Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

台灣北部地區大專院校餐廳管理現況及其影響因素之調查研究

[[abstract]]本研究之主要目的在探討臺灣北部地區大專院校學生餐廳管理之現況，進而探求影響 學生餐廳管理之有關因素，研究中利用問卷調查，深入訪談，及環境觀察等方法，分 別對各校負責餐廳督導業務的學校決策人員，用餐學生，餐廳業務執行人員及學生餐 廳等進行資料之蒐集，其結果如下： 一、行政方面 各校對於餐廳督導之業務一般為個單位共同管理，各單位之間有權責劃分不清之慫象 ，缺乏專業人員專責管理；大部份的學校，未編列經費用於改善餐廳，其督導人員之 專業知識普遍不足，多為兼職，對此督導工作投入的時間不多，工作意原低落，未發 揮管理的功能。 二、環境方面： 目前各校餐廳在容量上仍嫌不足，有些學校在設計之初即未考慮到衛生的因素，致造 成衛生情況不佳。 三、服務方面： 多數學校對餐廳在提供學生膳食營養方面，缺少長期的規書，對食品原料之品質管制 不良，學生、學校決策人員及餐廳業務執行人員對價格的認同差距不大。 四、教育方面： 在學生方面，學生本身缺乏足夠的營養、衛生知識，學校中又缺乏專業課程，大部份 的學生其飲食行為不佳，但其在選擇菜式時，以衛生為首要考慮因素者最多，有83.9 % 的學生到餐廳中用餐之最主要誘因是方便。在廚工訓練方面，雖有施行但並未達到 提升工作人員衛生習慣之預期效果。

Maritime broadband communication: Wireless channel measurement and characteristic analysis for offshore waters

For a long time, the development of maritime communication has been restricted by the low data rate, high-latency and high cost of the current communication systems. The upgrade of new generation mobile communication technologies is attracting more and more attention to conduct a shore-based broadband mobile communication network with high-latency and high reliability to serve the maritime industries. This paper presents a solution by means of building a ship-to-infrastructure (S2I) and a ship-to-ship (S2S) wireless communication networks for an offshore region. We characterize the S2I and S2S channels at 5.9 GHz band based on the channel measurements in realistic environments. The channel characteristics, including power delay profile, delay spread, propagation path loss, are extracted and analyzed. In view of the difference between marine and terrestrial communications, we analyze the influencing factors of the offshore water, including effective reflection, divergence and shadowing from the water surface, and diffraction loss caused by the earth curvature. We also predict the power coverage range and the channel capacity for S2I and S2S wireless communications. Finally, the communication performance is evaluated according to the channel measurement and characterization analysis. The research results can be a reference for the construction of maritime communication networks.Safety and Security Scienc

Influence of environmental factors on zooplankton assemblages in Bosten Lake, a large oligosaline lake in arid northwestern China

Water salinization in semi-arid and arid regions is threatening freshwater or oligosaline ecosystems. Anthropogenic processes enrich nutrients of aquatic systems causing significant environmental effects. Bosten Lake in Xinjiang Province, China is an interesting ecosystem featuring a salinity gradient from fresh to subsaline, as well as a nutrition gradient from oligotrophic to mesotrophic. In the present study, we focused on the effects of salinity and nutrients in Bosten Lake by investigating the zooplankton assemblages and environmental factors from different sampling times. A total of 74 zooplankton taxa were found, consisting of 34 rotifers, 26 protists, 10 cladocerans, and 4 copepods. Although no significant differences were found among different sampling sites, zooplankton species richness, diversity, and evenness showed significant differences between sampling times, with August samples showing highest values along with water temperature and total nitrogen. Principal component analysis and representational difference analysis results showed that zooplankton abundance is correlated with water temperature and nitrogen, but showed no significant relationship with water mineralization or conductivity. The subsaline-tolerating zooplankton species in Bosten Lake made their community insensitive to salinity. The decrease of total nitrogen concentration in Bosten Lake probably implied a primary productivity increase, which subsequently caused the zooplankton diversity to increase in August.Water salinization in semi-arid and arid regions is threatening freshwater or oligosaline ecosystems. Anthropogenic processes enrich nutrients of aquatic systems causing significant environmental effects. Bosten Lake in Xinjiang Province, China is an interesting ecosystem featuring a salinity gradient from fresh to subsaline, as well as a nutrition gradient from oligotrophic to mesotrophic. In the present study, we focused on the effects of salinity and nutrients in Bosten Lake by investigating the zooplankton assemblages and environmental factors from different sampling times. A total of 74 zooplankton taxa were found, consisting of 34 rotifers, 26 protists, 10 cladocerans, and 4 copepods. Although no significant differences were found among different sampling sites, zooplankton species richness, diversity, and evenness showed significant differences between sampling times, with August samples showing highest values along with water temperature and total nitrogen. Principal component analysis and representational difference analysis results showed that zooplankton abundance is correlated with water temperature and nitrogen, but showed no significant relationship with water mineralization or conductivity. The subsaline-tolerating zooplankton species in Bosten Lake made their community insensitive to salinity. The decrease of total nitrogen concentration in Bosten Lake probably implied a primary productivity increase, which subsequently caused the zooplankton diversity to increase in August

