TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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Article A Copula-Based Classification Using Agglomerated Feature Selection_Extraction: An Application in Cervical Cancer Diagnostic(Ankara University, Faculty of Science, 2025-09-23) Kochan, Necla; Sheikhi, AyyubThe use of gene-expression datasets has significantly enhanced our understanding of complex diseases such as cancer. The importance of the relationship between genes in analyzing such datasets has been highlighted, indicating their crucial role in diagnosing the disease accurately. In this study, we investigate the associated copulas between attributes to extract fundamental block-related components. Subsequently, we perform a classification algorithm based on these components to classify a labeled target variable. Specifically, examining the practical implications and effectiveness of our approach in real-world scenarios, we provide a novel illustrative application in cervical cancer classification.Article Model-Based Feature Selection Using Structural Equation Modeling for Enhanced Classification Performance in High-Dimensional Datasets(Gazi University, 2025-09-01) Albayrak, Muammer; Turhan, KemalFeature selection is becoming more and more important for machine learning and data mining. Especially for high dimensional datasets, it is necessary to filter out irrelevant and unnecessary features to overcome the problems of overfitting and multidimensionality. We hypothesized that an effective feature selection can be made with a model-based approach using the Structural Equation Modeling (SEM) method. The dataset consists of 2969 samples and 117 features. First, a measurement model created was tested with confirmatory factor analysis (CFA) and the number of features was reduced to 58 by removing the statistically insignificant features. In SEM analysis, sub-feature sets consisting of 55, 52, 41 and 35 features were obtained by removing the variables whose relationship was below the threshold values determined for the standardized regression coefficient (SRC). The obtained sub-feature sets were tested with a multilayer perceptron (MLP) and their effect on performance was examined. Results were compared with random forest feature importance as baseline method. SEM and random forest have generally performed very closely. While sub-feature sets created with the random forest in two-class classification produced better results, the sub-feature sets created with the suggested SEM-based method in three and five-class classification provided better performance. These results showed that effective feature selection can be made with the proposed model-based approach using SEM. With this approach, it is possible to obtain sub-feature sets that form a model which statistically significant and consistent with field knowledge by including expert knowledge in the modeling process.Article Citation - Scopus: 1Evaluation of Response to Treatment in Breast Cancer-Related Lymphedema(Turkish Society of Physical Medicine and Rehabilitation, 2024-10-31) Eyigor, Sibel; Çınar, Ece; Tanigor, Goksel; İnbat, Menekse Ozgur; Güvercin, Ezgi Yıldız; Kabayel, Sedef Çalışkan; Çalışkan Kabayel, Sedef; Yıldız Güvercin, EzgiObjectives: The primary objective of this study was to assess and compare the response to the breast cancer-related lymphedema (BCRL) treatment with Breast Cancer-Related Lymphedema of the Upper Extremity (CLUE) scores, bioimpedance spectroscopy (BIS), and the volume-assessments /measurements. The secondary objective of the study was to investigate whether CLUE played a role in the treatment response and to examine its correlation with the other measures of lymphedema. Patients and methods: Between January 2019 and June 2019, a total of 40 patients (2 males, 38 females; mean age: 57.8±12.5 years; range, 45 to 70 years) who were diagnosed with unilateral Stage 2-3 BCRL and underwent treatment were included. The patients’ upper extremity volumes were assessed and the patients were evaluated with the CLUE score, the Disabilities of the Arm, Shoulder, and Hand Outcome Measure (QuickDASH) score, BIS, and hand grip strength before and after the complete decongestive therapy. Results: Correlation analyses revealed that CLUE total score and BIS values were correlated with the reduction in the volumes (p=0.04 and p<0.001, respectively). The CLUE total score was also found to be positively correlated with the BIS values (p<0.001). Hand grip strength and QuickDASH scores were not found to be correlated with the changes in the volume and CLUE total scores. Conclusion: The development of a structured clinical assessment such as CLUE provides clinicians for a standardized evaluation for BCRL. The diagnosis of subclinical lymphedema can be detected earlier by using the BIS and CLUE scale and lymphedema comorbidity and treatment costs can be reduced.Article Ramifications of Households Non-Farm Income on Agricultural Productivity: Evidence From Rural Area of Pakistan(2020) Rashidin, Md.salamun; Liu, Bin; Javed, SaraIn