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 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 Complications and Therapeutic Approaches in a Sciatic Nerve Injury Rat Model(2025-04-30) Adali, Yasemen; Barış, Elif; Daştan, Ali Engin; Öztürk, VolgaSciatic nerve injury (SNI) is a common model for studying peripheral nerve damage and regeneration. This study investigates the complications associated with acute nerve injury (ANI) by laceration of sciatic nerve in rats including infection, edema, and cannibalism, and evaluates the effectiveness of therapeutic interventions to modulate the observed complications. For this purpose eighteen female wistar albino rats were divided into three groups: control, sham-operated, and ANI. The ANI model induced with dissection and repair of the right sciatic nerve. Post-surgical care included the administration of diclofenac sodium for pain management. Observations were made for signs of infection, edema, hematoma, and survival rates within 10 days. The ANI group showed significant complications, including a 41.6% incidence of symptoms of pain (paraesthesia, allodynia, hyperalgesia, decreased activity, piloerection, excessive licking, un-groomed appearance) within 3 days, which increased to 60% by day 5. Edema was observed in 8.3% of the ANI rats, and 33.3% developed hematomas. Cannibalism rates also increased, particularly within 10 days post-injury. Survival rates in the ANI group decreased to 16.6% by day 10, indicating severe post-operative complications. The current study highlights the critical complications associated with ANI in rats, particularly the high rates of pain related symptoms (i.e. paresthesia and cannibalism). These findings suggest the need for improved post-operative care and highlight the importance of therapeutic interventions like opioid analgesics to mitigate these complications and enhance recovery outcomes in peripheral nerve injury models.Research Project Raw 264.7 Makrofaj Hücre Kültüründe Lipopolisakkarid ile Oluşturulan in Vitro Sepsis Modelinde Vareniklinin İnflamasyon ve Migrasyon Süreçleri Üzerine Alfa7 Nikotinik Asetilkolin Reseptörü Aracılı Etkileri(2020) Arici, M. Aylin; Barış, Elif; Efe, Hande; Tosun, Metiner; Gümüştekin, MukaddesVücutta oluşan sistemik bir inflamatuvar yanıt olan sepsiste gelişen inflamasyonun kontrolünde kolinerjik antiinflamatuvar yolak önemli bir işlev görmektedir. Çalışmamızda, fare RAW 264.7 makrofaj hücrelerinde lipopolisakkarit (LPS) ile oluşturulan in vitro inflamasyon modelinde bir alfa-7 nikotinik asetilkolin reseptör (?7nAChR) agonisti olan vareniklinin inflamatuvar sitokinler, hücre proliferasyonu ve migrasyonu üzerine etkileri araştırılmıştır. Makrofaj hücrelerine artan konsantrasyonlarda (0,1-0,5-0,8-1 µM) LPS uygulaması sonucunda 24 saatte değişen sitokin konsantrasyonuna göre etkin LPS dozu belirlenmiştir. Ardından, etkin LPS dozu kullanılarak artan konsantrasyonlarda vareniklinin (1-3-10-30 µM) 24 saat sonunda sitokin düzeylerini üzerine etkisi belirlenmiş ve deksametazonun etkisi ile karşılaştırılmıştır. Vareniklin varlığında nikotinik asetilkolin reseptörlerinin (nAChR) işlevi selektif olmayan nAChR antagonisti mekamilamin; ?7nAChR'lerin işlevi ise selektif ?7nAChR antagonisti metililkakonitin ile araştırılmıştır. Vareniklinin LPS ile uyarılan hücre proliferasyonu ve migrasyonuna olan etkisi gerçek zamanlı olarak incelenmiştir. LPS uygulamasından 24 saat sonra hücreler toplanmış ve ELISA ile IL-1ß, IL-6 ve TNF? seviyeleri belirlenmiştir. İlaç uygulamalarından 24 saat sonra gerçek zamanlı hücre proliferasyonu ve migrasyon testleri yapılmıştır. Vareniklin, konsantrasyona bağlı olarak (1-3-10-30 µM), deksametazon uygulamasına benzer şekilde, LPS uygulamasına bağlı 24 saat sonra artan IL-1ß, IL-6 ve TNF? düzeyleri azaltmıştır. Bulgularımız, vareniklinin LPS ile uyarılan IL-1ß, IL-6 ve TNF? düzeylerini çoğunlukla ?7nAChR aracılığı ile azaltığını düşündürmektedir. Ek olarak, vareniklin LPS kaynaklı hücre proliferasyonunu ve migrasyonunu inhibe etmektedir. Vareniklinin, antiproliferatif etkinliğinden farklı olarak, migrasyonu ?7nAChR aktivasyonu ile baskıladığı gözlenmektedir. Sonuç olarak bulgularımız, ?7nAChR agonisti vareniklinin kolinerjik antiinflamatuvar yolak üzerine etki ederek makrofaj proliferasyonu ve migrasyonunun yanı sıra sitokin salıverilişini de baskılayarak antiinflamatuvar etkinlik gösterdiğini düşündürmektedir.Article Exploring the Potential of Lavandula