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

Spatiotemporal Distribution of Irrigation Water Use Efficiency from the Perspective of Water Footprints in Heilongjiang Province

Water footprints can reflect the sources and utilities of water resources. Introducing the water footprint theory to evaluate irrigation water use efficiency can reflect agricultural water consumption more scientifically and accurately. This study analyzes the variation trends of the blue, green and gray water footprints of grains in different regions of Heilongjiang Province and selects the grain-sowing area, total agricultural machinery power, grain blue water footprint and green water footprints and absolute fertilizer amount as input indexes and the agricultural gross product and gray water footprint of grain as output indexes. A slacks-based measure–data envelopment analysis (SBM-DEA) model is used to estimate the irrigation water use efficiencies of 11 cities in Heilongjiang Province, analyze the corresponding spatiotemporal distribution and further decompose and calculate the irrigation water use efficiencies of the five economically underdeveloped second-level cities. The results suggest that the spatial distribution of the grain water footprint in Heilongjiang Province reflects coexisting areas of excess and scarcity. The irrigation water use efficiency showed a steady and slow downward trend from 2008 to 2018. The irrigation water use efficiency reflected significant spatial differences in Heilongjiang Province, with a pattern of high values in the southwest and low values in the northeast; these differences have gradually narrowed. The average irrigation water use efficiency in Heilongjiang Province was 0.821 and the irrigation water efficiencies of Harbin, Qiqihar and Jixi were at the forefront of the province. Jiamusi, Hegang, Shuangyashan, Yichun, and Mudanjiang are the five cities with below-provincial-average irrigation water use efficiencies. The irrigation water use efficiency of Heilongjiang Province mainly depends on the pure technical efficiency. In the future, technical inputs should be improved on the basis of optimizing the agricultural production layout, focusing on improving the pure technical efficiency. The research results obtained herein can provide a theoretical basis for agricultural water management in Heilongjiang Province

Cognitive evaluation of HUD interface layout for intelligent automotive based on Bayesian BWM and Gray-TOPSIS

To reduce drivers’ cognitive load during the driving process, The present study concentrates on the cognitive evaluation and analysis of the Head-Up Display (HUD) interface layout, aiming to enhance human cognitive efficiency. Initially, a combination of eye-tracking technology and cognitive load theory is used to investigate users’ attention allocation and changes in eye movement indicators, followed by the conversion of these indicators. A comprehensive HUD interface layout evaluation system is established, considering structural layout esthetics, task efficiency, and cognitive load. To achieve this, an intelligent cognitive evaluation method for the automotive HUD interface layout is proposed, based on the Bayesian BWM and Gray-TOPSIS. Bayesian BWM is employed to determine the weights of evaluation indicators, followed by Gray-TOPSIS to assess and rank the layout candidate solutions. Experimental results indicate that in the optimal layout design, users exhibit fewer eye movements, shorter gaze durations, esthetically pleasing interface structures, and lower cognitive loads. Furthermore, comparative experiments validate the effectiveness and stability of the Bayesian BWM and Gray-TOPSIS methods. These findings offer guidance and reference for further optimizing the layout of intelligent automotive HUD interfaces

The Critical Depth of Freeze-Thaw Soil under Different Types of Snow Cover

Snow cover is the most common upper boundary condition influencing the soil freeze-thaw process in the black soil farming area of northern China. Snow is a porous dielectric cover, and its unique physical properties affect the soil moisture diffusion, heat conduction, freezing rate and other variables. To understand the spatial distribution of the soil water-heat and the variable characteristics of the critical depth of the soil water and heat, we used field data to analyze the freezing rate of soil and the extent of variation in soil water-heat in a unit soil layer under bare land (BL), natural snow (NS), compacted snow (CS) and thick snow (TS) treatments. The critical depth of the soil water and heat activity under different snow covers were determined based on the results of the analysis, and the variation fitting curve of the difference sequences on the soil temperature and water content between different soil layers and the surface 5-cm soil layer were used to verify the critical depth. The results were as follows: snow cover slowed the rate of soil freezing, and the soil freezing rate under the NS, CS and TS treatments decreased by 0.099 cm/day, 0.147 cm/day and 0.307 cm/day, respectively, compared with that under BL. In addition, the soil thawing time was delayed, and the effect was more significant with increased snow cover. During freeze-thaw cycles, the extent of variation in the water and heat time series in the shallow soil was relatively large, while there was less variation in the deep layer. There was a critical stratum in the vertical surface during hydrothermal migration, wherein the critical depth of soil water and heat change gradually increased with increasing snow cover. The variance in differences between the surface layer and both the soil water and heat in the different layers exhibited “steady-rising-steady” behavior, and the inflection point of the curve is the critical depth of soil freezing and thawing. This critical layer is a demarcation point between frozen soil and non-frozen soil, delineating the boundary between soil water and heat migration and non-migration. Furthermore, with increasing snow cover thickness and increasing density, the critical depth gradually increased

