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Öğe Automated Classification of Skin Diseases Using Microscopic Images: A Machine Learning Approach(Wiley, 2025) Karapinar Senturk, Zehra; Guler, Recep; Ozcan, Yunus; Gamsizkan, MehmetThis study presents a machine learning-based approach for the automated classification of skin diseases, specifically targeting morphea and lichen sclerosus, using microscopic images. The proposed method involves a systematic workflow, including image preprocessing techniques such as resizing, Reinhard normalization, Gaussian filtering, and CLAHE histogram equalization to enhance image quality. Feature extraction was performed using Gray-Level Co-occurrence Matrix (GLCM) and histogram-based statistical methods, capturing texture and intensity characteristics of skin tissues. Several classification models, including Support Vector Machine (SVM), Artificial Neural Network (ANN), Decision Tree (DT), Random Forest (RF), K-Nearest Neighbors (K-NN), and Logistic Regression (LR), were evaluated using accuracy, precision, recall, and F1 score, with hyperparameter optimization via grid search. The experimental results revealed that the combined feature set (GLCM + Histogram) achieved the highest performance, with the RF and K-NN models yielding a 100% in all performance metrics, including accuracy, sensitivity, recall, and F1-score. The study introduces a novel approach by examining these two diseases simultaneously, offering a reliable tool to support dermatologists with accurate and quick diagnoses. Future work will focus on expanding the dataset, exploring advanced deep learning techniques, and integrating clinical metadata to enhance model generalizability.Öğe BRAF mutation, TERT promoter mutation, and HER2 amplification in sporadic or neurofibromatosis-related neurofibromas and malignant peripheral nerve sheath tumors: do these molecules have a signature in malignant transformation?(Wiley, 2020) Coskun, Sinem; Gamsizkan, Mehmet; Yilmaz, Ismail; Yalcinkaya, Ulviye; Sungur, Mehmet Ali; Buyucek, Seyma; Onal, BinnurPeripheral nerve sheath tumors may occur sporadically or related to neurofibromatosis (NF). Unless the mechanisms of tumorigenesis in NF related malignant peripheral nerve sheath tumors (MPNST) are better understood, it remained unclear in sporadic cases. We aimed to investigate the genetic route for malignancy in both individuals with NF-1 and sporadic ones to open a way for targeted therapies in the future. We investigated the role of HER2 with Dual ISH DNA Probe Cocktail test, BRAF mutation (exon 15) and TERT promoter mutation frequency with Sanger sequencing method in respectively 25 sporadic neurofibromas, 25 NF-1 related neurofibromas and 25 MPNST cases from two institutes. Categorical data were analyzed and summarized as frequency and percentage. Statistical analysis was done with SPSS v.22 statistical package, and the statistical significance level was considered as 0.05. We identified TERT promoter mutation only in one sporadic MPNST (4%) and no BRAF mutation in any case. HER2 amplification is found in 10/25 (40%) MPNST cases. No mutations or gene amplification detected in neurofibromas (p < 0.001). MPNSTs are sarcomas with poor prognosis and limited treatment options. TERT promoter mutations and HER2 amplification may play a putative role in therapeutic purposes.Öğe Clinicopathologic Features and Prognostic Significance of Immunohistochemistry and In Situ Hybridization Based Molecular Classification in Gastric Carcinoma(Begell House Inc, 2023) Issin, Gizem; Sayar, Ilyas; Demir, Fatih; Bakkaloglu, Irem Guvendir; Gamsizkan, Mehmet; Yildiz, Zeliha; Yilmaz, IsmailBackground/Aim: Gastric carcinoma (GC) is a highly heterogeneous disease with many subtypes that have different morphologic and molecular characteristics. In the current study, we analyzed immunohistochemical (IHC) and in situ hybridization (ISH) features of GCs and evaluated their association with prognosis and clinicopathological features. Materials and Methods: Three hundred cases analyzed by IHC and ISH for microsatellite stability, p53, e-cadherin, HER2, PD-L1 