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Use of large language models as artificial intelligence tools in academic research and publishing among global clinical researchers.
Sci Rep
December 2024
Department of Dermatology, Niazi Hospital, Lahore, Pakistan.
With breakthroughs in Natural Language Processing and Artificial Intelligence (AI), the usage of Large Language Models (LLMs) in academic research has increased tremendously. Models such as Generative Pre-trained Transformer (GPT) are used by researchers in literature review, abstract screening, and manuscript drafting. However, these models also present the attendant challenge of providing ethically questionable scientific information.
View Article and Find Full Text PDFDevelopment of a prognostic gene signature and exploration of P4HA1 in the modulation of cuproptosis in colorectal cancer.
Sci Rep
December 2024
School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China.
Cuproptosis, a newly identified form of cell death, has drawn increasing attention for its association with various cancers, though its specific role in colorectal cancer (CRC) remains unclear. In this study, transcriptomic and clinical data from CRC patients available in the TCGA database were analyzed to investigate the impact of cuproptosis. Differentially expressed genes linked to cuproptosis were identified using Weighted Gene Co-Expression Network Analysis (WGCNA).
View Article and Find Full Text PDFComputational biology assisted exploration of phytochemicals derived natural inhibitors to block BZLF1 gene activation of Epstein-Bar virus in host.
Sci Rep
December 2024
Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.
The Epstein-Barr virus (EBV) is widespread and has been related to a variety of malignancies as well as infectious mononucleosis. Despite the lack of a vaccination, antiviral medications offer some therapy alternatives. The EBV BZLF1 gene significantly impacts viral replication and infection severity.
View Article and Find Full Text PDFQuantifying the regulatory potential of genetic variants via a hybrid sequence-oriented model with SVEN.
Nat Commun
December 2024
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, 100871, Beijing, China.
Deciphering how noncoding DNA determines gene expression is critical for decoding the functional genome. Understanding the transcription effects of noncoding genetic variants are still major unsolved problems, which is critical for downstream applications in human genetics and precision medicine. Here, we integrate regulatory-specific neural networks and tissue-specific gradient-boosting trees to build SVEN: a hybrid sequence-oriented architecture that can accurately predict tissue-specific gene expression level and quantify the tissue-specific transcriptomic impacts of structural variants across more than 350 tissues and cell lines.
View Article and Find Full Text PDFSystematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population.
Nat Commun
December 2024
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.
Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we here deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). Sequencing of the ACE2 receptor binding motif and polybasic furin cleavage site of the Spike gene in over 70,000 patients revealed that population sweeps of canonical variants of concern (VOCs) occurred in repeating wavelets.
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