Molecular cloning and functional characterization of peptidoglycan recognition protein 6 in grass carp Ctenopharyngodon idella

Peptidoglycan recognition proteins (PGRPs) are pattern recognition molecules of innate immunity. In this study, a long-form PGRP, designated as gcPGRP6, was identified from grass carp Ctenopharyngodon idella. The deduced amino acid sequence of gcPGRP6 is composed of 464 residues with a conserved PGRP domain at the C-terminus. The gcPGRP6 gene consists of four exons and three introns, spacing approximately 2.7 kb of genomic sequence. Phylogenetic analysis demonstrated that gcPGRP6 is clustered closely with zebrafish PGLYRP6, and formed a long-type PGRP subfamily together with PGLYRP2 members identified in teleosts and mammals. Real-time PCR and Western blotting analyses revealed that gcPGRP6 is constitutively expressed in organs/tissues examined, and its expression was significantly induced in liver and intestine of grass carp in response to PGN stimulation and in CIK cells treated with lipoteichoic acid (LTA), polyinosinic polycytidylic acid (Poly I:C) and peptidoglycan (PGN). Immunofluorescence microscopy and Western blotting analyses revealed that gcPGRP6 is effectively secreted to the exterior of CIK cells. The over-expression of gcPGRP6 in CIK cells leads to the activation of NF-kappa B and the inhibition of intracellular bacterial growth. Moreover, cell lysates from CIK cells transfected with pTurbo-gcPGRP6-GFP plasmid display the binding activity towards Lys-type PGN from Staphylococcus aureus and DAP-type PGN from Bacillus subtilis. Furthermore, proinflammatory cytokine IL-2 and intracellular PGN receptor NOD2 had a significantly increased expression in CIK cells overexpressed with gcPGRP6. It is demonstrated that the PGRP6 in grass carp has a role in binding PGN, in inhibiting the growth of intracellular bacteria, and in activating NF-kappa B, as well as in regulating innate immune genes. (C) 2013 Elsevier Ltd. All rights reserved.Peptidoglycan recognition proteins (PGRPs) are pattern recognition molecules of innate immunity. In this study, a long-form PGRP, designated as gcPGRP6, was identified from grass carp Ctenopharyngodon idella. The deduced amino acid sequence of gcPGRP6 is composed of 464 residues with a conserved PGRP domain at the C-terminus. The gcPGRP6 gene consists of four exons and three introns, spacing approximately 2.7 kb of genomic sequence. Phylogenetic analysis demonstrated that gcPGRP6 is clustered closely with zebrafish PGLYRP6, and formed a long-type PGRP subfamily together with PGLYRP2 members identified in teleosts and mammals. Real-time PCR and Western blotting analyses revealed that gcPGRP6 is constitutively expressed in organs/tissues examined, and its expression was significantly induced in liver and intestine of grass carp in response to PGN stimulation and in CIK cells treated with lipoteichoic acid (LTA), polyinosinic polycytidylic acid (Poly I:C) and peptidoglycan (PGN). Immunofluorescence microscopy and Western blotting analyses revealed that gcPGRP6 is effectively secreted to the exterior of CIK cells. The over-expression of gcPGRP6 in CIK cells leads to the activation of NF-kappa B and the inhibition of intracellular bacterial growth. Moreover, cell lysates from CIK cells transfected with pTurbo-gcPGRP6-GFP plasmid display the binding activity towards Lys-type PGN from Staphylococcus aureus and DAP-type PGN from Bacillus subtilis. Furthermore, proinflammatory cytokine IL-2 and intracellular PGN receptor NOD2 had a significantly increased expression in CIK cells overexpressed with gcPGRP6. It is demonstrated that the PGRP6 in grass carp has a role in binding PGN, in inhibiting the growth of intracellular bacteria, and in activating NF-kappa B, as well as in regulating innate immune genes. (C) 2013 Elsevier Ltd. All rights reserved

Impact of Land Use Change on Hydrologic Processes in a Large Plain Irrigation District

