevine leaves (n = 56) taken from seven distinct regions in Türkiye using next-generation sequencing technology. Investigations were also conducted into the samples' chemical properties. Firmicutes was the dominant phylum, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Bacillaceae was the predominant family in the analyzed samples, followed by Clostridiaceae, Peptostreptococcaceae, and Enterobacteriaceae. Bacillus was the dominant genus, followed by Lysinibacillus and Clostridium sensu stricto. The samples exhibited differences in terms of pH, total acidity, and salt content. The pH values of the brined grapevine leaves ranged from 2.31 to 6.91, the acidity levels ranged from 0.09% to 1.80%, and the salt percentages ranged from 3.39% to 49.14%. This research provides pioneering information for bacterial community analysis of brined grapevine leaves. © 2025 Wiley-VHCA AG, Zurich, Switzerland.Article Citation - WoS: 1Citation - Scopus: 1Left Ventricular Geometry as a Predictor of Carotid Artery Stenosis Severity in Patients Undergoing Carotid Artery Stenting(Wiley, 2020) Karaduman, Bilge Duran; Ayhan, Huseyin; Keles, Telat; Bozkurt, EnginBackground and Aim Cerebrovascular diseases are the second most common cause of death worldwide. Moderate and severe carotid artery stenosis causes nearly 10% of all strokes. LV geometry is a familiar prognostic and diagnostic factor in several populations; yet, data on its role in carotid artery stenosis are unknown. In our study, we investigated the prognostic value of LV geometry in predicting carotid artery stenosis severity in patients undergoing carotid artery stenting. Methods Patients who underwent carotid artery stenting between January 2012 and January 2016 at our tertiary care center were evaluated retrospectively. Two hundred fifty-five patients who underwent carotid artery stenting were included in the study. Accessible echocardiographic documentation of ninety-eight patients was accessed and evaluated. Results LV normal geometry was detected in 37 (37.7%) of the 98 carotid artery stenting (CAS) patients, concentric hypertrophy in 13 (13.2%), eccentric hypertrophy in 9 (9.1%), and concentric remodeling in 39 (39.7%). By a majority, distal filter was used in normal geometry and eccentric hypertrophy groups (82.9% vs 100%, P: .017). Considering the relationship between carotid artery stenosis severity and LV geometry, we determined that the stenosis severity was statistically significantly higher in the concentric hypertrophy group (p:0.012). However, although no complications were detected in the concentric hypertrophy group, it did not reach statistical significance between the groups (P: .058). LVMi and as expected, Doppler velocity showed a significant correlation with stenosis severity (r = .23 vs .54; P: .021, <.001, respectively). Conclusion Echocardiographic evaluation of LV geometry provided prognostic information in the development of carotid artery stenosis. Abnormal LV geometry is an independent predictor in detecting the severity of carotid artery stenosis undergoing carotid artery stenting.
