Systematic comparison of Mendelian randomisation studies and randomised controlled trials using electronic databases by Jie Zheng, George Davey Smith, Tom R Gaunt, Maria K Sobczyk

“…Among intervention types that can be mimicked by MR, only trials of pharmaceutical interventions could be automatically matched to MR results due to insufficient annotation with Medical Subject Headings ontology. A manual survey of the literature highlighted the potential for triangulation across a number of exposure/outcome pairs if these challenges can be addressed.Conclusions We conclude that careful triangulation of MR with RCT evidence should involve consideration of similarity of phenotypes across study designs, intervention intensity and duration, study population demography and health status, comparator group, intervention goal and quality of evidence.…”
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In Silico Analysis of Common Long Noncoding RNAs in Schistosoma mansoni and Schistosoma haematobium by Serhat Sirekbasan, Tugba Gurkok Tan

“…LncRNAs target genes and their gene ontology annotation was performed. Results. In S. mansoni and S. haematobium, 5132 and 3589 lncRNA transcripts were detected, respectively. …”
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On quantitizing revisited by Anthony J. Onwuegbuzie

“…It discusses the variable adoption of quantitizing based on differing philosophical perspectives related to ontology, epistemology, axiology, and methodology. …”
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Experimental Turn in Philosophy by Natalia V. Zaitseva, Dmitry V. Zaitsev

“…This interpretation of experimental philosophy opens up the possibility of experimental philosophical research in any field, from epistemology or ontology to logic and philosophy of language, without a far-fetched division into analytical and experimental versions. …”
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Knowledge Representation and Digital Scholarly Editions in Theory and Practice by Tanya Clement

“…This discussion employs the language of knowledge representation in computation (through terms like domain, ontology, and logic) in order to situate this scholarly edition within two existing frameworks: theories of knowledge representation in computation and theories of scholarly textual editing.…”
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Transcriptome responses to Ralstonia solanacearum infection in tetraploid potato by Zhuo Chen, Shunwei Shao, Xi Zhu, Yu Zhang, Zhendong Lan, Hui Jin

“…Transcriptome sequencing reveals 659 differentially expressed genes between the two varieties, with the ethylene responsive factor family containing the most differentially expressed genes. Gene ontology and KEGG analyses provided further insights into the genetic basis and molecular mechanisms underlying plant defense against R. solanacearum disease. …”
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From ChatGPT to Sora: Analyzing Public Opinions and Attitudes on Generative Artificial Intelligence in Social Media by Wenyan Feng, Yuhang Li, Chunhao Ma, Lisai Yu

“…Word co-occurrence network analysis, topic modeling based on Latent Dirichlet Allocation (LDA), and emotional characteristics based on the DLUT Emotion Ontology and psycholinguistic analyses based on the Linguistic Inquiry and Word Count (LIWC) dictionary were employed to explore public views on these generative AI technologies. …”
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Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse by Minjung Kim, Youngseok Yu, Ji-Hoi Moon, InSong Koh, Jae-Hyung Lee

“…Using weighted gene coexpression network analysis, we identified 9 modules related to the early differentiation stage (days 2–8) and 7 modules related to the late differentiation stage (days 10–18). Gene ontology and KEGG pathway enrichment analysis revealed that the mRNA and lncRNA upregulated in the late differentiation stage are highly associated with osteogenesis. …”
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Rapid Identification and Systematic Mechanism of Flavonoids from Potentilla freyniana Bornm. Based on UHPLC-Q-Exactive Orbitrap Mass Spectrometry and Network Pharmacology by Wei Cai, Kailin Li, Shihan Qin, Pei Xiong, Jie Peng, Silin Shi, Zaiqi Zhang

“…Then, the core targets were predicted by protein-protein interaction network and network analysis. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were carried out via DAVID. …”
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Microarray Analysis Reveals a Potential Role of lncRNA Expression in 3,4-Benzopyrene/Angiotensin II-Activated Macrophage in Abdominal Aortic Aneurysm by Yingying Zhou, Jiaoni Wang, Yangjing Xue, Aili Fang, Shaoze Wu, Kaiyu Huang, Luyuan Tao, Jie Wang, Yigen Shen, Jinsheng Wang, Lulu Pan, Lei Li, Kangting Ji

