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Öğe Deep Learning-Assisted Detection and Classification of Thymoma Tumors in CT Scans(Mdpi, 2025) Kilic, Murat; Biyikli, Merve; Ozcelik, Salih Taha Alperen; Uzen, Huseyin; Firat, HuseyinBackground/Objectives: Thymoma is a rare epithelial neoplasm originating from the thymus gland, and its accurate detection and classification using computed tomography (CT) images remain diagnostically challenging due to subtle morphological similarities with other mediastinal pathologies. This study presents a deep learning (DL)-based model designed to improve diagnostic accuracy for both thymoma detection and subtype classification (benign vs. malignant). Methods: The proposed approach integrates a pre-trained VGG16 network for efficient feature extraction-capitalizing on its capacity to capture hierarchical spatial features-and an MLP-Mixer-based feature enhancement module, which effectively models both local and global feature dependencies without relying on conventional convolutional mechanisms. Additionally, customized preprocessing and post-processing methods are employed to enhance image quality and suppress redundant data. The model's performance was evaluated on two classification tasks: distinguishing thymoma from healthy cases and discriminating between benign and malignant thymoma. Comparative analysis was conducted against state-of-the-art DL models including ResNet50, ResNet34, SEResNeXt50, InceptionResNetV2, MobileNetV2, VGG16, InceptionV3, and DenseNet121 using metrics such as F1 score, accuracy, recall, and precision. Results: The model proposed in this study obtained its best performance in thymoma vs. healthy classification, with an accuracy of 97.15% and F1 score of 80.99%. In the benign vs. malignant task, it attained an accuracy of 79.20% and an F1 score of 78.51%, outperforming all baseline methods. Conclusions: The integration of VGG16's robust spatial feature extraction and the MLP-Mixer's effective feature mixing demonstrates superior and balanced performance, highlighting the model's potential for clinical decision support in thymoma diagnosis.Öğe Development of a model to predict the risk of early graft failure after adult-to-adult living donor liver transplantation: An ELTR study(Lippincott Williams & Wilkins, 2024) Giglio, Mariano Cesare; Dolce, Pasquale; Yilmaz, Sezai; Tokat, Yaman; Acarli, Koray; Kilic, Murat; Zeytunlu, MuratGraft survival is a critical end point in adult-to-adult living donor liver transplantation (ALDLT), where graft procurement endangers the lives of healthy individuals. Therefore, ALDLT must be responsibly performed in the perspective of a positive harm-to-benefit ratio. This study aimed to develop a risk prediction model for early (3 months) graft failure (EGF) following ALDLT. Donor and recipient factors associated with EGF in ALDLT were studied using data from the European Liver Transplant Registry. An artificial neural network classification algorithm was trained on a set of 2073 ALDLTs, validated using cross-validation, tested on an independent random-split sample (n=518), and externally validated on United Network for Organ Sharing Standard Transplant Analysis and Research data. Model performance was assessed using the AUC, calibration plots, and decision curve analysis. Graft type, graft weight, level of hospitalization, and the severity of liver disease were associated with EGF. The model (http://ldlt.shinyapps.io/eltr_app) presented AUC values at cross-validation, in the independent test set, and at external validation of 0.69, 0.70, and 0.68, respectively. Model calibration was fair. The decision curve analysis indicated a positive net benefit of the model, with an estimated net reduction of 5-15 EGF per 100 ALDLTs. Estimated risks>40% and<5% had a specificity of 0.96 and sensitivity of 0.99 in predicting and excluding EGF, respectively. The model also stratified long-term graft survival (p<0.001), which ranged from 87% in the low-risk group to 60% in the high-risk group. In conclusion, based on a panel of donor and recipient variables, an artificial neural network can contribute to decision-making in ALDLT by predicting EGF risk.Öğe The effect of clinicopathologic findings of hepatocellular carcinoma on posttransplant survival: a multcenter cohort from TASL liver transplantation special interest group(Elsevier, 2022) Akyildiz, Murat; Gencdal, Genco; Ince, Volkan; Harputluoglu, Muhsin Murat; Bozkurt, Birkan; Zeytunlu, Murat; Kilic, Murat[Abstract Not Available]Öğe Efficacy of Modified Talc Powder in Experimental Rat Model of Pleurodesis(Mdpi, 2026) Kilic, Murat; Ozhan, Onural; Yildiz, Azibe; Koytepe, Suleyman; Akyuz, Mustafa; Turkoz, Yusuf; Gokturk, NurcanBackground: Pleurodesis is a treatment method that aims to create permanent adhesion between the pleural layers to prevent recurrent fluid or air accumulation in the pleural cavity. Talc, one of the most commonly preferred agents in this procedure, is widely used in clinical practice. In this study, a new talc formulation with a modified surface to impart antibacterial and analgesic properties was experimentally evaluated for the first time. The main objective of the study was to comparatively assess the inflammatory and fibrotic responses following standard talc and modified talc applications. Methods: Thirty-six 12-week-old female Wistar albino rats were simply randomly divided into three different groups: control (n = 12), standard talc (n = 12), and modified talc (n = 12). Under anesthesia, 1 mL of physiological saline containing 17 mg of talc was injected