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Öğe Activity Classification of Small Drug Molecules Using Deep Neural Networks and Classical Machine Learning Models(2022) Kanberiz, Hatice; Korkmaz, Selçuk; Süt, NecdetObjective: The main goal in the early phase of drug discovery studies is to detect small drug molecules that show activity against a specific receptor. For this purpose, small drug molecules are classified as actives or inactives by performing high-throughput screening (HTS) experiments. The datasets obtained from these experiments are uploaded to the PubChem database. This database contains more than one million bioassays that are obtained through HTS experiments. Alternatively, classification models can be developed using datasets in the PubChem database. Material and Methods: In this study, we obtained 5 datasets with different degrees of imbalance structure from the PubChem database. We trained these datasets using deep neural networks (DNN) for the classification of small drug molecules as actives or inactives. The test set performances of DNN models were compared with the support vector machines (SVM) and random forest (RF) algorithms. Results: The DNN achieved better balanced accuracy (minimum-maximum: 0.764-0.865), recall (minimum-maximum: 0.630-0.823), F1-score (minimum-maximum: 0.496-0.843) and Matthews correlation coefficient (minimum-maximum: 0.439- 0.721) compared to the SVM and RF. Conclusion: Our results showed that the DNN is a well-performed machine learning algorithm that can be in the early phase of drug discovery studies since it performs better than traditional machine learning algorithms in the case of imbalanced class structures.Öğe The Acute Effect of Fructose on Cardiac Hemodynamic Responses and Infarcted Area in Isolated Rat Heart During Ischemia-Reperfusion(2023) Palabıyık, Orkide; Aydın, Muhammed Ali; Değer, Ecem Büşra; Korkmaz, Selçuk; Vardar, Selma ArzuIntroduction: This study aimed to investigate the effects of fructose on cardiac hemodynamics and infarct size and the role of the antioxidant mechanism in these effects in isolated rat hearts undergoing ischemiareperfusion. Patients and Methods: Isolated hearts obtained from female Wistar rats were perfused with Krebs-Henseleit solution containing 12 mM glucose or solution containing 12 mM fructose or 48 mM fructose and underwent lowflow ischemia followed by reperfusion on the Langendorff apparatus. Left ventricular developed pressure (LVDP), timedependent pressure changes (dp/dt max, dp/dt min) and heart rates were recorded at the 1st, 15th and 120th minutes of reperfusion following ischemia, and the percentage of the infarct area and the size of the risk area were determined. At the end of the reperfusion, total oxidant capacity (TOS), malondialdehyde (MDA) and glutathione (GSH) levels were examined in perfusion fluid samples. Results: Basal dp/dt max values were lower in the high fructose group compared to the glucose group (p= 0.032). When the hearts were perfused with 12 mM fructose, a significant increase was observed in the percentage of the ischemic area and risk area compared to equivalent glucose and high fructose (p< 0.001 and p< 0.001, respectively). MDA, GSH and TOS values were comparable in all groups. Conclusion: The present study shows that fructose perfusion plays a role in reduced ventricular contractile function relative to glucose in isolated rat hearts. This reduction triggered by fructose appears to be independent of antioxidant mechanisms. Furthermore, fructose perfusion at glucose-equivalent concentration causes a greater increase in infarct area in ischemic hearts, whereas an increase in fructose concentration appears to prevent this effect.Öğe Quantitative Assessment of Salivary Gland Parenchymal Vascularization Using Power Doppler Ultrasound and Superb Microvascular Imaging: A Potential Tool in the Diagnosis of Sjögren’s Syndrome(2020) Ustabaşıoğlu, Fethi Emre; Korkmaz, Selçuk; İlgen, Ufuk; Solak, Serdar; Kula, Osman; Turan, Sezin; Emmüngil, HakanBackground: Primary Sjögren’s syndrome is a chronic inflammatory autoimmune disease. Minor salivary gland biopsy is the gold standard for the diagnosis of primary Sjögren’s syndrome. Superb microvascular imaging, power Doppler ultrasound, and color Doppler of the salivary glands represent non-invasive, non-irradiating modality for evaluating the vascularity of the salivary glands in the diagnosis and follow-up of primary Sjögren’s syndrome. Aims: To evaluate the efficacy of superb microvascular imaging and vascularity index in salivary glands for the sonographic diagnosis of primary Sjögren’s syndrome. Study Design: Prospective case-control study. Methods: Twenty participants with primary Sjögren’s syndrome and 20 healthy subjects were included in the study. Both parotid glands and submandibular glands were