Meeting report: eGenomics: Cataloguing our Complete Genome Collection II

This article summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection II" workshop held November 10-11, 2005, at the European Bioinformatics Institute. This exploratory workshop, organized by members of the Genomic Standards Consortium (GSC), brought together researchers from the genomic, functional OMICS, and computational biology communities to discuss standardization activities across a range of projects. The workshop proceedings and outcomes are set to help guide the development of the GSC's Minimal Information about a Genome Sequence (MIGS) specification.     

Are restricted species checklists or ant communities useful for assessing plant community composition and biodiversity in grazed pastures?

Semi-natural grasslands in Sweden are species-rich, and their natural values are strongly dependent on continuous management, mainly by grazing. However, the large heterogeneity in vegetation within and between grassland sites must be taken into account when designing management and preservation schemes, calling for precise field monitoring and assessment of habitat type and land use history. We have evaluated different surrogate measures to assess community composition and biodiversity of the most common vegetation types in grazed semi-natural pastures. We compared the complete plant community, two reduced checklists intended for quick surveys of the plant community, and the ant community. The results suggest that the taxonomic resolution in a plant inventory is important for both biodiversity assessment and recognition of vegetation types. The extent of a reduced species checklist was of greater importance than its quality for describing the plant community. Reduced checklists should only be used if they comprise species with known affinity to the studied vegetation types. We also found that plants and ants experience grazed semi-natural grasslands in different ways. Ant communities did not resemble the communities deduced from plant inventories, or vegetation types recognised by field staff.     

Spatial and temporal analyses of water quality and phytoplankton biomass in an urbanized versus a relatively pristine salt marsh estuary

The robust growth of coastal communities in the southeastern United States is putting unique pressures on estuarine resources. Urbanization of estuarine systems may alter ecosystem function and thus affect the spatial scale and magnitude of nutrient concentrations and primary production temporally and spatially. We examined the spatial and temporal patterns of nutrient and chlorophyll a (Chl a) concentrations in two shallow well-mixed estuaries, (1) a developed estuary, Murrells Inlet (MI), South Carolina, and (2) a relatively pristine estuary, North Inlet (NI), South Carolina. The summer chlorophyll a maximum in MI was characteristically higher than in NI, which may be indicative of eutrophication. Correlations between salinity and inorganic nutrients (N and P) suggest that nutrient import from upland sources may be more pronounced in MI during stochastic precipitation events. Although inorganic nutrient concentrations between the estuaries were similar overall, during a wet period, inorganic N concentration in MI was increased to a greater extent than in NI, while only minimal increases in inorganic P were observed in both estuaries. Chlorophyll a concentrations decreased from the dry to wet period. Geographic Information System (GIS) plots of intensive spatial sampling in MI indicated spatial gradients of nutrient concentrations within this estuary that appeared to be consistent over time. These observations were investigated in more detail using regression analyses to examine the influences of coastal dilution and nutrient sources on relationships between water quality constituents. Results indicate the importance of stochastic rain events in affecting the linkages of estuarine processes to upland runoff in the urbanized estuary, MI.     

中国不同地理区域鸟兽物种丰富度的相关性

生物类群之间物种丰富度的相关性研究是当前物种多样性研究中的热点问题之一,目前,中国尚无相关的研究报道。我们收集了中国三种区域类型：动物地理亚区、行政区和保护区的鸟兽名录,分析了行政区与保护区、动物地理区和经纬度带中鸟兽物种数比值及其相关性。 结果表明：不同区域、动物地理区和经纬度带中鸟兽物种数都显著相关。保护区尺度鸟兽物种 数的相关系数为0.818和动物地理区中的华北区为0.768,其他所有区域和地理区域的鸟兽物 种数的相关系数都高于0.850。因此,鸟兽物种数的相关关系在一定程度上具有预测价值。我们发现不同区域鸟兽物种数比值无显著性差异;但是,不同区域间鸟兽物种数 比值差异显著。该比值在中国呈中间低四周高的分布趋势,其中东北地区最高。我们还利用历史累积调查数据与非历史累积调查数据进行了鸟兽物种数比值及其相关性分析,发现利用累积数据计算的相关性低于非累积数据计算的相关性,但利用累积数据计算的鸟兽物 种数比值高于非累积数据计算的比值。最后,探讨了为什么鸟类与兽类的物种数目会相关。我们根据物种－面积公式,S=CA^Z,导出了两个生物类群物种丰富度的相关关 系式。利用全国不同区域数据拟合,得到Z₁/Z₂＝0.913,Z₁/Z₂接近于1。于是 ,C₁/C2可视为近似等于R_am。本研究可推广到其他不同生物类群物种。物种数量的相关关系为快速评估区域的物种多样性提供了一条途径。     

Medical physics external beam plan review: What contributes to the variability?

