HOMSTRAD: a database of protein structure alignments for homologous families.

We describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned structures, which have been selected on the basis of quality of the X-ray analysis and accuracy of the structure. For each family, the database provides a structure-based alignment derived using COMPARER and annotated with JOY in a special format that represents the local structural environment of each amino acid residue. HOMSTRAD also provides a set of superposed atomic coordinates obtained using MNYFIT, which can be viewed with a graphical user interface or used for comparative modeling studies. The database is freely available on the World Wide Web at: http://www-cryst.bioc.cam. ac.uk/-homstrad/, with search facilities and links to other databases.     

Optimizing conditions for cryopreservation of an insect cell line

A cell line (UM-BGE-2) derived from embryos of the cockroach Blattella germanica was frozen to ?196 °C under a variety of conditions and cell viability was assayed after warming. It was found that cell viability was affected by the cooling rate, the warming rate, the controlled cooling endpoint temperature, and the type and concentration of cryoprotectant. The best survival for cells suspended in Grace's tissue culture medium containing 1 M Me₂SO was obtained when cells were cooled at 1 °C/ min to at least ?90 °C before being placed in liquid nitrogen and warmed at more than 900 °C/min. Cultures initiated from these frozen cells produce typical growth curves and appear normal after several passages.     

在住院处深入开展以人为本与和谐共存服务理念的探讨

目的：为构建和谐的医患关系,为病人提供优质服务,结合住院处的实际情况,探讨在医院住院处深入开展以人为本与和谐共存服务理念的重要性和必要性。方法：详细介绍以人为本与和谐共存服务理念,简要概括医院住院处的工作职责及其在医院系统中的作用和地位,将以人为本与和谐共存服务理念与医院住院处的职责相结合,探讨该理念在提升住院处的工作职能、促进与患者的沟通交流、提升医院信誉、维护医院形象中的作用。结果：以人为本与和谐共存服务理念在指导住院处各项工作中确实有一定的引导作用。结论：将以人为本与和谐共存服务理念在提升住院处的工作职能相结合,可以很好地促进医务人员与患者的沟通交流,提升医院信誉,提高医院竞争力。     

Studies on the mode of action of calciferol: Biological activity of 1α,24R,25-trihydroxyvitamin D3 in the chick

The biological activity of 1α,24R,25-trihydroxyvitamin D₃ [1α,24R,25(OH)₃D₃] was elevated in comparison to the hormonally active form of vitamin D₃, 1α,25-dihydroxyvitamin D₃ [1α,25(OH)₂D₃], in the rachitic chick in terms of its ability to (a) stimulate intestinal calcium absorption, (b) mobilize bone calcium, (c) induce intestinal calcium binding protein, (d) modulate the level of enzyme activity of the renal 25-OH-D₃-1-hydroxylase system, and (e) interact with the intestinal cystosol-chromatin receptor system for the 1α,25(OH)₂D₃ receptor system. In each of these assays, the relative ratio of activity of 1α,24R,25(OH)₃D₃ to 1α,25(OH)₂D₃was (a) 25–50, (b) ca. 20, (c) 10, (d) 50, and (e) 36%, respectively.     

VitisMod:一个葡萄基因共表达数据库

葡萄转录组已在各种组织、发育阶段、生物胁迫、非生物胁迫和其他条件下被测定。目前,仍没有简单实用的网络工具来探索这些宝贵的数据。本文从美国国立生物技术信息中心的基因表达数据库(NCBI GEO)下载1019个基因表达芯片数据,进行权重基因共表达网络分析(WGCNA)。鉴定到41个基因共表达模块。功能富集分析发现这些模块具有不同的功能,并与实验/表型相关。通过模块内连接度筛选枢纽基因,这些基因可能具有重要功能。通过关联推定(Guilt-by-association)原理对模块内功能未知的基因进行功能预测。最后,构建了免费的网络工具VitisMod,为葡萄的基因功能研究提供新资源,网址为：http://bioinformatics.fafu.edu.cn/grape。     

Prescribed fires in Artemisia tridentata ssp. vaseyana steppe have minor and transient effects on vegetation cover and composition

