Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 5Citation - Scopus: 6Sequence Identification and in Silico Characterization of Novel Thermophilic Lipases From Geobacillus Species(WILEY, 2023) Sürmeli, Yusuf; Tekedar, Hasan Cihad; Sanli-Mohamed, GulsahMicrobial lipases are utilized in various biotechnological areas, including pharmaceuticals, food, biodiesel, and detergents. In this study, we cloned and sequenced Lip21 and Lip33 genes from Geobacillus sp. GS21 and Geobacillus sp. GS33, then we in silico and experimentally analyzed the encoded lipases. For this purpose, Lip21 and Lip33 were cloned, sequenced, and their amino acid sequences were investigated for determination of biophysicochemical characteristics, evolutionary relationships, and sequence similarities. 3D models were built and computationally affirmed by various bioinformatics tools, and enzyme-ligand interactions were investigated by docking analysis using six ligands. Biophysicochemical property of Lip21 and Lip33 was also determined experimentally and the results demonstrated that they had similar isoelectric point (pI) (6.21) and T-m (75.5(degrees)C) values as T-m was revealed by denatured protein analysis of the circular dichroism spectrum and pI was obtained by isoelectric focusing. Phylogeny analysis indicated that Lip21 and Lip33 were the closest to lipases from Geobacillus sp. SBS-4S and Geobacillus thermoleovorans, respectively. Alignment analysis demonstrated that S144-D348-H389 was catalytic triad residues in Lip21 and Lip33, and enzymes possessed a conserved Gly-X-Ser-X-Gly motif containing catalytic serine. 3D structure analysis indicated that Lip21 and Lip33 highly resembled each other and they were alpha/beta hydrolase-fold enzymes with large lid domains. BAN Delta IT analysis results showed that Lip21 and Lip33 had higher thermal stability, compared to other thermostable Geobacillus lipases. Docking results revealed that Lip21- and Lip33-docked complexes possessed common residues (H112, K115, Q162, E163, and S141) that interacted with the substrates, except paranitrophenyl (pNP)-C10 and pNP-C12, indicating that these residues might have a significant action on medium and short-chain fatty acid esters. Thus, Lip21 and Lip33 can be potential candidates for different industrial applications.Article Citation - WoS: 4Citation - Scopus: 4A New Shapley-Based Feature Selection Method in a Clinical Decision Support System for the Identification of Lung Diseases(MDPI, 2023) Kababulut, Fevzi Yasin; Kuntalp, Damla Gurkan; Düzyel, Okan; Özcan, Nermin; Kuntalp, MehmetThe aim of this study is to propose a new feature selection method based on the class-based contribution of Shapley values. For this purpose, a clinical decision support system was developed to assist doctors in their diagnosis of lung diseases from lung sounds. The developed systems, which are based on the Decision Tree Algorithm (DTA), create a classification for five different cases: healthy and disease (URTI, COPD, Pneumonia, and Bronchiolitis) states. The most important reason for using a Decision Tree Classifier instead of other high-performance classifiers such as CNN and RNN is that the class contributions of Shapley values can be seen with this classifier. The systems developed consist of either a single DTA classifier or five parallel DTA classifiers each of which is optimized to make a binary classification such as healthy vs. others, COPD vs. Others, etc. Feature sets based on Power Spectral Density (PSD), Mel Frequency Cepstral Coefficients (MFCC), and statistical characteristics extracted from lung sound recordings were used in these classifications. The results indicate that employing features selected based on the class-based contribution of Shapley values, along with utilizing an ensemble (parallel) system, leads to improved classification performance compared to performances using either raw features alone or traditional use of Shapley values.Article Citation - WoS: 2Citation - Scopus: 4Identification of Turkish Extra Virgin Olive Oils Produced in Different Regions by Using Nmr (h-1 and C-13) and Irms (c-13/C-12)(Wiley, 2023) Sevim, Didar; Köseoğlu, Oya; Ertaş, Hasan; Özdemir, Durmuş; Ulaş, Mehmet; Günnaz, Salih; Çelenk, Veysel UmutIsotope ratio mass spectroscopy (IRMS) and nuclear magnetic resonance (NMR) spectroscopy techniques are two of the analytical methods that are used to characterize food products. The aim of this study is to classify extra virgin olive oil (EVOO) samples collected from different regions of Turkey based on H-1 and C-13 NMR spectra along with IRMS d(13)C carbon isotope ratio data by using chemometrics multivariate data analysis methods. A total of 175 EVOO samples were analyzed in 2014/15 and 2015/16 harvest seasons. Multivariate classification and clustering models were used to identify geographical and botanical origins of the EVOOs. IRMS results showed that there was no significant difference in terms of d(13)C values between the years in terms of harvest year (p > 0.05), only extraction phase and variety were statistically significant factors (p < 0.05). The interactions of the factors showed that the harvest year x variety interaction is important. The outcomes of this research clearly indicated that considering the partial least squares discriminant analysis result with NMR spectra, the percent