PurposeIn this article we report on the results of a survey of physics plan review practices conducted by the Cancer Care Ontario Communities of Practice and the variations in practice between and within centers.MethodsThe medical physicists at each center worked together to complete the survey and submit a single response for that center. A 4-point Likert scale, used to report the variation in practice at each center, was quantified into two parameters: “Intra-center variation”, the distribution of responses within the center, and “Variation between centers”, the difference between the center’s response and the provincial mean. These metrics were correlated with center characteristics to identify factors that impacted on variations in practice.ResultsBolus and heterogeneity correction were the only two items checked by all physicists in all centers. In more than half of the centers, image registration and DVH binning are not likely checked by physics. A significant difference in the variation between centers is observed for centers that used a single vendor’s products. Centers that used an official checklist indicated higher levels and a wider range of Intra-center variation. Higher workload did not affect the variation in checking patterns between physicists in the same center.ConclusionsThe effect of a center’s resources on their checking practice suggest that local environment and workflow be accounted for when implementing TG275 guidelines. The observation that standardized checklists did not reduce checking variability point to the importance of following the checklist development guidelines in MPPG4 to avoid ineffective checklists.     

Some new species and a first checklist of corticioid fungi (Basidiomycota) from Chile

Gloeocystidiellum rajchenbergii, Hypochnicium patagonicum, Pteridomyces valdivianus, and Stereum greslebinii are described as new species from the Chilean Patagonia. An annotated checklist of corticioid fungi from Chile, listing 94 species with notes on distribution and ecology, scheduled for regular update, is available from http://corticioids.webs.com/checklists.htm.     

江西省野生维管植物名录

为了全面了解江西省野生维管植物资源的现状并为开展相应的生物多样性保护实践提供基础资料, 本文在前人的基础上, 通过进一步的文献收集、标本考证、数据分析, 并结合作者的野外调查结果, 按照维管植物最新的分类系统整理出江西省野生维管植物名录, 并根据标本信息核实了每个物种县市级的分布信息。结果显示, 江西省共有野生维管植物214科1,253属4,761种(含种下等级), 其中石松类与蕨类植物35科103属444种, 裸子植物5科21属36种, 被子植物174科1,129属4,281种。石松类与蕨类植物中, 物种数最多的前5个科为鳞毛蕨科(84种)、水龙骨科(55种)、凤尾蕨科(49种)、蹄盖蕨科(47种)和金星蕨科(47种), 最多的属是鳞毛蕨属(Dryopteris, 40种); 裸子植物中物种数最多的科和属为松科(7属12种)和松属(Pinus, 5种); 被子植物是江西省野生维管植物的最主要组成部分, 分别占科、属、种总数的81.3%、90.1%和89.9%, 其中种数最多的前5个科分别是禾本科(315种)、菊科(241种)、蔷薇科(228种)、唇形科(200种)和豆科(197种), 前6个属依次是薹草属(Carex, 71种)、悬钩子属(Rubus, 66种)、冬青属(Ilex, 56种)、蓼属(Persicaria, 40种)、珍珠菜属(Lysimachia, 37种)和杜鹃花属(Rhododendron, 37种)。江西省维管植物调查呈现出地区不均衡性, 建议增加后续调查工作的广度和深度, 尤其在武夷山脉、赣南山区、鄱阳湖湿地等生物多样性较高或较特殊的地区进行补充采集。同时, 本文呼吁加强专科专属的分类学研究, 为后续名录的修订与完善奠定基础。     

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics,March 2011

Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of ‘fitness for use’ for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC’s standard checklists for genomics and metagenomics and (b) TDWG’s Darwin Core standard, used primarily in taxonomy and systematic biology.     