stoechas in Smoking Cessation: A Molecular Docking Study of α4β2 Nicotinic Acetylcholine Receptor Interactions(Istanbul Univ, Fac Pharmacy, 2025-05-07) Barış, Elif; Portakal, Hüseyin SaygınBackground: Lavandula stoechas, commonly known as lavender, has traditionally been used in various therapeutic applications, including smoking cessation. The molecular interaction of Lavandula stoechas compounds with the α4β2 nicotinic acetylcholine receptors, which are crucial for smoking cessation, is not well understood. This study aims to analyze these interactions and compare them with the known smoking cessation drug varenicline tartrate. Methods: Molecular docking analysis was performed on essential compounds of Lavandula stoechas to assess their binding affinities to the α4β2 nicotinic acetylcholine receptors. The study utilized the crystal structure of the receptor and conducted virtual drug screening using AutoDock Vina in the PyRx Virtual Screening Tool. ADME (Absorption, Distribution, Metabolism, and Excretion) and toxicity profiles were also predicted using in silico methods. Results: The molecular docking revealed that several Lavandula stoechas compounds exhibited signif7 icant binding affinities to the α4β2 receptor. Compounds with the highest binding affinities were identified and compared with varenicline. The ADME and toxicity profiles indicated that these compounds had more favorable properties than varenicline, suggesting their potential as alternative smoking cessation agents. Discussion: The findings demonstrate that Lavandula stoechas contains compounds with significant binding affinities to the α4β2 nicotinic acetylcholine receptors, similar to varenicline. This indicates a potential role for Lavandula stoechas in smoking cessation therapy. The favorable ADME and toxicity profiles of these compounds further support their potential as alternatives to current smoking cessation drugs. This study paves the way for further research into the therapeutic applications of Lavandula stoechas in smoking cessation.Article Aile Hekimlerinin Sağlıklı Yaşam Biçimi Davranışlarının ve Klinik Uygulamalarında Yaşam Biçimi Tıbbının Değerlendirilmesi(Galenos Publishing House, 2025-04-15) Semin, Ilgi; Kazdağlı, Hasan; Gökdemir, Özden; Semin, Makbule IlgiAmaç: Bu çalışmanın amacı, aile hekimlerinin sağlıklı yaşam biçimi davranışlarını değerlendirmek ve klinik uygulamalarında yaşam biçimi tıbbına yönelik katılımlarını incelemektir. Yöntemler: Temmuz 2018 ile Ağustos 2019 tarihleri arasında aile hekimlerinden veri toplamak amacıyla çevrimiçi bir anket geliştirildi. Tanımlayıcı ve korelasyonel bir araştırma deseni kullanıldı. Çalışmada uygulanan anket, “katılımcıların kişisel bilgileri” ve “Sağlıklı Yaşam Biçimleri Davranış Ölçeği-II”i içermektedir. Kesitsel bir çalışma olarak tasarlanan bu araştırmada, örneklem kolayda örnekleme metodu ile sekiz ülkeden belirlenmiştir, ve anketler katılımcılara elektronik ortamda uygulanmıştır. Katılımcılara anketin süresi, veri saklama işlemleri, saklama süresi, araştırmacıların kimliği ve çalışmanın amacı hakkında bilgi verilmiştir. Bulgular: Çalışmaya 131 aile hekimi katılmış olup, erkek katılımcı oranı daha yüksek bulunmuştur. Sigara içme sıklığının Türk aile hekimleri arasında anlamlı derecede yüksek olduğu tespit edilmiştir (p=0,013). Ancak, ölçek toplam puanı veya altı boyutta alınan puanlar açısından aile hekimleri arasında istatistiksel olarak anlamlı bir fark bulunmamıştır. Sonuç: Çoğu aile hekimi, bu alanda daha fazla eğitim almak istediklerini belirtmiştir, bu da tıp fakültelerinin müfredatına eğitim müdahalelerin dahil edilmesi gerekliliğini göstermektedir. Ayrıca, iyi yapılandırılmış web tabanlı kitlesel çevrimiçi kurslar, aile hekimlerinin sağlıklı yaşam biçimi davranışları ve yaşam biçimi tıbbı uygulamalarına yönelik eğitim gereksinimlerini karşılamada etkili bir çözüm olabilir.Research Project İnsan Primer Fibroblast Hücre Kültür Karakterizasyonu İçin Biyosensör Geliştirilmesi(2021) Akdoğan, Gül; Demirdover, Cenk; Uygun, Zihni Onur; Sağın, Ferhan GirginHücre Kültürü, deneysel çalışmaların vazgeçilmez araçlarından biridir. Üç boyutlu organizmanın doğrudan kullanılamadığı pek çok deneysel çalışmanın uygulanabilir modeli olarak tercih edilmektedir. Herhangi bir doku parçası mekanik ya da enzimatik yollarla belirli hücreler elde etmek için kültüre edilebilir. Bu kültür işlerinin inceliklerinin yanında, primer kültürlerde ayrıca dikkat edilmesi gereken en