Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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  • Article
    Citation - Scopus: 4
    Quasi-Supervised Strategies for Compound-Protein Interaction Prediction
    (John Wiley and Sons Inc, 2022) Çakı, O.; Karaçalı, B.
    In-silico compound-protein interaction prediction addresses prioritization of drug candidates for experimental biochemical validation because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning (QSL) algorithm. In this framework, potential interactions are predicted by estimating the overlap between a true positive dataset of compound-protein pairs with known interactions and an unknown dataset of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure. We also address the class-imbalance problem by modifying the conventional cost function of the QSL algorithm. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations. © 2021 Wiley-VCH GmbH.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 2
    Recycling of Gas-To Sludge as a Potential Organic Amendment: Effect on Soil and Cotton Properties Under Hyperarid Conditions
    (Academic Press, 2023) Mabrouk, O.; Hamdi, H.; Sayadi, S.; Al-Ghouti, M.A.; Abu-Dieyeh, M.; Kogbara, R.; Al-Sharshani, A.
    Gas-to-liquid (GTL) sludge is a specific wastewater treatment by-product, which is generated during the industrial process of natural gas conversion to transportation fuels. This least studied sludge is pathogen-free and rich in organic carbon and plant nutrients. Therefore, it can be reused for soil enhancement as a sustainable management strategy to mitigate landfill gas emissions. In this field study, we compared the performance of soil treatments with GTL sludge to the more conventional chemical fertilizers and cow manure compost for the cultivation of cotton under hyperarid conditions. After a complete growing season, GTL sludge application resulted in the enhancement of soil properties and plant growth compared to conventional inputs. As such, there was a significant dose-dependent increase of soil organic matter (4.01% and 4.54%), phosphorus (534 and 1090 mg kg−1), and cumulative lint yield (4.68 and 5.67 t ha−1) for GTL sludge application rates of 1.5% and 3%, respectively. The produced fiber quality was adequate for an upland cotton variety (Gossypium hirsutum var. MAY 344) and appeared more dependent on the prevailing climate conditions than soil treatments. On the other hand, the adverse effects generally related to industrial sludge reuse were not significant and did not affect the designed agro-environmental system. Accordingly, plants grown on GTL sludge-amended soils showed lower antioxidant activity despite significant salinity increase. In addition, the concentrations of detected heavy metals in soil were within the standards’ limits, which did not pose environmental issues under the described experimental conditions. Leachate analysis revealed no risks for groundwater contamination with phytotoxic metals, which were mostly retained by the soil matrix. Therefore, recycling GTL sludge as an organic amendment can be a sustainable solution to improve soil quality and lower carbon footprint. To reduce any environmental concerns, an application rate of 1.5% could be provisionally recommended since a two-fold increase in sludge dose did not result in a significant yield improvement. © 2023 Elsevier Ltd