expression, and Epstein-Barr virus (EBV) status. Cases were classified into five subgroups based on expression profile. The relationships between subgroups, clinicopathological features, and survival were determined. Results: Ten ( 3.3%) cases were classified as EBV-associated, 45 (15%) as microsatellite instable (MSI), 73 (24.3%) as EBV-/ microsatellite-stable (MSS)/epithelial-mesenchymal-transformation (EMT)-like, 75 (25%) as EBV-/MSS/ non-EMT-like/p53+, and 97 (32.3%) as EBV-/MSS/non-EMT-like/ p53-. The MSI subtype had the best overall survival (OS). In contrast, the EBV-/MSS/EMT-like subtype had the poorest OS. The MSI subtype was also related with old age of the patient and antrum-corpus localized tumors, whereas the EBV-/MSS/EMT-like was associated with young age, larger tumor size, and advanced stage presentation. PD-L1 positivity is highly correlated with MSI and EBV-associated subtypes. Conclusion: Our data demonstrated a link between IHC/ISH characteristics of GC and clinical outcomes. IHC/ISH based molecular classification may be helpful in predicting the survival.Öğe Comment on Mahmood, M.N. Direct Immunofluorescence of Skin and Oral Mucosa: Guidelines for Selecting the Optimum Biopsy Site. Dermatopathology 2024, 11, 52–61(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Demiral, Şebnem; Ozcan, Yunus; Gamsizkan, Mehmet[No abstract available]Öğe The Comparative Dermal Stimulation Potential of Constant-Volume and Constant-Amount Diluted Calcium Hydroxylapatite Injections Versus the Concentrated Form(Lippincott Williams & Wilkins, 2023) Botsali, Aysenur; Erbil, Hakan; Esme, Pelin; Gamsizkan, Mehmet; Aksoy, Ali Okan; Caliskan, ErcanINTRODUCTION Biostimulation properties of diluted and hyperdiluted calcium hydroxylapatite (CaHA) injections have become increasingly popular. However, the existing data are insufficient to certify a particular dose-response pattern.OBJECTIVE To assess and compare the dermal stimulation potentials of different concentrations of CaHA injections.MATERIALS AND METHODS Two independent experiments (Experiment-1: constant injection volume vs Experiment-2: constant CaHA amount) included 4 study groups each, and these experimental groups were placed consecutively on the abdominal skin of a juvenile Yorkshire pig. Histopathological and immunohistochemical stainings were performed on punch biopsy materials collected 4 months after the injection day.RESULTS The fibroblast count significantly decreased upon dilution from 1:3 to 1:19 in experiment 1 (p = .000) but still higher than the control group. In experiment 1, the collagen density of the concentrated form was more elevated than the 1:19 dilution and the negative control groups (p = .034 and .000, respectively) but similar to the 1:3 dilution (p = .123). No significant difference was observed between the groups regarding collagen density with a standard amount of CaHA (0.2 mL, 30%) (p > .05).CONCLUSION Despite the efficacy being more pronounced till 1:3 dilution, hyperdiluted CaHA at any dilution ratio up to 1:19 can provide a higher fibroblast count than the negative control group.Öğe Comparison of histopathological and biomechanical changes of ligamentum mucosum in patients with anterior cruciate ligament rupture(Turkish Joint Diseases Foundation, 2024) Turhan, Yalcin; Arican, Mehmet; Karaduman, Zekeriya Okan; Sungur, Mehmet Ali; Gamsizkan, MehmetObjectives: The aim of this study was to identify the biomechanical and histopathological changes of ligamentum mucosum (LM) in patients with intact versus ruptured anterior cruciate ligament (ACL). Patients and methods: A total of 67 patients (45 males, 22 females; mean age: 33.2 +/- 7.9 years; range, 18 to 45 years) who underwent arthroscopic knee surgery for intraarticular pathologies between July 2022 and January 2023 were prospectively analyzed. The patients with LM were divided into two groups as the ACL intact group (n=31) and ACL ruptured group (n=36). Biomechanical tests and histopathological examinations were performed in all LM patients. Results: Age and body mass index distributions were similar between the groups (p>0.05). Peak force values of the LM in the ACL ruptured group were significantly higher than the ACL intact group (p=0.037). No significant difference was found between the groups in terms of collagen index (p=0.103) and fibroblast count (p=0.821). Conclusion: The peak force values of the LM were significantly higher in the ACL ruptured group as compared to the ACL intact group, which is probably due to the adaptation of LM in patients with ACL rupture against increased deforming forces to maintain knee stability.