success of the model in the South Marmara, North Aegean, and South Aegean region samples were 95%, 95.7%, and 96.4% in the model set, respectively. The results showed that by using classification and clustering models, geographic marking and labeling of these oils can be carried out regardless of differences in year and production systems (2 and 3 phase extraction system) according the NMR analysis.Article Citation - WoS: 11Citation - Scopus: 11The Utilization of Supervised Classification Sampling for Environmental Monitoring in Turin (italy)(MDPI, 2021) Salata, StefanoIn a world threatened by climate change, the need to observe the land transformation is crucial to set environmental policies. One of the most prominent issues of environmental monitoring is the availability of updated and reliable land use data. The last land-use release in Piedmont Region (Italy) is in 2010, while the most updated Normalized Difference Vegetation Index is in 2016. To overcome this limit, in this study, a supervised classification sampling has been applied on a Sentinel-2 image produced by the Copernicus Program on 29 September 2020, using Esri ArcGIS (ver.10.8 Redlands, California, US) by accessing via ONDA-DIAS services to L2A products. After land classification, three maps were generated-the Habitat Quality, the Habitat Decay, and the Normalized Difference Vegetation Index. This study aimed at classifying the environmental status in five classes ranging from critical to health with a double perspective-(i) to make a comparative metropolitan assessment between municipalities and (ii) to evaluate the quality of urban public green areas in the city of Turin while defining a different kind of intervention. Results indicate that products derived from supervised classification sampling can be applied in a wide range of applications while reaching seasonal monitoring of the environmental status and delivering just-in-time solutions.Article Citation - WoS: 23Citation - Scopus: 28Classification of Turkish Monocultivar (ayvalık and Memecik Cv.) Virgin Olive Oils From North and South Zones of Aegean Region Based on Their Triacyglycerol Profiles(John Wiley and Sons Inc., 2013) Gökçebag, Mümtaz; Dıraman, Harun; Özdemir, DurmuşIn this study, a total of 22 domestic monocultivar (AyvalIk and Memecik cv.) virgin olive oil samples taken from various locations of the Aegean region, the main olive growing zone of Turkey, during two (2001-2002) crop years were classified and characterized by well-known chemometric methods (principal component analysis [PCA] and hierarchical cluster analysis [HCA]) on the basis of their triacylglycerol (TAG) components. The analyses of TAG components (LLL and major fractions LOO, OOO, POO, PLO, SOO, and ECN 42-ECN 50) in the oil samples were carried out according to the HPLC method described in a European Union Commission (EUC) regulation. In all analyzed samples the value of trilinolein (LLL), the least abundant TAG, did not exceed the maximum limit of 0.5 % given by the EUC regulation for different olive oil grades. The ranges of abundant TAG, namely LOO, OOO, POO, PLO, and SOO, were 13.30-16.08, 37.27-46.36, 21.39-23.24, 4.93-7.03, and 4.72-6.00 %. The TAG data of Aegean virgin olive oils were similar to those of products from important olive-oil-producing Mediterranean countries was determined. Also, the estimation of major fatty acids (FA) was carried out by using a formula based on TAG data. The PCA results showed that some TAG components have an important role in the characterization and geographical classification of 22 monocultivar virgin olive oil. The Aegean virgin olive oil samples were successfully classified and discriminated into two main groups as the North and South (growing) subzones or AyvalIk and Memecik olives (cultivars) according to the HCA results based on experimental TAG data and calculated major FA profile.Article Citation - WoS: 14Citation - Scopus: 16Classification of Turkish Extra Virgin Olive Oils by a Saw Detector Electronic Nose(John Wiley and Sons Inc., 2011) Kadiroğlu, Pınar; Korel, Figen; Tokatlı, FigenAn electronic nose (e-nose), in combination with chemometrics, has been used to classify the cultivar, harvest year, and geographical origin of economically important Turkish extra virgin olive oils. The aroma fingerprints of the eight different olive oil samples [Memecik (M), Erkence (E), Gemlik (G), Ayvalik (A), Domat (D), Nizip (N), Gemlik-Edremit (GE), Ayvalik-Edremit (AE)] were obtained using an e-nose consisting a surface acoustic wave detector. Data were analyzed by principal component analysis (PCA) and discriminant function analysis (DFA). Classification of cultivars using PCA revealed that A class model was correctly discriminated from N in two harvest years. The DFA classified 100 and 97% of the samples correctly according to the cultivar in the 1st and 2nd harvest years, respectively. Successful separation among the harvest years and geographical origins were obtained. Sensory analyses were performed for determining the differences in the geographical origin of the olive oils and the preferences of the panelists. The panelists could not detect the differences among olive oils from two different regions. The cultivar, harvest year, and geographical origin of extra virgin olive oils could be discriminated successfully by the e-nose.