evaluated by superb microvascular imaging, power Doppler ultrasound, and color Doppler. The diagnostic accuracy of superb microvascular imaging was compared using these techniques. Results: In the patient group, the vascularity index values of superb microvascular imaging in parotid glands and submandibular glands were 3.5±1.66, 5.06±1.94, respectively. While the same values were 1.0±0.98 and 2.44±1.34 in the control group (p?0.001). In the patient group, the vascularity index values of power Doppler ultrasound in parotid glands and submandibular glands were 1.3±1.20 and 2.59±1.82, respectively. While the same values were 0.3±0.32 and 0.85±0.68 in the control group (p?0.001). The superb microvascular imaging vascularity index cut-off value for the diagnosis of primary Sjögren’s syndrome in parotid glands that maximizes the accuracy was 1.85 (area under the curve: 0.906; 95% confidence interval: 0.844, 0.968), and its sensitivity and specificity were 87.5% and 72.5%, respectively. While the superb microvascular imaging vascularity index cut-off value for the diagnosis of primary Sjögren’s syndrome in submandibular gland that maximizes the accuracy was 3.35 (area under the curve: 0.873; 95% confidence interval: 0.800, 0.946), its sensitivity and specificity were 82.5% and 70%, respectively. Conclusion: Superb microvascular imaging with high reproducibility of the vascularity index has a higher sensitivity and specificity than the power Doppler ultrasound in the diagnosis of primary Sjögren’s syndrome. It can be a noninvasive technique in the diagnosis of primary Sjögren’s syndrome when used with clinical, laboratory and other imaging methods.Öğe Small Drug Molecule Classification Using Deep Neural Networks(2019) Korkmaz, SelçukObjective: Early phase of drug discovery studies include a virtual screening phaseof detecting active molecules among a large number of small drug molecules. The number ofpublicly available datasets for drug molecules are growing exponentially every year thanks to thedatabases, such as PubChem and ChEMBL. Therefore, there is a strong need for analyzing andretrieving useful information from these datasets using automated processes. For this purpose,machine learning algorithms are often used for activity prediction of small drug compounds, since they are faster and comparatively cheaper. Deep neural networks has emerged as a powerfulmachine learning method with great advantages to deal with high-dimensional big datasets. Material and Methods: In this study, we applied different settings of deep neural networks modelsto reveal the effects of learning rate, batch size and minority class weight on performance of thenetwork. Results: Small learning rate and large batch size are found to be the most importantfactors that improve performance of the deep neural network. The best performed model yielded89% accuracy and 0.78 area under the curve value. Conclusion: Findings of this study is promising for use of deep neural networks in virtual screening of small drug compounds from publiclyavailable databases.Öğe ÜNİVERSİTE ÖĞRENCİLERİNDE DÜZENLİ KAHVALTI TÜKETİMİ İLE ANTROPOMETRIK ÖLÇÜMLER ARASINDAKİ İLİŞKİ(2017) Öner, Neslihan; Caferoğlu, Zeynep; Korkmaz, SelçukAmaç: Bu çalışma, Erciyes Üniversitesinde öğrenim gören öğrencilerin düzenli kahvaltı tüketim alışkanlığının antropometrik ölçümler ile ilişkisini değerlendirmek amacıyla yapılmıştır. Gereç ve Yöntem: Çalışmaya beslenme eğitimi alan ve almayan toplam on fakülte de öğrenim gören ve yaş ortalaması 21.16±1.56 yıl olan 269 gönüllü kız öğrenci dâhil edilmiştir. Veriler anket formu ile 2016 yılının Ocak ve Nisan ayları arasında toplanmıştır. Öğrencilerin ağırlık, boy, bel, kalça ve boyun çevreleri ölçülmüştür. Normal dağılıma uygunluk Shapiro-Wilk testi, histogram ve Q-Q grafikleri ile değerlendirilerek; gruplar arası karşılaştırmalar da t testi kullanılmıştır. Kategorik değişkenler ise Ki-kare testi kullanılarak analiz edilmiştir.Düzenli kahvaltı tüketimi ile antropometrik ölçümler arasındaki ilişki, binarylojistik regresyon analizi ile incelenmiştir. Bulgular: Öğrencilerin %38.3'ü öğrenim gördükleri bölümde beslenme eğitimi alırken, %61.7'si herhangi bir beslenme eğitimi almamaktadır. Beslenme eğitimi alan öğrencilerin vücut ağırlığı, BKİ, bel, kalça ve boyun çevresi ortancası almayanlara göre anlamlı olarak daha yüksek bulunmuştur (p<0.05). Haftalık kahvaltı tüketim sıklığı 5.32±2.02 kezdir. Beslenme eğitimi alan öğrenciler arasında düzenli kahvaltı tüketim oranı %74.8 ve almayanlar arasında %64.5'tir (p>0.05). BKİ sınıflamasına göre hafif şişman öğrencilerin normal öğrencilere göre düzensiz kahvaltı yapma riskinin yaklaşık dört kat daha fazla olduğu bulunmuştur (Odds oranı = 3.967, p=0.001). Sonuç: Üniversite öğrencilerine verilen beslenme eğitimi kapsamında kahvaltı ve önemi konusuna ağırlık verilmelidir.