Öğe Diagnosis of Lichen Sclerosus, Morphea, and Vasculitis Using Deep Learning Techniques on Histopathological Skin Images(Sakarya University, 2025) Güler, Recep; Karapinar Şentürk, Zehra; Gamsizkan, Mehmet; Ozcan, YunusSkin diseases are very common all over the world. The examination can be done by photographing the relevant area or taking a tissue sample to diagnose skin diseases. Examining tissue samples allows examination at the cellular level. This study discussed three skin diseases: lichen sclerosus, morphea, and cutaneous small vessel vasculitis (vasculitis). For this problem, which does not have an open-access dataset in the literature, a dataset consisting of histopathological images belonging to each class was created. Convolutional neural network models were created for this three-class classification problem, and their results were evaluated. In addition, in this problem where it is difficult to obtain sample images, the efficiency of transfer learning methods was evaluated with a limited number of examples. For this purpose, tests were performed with VGG16, ResNet50, InceptionV3, and EfficientNetB4 models, and the results were given. Among all the results, the accuracy value of the VGG16 model was 0.9755 and gave the best result. However, although the accuracy value was quite good, precision, recall, and f1-score metrics values were around 0.65. This shows deficiencies in how often the model correctly predicts the positive class and how well it predicts all positive examples in the dataset. © 2025 Elsevier B.V., All rights reserved.Öğe Effects of Drone Brood Homogenate on Wound Healing: An Experimental Study on Rats(Wiley, 2025) Arican, Mehmet; Kekecoglu, Meral; Turhan, Yalcin; Caprazli, Tugce; Gamsizkan, Mehmet; Karaduman, Zekeriya OkanBackground Wound healing is one of the most interesting topics in orthopaedic surgery, and there are many studies on the factors and mechanisms affecting this process. Objectives To evaluated the macroscopic and histopathological results of drone larvae homogenate (DLH) on wound healing in a full-thickness wound model. Methods Thirty male wistar rats (6-8 weeks, 250 +/- 50 g) were used. A uniform circular full-thickness wound of approximately 18.44 +/- 1.45 (control), 19.02 +/- 1.24 (silverdin), 19.37 +/- 1.28 (DLH) mm2 was excised on the back of each rat. They were divided into control (n: 10), silverdin (n: 10) and DLH (n: 10) groups. DLH, collected from the beehive for 3-7 days in late spring and ready for use after homogenization and lyophilization. Two mL of physiological saline, silver sulfadiazine 1% and DLH were applied to the control, silverdin and DLH groups, respectively, and a thin layer that completely covered the wound, and repeated every 2 days for all groups for 14 days. The condition of the lesions was observed every 2 days and the amount of contraction and granulation tissue formed in the lesion was recorded. The lesioned areas was examined histopathologically. Results There was no statistically significant difference in lymphocyte, fibroblast, scar thickness, polymorphonuclear leukocyte (PMNL), minivascular density (CD34) and transforming growth factor-beta 1 (TGF-beta 1) among the control, silverdin and DLH groups (p = 0.771, 0.434, 0.07, 0.396). The scar density of the DLH group was found to be higher than the control and silverdin groups (p = 0.003). The average wound diameter of the control group (6.87 +/- 0.93 mm2) on the 10th day was found to be higher than the silverdin (4.39 +/- 1.15 mm2) and DLH groups (4.16 +/- 0.55 mm2) (p = 0.0001). Conclusions DLH has a positive effect on wound healing, especially by ensuring early wound contraction and wound scar formation.