önemli nokta, heterojen bir hücre topluluğunun içinden kendi ilgilendiğimiz hücre topluluğunun karakterizasyonunu yaparak deneylere bu hücreler üzerinden devam edebilmektir. Bu projede, ticari olarak elde edilebilen hücre hattının, ya da stabil ve kanıtlanmış bir deney hayvanı modelinin bulunmadığı durumlarda sıklıkla tercih edilen ve insandan doğrudan elde edilen primer kültürler üzerinde durulmuştur. Bu projenin amacı; çeşitli dokulardan elde edilen primer fibroblast hücre kültürlerinin karakterizasyonu için fibroblast biyobelirteci olarak bilinen ısı şok proteini 47 (HSP47) proteinini tanıyan bir biyosensör geliştirilmesinin sağlanmasıdır. Biyosensörler, analit ve biyoaktif molekül ilişkisine dayalı olarak geliştirilen ucuz, güvenilir ve hızlı ölçüm sistemleridir. HSP47 biyosensörünün geliştirilmesi için, spesifik moleküller olan antikorların, dönüştürücü yüzeyinin modifikasyonundan sonra yüzeye immobilize edilmesi ve bundan sonra da HSP-47 molekülü ile antikor arasındaki afiniteye bağlı olarak yüzeyin elektrokimyasal olarak incelenmesi gerçekleştirilmiştir. Bunun için altın nanopartikül elektrotlar kullanılmış ve grafen oksit ile modifiye edilmişlerdir. Biyosensörün performansı hem standartlarda hem de hücrelerde test edilmiştir. Biyosensörün düşük tespit limiti (LOD) ve lineer tespit limiti (LOQ) sırasıyla 0,06 ng/mL ve 0,183 ng/mL olarak hesaplandı. Doğrusal ölçüm aralığı 10-160 pg/mL arasında elde edildi. Böylece literatürde ilk kez HSP47?nin primer fibroblast kültürlerinde belirlenmesi için impedimetrik bir biyosensör geliştirilmiş oldu.Article Prolonged Β-Hydroxybutyrate Ketosis Enhances Ponatinib Response of K562 Chronic Myeloid Leukaemia Cells(Dokuz Eylul Univ inst Health Sciences, 2025-01-31) Özkaya, Ali Burak; Geyik, Öykü Gönül; Malcanlı, SenanurPurpose: Ketosis is a metabolic state characterized by production of ketone bodies, including acetoacetate, β-hydroxybutyrate (BHB), and acetone, in response to reduced blood glucose levels. BHB stands out as the principal ketone body in nutritional ketosis which has diverse therapeutic implications for metabolic, nondegenerative and neoplastic disorders. In current study we investigated the impact of ketosis on chronic myeloid leukaemia (CML) cell viability and drug response. Materials and Methods: We investigated the impact of BHB-mediated ketosis on the viability of K562 cells, an in vitro model of CML, and explored the influence of BHB on the sensitivity of these cells to ponatinib, a multi-targeted tyrosine kinase inhibitor used in CML treatment. We used MTT assay to measure cell viability and Hoechst/PI assay to measure cell death. Results: Our findings reveal that BHB concentrations ranging from 1 mM to 5 mM, which fall within the physiological range of ketosis, elicit a minimal yet concentration-dependent reduction in cell viability. We also observed that while a 24-hour pre-treatment with BHB did not enhance the response of K562 cells to ponatinib, prolonged ketosis (4 days) improved response of cells to the drug by decreasing final cell viability from 25.15% to 13.12%. The primary mode of viability inhibition by ponatinib was cell death which was further intensified by exposure to prolonged ketosis. Conclusion: Ketosis induced by ketogenic diet of ketone body supplementation is considered as safe and effective adjuvant cancer therapy options and here, we report its potential effectiveness in the context of CML.Article Citation - WoS: 2Citation - Scopus: 2Right Vagotomy Alters Heart Rate Variability Temporarily and Increases Total Choline Levels in Rats(Walter de Gruyter GmbH, 2024-07-01) Barış, Elif; Ozel, Hasan Fehmı; Kazdağlı, Hasan; Özbek, MustafaObjectives: The variability in the time intervals between heartbeats, known as heart rate variability (HRV), serves as a reflection of the intricate interplay between the sympathetic and parasympathetic neural systems. While the potential asymmetric effects of the left and right branches of the vagus nerve remain uncertain, this study aims to investigate the impact of unilateral, bilateral, and atropine interventions on HRV parameters and choline levels within cardiac tissue. Methods: 40 male adult Wistar albino rats were randomly assigned to the five groups (each n=8): sham-operated, atropine, right vagotomy, left vagotomy, and bilateral vagotomy. Heart rate variability (HRV) analyses were conducted, and the levels of total choline/acetylcholine in heart tissues were