Weighting and Congruence: A Case Study Based on Three Mitochondrial Genes in Pitvipers

Weighting strategies in a total evidence approach are often conducted in order to remove homoplasy, with the implicit hope to increase congruence between data partitions. Incongruence was measured using the test of Farriset al.(J. S. Farris, M. Källersjö, A. G. Kluge, and C. Bult, 1995,Cladistics10, 315–319) within and between three mitochondrial genes from pitvipers (Crotalinae) in partitioning each codon position for the coding genes. Incongruence between codon positions of a gene can be worse than incongruence between genes at analogous positions. Third positions of codons behave very differently in terms of incongruence from one gene to another while showing similar patterns in saturation tests. Instead of removing characters in order to discard homoplasy, which is hopeless and does not increase general congruence, we advocate for the removal of those substitutions that are incongruent with the rest. The genusCalloselasmaand its sister group the genusHypnaleare the most basal Crotalinae. Asiatic pitvipers are paraphyletic, while American pitvipers are monophyletic.     

LCA Case Study of zinc hydro and pyro-metallurgical process in China

Goal, Scope and Background  China is one of the main producers of metallic zinc and its annual production has been becoming the largest in the world since the year 2000. To improve the environmental situation of zinc production in China, a life cycle assessment was performed for hydro and pyro-metallurgical processes, based on the case study of Zhuzhou Smelter and Shaoguan metallurgical plant, respectively. Methods  The system is modeled into several sub-modules so as to identify the source of environmental impacts. Results and Discussion  The main results of LCA study are summarized as follows: (1) Hydro-metallurgical process is superior to pyro-metallurgical process in GWP and inferior to pyro-metallurgical process in GER and ACP. (2) Compared with the advanced foreign zinc metallurgical process, the GWP, ACP and HME of the zinc metallurgical process in China are much higher. (3) In hydro-metallurgical processes, residue treatment and auxiliary processes are the main contributors of ACP and GWP, which are the key sub-modules, and should be improved. In pyro-metallurgical processes, the main sub-modules needing improvement are smelting, power and electricity generation. (4) Electricity is the main energy consumption in the hydro-metallurgical processes, accounting for 60% of GER. In pyro-metallurgical process, main energy sources are metallurgical coke and anthracite, both also accounting for 60% of GER. Conclusions  According to the discovery of LCA study, three main measures to improve the environmental performance of zinc products were proposed: 1) Regulating the structure of energy sources of Shaoguan Smelter, 2) removing SO^b2 in low concentration from flue gas by absorption with zinc oxide, and 3) adjusting the material structure of Walze rotary furnace.     

Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans

Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choic of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objectively which approach is best. Using a cytochrome b data set from cetaceans and artiodactyls, we examined the effects of a suite of parameter settings on the outcome of phylogenetic analyses. We tested 2968 combinations among the seven parameters that most often vary among phylogenetic studies. It is our contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings. Portions of this data set have been used in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales.     

Perceptions on LCA implementation: evidence from a survey on adopters and nonadopters in Italy

Purpose

This paper introduces the results of an Italian survey on the implementation of life cycle assessment (LCA). Both LCA adopters and nonadopters were involved, in order to understand the main benefits and barriers to the adoption of LCA and how the experiences of LCA adopters differ from the expectations of nonadopters.

Methods

Approximately 2000 Italian companies were contacted and 122 companies participated in the online survey, which represent the 6.5 % of the statistical population of our study. To define the statistical population, firms that had implemented an LCA or an environmental initiative according to an official international standard were only considered. Statistically significant differences in answers between LCA adopters and nonadopters were tested by performing the Mann–Whitney test.

Results and discussion

Companies recognize that LCA can provide useful information to drive strategic decisions and product design, and it is perceived as an opportunity to improve the current monitoring systems. In addition, companies recognize the potential of LCA in marketing, making the communication of green attributes more substantial and robust. Focusing on the barriers experienced by LCA adopters, data collection can be cited. Communication issues also pose a barrier to the further implementation of LCA. The analysis of the results and the comparison of the results for the two groups of respondents highlight that on average, the difficulties are considered as more important than the benefits and that nonadopters tend to overestimate the difficulties and underestimate the benefits connected to the implementation of LCA.

Conclusions

The findings shed light on LCA-related issues both for companies and public servants. The misconception of LCA by nonadopters suggests that an increased awareness is the key to the success of LCA and to its more widespread adoption by companies. It is essential to create and disseminate know-how and sensitize companies to the real barriers and benefits of adopting an LCA. The awareness of potential LCA adopters can be raised by training and education initiatives, as well as by increased possibilities to experiment with these kinds of tools (public programs for financial support, fiscal incentives). On the other hand, market and communication research would contribute to better understand how the environmental impacts of products can be more effectively communicated to clients and consumers.

