Numerical approaches towards life cycle interpretation five examples

The ISO-standard for LCA distinguishes four phases, of which the last one, the interpretation, is the least elaborated. It can be regarded as containing procedural steps (like a completeness check) as well as numerical steps (like a sensitivity check). This paper provides five examples of techniques that can be used for the numerical steps. These are the contribution analysis, the perturbation analysis, the uncertainty analysis, the comparative analysis, and the discernibility analysis. All five techniques are described at a non-technical level with respect to basic concept, possibilities, tabular and graphical representation, restriction and warnings, and all are illustrated with a simple example.     

影响水稻光合日变化的酶和相关因素的分析

水稻叶片的最大光合速率出现在上午１０：００时,Ｒｕｂｉｓｃｏ初始活力也在此时达到最大,然后逐渐降低,下午１４：００时略上升后又下降．Ｒｕｂｉｓｃｏ初始活力与光合速率之间极显著相关,相关系数为 ０．９４７４．运用相关性分析、回归分析、通径分析,对晴（有时有云）天气水稻叶片的光合速度、光合关键酶及有关因素的日变化进行综合评估,结果发现中午光合下降主要来自气孔限制,同时Ｒｕｂｉｓｃｏ活性也下降;Ｒｕｂｉｓｃｏ活性是影响光合日变化的又一重要生化因子．体内Ｒｕｂｉｓｃｏ活性受Ｒｕｂｉｓｃｏ活化酶的调节．     

Discrimination of higher plant calluses based on embryogenic capacity and taxonomic classification by pyrolysis mass spectrometry

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum, and has been widely applied to the discrimination of closely related microbial strains. Minimally prepared samples of embryogenic and non-embryogenic calluses derived from various higher plants (sweet potato, morning glory, Korean ginseng, Siberian ginseng, and balloon flower) were subjected to PyMS for spectral fingerprinting. A dendrogram based on the unweighted pair group method, with arithmetic mean of pyrolysis mass spectra, divided the calluses into Siberian ginseng embryogenic callus and the others, which were subsequently divided into embryogenic and non-embryogenic callus groups, regardless of plant species from which the calluses were derived. In the non-embryogenic callus group, the dendrogram was in agreement with the known taxonomy of the plants. These results indicate that PyMS analysis could be applied for discriminating plant calluses based on embryogenic capacity and taxonomic classification.     

Intraspecific variation in Licuala glabra Griff. (Palmae) in Peninsular Malaysia– a morphometric analysis

We studied vegetative and reproductive characters of 74 herbarium specimens of Licuala glabra Griff. (Palmae) collected from 22 localities throughout Peninsular Malaysia. To test the null hypothesis that there are no distinct groups within the species, cluster analysis (nearest neighbour), principal coordinates and principal components analyses were performed on the set of 43 qualitative and quantitative characters. The results obtained suggested that: (1) there are three infraspeciflc groups within the species, viz., the two published varieties glabra and selangorensis as well as a possible third novel taxon; (2) there is clustering of individuals corresponding to their geographic localities; (3) clusters generated using only reproductive characters indicate a biogeographic distribution of populations correlated with the mountain ranges in the peninsula.     

Fish ecoregions of Kansas: stream fish assemblage patterns and associated environmental correlates

Synopsis Principal components analysis was performed on fish presence/absence data for 39 common fish species from 410 stream sites in Kansas. The analysis confirmed ten ecologically meaningful fish assemblages, based on species associations. Factor scores based on these assemblages were then clustered into six geographic areas or fish ecoregions. Canonical discriminant analysis identified environmental variables that distinguished the derived fish ecoregions. Mean annual runoff, mean annual growing season, and discharge appear most important. Mean width, mean depth, chloride concentration, water temperature, substrate type, gradient, and percent of pool habitat were less important. Correspondence exists between these fish ecoregions and the patterns of physiographic regions, river basins, geology, soil, and potential natural vegetation in Kansas. The multivariate statistical approach used to classify fish ecoregions should have considerable potential value for fish assessment and management purposes in areas other than the state of Kansas.     

Normal Approximations of Exact Tests in Configural Frequency Analysis

The most common tests for types and antitypes in configural frequency analysis are normal approximations of exact tests. In the paper such statistics under the complete independence model and under the fixed margins model are discussed. It turns out that these test statistics are not acceptable when the number of simultaneously performed tests is large or when the expected frequencies are small. In these cases, the use of exact tests is advocated and some existing computer programs for such tests are indicated. A normal approximation based on the strong version of the De Moivre-Laplace limit theorem is also discussed. Empirical examples are given from longitudinal data describing psychological development of boys.     