“…The function of differential mRNAs was determined by pathway and Gene Ontology analysis. Eight pathways associated with inflammation were upregulated, and seven pathways including cell apoptosis were downregulated. …”
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Gene Expression Changes in Venous Segment of Overflow Arteriovenous Fistula by Yasuhiro Hashimoto, Akiko Okamoto, Hisao Saitoh, Shingo Hatakeyama, Takahiro Yoneyama, Takuya Koie, Chikara Ohyama

“…The cDNA microarray analysis identified 397 upregulated genes and 456 downregulated genes. Gene ontology analysis with GeneSpring GX software revealed that biological developmental processes and glycosaminoglycan binding were the most upregulated. …”
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The Motives behind the Skepticism of Conventional Medicine Advocates towards Traditional Persian Medicine: An Expert Opinion by Majid Nimrouzi, Zahra Salehi, Faranak Alembizar

“…Some critiques are because of a knowledge gap between ontology and epistemology of complementary medical approaches and conventional medicine. …”
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A Comparison of Computational Approaches for Intron Retention Detection by Jiantao Zheng, Cuixiang Lin, Zhenpeng Wu, Hong-Dong Li

“…We also describe the use of differential analysis methods to identify disease-associated IRs and compare differential IRs along with their Gene Ontology enrichment, which is illustrated on an Alzheimer’s disease RNA-Seq dataset. …”
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Multitarget Effects of Danqi Pill on Global Gene Expression Changes in Myocardial Ischemia by Qiyan Wang, Hui Meng, Qian Zhang, Tianjiao Shi, Xuefeng Zhang, Mingyan Shao, Linghui Lu, Jing Wang, Wei Wang, Chun Li, Yong Wang

“…Differentially expressed genes among the sham group, model group, and DQP group were analyzed. The gene ontology enrichment analysis and pathway analysis of differentially expressed genes were carried out. …”
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Enabling Semantic Technology Empowered Smart Spaces by Jussi Kiljander, Arto Ylisaukko-oja, Janne Takalo-Mattila, Matti Eteläperä, Juha-Pekka Soininen

“…The proposed solutions include ontologies, system models, and guidelines for building smart spaces with the M3 semantic information sharing platform. …”
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The anti-melanoma roles and mechanisms of tricholoma isoflavone derivative CA028 by Cheng Liang, Jianfu Jiang, Jinkai Li, Xiao Lin, Wenjun Huang, Keng Po Lai, Jian Chen

“…The results of gene ontology highlighted the involvement of CA028’s targets in the cell proliferation, cell apoptosis, and migration ability of melanoma cells. …”
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A Method for Trust Quantification in Cloud Computing Environments by Xiaohui Li, Jingsha He, Bin Zhao, Jing Fang, Yixuan Zhang, Hongxing Liang

“…In this paper, we propose a method for trust quantification based on fuzzy comprehensive evaluation theory for cloud computing to protect user data through trust quantification of cloud services after we introduce trust ontology for cloud services and define user preference trust values. …”
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Human Periodontal Ligament Stem Cell-Derived Exosomes Promote Bone Regeneration by Altering MicroRNA Profiles by Ting Liu, Wenyun Hu, Xue Zou, Jingchen Xu, Shushu He, Le Chang, Xinyi Li, Yuanyuan Yin, Mi Tian, Ziyu Li, Jialiang Zhou, Xiaoge Jiang, Song Chen

“…The results of Gene Ontology analysis and pathway analysis demonstrated that the target genes of differentially expressed exosomal miRNAs participate in the regulation of a variety of biological processes, such as catalytic activity, protein binding, metabolic processes, cell development, and differentiation, and are enriched in osteogenic differentiation-related pathways, such as MAPK signaling, AMPK signaling, and insulin signaling pathways. …”
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Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq by Zehra Omeroğlu Ulu, Salih Ulu, Soner Dogan, Bilge Guvenc Tuna, Nehir Ozdemir Ozgenturk

“…These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. …”
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Transcriptomics reveals substance biosynthesis and transport on membranes of Listeria monocytogenes affected by antimicrobial lipopeptide brevilaterin B by Yangliu Liu, Yawei Ning, Zhou Chen, Panpan Han, Tongxin Zhi, Siting Li, Aijin Ma, Yingmin Jia

“…Transcriptomic analysis showed 1779 difference expressed genes, including 895 up-regulated and 884 down-regulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that brevilaterin B influenced multiple pathways of L. monocytogenes, including peptidoglycan biosynthesis, membrane transport (ATP-binding cassette transports, ion transport), cellular metabolism (amino acid and lipid metabolism), ATP synthesis, and activation of the stress response (quorum sensing and bacterial chemotaxis). …”
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