SciCombinator

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131

Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases of genomic variation.

131

The violation of a Bell inequality not only attests to the nonclassical nature of a system but also holds a very unique status within the quantum world. The amount by which the inequality is violated often provides a good benchmark on how a quantum protocol will perform. Acquiring images of such a fundamental quantum effect is a demonstration that images can capture and exploit the essence of the quantum world. Here, we report an experiment demonstrating the violation of a Bell inequality within observed images. It is based on acquiring full-field coincidence images of a phase object probed by photons from an entangled pair source. The image exhibits a violation of a Bell inequality with S = 2.44 ± 0.04. This result both opens the way to new quantum imaging schemes based on the violation of a Bell inequality and suggests promise for quantum information schemes based on spatial variables.

130

Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a ‘chromatin-RNA in situ reverse-transcription sequencing’; (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements by combining the simplicity of RNA biotin labeling with the specificity of the CRISPR/Cas9 system. Using gene-specific gRNAs, we describe a pluripotency-specific lncRNA interacting network in the promoters of Sox2 and Pou5f1, two critical stem cell factors that are required for the maintenance of pluripotency. The promoter-interacting lncRNAs were specifically activated during reprogramming into pluripotency. Knockdown of these lncRNAs caused the stem cells to exit from pluripotency. In contrast, overexpression of the pluripotency-associated lncRNA activated the promoters of core stem cell factor genes, and enhanced fibroblast reprogramming into pluripotency. These CRIST-seq data suggest that the Sox2 and Pou5f1 promoters are organized within a unique lncRNA interaction network that determines the fate of pluripotency during reprogramming. This CRIST approach may be broadly used to map lncRNA interaction networks at target loci across the genome.

130

Plenty of genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms (SNPs) for coronary artery disease (CAD) and blood pressure (BP). However, these SNPs only explain a small proportion of the heritability of two traits/diseases. Although high BP is a major risk factor for CAD, the genetic intercommunity between them remain largely unknown. To recognize novel loci associated with CAD and BP, a genetic-pleiotropy-informed conditional false discovery rate (cFDR) method was applied on two summary statistics of CAD and BP from existing GWASs. Stratified Q-Q and fold enrichment plots showed a high pleiotropic enrichment of SNPs associated with two traits. Adopting a cFDR of 0.05 as a threshold, 55 CAD-associated loci (25 variants being novel) and 47 BP loci (18 variants being novel) were identified, 25 of which were pleiotropic loci (13 variants being novel) for both traits. Among the 32 genes these 25 SNPs were annotated to, 20 genes were newly detected compared to previous GWASs. This study showed the cFDR approach could improve gene discovery by incorporating GWAS datasets of two related traits. These findings may provide novel understanding of etiology relationships between CAD and BP.

130

Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depends on the analysis of sequence homology at the nucleotide or protein level.

130

YouTube™ ( http://www.youtube.com ), as a very popular video site around the world, is increasingly being used for health information. The objectives of this review were to assess the overall usefulness of information on food poisoning presented on YouTube™ for patients.

130

Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For this, it is necessary to characterize human phenotypes at the molecular and functional levels, by exploiting gene annotations and known relations among genes, diseases and phenotypes. This characterization makes it possible to implement tools for retrieving functions shared among phenotypes, co-occurring in the same patient and facilitating the formulation of hypotheses about the molecular causes of the disease.

130

By definition, effect of synonymous single-nucleotide variants (SNVs) on protein folding and function are neutral, as they alter the codon and not the encoded amino acid. Recent examples indicate tissue-specific and transfer RNA (tRNA)-dependent effects of some genetic variations arguing against neutrality of synonymous SNVs for protein biogenesis.

124

We report on measurements of external gamma radiation on 9 islands in 4 atolls in the northern Marshall Islands, all of which were affected by the US nuclear testing program from 1946 to 1958 (Enjebi, Ikuren, and Japtan in Enewetak Atoll; Bikini and Enyu in Bikini Atoll; Naen in Rongelap Atoll; and Aon, Elluk, and Utirik in Utirik Atoll). We also report americium-241, cesium-137, plutonium-238, and plutonium-239,240 activity concentrations in the soil samples for 11 islands in 4 northern atolls (Enewetak, Japtan, Medren, and Runit in Enewetak Atoll; Bikini and Enyu in Bikini Atoll; Naen and Rongelap in Rongelap Atoll; and Aon, Elluk, and Utirik in Utirik Atoll) and from Majuro Island, Majuro Atoll in the southern Marshall Islands. Our results show low external gamma radiation levels on some islands in the Enewetak Atoll and Utirik Atoll, and elevated levels on Enjebi Island in the Enewetak Atoll, on Bikini Atoll, and on Naen Island in the Rongelap Atoll. We perform ordinary kriging on external gamma radiation measurements to provide interpolated maps. We find that radionuclides are absent from all Majuro soil samples, and that they are present at highest activity concentrations in samples from Runit and Enjebi islands (Enewetak Atoll), Bikini Island (Bikini Atoll), and Naen Island (Rongelap Atoll). We contextualize all results by making comparisons between islands and to various standards, as well as to regions of the world affected by nuclear accidents. We also discuss implications for informed decision-making by the Marshallese and local atoll governments and their people on issues pertaining to island resettlement.

109

To systematically quantify the prevalence, severity, and nature of preventable patient harm across a range of medical settings globally.