intrapleurally into the right hemithorax. The presence of pneumothorax after the procedure was assessed by chest radiography. After a 12-day follow-up period, the animals were euthanized. Bronchoalveolar lavage (BAL) fluid samples, blood samples, and lung and pleural tissue samples were collected for biochemical, histopathological, and immunohistochemical analyses. Results: Modified talc application resulted in a significant increase in both visceral and parietal pleural thickness (p < 0.05). Granulation tissue formation and collagen deposition were significantly higher in the modified talc group. In addition, TGF-beta expression and CD68-positive macrophage count increased significantly in the modified talc group (p < 0.05). Inflammatory changes in the lung parenchyma were limited and not statistically significant. Conclusions: The modified talc formulation enriched with lidocaine and antibacterial agents produced a stronger inflammatory and fibrotic response compared to standard talc. These findings indicate that modified talc may increase the effectiveness of pleurodesis. Furthermore, the absence of significant lung parenchymal damage suggests that this treatment is locally effective and feasible. However, further long-term and advanced studies are needed to translate these results into clinical use.Öğe Grad-CAM Enhanced Explainable Deep Learning for Multi-Class Lung Cancer Classification Using DE-SAMNet Model(Mdpi, 2026) Kilic, Murat; Biyikli, Merve; Yelman, Abdulkadir; Firat, Huseyin; Uzen, Huseyin; Cicek, Ipek Balikci; Sengur, AbdulkadirBackground/Objectives: Lung cancer (LC) is the leading cause of cancer-related mortality worldwide, making early and accurate diagnosis crucial for improving patient outcomes. Although chest computed tomography (CT) enables detailed assessment of lung abnormalities, manual interpretation is time-consuming, requires expert expertise, and is prone to diagnostic variability. To address these challenges, this study proposes DE-SAMNet, a hybrid deep learning framework for automated multi-class LC classification from CT scans. Methods: The model integrates two pre-trained convolutional neural networks-DenseNet121 and EfficientNetB0-operating in parallel to extract complementary multi-scale features. A Spatial Attention Module (SAM) is applied to each feature stream to emphasize clinically important regions. Final classification is performed through a compact fusion mechanism involving global average pooling, batch normalization, and a fully connected layer. DE-SAMNet was evaluated on two datasets: a public dataset (IQ-OTH/NCCD) with benign, malignant, and normal cases, and a private clinical dataset including benign, malignant, cystic, and healthy cases. Results: On the public dataset, the model achieved a 99.00% F1-score, 98.41% recall, 99.64% precision, and 99.54% accuracy. On the private dataset, it obtained 95.96% accuracy, 95.99% precision, 96.04% F1-score, and 96.21% recall, outperforming existing approaches. To enhance reliability, explainable AI (XAI) techniques such as Grad-CAM were used to visualize the model's decision rationale. The resulting heatmaps effectively highlight lesion-specific regions, offering transparency and supporting clinical interpretability. Conclusions: This explainability strengthens trust in automated predictions and demonstrates the clinical potential of the proposed system. Overall, DE-SAMNet delivers a highly accurate and interpretable solution for early LC detection.Öğe Immunohistochemical Expressions of the Antimicrobial Peptides (hBD-3 and hCAP-18/LL-37) in Colon, Stomach and Lung Adenocarcinomas(Akad Doktorlar Yayinevi, 2015) Kilic, Murat; Oguztuzun, Serpil; Simsek, Gulcin; Cakir, EbruThis study investigated the immunohistochemical staining characteristics of human beta defensin-3 (hBD-3) and human cationic antimicrobial peptide-18/cathelicidin (hCAP-18/LL-37) in colon, stomach and lung adenocarcinomas and normal tissues (periphery to tumor tissues) from 22, 24 and 24 patients, respectively. Expressions of hBD-3 and hCAP-18/LL-37 were assessed by immunohistochemistry for colon, stomach and lung adenocarcinomas of 70 patients from Ataturk Chest Diseases and Thoracic Surgery Training and Research Hospital and Kecioren Training and Research Hospital. both located in Ankara, Turkey. The differences between the expressions of hBD-3 and hCAP-18/LL-37 in normal and carcinoma tissues were analyzed by Mann-Whitney U Test. When the normal and tumor tissues of these cases were compared according to their staining intensity of positive staining, the hBD-3 and hCAP-18/LL-37 expressions in colon, stomach and lung adenocarcinomas cells were significantly higher than those in normal cells (p<0.05). Immunostaining of HBD-3 and hCAP-18/LL-37 was found to be a marker of malignancy in colon, stomach and lung adenocarcinomas. The expressions of hBD-3 and hCAP-18/LL-37 were, for the first time, shown to be significantly altered in colon, stomach and lung adenocarcinomas as compared to controls. In conclusion, the present findings suggest that beside the antimicrobial activity of Antimicrobial Peptides (AMPs), hBD-3 and hCAP-18/LL-37 can also play a role in the pathogenesis of colon, stomach and lung adenocarcinomas.