     

胚胎发育早期转基因的PCR检测研究

转基因在受精卵中的整合时间对于转基因动物的建立十分重要。采用ＷＡＰ基因调控序列指导的人Ｇ－ＣＳＦ基因为构件,对小鼠受精卵进行显微注射。对培养至１细胞期、２细胞期和８细胞期的胚胎进行ＰＣＲ检测。结果表明,三个时期转基因的检出率分别为１００％、７７．７７％和４４．４４％。说明随着培养时间的增加,转基因逐渐丢失。     

Measuring Client Experiences in Maternity Care under Change: Development of a Questionnaire Based on the WHO Responsiveness Model

BackgroundMaternity care is an integrated care process, which consists of different services, involves different professionals and covers different time windows. To measure performance of maternity care based on clients'' experiences, we developed and validated a questionnaire.ConclusionsThe ReproQ appears suitable for assessing quality of maternity care from the clients'' perspective. Recruitment of disadvantaged groups requires additional non-digital approaches.     

Systematic Review and Meta-Analysis of Validation Studies on a Diabetes Case Definition from Health Administrative Records

Objectives

Health administrative data are frequently used for diabetes surveillance. We aimed to determine the sensitivity and specificity of a commonly-used diabetes case definition (two physician claims or one hospital discharge abstract record within a two-year period) and their potential effect on prevalence estimation.

Methods

Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we searched Medline (from 1950) and Embase (from 1980) databases for validation studies through August 2012 (keywords: “diabetes mellitus”; “administrative databases”; “validation studies”). Reviewers abstracted data with standardized forms and assessed quality using Quality Assessment of Diagnostic Accuracy Studies (QUADAS) criteria. A generalized linear model approach to random-effects bivariate regression meta-analysis was used to pool sensitivity and specificity estimates. We applied correction factors derived from pooled sensitivity and specificity estimates to prevalence estimates from national surveillance reports and projected prevalence estimates over 10 years (to 2018).

Results

The search strategy identified 1423 abstracts among which 11 studies were deemed relevant and reviewed; 6 of these reported sensitivity and specificity allowing pooling in a meta-analysis. Compared to surveys or medical records, sensitivity was 82.3% (95%CI 75.8, 87.4) and specificity was 97.9% (95%CI 96.5, 98.8). The diabetes case definition underestimated prevalence when it was ≤10.6% and overestimated prevalence otherwise.

Conclusion

The diabetes case definition examined misses up to one fifth of diabetes cases and wrongly identifies diabetes in approximately 2% of the population. This may be sufficiently sensitive and specific for surveillance purposes, in particular monitoring prevalence trends. Applying correction factors to adjust prevalence estimates from this definition may be helpful to increase accuracy of estimates.     

microRNA的实验和生物信息学开发方法

mircroRNA是一类约22nt的内源小分子RNA,普遍存在于真核生物体内,它通过与靶基因互补结合来调控基因表达,从而对生物体的生长、发育等起到重要的调节作用。随着生物学技术的不断发展,mircroRNA研究的越发深入,越来越多的mircroRNA被开发出来。本文结合了mircroRNA的生理特点,从RNA、DNA和生物信息学预测这3个方面归纳总结有关开发microRNA的方法,以及由此衍生出来的相关的研究方法。通过对这些研究方法的分类总结,不但为mircroRNA以后的研究工作奠定良好的基础,而且有利于新技术的研发。     

Development and Application of a New Method To Extract Bacterial DNA from Soil Based on Separation of Bacteria from Soil with Cation-Exchange Resin

A new method for the extraction of bacterial DNA from soil has been developed. Soil samples of 50 g were dispersed, and bacteria were released by use of a cation-exchange resin; subsequently, bacteria were separated from soil particles by low-speed centrifugation and lysed with lysozyme and ionic detergent, and the DNA was then purified by CsCl-ethidium bromide equilibrium density centrifugation. The extracted DNA was of high molecular weight and sufficiently pure for restriction enzyme digestion, DNA-DNA hybridization, and amplification by the polymerase chain reaction. The advantages of the new method are that the separation of bacteria from soil is considerably faster than by repeated blending, more samples can be handled, and furthermore no aerosols are formed during separation. Also, we investigated whether the CsCl-ethidium bromide equilibrium density centrifugation could be replaced by purification using Gene-Clean. However, this method produced DNAs which were insufficiently pure for several types of analysis. The new method was used to study survival of a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading Pseudomonas cepacia DBO1 (pRO101) in unamended soil and in soil amended with 2,4-D. We found that the degrading strain, irrespective of inoculation level, was able to grow to the same high numbers in soil amended with 2,4-D, while the strain in nonamended soil were maintained at the inoculation level. Detection based on DNA extraction and subsequent dot blot DNA-DNA hybridization was in accordance with detection by plating on selective medium.     