Resources Evaluation of Seed Plants in Yulong Snow Mountain,Lijiang, Northwestern Yunnan

Yulong Snow Mountain (Jade Dragon Snow Mountain), located in northwestern Yunnan, is belonging to one of three biodiversity centers of China. In this paper, we analyzed the composition of seed plant resource species in Yulong Snow Mountain based on databases and checklists of seed plants, and specimens collected recently in this area. More than 2815 seed plant species in Yulong Snow Mountain region were recorded, among which 96 species are endangered. Furthermore, we classified and evaluated these plant resources based on their use and biological characteristics. In addition, we propose a systematic and sustainable approach to solve the conflicts between the conservation and the economical development. This study updated the checklist of seed plants of Lijiang Alpine Botanical Garden, while also documented the basic information of plant resources in Yulong Snow Mountain. These findings provided scientific basis for future research and conservation.     

基于主因子分析的生态社区评价方法研究——以上海外环以内区域为例

从生态系统和可持续发展理论出发,构建了生态社区评价的指标体系,运用主因子分析方法建立了生态社区评价模型;并在遥感与GIS技术支持下,对上海中心城区做了生态社区评价研究.结果表明,在空间格局上,社区生态水平差异明显,无论是在社区内部还是社区之间,各主因子分布极不平衡;总体看来,浦西核心区的大部分社区,其规模结构比较合理,服务设施比较完善,然而部分社区的生态环境质量急需要改善,部分社区的居住条件也需要进一步完善;而浦东一些社区,尽管生态指数较高,生态环境质量较好,但由于基础配套设施不够健全,规模结构不够均衡,道路交通系统尚待进一步完善.     

线虫群落对抚顺煤矸石山周边土壤可溶性盐污染的响应

于2006年5月对抚顺西露天矿西舍场煤矸石山周边的次生盐渍化样地进行可溶性盐含量和土壤线虫调查,经淘洗-过筛-离心漂浮法提取土壤线虫,应用线虫多样性指数和功能类群指数研究该区域土壤线虫群落的特征及差异。研究结果表明,抚顺西露天矿西舍场矸石山周围环境受到了煤矸石风化产生的以硫酸钠为主的可溶性盐污染, 但污染程度不高,土壤整体健康状况良好;共鉴定出线虫29属,其中Acrobeloides、Cervidellus 和Mesorhabtidis为优势属,随采样点距矸石山距离的增加线虫优势属也有所变化;研究区域中食细菌线虫和植物寄生线虫的绝对丰度高于食真菌线虫和捕食-杂食线虫的绝对丰度;土壤pH、矿化度、HCO₃^-、Cl^-、SO₄^2-、NO₃^-与线虫生态指数间存在显著相关关系。因此,通过开展线虫群落对土壤可溶性盐污染的响应研究,能为促进土壤生态系统健康发展提供科学依据。     

获取生物物种名录信息的R程序包SP2000

物种名录为衡量区域和全球生物多样性提供了数据基础。随着互联网的兴起与发展, 人们将地球上已知的动物、植物、微生物等类群的物种名录信息存储到公共数据平台中, 并对物种名录进行快速及时地更新, 这极大地促进了分类学、保护生物学和宏观生态学等学科的发展, 成为政府或国际组织开展物种保育现状评估、红色名录编撰和生物多样性保护的重要依据。物种2000中国节点(http://www.sp2000.org.cn)和Catalogue of Life网站(http://www.catalogueoflife.org)分别是中国和全球最大的生物物种名录数据平台, 截至2020年6月4日, 其收录的物种数分别为122,280种和1,829,672种。然而这些数据平台仅提供物种查询、检索、下载等基本功能, 难以满足使用者准确、快速地批量获取所需生物物种名录数据信息的需求, 制约了这些大数据平台在生物多样性研究和保护中的作用。因此, 我们选取R语言开发了程序包SP2000, 旨在帮助用户批量获取中国或全球生物物种名录信息。该程序包具有跨Windows、MacOS、Linux等多个系统运行、操作便捷、代码开源等特点。为了方便用户使用, 本文详细介绍了SP2000的基本原理、特点及使用指南, 包括程序包的下载、安装、运行和参数设置等。     

Assessing the Assessment in Emergency Care Training

Objective

Each year over 1.5 million health care professionals attend emergency care courses. Despite high stakes for patients and extensive resources involved, little evidence exists on the quality of assessment. The aim of this study was to evaluate the validity and reliability of commonly used formats in assessing emergency care skills.