Öğe The influence of pneumothorax, pneumomediastinum, and other factors on the mortality and morbidity in patients with viral infections(2024) Kilic, Murat; Karatepe, UmitAim: This study examines the effects of pneumothorax and pneumomediastinum on the mortality and morbidity of patients with respiratory virus infections. It analyses blood parameters and the Systemic Immune Inflammation Index (SII) in patients who acquired these complications compared to those who did not. Materials and Methods: We conducted a retrospective assessment of 2246 COVID19 patients who received treatment at our medical facility between August 2020 and February 2021. This study included a total of 118 patients who were admitted to the hospital due to a respiratory virus illness. The patients were categorised into two groups: one consisting of individuals who experienced pneumothorax and/or pneumomediastinum, and the other consisting of individuals who did not acquire these complications. Both groups had an equal number of participants. The study analysed many factors including metabolic profiles, hemogram results, length of hospital stay, SII levels, and the incidence of pneumothorax, with a focus on their association with morbidity and mortality outcomes. Results: Significantly, female patients who experienced pneumothorax during COVID19 treatment exhibited a worse mortality rate. Patients with pneumothorax had elevated leukocyte and neutrophil counts, along with heightened systemic immune-inflammation index (SII) and decreased levels of total protein and albumin. The data highlight the potential importance of specific blood measurements, as well as the presence of pneumothorax, as indications for death in patients with respiratory virus infections. Conclusion: For enhanced patient outcomes, it is important to closely monitor and manage female patients who get pneumothorax after receiving therapy for respiratory virus infection.Öğe The Arthroscopic Wafer Procedure in Patients with Ulnar Impaction Syndrome(Thieme Medical Publ Inc, 2025) Ergen, Emre; Ertem, Kadir; Al, Firat; Kilic, Murat; Kabadayi, Bilal; Cicek, Ipek Balikci; Ozdes, Huseyin UtkuAim We aimed to show the outcomes of patients with ulnar impaction syndrome who had surgical treatment with the arthroscopic wafer procedure between 2013 and 2024. Materials and Methods We analyzed data from 22 patients (22 wrists) treated with the arthroscopic wafer procedure. Visual analogue scale (VAS) score, Disabilities of Arm, Shoulder and Hand (DASH), and Mayo Wrist scoring systems were used for clinical evaluation, grip strength, and wrist range of motion (ROM) were compared with the nonoperative side, local tenderness examination at triangular fibrocartilage complex location between pisiform bone and ulnar head and ulnar grind test were evaluated. Patients were also asked to rate their satisfaction with the surgery. In radiological evaluations, preoperative and postoperative ulnar variance was measured. Results The mean follow-up period was 58.6 months. The mean VAS score was 2.86, the mean DASH score was 24.58, and the mean MAYO score was 72.64. There was no significant difference in wrist ROM between the operated side and the contralateral side ( p > 0.05). The mean time to return to work after surgery was 6 weeks. A total of 77.3% of the patients had good or very good results. No complications were encountered in our study. Conclusion According to our study findings, arthroscopic wafer procedure as a minimally invasive method provided satisfactory clinical and functional results with lower complication rates in patients with ulnar impaction syndrome.Öğe Ultrasonographic Assessment of the Diaphragm and the Effects of Smoking on Respiratory Function in Individuals Attending a Smoking Cessation Center(Mdpi, 2026) Utus, Ahmet; Ozyilmaz, Semiramis; Karatas, Turgay; Dag, Nurullah; Ural, Gurkan; Balikci Cicek, Ipek; Kilic, MuratBackground: Smoking adversely affects pulmonary function and systemic health; however, its impact on diaphragm muscle morphology and its relationship with functional capacity and psychosocial outcomes in individuals without clinically diagnosed respiratory disease remain unclear. This study aimed to evaluate diaphragm muscle thickness in smokers and to investigate its associations with pulmonary function, functional capacity, sleep quality, and depression. Methods: This cross-sectional observational study included 20 smokers and 20 age-matched never-smokers. Pulmonary function was assessed using spirometry. Functional capacity was evaluated with the 6-Minute Walk Test (6 MWT) and the 30 s sit-to-stand test (30 s STST). Sleep quality and depression were assessed using the Pittsburgh Sleep Quality Index (PSQI) and the Beck Depression Inventory (BDI). Inspiratory and expiratory diaphragm muscle thicknesses were measured by ultrasonography. Between-group comparisons and correlation analyses were performed. Results: Smokers exhibited significant impairments in all assessed parameters except expiratory diaphragm thickness compared with controls (p < 0.05). Large to very large effect sizes were observed for FEV1, FEF25-75%, functional capacity, and inspiratory diaphragm thickness. Inspiratory diaphragm thickness showed moderate to strong positive correlations with pulmonary function parameters and a very strong positive correlation with functional capacity, while strong negative correlations were observed with sleep quality and depression (p < 0.05). Smoking duration was strongly associated with poorer functional and psychosocial outcomes. Conclusions: Smoking is associated with early and multidimensional impairments in diaphragm muscle morphology, pulmonary function, functional capacity, and psychosocial status, even in individuals without overt respiratory disease. Reduced inspiratory diaphragm thickness may represent an early and clinically meaningful marker of smoking-related respiratory muscle dysfunction.