Land use is the main factor that influences catchment hydrologic processes, and a better understanding of its effect is important for future land use planning and water resource management. By applying the Soil and Water Assessment Tool (SWAT), we assessed the effects of land use changes on major hydrologic processes (evapotranspiration (ET), discharge, river) on a large plain irrigation district, the Hetao Irrigation District (HID), China. The results indicated that SWAT was a useful tool for simulating the effects of land use changes on regional hydrologic processes. Human activities were the main factors that directly influenced land use in the HID. Land use changes had important impacts on the hydrologic processes of the HID. During 1995-2010, the land use changed greatly in the HID, leading to the changes in ET and discharge. The peak value of ET coincided with the exuberant crop growth period in the maximized sown crop area. In 1995s, wheat maximized the sown area and ET peaked in June; when sunflower and corn maximized the sown area in 2010s, ET peaked in July and August. The increased ET reduced discharge in the same period in the HID. Land use change affected the period and quantity of water diversion in the irrigation district. The quantity of water diverted in 1995 was greater than that in 2010, indicating that land use change significantly impacted the water quantity of the river, which was the water source of the irrigation district. This study will be a reference for future land use planning and water resource management in the irrigation district

Brain structural plasticity in survivors of a major earthquake

Background: Stress responses have been studied extensively in animal models, but effects of major life stress on the human brain remain poorly understood. The aim of this study was to determine whether survivors of a major earthquake, who were presumed to have experienced extreme emotional stress during the disaster, demonstrate differences in brain anatomy relative to individuals who have not experienced such stressors. Methods: Healthy survivors living in an area devastated by a major earthquake and matched healthy controls underwent 3-dimentional high-resolution magnetic resonance imaging (MRI). Survivors were scanned 13-25 days after the earthquake; controls had undergone MRI for other studies not long before the earthquake. We used optimized voxel-based morphometry analysis to identify regional differences of grey matter volume between the survivors and controls. Results: We included 44 survivors (17 female, mean age 37 [standard deviation (SD) 10.6] yr) and 38 controls (14 female, mean age 35.3 [SD 11.2] yr) in our analysis. Compared with controls, the survivors showed significantly lower grey matter volume in the bilateral insula, hippocampus, left caudate and putamen, and greater grey matter volume in the bilateral orbitofrontal cortex and the parietal lobe (all p < 0.05, corrected for multiple comparison). Limitations: Differences in the variance of survivor and control data could impact study findings. Conclusion: Acute anatomic alterations could be observed in earthquake survivors in brain regions where functional alterations after stress have been described. Anatomic changes in the present study were observed earlier than previously reported and were seen in prefrontal-limbic, parietal and striatal brain systems. Together with the results of previous functional imaging studies, our observations suggest a complex pattern of human brain response to major life stress affecting brain systems that modulate and respond to heightened affective arousal

The on-orbit calibration of DArk Matter Particle Explorer

The DArk Matter Particle Explorer (DAMPE), a satellite-based cosmic ray and gamma-ray detector, was launched on December 17, 2015, and began its on-orbit operation on December 24, 2015. In this work we document the on-orbit calibration procedures used by DAMPE and report the calibration results of the Plastic Scintillator strip Detector (PSD), the Silicon-Tungsten tracKer-converter (STK), the BGO imaging calorimeter (BGO), and the Neutron Detector (NUD). The results are obtained using Galactic cosmic rays, bright known GeV gamma-ray sources, and charge injection into the front-end electronics of each sub-detector. The determination of the boundary of the South Atlantic Anomaly (SAA), the measurement of the live time, and the alignments of the detectors are also introduced. The calibration results demonstrate the stability of the detectors in almost two years of the on-orbit operation

The on-orbit calibration of DArk Matter Particle Explorer

The DArk Matter Particle Explorer (DAMPE), a satellite-based cosmic ray and gamma-ray detector, was launched on December 17, 2015, and began its on-orbit operation on December 24, 2015. In this work we document the on-orbit calibration procedures used by DAMPE and report the calibration results of the Plastic Scintillator strip Detector (PSD), the Silicon-Tungsten tracKer-converter (STK), the BGO imaging calorimeter (BGO), and the Neutron Detector (NUD). The results are obtained using Galactic cosmic rays, bright known GeV gamma-ray sources, and charge injection into the front-end electronics of each sub-detector. The determination of the boundary of the South Atlantic Anomaly (SAA), the measurement of the live time, and the alignments of the detectors are also introduced. The calibration results demonstrate the stability of the detectors in almost two years of the on-orbit operation

The on-orbit calibration of DArk Matter Particle Explorer

The DArk Matter Particle Explorer (DAMPE), a satellite-based cosmic ray and gamma-ray detector, was launched on December 17, 2015, and began its on-orbit operation on December 24, 2015. In this work we document the on-orbit calibration procedures used by DAMPE and report the calibration results of the Plastic Scintillator strip Detector (PSD), the Silicon-Tungsten tracKer-converter (STK), the BGO imaging calorimeter (BGO), and the Neutron Detector (NUD). The results are obtained using Galactic cosmic rays, bright known GeV gamma-ray sources, and charge injection into the front-end electronics of each sub-detector. The determination of the boundary of the South Atlantic Anomaly (SAA), the measurement of the live time, and the alignments of the detectors are also introduced. The calibration results demonstrate the stability of the detectors in almost two years of the on-orbit operation