Pakistan, agriculture sector currentlycontributesup to 28 percent to in GDP. Due tothe development ofmodern scienceand technology, rural household source of income is altering. Lots of research suggested that non-farm income is the main source of income for rural area. This study investigates the effects of non-farm income on agriculture productivity in Pakistan. The current research accumulated data from Pakistan Social and Living Standards Measurement Survey (PSLM) 2014-15. Pakistan Federal Bauru of Statistics has developed its own sampling frame for rural and urban areas. Researcher used the Heckman’s two-step procedure to tackle the problem of endogeneity and selection bias. The first phase of probit regression coefficient indicatesthatthe availability of banks, motorable roads, forest, telecommunication substructure, montane grasslands and shrublands zone are substantial to clarify the non-farm income. On the other hand, the second stage of OLS regression exhibited a significant negative association between non-farm income and per-capitafarm income.Article Demansın Davranışsal ve Psikolojik Belirtileri Bilgi Ölçeği’nin Türkçe Versiyonunun (DDPB-T) Geçerliliği ve Güvenilirliği: Bakıcılar Arasında Psikometrik Bir Değerlendirme(Turkiye Sinir ve Ruh Sagligi dernegi, 2024) Var, Levent; Güllüoğlu, Halil; Uysal, Hasan Armağan; Poyraz, Turan; Başaran, Simay; Eşkut, NeslihanAmaçArticle Duchenne Muscular Dystrophy Patients Diagnosed at the Asymptomatic Stage: What Are the Benefits of Early Diagnosis(Turkish Society of Physical Medicine and Rehabilitation, 2024-11-14) Sertpoyraz, Filiz Meryem; Tanigor, Goksel; Baydan, Figen; Kale, Murat Yildirim; Tanigoer, GoekselObjectives: This study aimed to demonstrate whether a diagnosis given at the asymptomatic stage of patients with DMD can affect the clinical outcomes and to define the clinical characteristics of the patients. Patients and methods: The cross-sectional study was conducted with 136 male patients (mean age: 8.8±3.7 years; range, 3 to 17 years) with DMD between March 2022 and February 2023. The patients were diagnosed through clinical presentation, pathology studies, and genetic testing. The demographic, clinical, and the laboratory data of the patients were recorded. The patients were evaluated in two groups: those diagnosed at the asymptomatic stage due to elevated creatine kinase (CK) and those diagnosed due to clinical symptoms. Patients were further stratified according to their age groups: those younger than 10 years and those aged 10 years or older. Hand grip, quadriceps muscle strength, and Vignos and Brooke motor functional assessment scales of the two groups were compared. Results: In patients who were diagnosed with CK levels, CK elevation was significantly more common than other findings. When the age at diagnosis was evaluated, the age at diagnosis in those diagnosed with CK levels was statistically significantly lower than in those diagnosed with clinical findings. No significant difference was detected in clinical findings between the groups under the age of 10 years. Among patients aged 10 years or older, hand muscle strength, quadriceps muscle strength, and Vignos and Brooke motor function scale scores were significantly better in those diagnosed with CK levels compared to those diagnosed with clinical findings. Conclusion: This study shows that early diagnosis in the preclinical period, which enables earlier medical treatment and rehabilitation, may have a positive effect on motor functions and the course of the disease.Article Can Volumetric Magnetic Resonance Imaging Evaluations Be Helpful in the Follow-Up of Cognitive Functions in Cognitively Normal Parkinson's Disease Patients?(Tubitak Scientific & Technological Research Council Turkey, 2024-08-23) Uysal, Hasan Armağan; Hunerli, Duygu; Çakmur, Raif; Dönmez Çolakoğlu, Beril; Ada, Emel; Yener, Görsev; Çolakoğlu, Beril DönmezBackground/aim: In this study, besides the evaluation of gray and white matter changes in cognitively normal Parkinson's disease (PDCN) patients with volumetric magnetic resonance imaging (MRI) parameters, it was tried to show that some neuropsychological tests may be impaired in PD-CN patients. Materials and methods: Twenty-six PD-CN patients and 26 healthy elderly (HC) participants were included in the current study. Global cognitive status was assessed using the mini-mental state examination (MMSE), and the Montreal cognitive assessment scale (MoCA). Attention and executive functions were evaluated using the Wechsler memory scale-revised (WMS-R) digit span test and trail making test (TMT) part A and part B, the Stroop test, semantic and phonemic fluency tests, and clock drawing test. Magnetic resonance imaging (MRI) was acquired according to the Alzheimer's disease neuroimaging initiative (ADNI) protocol. Results: There were no significant differences among groups regarding age, sex, handedness, and years of education. In the comparison of the PD-CN group and the HC group, there was a statistical decrease in the total animal scores, lexical fluency, TMT part A and TMT part