Publications by authors named "J K McDaniel"
Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a benchmark containing mosaic variants in the Genome in a Bottle Consortium (GIAB) HG002 reference material DNA from a large batch of a normal lymphoblastoid cell line. First, we used a somatic variant caller with high coverage (300x) Illumina whole genome sequencing data from the Ashkenazi Jewish trio to detect variants in HG002 not detected in at least 5% of cells from the combined parental data.
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- - In anodic electrosynthesis, cation radicals are important intermediates that can be attacked by nucleophiles or undergo deprotonation, affecting the yield of chemical products based on competing pathways.
- - The study uses computational methods to analyze how methanol influences the trapping of enol ether cation radicals, revealing that methanol enhances the rate of specific reactions through a second-order kinetic process.
- - The formation of a "Zundel-like" conformation with methanol assists both intramolecular and solvent-mediated attacks on the cation radicals, leading to very low energy barriers for these reactions and resulting in unique kinetics based on the structure of the substrate.
In this study, we investigate the quaternary ammonium-based ionic liquid (QAIL), methyltrioctylammonium bis(trifluoromethylsulfonyl)imide, [N][TFSI], utilizing small angle neutron scattering (SANS) measurements and polarizable molecular dynamics (MD) simulations to characterize the short- and long-range liquid structure. Scattering structure factors show signatures of three length scales in reciprocal space indicative of alternating polarity ( ∼ 0.44 Å), charge ( ∼ 0.
View Article and Find Full Text PDFBackground: Research suggests that systemic inflammation may link loneliness to adverse health outcomes, yet there is a gap in comprehensively reviewing recent evidence on the relationship between loneliness and biological measures of inflammation in adults. This scoping review synthesizes current research to address the question: Is there a definitive link between loneliness and biological markers of inflammation in adults?
Methods: Following the methods outlined by Arksey and O'Malley, we developed a protocol, defined our research question, and systematically searched PubMed, CINAHL, Embase, and Scopus for English-language studies conducted from 2018 to 2023 exploring the relationship between loneliness and biomarkers of inflammation in adults.
Results: Twelve studies meeting the inclusion criteria displayed heterogeneity in terms of sample characteristics, loneliness scales, and inflammatory biomarkers.
Article Synopsis
- * The authors introduce "stratifications," or specific BED files, that outline different genomic contexts for GRCh37/38 and the new T2T-CHM13 reference, which includes previously challenging regions to sequence.
- * They also compare the performance of sequencing benchmarks across these references, showing how difficult regions in CHM13 impact the overall performance, and provide a snakemake pipeline for generating stratifications to aid in optimizing sequencing platforms.