Question: What is the impact of prescribed fires on the cover and composition of vegetation in Artemisia tridentata ssp. vaseyana steppe? Location: United States Department of Agriculture, Agricultural Research Service, United States Sheep Experiment Station, eastern Idaho (44°14′44′’ N, 112°12′47′’ W). Methods: Multiple prescribed fires were lit in 2002 and 2003 in an Artemisia tridentata ssp. vaseyana (mountain big sagebrush) steppe ecosystem that was relatively free of exotic plants. Measurements of cover components and plant species frequencies were taken pre‐ and for 2 to 3 years post‐fire. Results: Cover of forbs and grasses returned to pre‐fire levels after two years. Shrub cover declined from 36 to 6% in the first year post‐fire. Fire reduced the frequencies of three species, A. tridentata ssp. vaseyana, Festuca idahoensis, and Cordylanthus ramosus, of rangeland plants. Frequencies of four plant species, Hesperostipa comata, Polygonum douglasii, Chenopodium fremontii and Chenopodium leptophyllum increased, but only P. douglasii increased for more than a year. Conclusion: This study demonstrates that in an Artemisia tridentata ssp. vaseyana steppe ecosystem without significant non‐native species or anthropogenic disturbances vegetative cover and species composition of the herbaceous community are only minimally altered by fire. The herbaceous component returned to pre‐fire conditions within three years of a fire.     

某三级甲等医院实施单病种质量管理的效果分析

目的：分析单病种质量管理对三级甲等医院临床医疗质量控制的干预效果。方法：介绍实施单病种质量管理的具体措施,回 顾性分析出院人次、平均住院日及住院费用。结果：实施单病种质量管理规范了医师诊疗行为并改进了医疗服务质量,缩短了平 均住院日,降低了医疗费用;但医务人员对单病种质量管理的认识不够深入,单病种诊断标准不够规范,单病种限价对医疗质量 具有潜在的影响。结论：应在不断总结单病种质量管理经验的基础上,完善单病种质量管理,促进我国医疗行业持续、健康的发 展。     

DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning

Protein nitration and nitrosylation are essential post-translational modifications(PTMs)involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases.Therefore, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specificscoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65 for tyrosine nitration, 0.80 for tryptophan nitration, and 0.70 for cysteine nitrosylation, respectively,demonstrating the robustness and reliability of our tool. Also, when tested in the independent dataset, DeepNitro is substantially superior to other similar tools with a 7%à42% improvement in the prediction performance. Taken together, the application of deep learning method and novel encoding schemes, especially the position-specific scoring feature, greatly improves the accuracy of nitration and nitrosylation site prediction and may facilitate the prediction of other PTM sites. DeepNitro is implemented in JAVA and PHP and is freely available for academic research at http://deepnitro.renlab.org.     

Predict prokaryotic proteins through detecting N-formylmethionine residues in protein sequences using support vector machine

Identifying prokaryotes in silico is commonly based on DNA sequences. In experiments where DNA sequences may not be immediately available, we need to have a different approach to detect prokaryotes based on RNA or protein sequences. N-formylmethionine (fMet) is known as a typical characteristic of prokaryotes. A web tool has been implemented here for predicting prokaryotes through detecting the N-formylmethionine residues in protein sequences. The predictor is constructed using support vector machine. An online predictor has been implemented using Python. The implemented predictor is able to achieve the total prediction accuracy 80% with the specificity 80% and the sensitivity 81%.     

中国陆地生态系统服务价值测量

利用遥感技术,结合生态学方法,在对生态参数遥感测量的基础上,计算了中国陆地生态系统2000年的生态服务价值.结果表明,中国陆地生态系统2000年所产生的生态服务价值为9.17×10¹²元,总体空间分布由东向西递减、由中部向东北和南部递增,与植被的地带性分布梯度基本一致;森林的平均单位面积价值最高,为18789元·hm^-2,占总生态服务价值的40.80%;其次是灌丛(13789元·hm^-2)和耕地(13054元·hm^-2),分别占总生态服务价值的10.79%和24.23%.从生态系统服务功能来看,气体调节价值的贡献率最大,占总价值的45.16%;其次是水土保持价值(28.83%)和涵养水源价值(14.44%);有机物质生产和营养物质循环的价值最小,其贡献率为11.57%.生态遥感测量方法克服了传统生态统计方法以点代面的缺点,计算结果能更加客观地反映生态系统服务价值及其空间分布,但该方法本身也存在一些不确定性,对生态系统各项服务功能及其价值的评估只是保守和粗略的估计,有待于深入研究.