Öğe The Effects of Phenyramidol and Diclofenac Treatment on Fracture Healing in Rats(Korean Orthopaedic Assoc, 2024) Celik, Mucahit; Karaduman, Zekeriya Okan; Turhan, Yalcin; Arican, Mehmet; Gamsizkan, Mehmet; Saglam, Sonmez; Uludag, VeyselBackground: Fracture healing or nonunion refers to a process in which many factors interact. In this study, we aimed to evaluate the radiological, histological, and biomechanical effects of phenyramidol and diclofenac, which are frequently used to treat post-fracture ture pain worldwide, on fracture healing and nonunion in a rat femur fracture model. Methods: In this study, 72 male Wistar-Albino rats aged 2-3 months and weighing 250 +/- 30 g were divided into 4 main groups. The rats were divided into 12 subgroups according to the early, middle, and late periods. A fracture model was created in rat femurs, and surgical fixation was performed. Postoperative analgesic treatment protocols included phenyramidol, diclofenac, phenyramidol + diclofenac, and the control group. The rats were sacrificed on the fifteenth, thirtieth, and forty-fifth days and were evaluated radiologically, histopathologically, and biomechanically. Results: Scoring was conducted independently by 2 orthopedists not involved in the study. When the results were analyzed statistically, no statistically significant difference was observed between the fifteenth and thirtieth day radiology score values of the control, diclofenac, phenyramidol, and Phenyramidol + diclofenac groups (p > 0.05), but there was a statistically significant difference (p < 0.05) between the forty-fifth day radiology score values of the control, diclofenac, phenyramidol, and phenyramidol + diclofenac groups. Conclusions: Our study shows that the use of diclofenac or phenyramidol alone negatively affects postoperative fracture healing. However, this effect was less pronounced in the combined treatment group. Histologic examination revealed that neither treatment had a significant effect on healing. There were statistical differences in biomechanical and radiologic properties between the phenyramidol and diclofenac groups; in particular, the diclofenac group had lower biomechanical properties.Öğe Intraoperative Dermatoscopic Features of Subungual Exostosis(Mashhad Univ Med Sciences, 2020) Elmas, Omer Faruk; Kilitci, Asuman; Uyar, Belkiz; Gamsizkan, Mehmet[Abstract Not Available]Öğe Investigation of the Relationship of Two-Glass Test with Prostate Biopsy and Presence and Grade of Asymptomatic Prostate Inflammation in Men with Serum Prostate-Specific Antigen Level Between 2.5-10 ng/ml(Duzce Univ, Fac Medicine, 2024) Yuksel, Alpaslan; Tekin, Ali; Senoglu, Yusuf; Baba, Dursun; Gamsizkan, MehmetObjective: Prostate-specific antigen (PSA) is utilized as a marker to detect prostate cancer. Elevated PSA levels often lead to prostate biopsy to assess the potential presence of cancer. However, PSA elevation is not specific to cancer and can be caused by various conditions, including benign prostatic hyperplasia (BPH), urinary tract infections, and chronic prostatitis. Notably, approximately 66% of patients undergoing biopsy do not have prostate cancer, leading to unnecessary procedures and associated complications. Chronic prostatitis is detected in around 40% of these biopsies. The two-glass test involves examining urine before and after a rectal examination to diagnose chronic prostatitis. This study aims to investigate the effectiveness of the two-glass test in predicting prostatitis and inflammation in patients with PSA levels between 2.5-10 ng/ml who have undergone prostate needle biopsy. Materials and Methods: The study included fifty-two male patients aged between 50 and 78 years with PSA levels between 2.5 and 10 ng/ml who presented to our clinic. All patients underwent the EPS-two-glass test and prostate biopsy. EPS (expressed prostatic secretion) is obtained by collecting fluid from the urethra after prostate massage, while VB-3 (voided bladder-3) is urine collected