B scores in the PD-CN group. Subcortical gray matter volumes (GMV) were significantly lower in PD-CN patients. The PD-CN group had a significantly reduced total volume of right putamen and left angular gyrus compared to that in the HC group. We observed that putamen and angular gyrus volumes were lower in PD-CN patients. On the other hand, TMT part B may be a useful pretest in detecting the conversion of mild cognitive impairment in PD. Conclusion: Significant MRI volumetric measurements and neuropsychological test batteries can be helpful in the clinical follow-up in PD-CN patients.Article Citation - Scopus: 1Yaşlanmanın Yüz ve İsim Tanıma Üzerindeki Etkisi: Bir fMRI Çalışması(Turkish Association of Nervous and Mental Health, 2023) Haznedaroğlu, Damla İşman; Gönül, Ali Saffet; Eroğlu, Seda; Uslu, Özgül; Oğuz, Kaya; Erata, Mehmet Can; Kan, Öykü Yavuz; Erdogan, YigitAmaç: Bu çalışmanın amacı ilerleyen yaşla birlikte bellek görevi sırasında beyindeki fonksiyonel değişiklikleri tespit etmek ve bu değişikliklerin bellek performansıyla ilişkisini incelemektir. Yöntem: Çalışmaya Genç Yetişkin Grup (GYG; N=20; 20-25 yaş) ve İleri Yaş Grup (İYG; N=18; 60-70 yaş) olmak üzere iki grup dahil edilmiştir. Gruplara Montreal Bilişsel Değerlendirme (MoCA) puanları 21’in üstünde olan ve birinci dereceden akrabalarında Alzheimer Hastalığı öyküsü olmayan kişiler dahil edilmiştir. Katılımcılara yüz ve isimlerin öğrenildiği kodlama, yüz tanıma ve isim tanıma alt görevlerini içeren bellek görevi sırasında Fonksiyonel Manyetik Rezonans Görüntüleme (fMRG) çekimi yapılmıştır. Bulgular: GYG’a göre, İYG’de yüz tanıma görevinde sol posterior singulat korteks, sol süperior frontal korteks, sol fusiform yüz tanıma alanında; isim tanıma görevinde sol süperior frontal korteks, sağ prefrontal korteks, sol anterior+posterior singulat kortekste aktivite artışı bulunmuştur. İYG yüz tanıma ve isim tanıma bellek testlerinde daha düşük doğru sayısına sahiptir (sırasıyla p=0,026; p=0,001). Sonuç: Bulgular İYG’de bellek görevi sırasında beyinde daha yaygın bir aktivasyon ortaya çıktığını tespit etmiştir. Bu durum ilerleyen yaşla birlikte bellekteki bilgiler hatırlanırken kişilerin daha fazla nöral ve bilişsel kaynağa ihtiyaç duyduğunu göstermektedir.Article Expressions of the Satellite Repeat Hsat5 and Transposable Elements Are Implicated in Disease Progression and Survival in Glioma(Tubitak Scientific & Technological Research Council Turkey, 2024-08-23) Köse, Sıla Naz; Yaraş, Tutku; Bursalı, Ahmet; Oktay, Yavuz; Yandım, Cihangir; Karakulah, GökhanThe glioma genome encompasses a complex array of dysregulatory events, presenting a formidable challenge in managing this devastating disease. Despite the widespread distribution of repeat and transposable elements across the human genome, their involvement in glioma's molecular pathology and patient survival remains largely unexplored. In this study, we aimed to characterize the links between the expressions of repeat/transposable elements with disease progression and survival in glioma patients. Hence, we analyzed the expression levels of satellite repeats and transposons along with genes in low-grade glioma (LGG) and high-grade glioma (HGG). Endogenous transposable elements LTR5 and HERV_a-int exhibited higher expression in HGG patients, along with immune response-related genes. Altogether, 16 transposable elements were associated with slower progression of disease in LGG patients. Conversely, 22 transposons and the HSAT5 satellite repeat were linked to a shorter event-free survival in HGG patients. Intriguingly, our weighted gene coexpression network analysis (WGCNA) disclosed that the HSAT5 satellite repeat resided in the same module network with genes implicated in chromosome segregation and nuclear division; potentially hinting at its contribution to disease pathogenesis. Collectively, we report for the first time that repeat and/or transposon expression could be related to disease progression and survival in glioma. The expressions of these elements seem to exert a protective effect during LGG-to-HGG progression, whereas they could have a detrimental impact once HGG is established. The results presented herein could serve as a foundation for further experimental work aimed at elucidating the molecular regulation of glioma genome.Article Observing Conductance Quantization by a Novel Magnetic Control System(Gazi Univ, 2024-06-01) Ozturk, Yavuz; Çiğdem, Dila; Karakaya, Bilge Toprak; Değimli, Duru; Çelikoğlu, Meltem Gönülol; Gonulol, MeltemIn this study, a novel magnetic system that allows observing quantized conductance for undergraduate and graduate laboratories is presented. Bending of a magnetic cylindrical beam, like a cantilever, is controlled by an electromagnet to provide contact between needle type electrode and a plane of conductor. It is shown that by using the beam bending, it is possible to displace an object on the beam in nanometer and micrometer scale. The measured quantized conductance results prove that the designed system can be used for demonstration of the quantized conductance.