Methods

Residents were assessed at the end of a 2-week emergency course; a subgroup was videotaped. Psychometric analyses were conducted to assess the validity and inter-rater reliability of the assessment instrument, which included a checklist, a 9-item competency scale and a global performance scale.

Results

A group of 144 residents and 12 raters participated in the study; 22 residents were videotaped and re-assessed by 8 raters. The checklists showed limited validity and poor inter-rater reliability for the dimensions “correct” and “timely” (ICC = .30 and.39 resp.). The competency scale had good construct validity, consisting of a clinical and a communication subscale. The internal consistency of the (sub)scales was high (α = .93/.91/.86). The inter-rater reliability was moderate for the clinical competency subscale (.49) and the global performance scale (.50), but poor for the communication subscale (.27). A generalizability study showed that for a reliable assessment 5–13 raters are needed when using checklists, and four when using the clinical competency scale or the global performance scale.

Conclusions

This study shows poor validity and reliability for assessing emergency skills with checklists but good validity and moderate reliability with clinical competency or global performance scales. Involving more raters can improve the reliability substantially. Recommendations are made to improve this high stakes skill assessment.     

A Quick Guide for Building a Successful Bioinformatics Community

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).     

Hydrogen sulfide mitigates cardiac remodeling during myocardial infarction via improvement of angiogenesis

Exogenous hydrogen sulfide (H2S) leads to down-regulation of inflammatory responses and provides myocardial protection during acute ischemia/reperfusion injury; however its role during chronic heart failure (CHF) due to myocardial infarction (MI) is yet to be unveiled. We previously reported that H2S inhibits antiangiogenic factors such, as endostatin and angiostatin, but a little is known about its effect on parstatin (a fragment of proteinase-activated receptor-1, PAR-1). We hypothesize that H2S inhibits parstatin formation and promotes VEGF activation, thus promoting angiogenesis and significantly limiting the extent of MI injury. To verify this hypothesis MI was created in 12 week-old male mice by ligation of left anterior descending artery (LAD). Sham surgery was performed except LAD ligation. After the surgery mice were treated with sodium hydrogen sulfide (30 μmol/l NaHS, a donor for H2S, in drinking water) for 4 weeks. The LV tissue was analyzed for VEGF, flk-1 and flt-1, endostatin, angiostatin and parstatin. The expression of VEGF, flk-1 and flt-1 were significantly increased in treated mice while the level of endostatin, angiostatin and parstatin were decreased compared to in untreated mice. The echocardiography in mice treated with H2S showed the improvement of heart function compared to in untreated mice. The X-ray and Doppler blood flow measurements showed enhancement of cardiac-angiogenesis in mice treated with H2S. This observed cytoprotection was associated with an inhibition of anti-angiogenic proteins and stimulation of angiogenic factors. We established that administration of H2S at the time of MI ameliorated infarct size and preserved LV function during development of MI in mice. These results suggest that H2S is cytoprotective and angioprotective during evolution of MI.     

ILCD Handbook Public Consultation Workshop

Introduction

The European Commission is supporting the development of the International Reference Life Cycle Data System (ILCD). This consists primarily of the ILCD Handbook and the ILCD Data Network. This paper gives an insight into the scientific positions of business, governments, consultants, academics, and others that were expressed at this public consultation workshop.

Workshop focus

The workshop focused on four of the topics of the main guidance documents of the ILCD Handbook: (1) general guidance on life cycle assessment (LCA); (2) guidance for generic and average life cycle inventory (LCI) data sets; (3) requirements for environmental impact assessment methods, models and indicators for LCA; and (4) review schemes for LCA.

Workshop participation

This consultation workshop was attended by more than 120 participants during the 4 days of the workshop. Representatives came from 23 countries, from both within and outside the European Union.

Workshop structure

Approximately half of the participants were from business associations or individual companies. Another 20% were governmental representatives. Others came predominantly from consultancies and academia.

Results

This public consultation workshop provided valuable inputs into the overall ILCD Handbook developments as well as for further development. This paper focuses on some of the main scientific issues that were raised.     