after a massage. These samples are used to detect prostate infection. Prostate inflammation was deemed significant if >= 10 leukocytes were observed under the microscope. Patients were categorized into three groups based on pathology results: prostate cancer, BPH, and chronic prostatitis. The chronic prostatitis group was further classified based on histopathological calcification described by Nickel. Results: Chronic prostatitis was detected in 38% of the study participants. VB3 positivity was significantly higher in the chronic prostatitis group compared to the other groups (p = 0.028). Although no significant difference was observed in the prevalence of inflammation and PSA elevation, PSA levels were higher in the multifocal inflammation subgroup compared to the focal inflammation group. Conclusions: The relationship between chronic prostatitis and PSA elevation remains unclear. Although this study did not find a statistical relationship between inflammation and PSA elevation, the significant correlation between chronic prostatitis and VB3 positivity suggests a potential link. These findings can serve as a foundation for further research aimed at reducing unnecessary biopsies.Öğe KRAS, BRAF, PIK3CA mutation frequency of radical prostatectomy samples and review of the literature(Taylor & Francis Ltd, 2021) Bahcivan, Atike; Gamsizkan, Mehmet; Coskun, Sinem Kantarcioglu; Cangur, Sengul; Yuksel, Alpaslan; Ceyhan, Aysegul; Onal, BinnurObjective The molecular basis of prostate cancer is highly heterogeneous. Our study aimed to perform the mutation analysis of KRAS, BRAF, PIK3CA, and immunohistochemical (IHC) evaluation of EGFR, HER2, p16, and PTEN to demonstrate new areas for targeted therapies. Methods A total of 24 prostatectomy samples diagnosed with adenocarcinoma were analyzed by microarray hybridization. Also, these samples were IHC stained for EGFR, HER2, P16, and PTEN. The cases were divided into two groups based on low and high Gleason scores. All findings were compared with the clinicopathological parameters of the patients. Results While KRAS mutation was in 3/24 (12.5%) of our cases, BRAF and PIK3CA mutations were not detected. There was no significant difference between the groups in terms of KRAS mutation frequency. HER2 was immunohistochemically negative in all samples. There was no correlation between EGFR, P16 immunopositivity, and clinicopathological features. Conclusion KRAS mutation frequency is similar to those in Asian populations. BRAF and PIK3CA mutation frequencies have been reported in the literature in the range of 0-15% and 0-10.4%, respectively, consistent with our study findings. HER2 immunoexpression is a controversial issue in the literature. EGFR and p16 expressions may not correlate with the stage.Öğe Novel mutation identified in the DDB2 gene in patients with xeroderma pigmentosum group-E(Wiley, 2020) Karagun, Ebru; Eroz, Recep; Gamsizkan, Mehmet; Baysak, Sevim; Eyup, Yavuz; Ozcan, YunusBackground Xeroderma pigmentosum (XP) is a rare photosensitive syndrome, which is divided into eight complementation groups (XP-A to XP-G and XPV) and characterized by skin cancers diagnosed at early age. A family of seven members (age range between 5 and 47 years) with carriers of the novel nonsense mutation that causes XP-E type were included in the current study. Methods DNA was isolated from peripheral blood samples of the proband, and cancer predisposition genes were sequenced with next-generation sequencing. The demographic features and the laboratory, clinical, and histopathological findings of patients were evaluated. Results In the proband, squamous cell carcinoma was first diagnosed in the right-eye cornea at the age of 13 years and then in the left-eye cornea at the age of 15 years. Later, the patient was diagnosed with basosquamous cell carcinoma on the dorsum of the nose at the age of 18 years. After genetic analysis, a novel nonsense c.1063C>T(p.Arg355Ter) pathogenic variation that causes XP-E type was detected as homozygous in the DDB2 gene of the proband and her siblings, 11 and 5 years of age, and as heterozygous in her parents and a 22-year-old brother. Conclusion Because of the occurrence of early termination codon, truncated nonfunctional proteins or proteins with deleterious loss or gain-of-function activities are synthesized in nonsense mutation. Thus, to avoid the development of pathological lesions, it is important that such patients with nonsense mutation stay away from agents that might cause DNA damage and develop an appropriate lifestyle according to this condition.