181 research outputs found
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The Expanding Landscape of Alternative Splicing Variation in Human Populations.
Alternative splicing is a tightly regulated biological process by which the number of gene products for any given gene can be greatly expanded. Genomic variants in splicing regulatory sequences can disrupt splicing and cause disease. Recent developments in sequencing technologies and computational biology have allowed researchers to investigate alternative splicing at an unprecedented scale and resolution. Population-scale transcriptome studies have revealed many naturally occurring genetic variants that modulate alternative splicing and consequently influence phenotypic variability and disease susceptibility in human populations. Innovations in experimental and computational tools such as massively parallel reporter assays and deep learning have enabled the rapid screening of genomic variants for their causal impacts on splicing. In this review, we describe technological advances that have greatly increased the speed and scale at which discoveries are made about the genetic variation of alternative splicing. We summarize major findings from population transcriptomic studies of alternative splicing and discuss the implications of these findings for human genetics and medicine
Population and allelic variation of A-to-I RNA editing in human transcriptomes.
BackgroundA-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing.ResultsIn order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis. We identify 1054 RNA editing events associated with cis genetic polymorphisms. Additionally, we find that a subset of these polymorphisms is linked to genome-wide association study signals of complex traits or diseases. Finally, compared to random cis polymorphisms, polymorphisms associated with RNA editing variation are located closer spatially to their respective editing sites and have a more pronounced impact on RNA secondary structure.ConclusionsOur study reveals widespread cis variation in RNA editing among genetically distinct individuals and sheds light on possible phenotypic consequences of such variation on complex traits and diseases
Automated Paper Screening for Clinical Reviews Using Large Language Models
Objective: To assess the performance of the OpenAI GPT API in accurately and
efficiently identifying relevant titles and abstracts from real-world clinical
review datasets and compare its performance against ground truth labelling by
two independent human reviewers.
Methods: We introduce a novel workflow using the OpenAI GPT API for screening
titles and abstracts in clinical reviews. A Python script was created to make
calls to the GPT API with the screening criteria in natural language and a
corpus of title and abstract datasets that have been filtered by a minimum of
two human reviewers. We compared the performance of our model against
human-reviewed papers across six review papers, screening over 24,000 titles
and abstracts.
Results: Our results show an accuracy of 0.91, a sensitivity of excluded
papers of 0.91, and a sensitivity of included papers of 0.76. On a randomly
selected subset of papers, the GPT API demonstrated the ability to provide
reasoning for its decisions and corrected its initial decision upon being asked
to explain its reasoning for a subset of incorrect classifications.
Conclusion: The GPT API has the potential to streamline the clinical review
process, save valuable time and effort for researchers, and contribute to the
overall quality of clinical reviews. By prioritizing the workflow and acting as
an aid rather than a replacement for researchers and reviewers, the GPT API can
enhance efficiency and lead to more accurate and reliable conclusions in
medical research.Comment: 15 pages, 2 figures, 4 table
RNA editing in the human ENCODE RNA-seq data
RNA-seq data can be mined for sequence differences relative to the reference genome to identify both genomic SNPs and RNA editing events. We analyzed the long, polyA-selected, unstranded, deeply sequenced RNA-seq data from the ENCODE Project across 14 human cell lines for candidate RNA editing events. On average, 43% of the RNA sequencing variants that are not in dbSNP and are within gene boundaries are A-to-G(I) RNA editing candidates. The vast majority of A-to-G(I) edits are located in introns and 3′ UTRs, with only 123 located in protein-coding sequence. In contrast, the majority of non–A-to-G variants (60%–80%) map near exon boundaries and have the characteristics of splice-mapping artifacts. After filtering out all candidates with evidence of private genomic variation using genome resequencing or ChIP-seq data, we find that up to 85% of the high-confidence RNA variants are A-to-G(I) editing candidates. Genes with A-to-G(I) edits are enriched in Gene Ontology terms involving cell division, viral defense, and translation. The distribution and character of the remaining non–A-to-G variants closely resemble known SNPs. We find no reproducible A-to-G(I) edits that result in nonsynonymous substitutions in all three lymphoblastoid cell lines in our study, unlike RNA editing in the brain. Given that only a fraction of sites are reproducibly edited in multiple cell lines and that we find a stronger association of editing and specific genes suggests that the editing of the transcript is more important than the editing of any individual site
Disability and Health in African Americans: Population Research and Implications for Occupational Therapy Community-Based Practice
Background: Population-based research and community-based interventions are integral to occupational therapy’s scope of practice, yet they are underdeveloped in actual implementation. Therefore, this paper focuses on some health challenges facing the African American population, guided by the Person-Environment-Occupation-Performance Model.
Method: Using data from an observational cross-sectional nationwide telephone survey of African American adults, we examined differences between African Americans who are receiving disability payments (RDP) and those who are employed full time (FTE) on several physical health behaviors and psychosocial health indicators. We further compared the differences between African Americans RDP versus those FTE on those physical health behaviors and psychosocial health indicators across five US regions.
Results: Findings suggest that African Americans RDP are engaging in fewer positive physical health behaviors and experiencing worse psychosocial health compared to their counterparts FTE. There are also nuanced regional variations in the differences between African Americans RDP and FTE in physical health behaviors and psychosocial health indicators.
Conclusion: This research highlighted some health challenges of African Americans RDP and FTE using a regional lens, demonstrating the value of OT population-based research. There is a need for OT population-specific community-based practice to address the health disparities of underserved and minority populations, such as African Americans
Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver
BackgroundRNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored.ResultsDeep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1-deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels for 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1-deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1-deficient mice, demonstrating that Apobec-1 is required.ConclusionsThese studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific
Long-term Observations in Acoustics - the Ocean Acoustic Observatory Federation
The Ocean Acoustic Observatory Federation (OAOF)
includes several laboratories and universities: the
Institute of Geophysics and Planetary Physics (IGPP) and
the Marine Physical Laboratory (MPL) at the Scripps
Institution of Oceanography, the Pacific Meteorological
and Environmental Laboratory (PMEL) of NOAA, the
Naval Postgraduate School (NPS), and the Applied
Physics Laboratory at the University of Washington
(UW/APL)
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