The genome of the extremophile crucifer Thellungiella parvula

Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance.     

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder

Transitional cell carcinoma (TCC) is the most common type of bladder cancer. Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer.     

Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1

We report a genome-wide association study for open-angle glaucoma (OAG) blindness using a discovery cohort of 590 individuals with severe visual field loss (cases) and 3,956 controls. We identified associated loci at TMCO1 (rs4656461[G] odds ratio (OR) = 1.68, P = 6.1 × 10(-10)) and CDKN2B-AS1 (rs4977756[A] OR = 1.50, P = 4.7 × 10(-9)). We replicated these associations in an independent cohort of cases with advanced OAG (rs4656461 P = 0.010; rs4977756 P = 0.042) and two additional cohorts of less severe OAG (rs4656461 combined discovery and replication P = 6.00 × 10(-14), OR = 1.51, 95% CI 1.35-1.68; rs4977756 combined P = 1.35 × 10(-14), OR = 1.39, 95% CI 1.28-1.51). We show retinal expression of genes at both loci in human ocular tissues. We also show that CDKN2A and CDKN2B are upregulated in the retina of a rat model of glaucoma.     

PsmArena: Partitioned Shared Memory for NUMA-Awareness in Multithreaded Scientific Applications

The Distributed Shared Memory(DSM) architecture is widely used in today's computer design to mitigate the ever-widening processing-memory gap, and it inevitably exhibits Non-Uniform Memory Access(NUMA) to shared-memory parallel applications. Failure to adapt to the NUMA effect can significantly downgrade application performance, especially on today's manycore platforms with tens to hundreds of cores. However, traditional approaches such as first-touch and memory policy fall short in false page-sharing, fragmentation, or ease of use. In this paper, we propose a partitioned shared-memory approach that allows multithreaded applications to achieve full NUMA-awareness with only minor code changes and develop an accompanying NUMA-aware heap manager which eliminates false page-sharing and minimizes fragmentation. Experiments on a 256-core cc-NUMA computing node show that the proposed approach helps applications to adapt to NUMA with only minor code changes and improves the performance of typical multithreaded scientific applications by up to 4.3 folds with the increased use of cores.     

Long Text Classification Algorithm Using a Hybrid Model of Bidirectional Encoder Representation from Transformers-Hierarchical Attention Networks-Dilated Convolutions Network

Text format information is full of most of the resources of Internet,which puts forward higher and higher requirements for the accuracy of text classification.T...     

中上层浮鱼礁最优单锚系泊方式研究

中上层人工生境建设是我国南方海洋牧场发展模式的重要组成部分,以单锚系泊的中上层浮鱼礁为研究对象,探讨保证结构安全和聚鱼效果的最优锚泊方式.首先基于波浪水槽中浮鱼礁物理模型试验验证了现有数值模型的准确性.而后针对浮鱼礁单锚系泊方式,详述了数值模型中单锚系泊方式的处理方法和出水条件的判别方法,重点探讨了浮鱼礁浮架底部中心至...     

试谈环境科学术语统一性

贵刊2005年第7卷第2期开展了关于"生态环境建设"提法的讨论,这对环境科学基础理论研究和科技名词规范及统一,是有促进作用的.现仅就一些较有影响的辞书所反映的环境科学术语概念不统一的问题,试举几例,供研讨.     

DPSIR model-based evaluation index system for geographic national conditions

Establishing a reasonable evaluation index system is the basis and premise for the scientific evaluation of geographic national conditions. By analyzing the DPSIR model and its correlation and relation with the evaluation index system, the indexes for geographic national conditions were selected from the aspects of resources, ecology, environment, economy, society, etc to build an evaluation index system for geographic national conditions that consists of three hierarchies: index, criterion, and target levels. Furthermore, the index system was analyzed in terms of index integrity, low overlapping of elements, non-existence of isolated indexes, hierarchy of index system, etc., for the purpose of demonstrating that the DPSIR model-based evaluation index system for geographic national conditions meets the principles of index system establishment.     

Internet路由前缀宣告的特征挖掘与分析

基于大量的历史BGP路由表快照,对BGP路由宣告信息进行深度挖掘.提出了前缀宣告稳定性度量方法,验证了绝大多数路由宣告是稳定的,历史上发生的路由劫持事件都是瞬时的(不具备稳定性);设计了前缀宣告的相似性测度算法,对大量历史BGP路由宣告进行了分析,结果表明大多数大型AS宣告的路由前缀具有自相似性,即,同一个AS宣告的多个路由前缀有一定的连续性.基于以上两个特征,从历史路由信息中可进一步提取前缀宣告的可信集,构造BGP路由宣告的可信知识库,为后续的路由前缀劫持检测和路由安全监测提供依据.