Öğe Refining diagnosis is the prerequisite for the correct treatment: The cytodiagnostic utility of SOX10 in the diagnosis of metastatic melanoma(Wiley, 2021) Kilitci, Asuman; Elmas, Omer Faruk; Demirbas, Abdullah; Gamsizkan, Mehmet; Atasoy, Mustafa; Tursen, Umit; Lotti, Torello[Abstract Not Available]Öğe Short- and long-term effects of rapamycin on ischemic damage and apoptotic changes in torsion of rat testes(Springer, 2021) Kabaklioglu, Murat; Kaya, Murat; Sahin, Ibrahim Ethem; Gamsizkan, Mehmet; Bahcivan, Atike; Eroz, RecepRapamycin has antioxidant defense mechanisms and immune suppressive effects. To detect the short- and long-term effects of rapamycin on ischemic damage and apoptotic changes in torsion of rat testes, mature male albino Wistar rats (n = 48) were included in the study as control, sham, early torsion-detorsion (T/D), early rapamycin treatment, early rapamycin control, late T/D, late rapamycin treatment, and late rapamycin control. The right testis was rotated 720 degrees in a clockwise direction during 4 h in operation groups. Rapamycin was administered orally three times: 30 min before detorsion and 24 and 48 h after detorsion. The animals were killed on the third day in early groups and on the tenth day in late groups after detorsion. Statistically significant differences among all groups were detected for SOD and TBARS, mean seminiferous tubule diameter (MSTD) and Cosentino's histologic score (CHS), caspase 3, bax, average number of apoptotic cells per tubule (ANPCT), and percentage of apoptotic tubule (PAT) values. ANPCT values were 10% lower in the rapamycin treatment groups compared with the untreated T/D groups, and the PAT values were also approximately 1.3 times lower. Although short-term usage of rapamycin may reduce to the tubular injury caused by I/R conversely to apoptosis in the testicular tissue after testicular torsion, rapamycin may have the potential to increase the long-term apoptosis with/without testicular torsion and a subsequent regression in fertility.Öğe Systemic tranexamic acid promotes bone healing in a rat model of femur fracture(Turkish Joint Diseases Foundation, 2020) Karaduman, Zekeriya Okan; Arican, Mehmet; Turhan, Yalcin; Turhal, Ozan; Orhan, Zafer; Gamsizkan, MehmetObjectives: This study aims to investigate the effect of tranexamic acid (TXA) on the union of closed femoral fractures using radiological and histological methods in an experimental rat model. Materials and methods: This experimental study was conducted between June 2017 and February 2018. Closed femoral fractures were created in 36 male Wistar albino rats (age: three months [range. 2.5-3.5 months]. weighing 200 grams [range. 180-220 grams]). Half of the animals randomly divided into two groups were administered intravenous single dose of TXA (30 mg/kg). whereas the animals in the control group did not receive any medication. The animals in the two groups were randomly divided into three groups with six animals each and cervical dislocation was performed at days 15, 30, and 45, and radiological and histopathological healing scores were compared. Results: When the mean radiological scores of the TXA and control groups were compared. a statistically significant difference was found in favor of the TXA group at day 15 (p=0.019). but no significant difference was found in the mean scores on days 30 and 45 (p=0.138 and p=0.269. respectively). Histopathological examination also showed a statistically significant difference between the 15-day mean score values in favor of the TXA group (p=0.017). Conclusion: The use of systemic TXA accelerates early bone formation and fracture healing.
