Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

The effects of the tylosin and Cd on soil enzyme activity

Soil microbial environment have been affected by different concentration heavy metals Cd (HM) and tylosin (TYL) and combination of TYL and HM interactions. Degradation of TYL was caused certain inhibition due to the addition of HM. The germination index of seed had been inhibited owing to the toxic effects of HM and TYL, but we found that the low concentrations of HM (4 mg/kg), the germination index higher than the soil which unadded HM and TYL in it. The soil enzyme activity was significantly suppressed by the addition of HM and TYL. Actinomycete was inhibited by high concentrations of HM for a long time. The studies demonstrated that the pollution of the soil micro-environment has been serious than only add HM or TYL in the soil

Spatial–temporal variations of NDVI and its response to climate in China from 2001 to 2020

Vegetation plays an important role in global or regional environmental change. In this study, the spatial–temporal variations of NDVI and its response to climate in China and its seven sub-regions were investigated based on MODIS NDVI data, ERA5-land precipitation (PRE) and temperature (TEM) data from 2001 to 2020. The inter-annual growth rate of NDVI in China was 0.0021/yr in the past 20 years. The inter-annual growth rates of NDVI in seven sub-regions had significant differences at regional or seasonal scales. The ratio of improved vegetation area to the total studied area reached about 70%. In summer, vegetation degradation was concentrated in East China and Southwest China. The vegetation in Central China and South China improved more obviously in autumn than in the other seasons. The vegetation of Northeast China had a remarkable degradation in autumn and winter, especially in winter. The influence degree of PRE (q = 0.54, P < 0.01) was greater than that of TEM (q = 0.27, P < 0.01) in the control of the spatial distribution of NDVI. The interaction influence degree q of PRE $\cap$ TEM was about 0.71 in the last 20 years. However, the PRE and TEM played different roles in vegetation growth in seven sub-regions

Cost-Effective Resource Provisioning for Real-Time Workflow in Cloud

In the era of big data, mining and analysis of the enormous amount of data has been widely used to support decision-making. This complex process including huge-volume data collecting, storage, transmission, and analysis could be modeled as workflow. Meanwhile, cloud environment provides sufficient computing and storage resources for big data management and analytics. Due to the clouds providing the pay-as-you-go pricing scheme, executing a workflow in clouds should pay for the provisioned resources. Thus, cost-effective resource provisioning for workflow in clouds is still a critical challenge. Also, the responses of the complex data management process are usually required to be real-time. Therefore, deadline is the most crucial constraint for workflow execution. In order to address the challenge of cost-effective resource provisioning while meeting the real-time requirements of workflow execution, a resource provisioning strategy based on dynamic programming is proposed to achieve cost-effectiveness of workflow execution in clouds and a critical-path based workflow partition algorithm is presented to guarantee that the workflow can be completed before deadline. Our approach is evaluated by simulation experiments with real-time workflows of different sizes and different structures. The results demonstrate that our algorithm outperforms the existing classical algorithms

Real‐Time Quantification of Cell Mechanics and Functions by Double Resonator Piezoelectric Cytometry – Theory and Study of Cellular Adhesion of HUVECs

Abstract Cell mechanics is closely associated with cellular structure and function. However, the inability to measure both cellular force and viscoelasticity of statistically significant number of cells noninvasively remains a challenge for quantitative characterizations of various cellular functions and practical applications. Here a double resonator piezoelectric cytometry (DRPC), using AT and BT cut quartz crystals of the same frequency and surface morphology is developed to simultaneously quantify the cells‐generated forces (ΔS) and viscoelastic moduli (G′, G″) of a population of isolated single cells or cells with different degrees of cell‐cell interactions in a non‐invasive and real time manner. DRPC captures the dynamic mechanical parameters ΔS and G′, G″ during the adhesions of human umbilical vein endothelial cells (HUVECs) under different ligand densities of adhesion molecules fibronectin or Arg‐Gly‐Asp (RGD) modified on the gold surfaces of 9 MHz AT and BT cut quartz crystals, and different seeding densities of HUVECs. It is found that both the ligand density and cell seeding density affect the magnitudes of ΔS and G′, G″ and their correlations are revealed for the first time by DRPC. The validity of DRPC is further verified by mechanical changes of the cells in response to treatments with cytoskeleton regulators