Myo-Inositol Treatment and GABA-A Receptor Subunit Changes After Kainate-Induced Status Epilepticus

Identification of compounds preventing the biochemical changes that underlie the epileptogenesis process is of great importance. We have previously shown that myo-Inositol (MI) daily treatment prevents certain biochemical changes that are triggered by kainic acid (KA)-induced status epilepticus (SE). The aim of the current work was to study the further influence of MI treatment on the biochemical changes of epileptogenesis and focus on changes in the hippocampus and neocortex of rats for the following GABA-A receptor subunits: α1, α4, γ2, and δ. After SE, one group of rats was treated with saline, while the second group was treated with MI. Control groups that were not treated by the convulsant received either saline or MI administration. 28–30 h after the experiment, a decrease in the amount of the α1 subunit was revealed in the hippocampus and MI had no significant influence on it. On the 28th day of the experiment, the amount of α1 was increased in both the KA? and KA + MI-treated groups. The α4 and γ2 subunits were strongly reduced in the hippocampus of KA-treated animals, but MI significantly halted this reduction. The effects of MI on α4 and γ2 subunit changes were significantly different between hippocampus and neocortex. On the twenty-eighth day after SE, a decrease in the amount of α1 was found in the neocortex, but MI treatment had no effect on it. The obtained results indicate that MI treatment interferes with some of the biochemical processes of epileptogenesis.     

Arjunolic acid ameliorates reactive oxygen species via inhibition of p47phox-serine phosphorylation and mitochondrial dysfunction

Impaired cardiovascular function during acute myocardial infarction (MI) is partly associated with recruitment of activated polymorphonuclear neutrophils. The protective role of arjunolic acid (AA; 2,3,23-trihydroxy olean-12-en-28-oic acid) is studied in the modulation of neutrophil functions in vitro by measuring the reactive oxygen species (ROS) generation. Neutrophils were isolated from normal and acute MI mice to find out the efficacy of AA in reducing oxidative stress. Stimulation of neutrophils with phorbol-12-myristate-13-acetate (PMA) resulted in an oxidative burst of superoxide anion (O₂⁻) and enhanced release of lysosomal enzymes. The treatment of neutrophils with PMA induced phosphorylation of Ser345 on p47^phox, a cytosolic component of NADPH oxidase. Furthermore, we observed activated ERK induced phosphorylation of Ser345 in MI neutrophils. Treatment with AA significantly inhibited the phosphorylation of P47^phox and ERK in the stimulated controls and MI neutrophils. Oxidative phosphorylation activities in MI cells were lower than in control, while the glycolysis rates were elevated in MI cells compared to the control. In addition, we observed AA decreased intracellular oxidative stress and reduced the levels of O₂⁻ in neutrophils. This study therefore identifies targets for AA in activated neutrophils mediated by the MAPK pathway on p47^phox involved in ROS generation.     

Geographical patterns of parasite infracommunities in the rough scad, Trachurus lathami Nichols, in the Southwestern Atlantic ocean

We assessed temporal variability in parasite infections of rough scad (Trachurus lathami) in 3 samples from Miramar (MI) in 2008, separated by periods of 1 mo, and 2 samples from Villa Gesell (VG), 1 each in 2008 and 2009 (Buenos Aires Province, Argentina), respectively. A sample was also obtained from Cabo Frio (CF) (Brazil) in 2009 to compare differences in parasite communities between fish from this locality and each Argentinean locality. All rough scad were parasitized by at least 1 of 27 parasite species. Similarity-based multivariate analysis revealed significant differences between localities, but temporal homogeneity in each Argentinean locality. Overall, prevalence and abundance of parasite species were most similar between samples from MI and VG, while the greatest differences occurred between samples from MI and CF. A canonical analysis of principal coordinates showed significant differences among samples. Grillotia carvajalregorum was the most important species in determining the position of Argentinean samples, especially those from MI, while Ectenurus virgulus , Raphidascaris sp., and Hysterothylacium sp. were the most important species related to fish from CF. The parasite assemblage of T. lathami showed a notable temporal persistence within the same locality and a high variability at the spatial scale, suggesting the existence of 3 independent stocks of T. lathami in South Atlantic waters.