Microstructure and Wear Resistance of TiCp/Ti6Al4V Composite Coatings by Follow-Up Ultrasonic-Assisted Laser Additive Manufacturing

With the increasing demand for the high agility and fast response of high-level equipment in the aerospace and energy power fields, it is increasingly urgent to improve the performance of the high-temperature and wear resistance of the corresponding high-level components. Ceramic-reinforced titanium matrix composites have excellent high-temperature and wear resistance, but, in laser additive manufacturing, the primary ceramic phase is coarse, and the morphology of the ceramic phase is difficult to control, which limits their further development. In this investigation, a follow-up ultrasonic-assisted laser-additive-manufacturing method was proposed to prepare a 30 wt.% TiC/Ti6Al4V composite coating on a Ti6Al4V surface. Under the effects of ultrasonic cavitation and acoustic streaming, the content of the unmelted TiC was reduced, the dendritic primary TiC in the solidification process was broken and the distribution uniformity of the primary TiC was improved. The content of the unmelted TiC in the composite coating decreased significantly under ultrasonic action, and it was only 50.23% of that without ultrasonic action. At the same time, the average size of the dendritic primary TiC in the composite coating decreased from 61.59 &mu;m to 27.04 &mu;m, which was 56.10% smaller than that without ultrasonic action. The average microhardness of the composite coating reached the maximum of 656.70 HV0.2 under ultrasonic power, and it was 83.21% higher than that of the Ti6Al4V substrate, and 26.44% higher than that of the composite coating without ultrasonic power. Due to the ultrasonic-cavitation and acoustic-streaming effects, the content of the unmelted TiC obviously decreased, so that the average friction coefficient of the composite coating increased, and the wear mechanism changed from abrasive wear to adhesive wear

Effect of casting temperature on the solidification process and (micro)structure of Zr-based metallic glasses

Bulk metallic glasses (BMGs) bear versatile advantages compared to traditional crystalline metallic materials. However, preparation of large size BMG components remains a great challenge due to the lack of understanding the casting dynamics of BMGs. The present work investigates the dynamics of the solidification process during casting of a Zr41.2Ti13.8Cu12.5Ni10Be22.5 BMG by measuring the time-dependent temperature evolution and constructing distance–time curves showing the progress of solidification. The experimentally probed temperature evolution proves that a higher casting temperature causes a lower cooling rate and induces more pronounced nanocrystal phase formation in the final BMG casting. Thus, optimization of the casting temperature is crucial for casting BMG components. The solidification coefficient K of the studied Zr-based BMG in copper mold was determined. The solidification time can be calculated with model: τ=M2K2. The solidification of the Zr-based BMG occurs in a narrow transition layer region following a “layer-by-layer” solidification mode. This feature is vital for designing the casting process appropriately to avoid the formation of casting defects in BMG components. The present work sheds new light on the solidification mechanism of bulk glass-forming liquids and underlines the importance of optimizing the technology and processing conditions for fabrication of BMG components with practical applications

Flexible Diodes/Transistors Based on Tunable p-n-Type Semiconductivity in Graphene/Mn-Co-Ni-O Nanocomposites

We report a novel Mn-Co-Ni-O (MCN) nanocomposite in which the p-type semiconductivity of Mn-Co-Ni-O can be manipulated by addition of graphene. With an increase of graphene content, the semiconductivity of the nanocomposite can be tuned from p-type through electrically neutral to n-type. The very low effective mass of electrons in graphene facilitates electron tunneling into the MCN, neutralizing holes in the MCN nanoparticles. XPS analysis shows that the multivalent manganese ions in the MCN nanoparticles are chemically reduced by the graphene electrons to lower-valent states. Unlike traditional semiconductor devices, electrons are excited from the filled graphite band into the empty band at the Dirac points from where they move freely in the graphene and tunnel into the MCN. The new composite film demonstrates inherent flexibility, high mobility, short carrier lifetime, and high carrier concentration. This work is useful not only in manufacturing flexible transistors, FETs, and thermosensitive and thermoelectric devices with unique properties but also in providing a new method for future development of 2D-based semiconductors