Development of a Genotyping Method for Potato Scab Pathogens Based on Multiplex PCR

Scab disease significantly damages potato and other root crops. Streptomyces scabiei, S. acidiscabiei, and S. turgidiscabiei are the best-known causal agents of this disease. We have developed a novel genotyping method for these potato scab pathogens using multiplex PCR, whose benefits include rapid and easy detection of multiple species. We designed a species-specific primer set (6 primers, 3 pairs) for the 16S rRNA genes and 16S–23S ITS regions of these potato scab pathogens. The specificity of the primer set was confirmed by testing 18 strains containing potato scab pathogens, other Streptomyces species, and strains of other genera. The application of the developed method to potato field soil and potato tissue samples resulted in the clear detection and identification of pathogens. Since this method is applicable to a large number of environmental samples, it is expected to be useful for a high-throughput analysis of soil and plant tissues of scab disease.     

基于 LUX 引物的 HBV 实时 PCR检测方法的建立

实时PCR技术因其快速、准确、灵敏度和重复性高、可减少交叉污染等特点而广泛应用于分子生物学和医学研究领域。本研究建立了一种基于LUX （Light Upon eXtension）引物的HBV病毒载量检测的实时定量PCR检测方法。通过检测系列稀释的HBV DNA（5-5×108拷贝/反应）来验证LUX实时分析的性能和灵敏度。结果表明该检测方法在Ct值和log10 HBV DNA浓度之间存在很好的线形关系,并且具有很高的灵敏度,检测低限可达每毫升血清中50拷贝的HBV。对91份阳性血清样品的检测和熔解曲线分析表明该方法具有很高的特异性。新建立的LUX实时检测方法为检测治疗效果、研究HBV病毒载量和疾病发展之间的关系提供了一种理想的工具。     

Noise assessment in LCA - a methodology attempt: A case study with various means of transportation on a set trip

The present work focuses on impact assessment of noise disturbance in the framework of LCA studies. A number of difficulties arose in the course of the study, namely expressing noise measurements in an easy-to-handle unit, imputing disturbance engendered by several simultaneous sources to every single source, handling additive quantities non-linearly, taking into account the space and time dependence of potential impacts associated with noise, It is shown how all these issues were tackled in a I.CA study that assessed different modes of transportation. The methodology developed takes into account the disturbance to noise level exceeding a set threshold and no other kinds of noise effects. It is obvious that disturbance due to noise emissions depends on people density in the neighborhood of the emission source. In this context, a “site-dependent approach” was taken, meaning that we did include local factors into the valuation. The methodology developed in this article may be extended to other types of emissions when it is necessary to integrate local factors in the assessment phase of LCA. This document is the property of Ecobilan and can not be reproduced without its prior authorization     

Community Based Fisheries Management and Fisher Livelihoods: Bangladesh Case Studies

Poor fishers in Bangladesh have been disadvantaged by policies that favored powerful people leasing fishing rights. Community-based management was expected to improve fisher access, livelihoods, and the sustainability of fisheries. The impacts of community management in three floodplain waterbodies differed according to the environment and property rights. Where a set of fishers jointly held exclusive rights to a small enclosed lake they increased production by stocking fish and shared the returns. This strategy is productive but attracts competition for profits and fish consumption was unchanged. Access to capture fisheries in floodplain waterbodies enables the poor to catch diverse small fish for their consumption. Yet sustainability requires limits on fishing. Fish sanctuaries were respected, yet catches per day fell when more people from several villages increased fishing effort in a large wetland, while a tightly knit community restored the fishery in a smaller floodplain. Community organizations will need recognition of their long-term use rights to overcome future threats.

Social Assessments for Better Development: Case Studies in Russia and Central Asia

Social Assessments for Better Development: Case Studies in Russia and Central Asia. Michael M. Cernea and Ayse Kudat. eds. Introduction by Johannes Linn and Ismail Serageldin. Washington, DC: The World Bank, 1997. 207 pp.     

Environmental assessment and improvement alternatives of a ventilated wooden wall from LCA and DfE perspective

Purpose  

The main goal of this paper was to analyse the environmental profile of a structural component of a wooden house: a ventilated wooden wall, by combining two environmental methodologies: one quantitative, the life cycle assessment (LCA) and another qualitative, the design for the environment (DfE).