Scopus İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395

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  • Conference Object
    Citation - Scopus: 9
    Production of Concrete Compatible Biogranules for Self-Healing Concrete Applications
    (EDP Sciences, 2019) Sonmez, Merve; Erşan, Yusuf Çaǧatay
    Recently, cost-efficient nitrate reducing biogranules were suggested as an alternative to axenic microbial cultures for development of microbial self-healing concrete. In a marine environment, biogranule containing microbial self-healing concrete showed simultaneous self-healing of cracks and immunisation against rebar corrosion. Yet, information about the production strategy of these biogranules and their compatibility with a mortar matrix is limited. This study presents the production of biogranules and their compatibility with mortar specimens when incorporated at dosages between 0.36% to 4.30% w/w cement (0.25% to 3% of bacteria w/w cement). In-house produced biogranules composed of 70% bacteria and 30% of minerals w/w of biogranule were used for the compatibility tests. In test mortars, calcium formate (CF) and calcium nitrate (CN) were used as regular nutrient admixtures, and nutrient content was set identical in every batch. Up to 2.9% incorporation, biogranules had no significant influence on the fresh properties of mortar. More than 2.9% incorporation caused poor workability and a 26% decrease in 3-Day compressive strength of biomortar specimens. Overall, the biogranules produced are compatible with a cementitious matrix up to 2.9% w/w cement, and even up to 3.6% if early age strength is not essential, which makes biogranules one of the most compatible microbial healing agents among the suggested agents in the literature. © 2021 Elsevier B.V., All rights reserved.
  • Article
    Citation - Scopus: 2
    Prediction of Colorectal Cancer Based on Taxonomic Levels of Microorganisms and Discovery of Taxonomic Biomarkers Using the Grouping-Scoring (G-S-M) Approach
    (Elsevier Ltd, 2025-03) Bakir-Güngör, Burcu; Temiz, Mustafa; Canakcimaksutoglu, Beyza; Yousef, Malik
    Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases. © 2025 Elsevier B.V., All rights reserved.
  • Conference Object
    Citation - WoS: 5
    Citation - Scopus: 6
    Optimizing Nutrient Content of Microbial Self-Healing Concrete
    (CRC Press-Taylor & Francis Group, 2019) Ersan, Y. C.; Akin, Y.
    Cracks in microbial self-healing concrete are autonomously sealed through microbial induced calcium carbonate precipitation (MICP). The biogenic production of dissolved inorganic carbon (i.e. CO2) is the main drive for MICP and it is limited by the bioavailability of the nutrients. When added as admixtures bioavailability of the nutrients becomes even more significant for crack sealing as they disperse in mortar and a considerable portion stays far from an individual crack. Therefore, determination of the nutrient bioavailability and optimization of the nutrient content is necessary to enhance self-healing performance of bioconcrete. This study defines an optimum nutrient content range for nitrate reduction based microbial self-healing concrete. Ca-formate and Ca-nitrate were used as nutrient admixtures and their wt/wt ratio was kept constant at 2.50: 1.00 while testing various nutrient doses. Variation in mortar properties and nutrient bioavailability was observed and the optimum nutrient content range was defined as 3.5% to 7% depending on the expectations.