quantified. Statistical analyses were performed to assess the results. Results: The bilateral vagotomy and atropine groups exhibited higher heart rates and high frequency power (HF), along with reduced low frequency power (LF). Total power (TP) remained relatively unchanged. In the bilateral vagot- omy group, DFAα1 was significantly elevated while DFAα2 was reduced significantly. SD1 and SampEn were significantly lower in both the bilateral vagotomy and atropine groups. Notably, the right vagotomy group displayed significant changes primarily in the 15th minute, particularly in time- domain parameters, HF, TP, and SD1, with a significant in- crease observed in total choline levels. Conclusions: Our results revealed that asymmetrical vagal innervation induces distinct effects on heart rate variability parameters and total choline/acetylcholine levels in heart tissues. Our findings suggest that compensatory hemody- namic recovery, possibly driven by contralateral vagal overactivity, may contribute to these observed results.Article Citation - WoS: 1Citation - Scopus: 1Differential Effects of Choline on TLR2/4 Mediated Signaling Through Possible Regulation of Toll-Interacting Protein in Hepatocellular Carcinoma Cell Lines(Walter de Gruyter GmbH, 2024-05-30) Barış, Elif; Demir, Ayse BanuObjectives: Toll-like receptor (TLR) mediated inflammatory status plays an important role in development and pro- gression of hepatocellular carcinoma (HCC). Toll-interacting protein (TOLLIP) has an inhibitory effect on TLR-mediated inflammatory signalling and expression profile of TOLLIP varies between malignancies including HCC. Cholinergic anti-inflammatory pathway (CAP) is an endogenous mech- anism that controls inflammatory status via α7nicotinic acetylcholine receptors (α7nAChR). This study aims to investigate the effect of CAP-acting agent choline on TOLLIP and its related TLR-mediated inflammatory response in HCC cells with distinct differentiation stages. Methods: The expression patterns of α7nAChR, TLR2/4, TOLLIP, IL6, NFkB genes were evaluated by RT-PCR and ELISA in the presence of choline, along with the real-time cell proliferation and migration in HEP3B and SNU449 HCC cell lines. The interaction between choline and TOLLIP assessed by using in-silico analyses. Results: Choline downregulated TOLLIP in Hep3B and SNU449 cells. However, the expressions of α7nAChR, NF-κB, IL-6, TLR2 and TLR4 showed a decreased pattern in well differentiated HEP3B cells, while an increased pattern in poorly differentiated SNU449 cells. Conclusions: Choline might exert differential effects in TLR2/4-dependent signalling based on the differentiation stages of the HCC cells, suggesting its potential therapeutic effects in earlier stages of HCC which might be result of its partial modulation of TOLLIP.Article Retrospective Evaluation of Covid-19 Incidence During Smoking Cessation Treatment With Varenicline(2024-03-27) Barış, Elif; Ömeroğlu Şimşek, Gökçen; Arıcı, Mualla Aylin; Gümüştekin, Mukaddes; Tosun, Metiner; Kılınç, Oğuz; Şimşek, GökçenBackground: Cholinergic anti-inflammatory pathway endogenously controls inflammatory processes through activation of the α7-nicotinic acetylcholine receptor (α7nAChR). Varenicline, used in smoking cessation therapy, is a full α7nAChR agonist with anti-inflammatory effects. In this study, the frequency of coronavirus disease (COVID-19) was evaluated in patients using varenicline as a smoking cessation treatment. Methods: In this retrospective cross-sectional study, records of the 111 patients admitted to Smoking Cessation Outpatient Clinic of XXXXX University Faculty of Medicine during the COVID-19 pandemic were evaluated. The development of COVID-19 disease according to the status of the patients being positive for SARS-COV-2 was evaluated comparatively in patients who received varenicline or not. Additionally, the disease symptoms were questioned. Results: SARS-CoV-2 PCR positivity was not detected in any of 38 patients who regularly used varenicline out of 68 patients evaluated. SARS-CoV-2 PCR positivity was detected in 13 (43.3%) of 30 patients who received other treatments or irregularly used varenicline (p<0.001). Conclusions: Patients under smoking cessation treatment did not develop COVID-19 during the period of varenicline use compared to non-users suggesting that the medication may have a protective role in the development of COVID-19 which might be further investigated by clinical trials.