To assess the reproducibility of CT-based Leaman score (CT-LeSc). CT-LeSc can non-invasively quantify total coronary atherosclerotic burden and is an independent long-term predictor of cardiac... Show moreTo assess the reproducibility of CT-based Leaman score (CT-LeSc). CT-LeSc can non-invasively quantify total coronary atherosclerotic burden and is an independent long-term predictor of cardiac events. Its calculation however relies on the subjective assessment of lesions using coronary computed tomography angiography and therefore is subject to intra- and inter-observer variability. Inter-observer reproducibility was assessed by calculating the CT-LeSc in 50 patients randomly selected from the SYNTAX III REVOLUTION and ABSORB trials by two separate teams, each made up of two cardiologists, who reported results by consensus. For intra-observer reproducibility, the CT-LeSc was calculated in same 50 patients on two occasions eight weeks apart, by the same team of two cardiologists. The level of agreement was measured by the weighted kappa statistic, with intra- and inter-observer variability used to evaluate the CT-LeSc’s reproducibility. The variables evaluated by weighted kappa statistics were total number of lesions; number of calcified lesions; number of non-calcified lesions; number of mixed lesions; number of obstructive lesions; number of non-obstructive lesions; and the total CT-LeSc in increments of ten and five. During assessment of inter-observer variability the mean ± standard deviation (SD) CT-LeSc calculated by the first and second team was 15.36 ± 5.57 versus 15.24 ± 5.16. The mean of the differences (precision) was 0.97, with a SD (accuracy) 1.17. The inter-observer variability was lowest for Leaman score in increments of five (weighted kappa 0.93), and highest for the total number of calcified lesions (weighted kappa 0.66). During assessment of intra-observer variability, the mean ± SD CT-LeSc were 16.61 ± 5.28 versus 16.82 ± 5.55. The mean ± SD of the differences was 1.28 ± 1.02. The intra-observer variability was the lowest for Leaman score in increments of five (weighted kappa 0.93), and the highest for the total number of lesions and calcified lesions (weighted kappa 0.65). CT-LeSc has substantial to near-perfect agreement for reproducibility. Show less
.Sensitive detection of weak acoustic signals at nanometer scale is challenging. Here, the authors present an acoustic detection system based on a single molecule as a probe, where frequency and... Show more.Sensitive detection of weak acoustic signals at nanometer scale is challenging. Here, the authors present an acoustic detection system based on a single molecule as a probe, where frequency and amplitude of acoustic vibrations can be extracted from its minute variations in distance to the surface of a plasmonic gold nanorod.Sensitive detection of local acoustic vibrations at the nanometer scale has promising potential applications involving miniaturized devices in many areas, such as geological exploration, military reconnaissance, and ultrasound imaging. However, sensitive detection of weak acoustic signals with high spatial resolution at room temperature has become a major challenge. Here, we report a nanometer-scale system for acoustic detection with a single molecule as a probe based on minute variations of its distance to the surface of a plasmonic gold nanorod. This system can extract the frequency and amplitude of acoustic vibrations with experimental and theoretical sensitivities of 10 pm Hz(-1/2) and 10 fm Hz(-1/2), respectively. This approach provides a strategy for the optical detection of acoustic waves based on molecular spectroscopy without electromagnetic interference. Moreover, such a small nano-acoustic detector with 40-nm size can be employed to monitor acoustic vibrations or read out the quantum states of nanomechanical devices. Show less
Yang, X.F.; Gao, S.H.; Guo, L.; Wang, B.; Jia, Y.Y.; Zhou, J.; ... ; Ye, K. 2021
Papaver species P. setigerum, P. rhoeas, and P. somniferum accumulates different levels of morphine and noscapine. Here, the authors report the improved genome assembly of P. somniferum and de novo... Show morePapaver species P. setigerum, P. rhoeas, and P. somniferum accumulates different levels of morphine and noscapine. Here, the authors report the improved genome assembly of P. somniferum and de novo assembly of the other two species, and reveal the evolution of the benzylisoquinoline alkaloids biosynthetic pathway.For millions of years, plants evolve plenty of structurally diverse secondary metabolites (SM) to support their sessile lifestyles through continuous biochemical pathway innovation. While new genes commonly drive the evolution of plant SM pathway, how a full biosynthetic pathway evolves remains poorly understood. The evolution of pathway involves recruiting new genes along the reaction cascade forwardly, backwardly, or in a patchwork manner. With three chromosome-scale Papaver genome assemblies, we here reveal whole-genome duplications (WGDs) apparently accelerate chromosomal rearrangements with a nonrandom distribution towards SM optimization. A burst of structural variants involving fusions, translocations and duplications within 7.7 million years have assembled nine genes into the benzylisoquinoline alkaloids gene cluster, following a punctuated patchwork model. Biosynthetic gene copies and their total expression matter to morphinan production. Our results demonstrate how new genes have been recruited from a WGD-induced repertoire of unregulated enzymes with promiscuous reactivities to innovate efficient metabolic pathways with spatiotemporal constraint. Show less
A balanced omega-6/omega-3 polyunsaturated fatty acid (PUFA) ratio has been linked to health benefits and the prevention of many chronic diseases. Current dietary intervention studies with... Show moreA balanced omega-6/omega-3 polyunsaturated fatty acid (PUFA) ratio has been linked to health benefits and the prevention of many chronic diseases. Current dietary intervention studies with different sources of omega-3 fatty acids (omega-3) lack appropriate control diets and carry many other confounding factors derived from genetic and environmental variability. In our study, we used the fat-1 transgenic mouse model as a proxy for long-term omega-3 supplementation to determine, in a well-controlled manner, the molecular phenotype associated with a balanced omega-6/omega-3 ratio. The fat-1 mouse can convert omega-6 to omega-3 PUFAs, which protect against a wide variety of diseases including chronic inflammatory diseases and cancer. Both wild-type (WT) and fat-1 mice were subjected to an identical diet containing 10% corn oil, which has a high omega-6 content similar to that of the Western diet, for a six-month duration. We used a multi-platform lipidomic approach to compare the plasma lipidome between fat-1 and WT mice. In fat-1 mice, an unbiased profiling showed a significant increase in the levels of unesterified eicosapentaenoic acid (EPA), EPA-containing cholesteryl ester, and omega-3 lysophosphospholipids. The increase in omega-3 lipids is accompanied by a significant reduction in omega-6 unesterified docosapentaenoic acid (omega-6 DPA) and DPA-containing cholesteryl ester as well as omega-6 phospholipids and triacylglycerides. Targeted lipidomics profiling highlighted a remarkable increase in EPA-derived diols and epoxides formed via the cytochrome P450 (CYP450) pathway in the plasma of fat-1 mice compared with WT mice. Integration of the results of untargeted and targeted analyses has identified a lipidomic biosignature that may underlie the healthful phenotype associated with a balanced omega-6/omega-3 ratio, and can potentially be used as a circulating biomarker for monitoring the health status and the efficacy of omega-3 intervention in humans. Show less
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we... Show moreThe 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research. Show less
