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Variant Call Format (VCF), the prevailing representation for germline genotypes in population sequencing, suffers rapid size growth as larger cohorts are sequenced and more rare variants are discovered. We present Sparse Project VCF (spVCF), an evolution of VCF with judicious entropy reduction and run-length encoding, delivering >10× size reduction for modern studies with practically minimal information loss. spVCF interoperates with VCF efficiently, including tabix-based random access. We demonstrate its effectiveness with the DiscovEHR and UK Biobank whole-exome sequencing cohorts.
Apache-licensed reference implementation github.com/mlin/spVCF.
Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.
The World Health Organization launched a recent global campaign to combat ageism, citing its ubiquity and insidious threat to health. The historical context that promoted this pernicious threat is understudied, and such studies lay the critical foundation for designing societal-level campaigns to combat it. We analyzed the trend and content of aging narratives over 210 years across multiple genres-newspaper, magazines, fiction, non-fiction books; and modelled the predictors of the observed trend.
A 600-million-word-dataset was created from the Corpus-of-Historical-American-English and the Corpus-of-Contemporary-American-English to form the largest structured historical corpus with over 150,000 texts from multiple genres. Computational linguistics and statistical techniques were applied to study the trend, content, and predictors of aging narratives.
Aging narratives have become more negative, in a linear fashion (p=.003), over 210 years. There are distinct shifts From uplifting narratives of heroism and kinship in the 1800s to darker tones of illness, death, and burden in the 1900s across newspapers, magazines, and non-fiction books. Fiction defied this trend by portraying older adults positively through romantic courtship and war heroism. Significant predictors of ageism over 210 years are the medicalization of aging, loss of status, warmth, competence, and social ostracism.
Though it is unrealistic to reverse the course of ageism, its declining trajectory can be ameliorated. Our unprecedented study lay the groundwork for a societal level campaign to tackle ageism. The need to act is more pressing given the Covid-19 pandemic where older adults are constantly portrayed as vulnerable.
Though it is unrealistic to reverse the course of ageism, its declining trajectory can be ameliorated. Our unprecedented study lay the groundwork for a societal level campaign to tackle ageism. The need to act is more pressing given the Covid-19 pandemic where older adults are constantly portrayed as vulnerable.Androgen receptor (AR) signaling continues to drive castration-resistant prostate cancer (CRPC) in spite of androgen deprivation therapy (ADT). Constitutively active shorter variants of AR, lacking the ligand binding domain, are frequently expressed in CRPC and have emerged as a potential mechanism for prostate cancer to escape ADT. ARv7 and ARv567es are 2 of the most commonly detected variants of AR in clinical samples of advanced, metastatic prostate cancer. It is not clear if variants of AR merely act as weaker substitutes for AR or can mediate unique isoform-specific activities different from AR. In this study, we employed LNCaP prostate cancer cell lines with inducible expression of ARv7 or ARv567es to delineate similarities and differences in transcriptomics, metabolomics, and lipidomics resulting from the activation of AR, ARv7, or ARv567es. While the majority of target genes were similarly regulated by the action of all 3 isoforms, we found a clear difference in transcriptomic activities of AR versus the variants, and a few differences between ARv7 and ARv567es. Some of the target gene regulation by AR isoforms was similar in the VCaP background as well. Differences in downstream activities of AR isoforms were also evident from comparison of the metabolome and lipidome in an LNCaP model. Overall our study implies that shorter variants of AR are capable of mediating unique downstream activities different from AR and some of these are isoform specific.
Most studies examining the components of the fear-avoidance model have examined processes at the group level. The current study used ecological momentary assessments to (a) investigate the group and intraindividual relationships between pain fear, avoidance, and pain severity, (b) identify any heterogeneity between these relationships, and (c) explore the role of moderators to explain such heterogeneity.
Seventy-one pediatric patients with chronic abdominal pain (M = 13.34 years, standard deviation = 2.67 years) reported pain fear, avoidance, and pain severity four times per day over 14 days.
Results indicated significant individual differences in the relationship between pain fear and pain avoidance predicting pain severity. Resatorvid Child age helped explain the heterogeneity in the relationships between pain avoidance and pain severity such that older children had a stronger and more positive relationship between these variables. The random effect between pain fear and pain severity also indicated a moderator ental differences.Cadmium (Cd) strongly inhibits root growth, especially the formation of lateral roots (LRs). The mechanism of Cd inhibition on LR formation in rice (Oryza sativa) remains unclear. In this study, we found that LR emergence in rice was inhibited significantly by 1 �M Cd and almost completely arrested by 5 �M Cd. Cd suppressed both the formation and subsequent development of the lateral root primordium (LRP). By using transgenic rice expressing the auxin response reporters DR5GUS and DR5revVENUS, we found that Cd markedly reduced the auxin levels in the stele and LRP. Cd rapidly downregulated the expression of the auxin efflux transporter genes OsPIN1b, OsPIN1c and OsPIN9 in the stele and LRP. The emergence of LRs in a rice cultivar with a null allele of OsHMA3 (Heavy Metal ATPase 3) was more sensitive to Cd than cultivars with functional alleles. Overexpression of functional OsHMA3 in rice greatly alleviated the inhibitory effect of Cd, but the protective effect of OsHMA3 was abolished by the auxin polar transport inhibitor 1-N-naphthylphthalamic acid.
Homepage: https://www.selleckchem.com/products/resatorvid.html
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