Some remarks about the analysis of active control studies

In an active-controlled trial, the experimental treatment can be declared to be non-inferior to the control if the confidence interval for the difference excludes a fixed pre-specified margin. Recently, some articles have discussed an alternative method where the data from the current study and placebo-controlled studies for the active control are combined together into a single test statistic to test whether a fixed fraction of the effect of the active control is preserved. It has been shown that, conditional on nuisance parameters from the active-controlled study, a fixed margin can be defined that will be operationally equivalent to this latter method. In this article, we will discuss statistical properties associated with these approaches. Specifically, the interim monitoring boundaries and level of evidence will be considered.     

Phenotypic evaluation of genetic variability and selection of yield contributing traits in chickpea recombinant inbred line population under high temperature stress

Heat is a major abiotic stress that drastically reduces chickpea yield. This study aimed to identify heat-responsive traits to sustain crop productivity by screening a recombinant inbred line (RILs) population at two locations in India (Ludhiana and Faridkot). The RIL population was derived from an inter-specific cross between heat-tolerant genotype GPF 2 (C. arietinum L.) and heat sensitive accession ILWC 292 (C. reticulatum). The pooled analysis of variance showed highly significant differences for all the traits in RILs and most of the traits were significantly affected by heat stress at both locations. High values of genotypic coefficient of variation (19.52–38.53%), phenotypic coefficient of variation (20.29–39.85%), heritability (92.50–93.90%), and genetic advance as a percentage of mean (38.68–76.74%) have been observed for plant height, number of pods per plant, biomass, yield, and hundred seed weight across the heat stress environments. Association studies and principal component analysis showed a significant positive correlation of plant height, number of pods per plant, biomass, hundred seed weight, harvest index, relative leaf water content, and pollen viability with yield under both timely-sown and late-sown conditions. Path analysis revealed that biomass followed by harvest index was the major contributor to yield among the environments. Both step-wise and multiple regression analyses concluded that number of pods per plant, biomass and harvest index consistently showed high level of contribution to the total variation in yield under both timely-sown and late-sown conditions. Thus, the holistic approach of these analyses illustrated that the promising traits provide a framework for developing heat-tolerant cultivars in chickpea.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-00977-5.     

分子水平的遗传多样性及其测量方法

遗传多样性水平是一项很重要的数据。目前从分子水平量化遗传多样性的方法以等位酶分析、ＲＦＬＰ分析和ＲＡＰＤ分析为代表。遗传变异在基因组中并非随机分布,所以取样方式对分析结果的影响不容忽视。本文叙述了遗传变异的产生和分布,并以此为基础比较了上述３种分析方法的理论与实践。     

凡纳滨对虾各月龄性状的主成分与判别分析

为了研究凡纳滨对虾各性状增长规律和判定最佳生长季节凡纳滨对虾的体格与月龄的关系,选择1～6月龄凡纳滨对虾各1000只,选择全长、体长、第一腹节背高、第三腹节背高、第一腹节背宽、头胸甲长和体重共7个性状,进行主成分与判别分析.结果表明:各月龄凡纳滨对虾性状之间均呈现显著的正相关(P<0.01), 其中以全长与体长的相关性最为明显,1月龄凡纳滨对虾体重与形态性状的相关系数较小.各月龄凡纳滨对虾的主成分有所不同,1～2月龄凡纳滨对虾的第一主成分为长度因子,第二主成分为宽度因子,第三主成分为高度因子;3月龄凡纳滨对虾的第一主成分与1～2月龄凡纳滨对虾一致,但第二主成分为高度因子,第三主成分为体重因子;4～6月龄凡纳滨对虾的第一主成分为体重因子,第二主成分为高度因子,第三主成分为宽度因子.1～3月龄凡纳滨对虾形态性状的增长优先于体重, 4～6月龄凡纳滨对虾体重优先于形态性状的增长.错过最佳生长季节的凡纳滨对虾的与体格大小相符的月龄可通过建立的判别式来判断,总的判别准确率为98.98%,其中2～4月龄凡纳滨对虾的判别准确率为100%.     

Numerical Approaches to Life Cycle Interpretation - The case of the Ecoinvent’96 database (10 pp)

Goal, Scope and Background To strengthen the evaluative power of LCA, life cycle interpretation should be further developed. A previous contribution (Heijungs & Kleijn 2001) elaborated five examples of concrete methods within the subset of numerical approaches towards interpretation. These methods were: contribution analysis, perturbation analysis, uncertainty analysis, comparative analysis, and discernibility analysis. Developments in software have enabled the possibility to apply the five example methods to explore the much-used Ecoinvent”96 database.Discussion of Methods The numerical approaches implemented in this study include contribution analysis, perturbation analysis, uncertainty analysis, comparative analysis, discernibility analysis and the newly developed key issue analysis. The data used comes from a very large process database: Ecoinvent’96, containing 1163 processes, 1181 economic flows and 571 environmental flows. Conclusions Results are twofold: they serve as a benchmark to the usefulness and feasibility of these numerical approaches, and they shed light on the question of stability and structure in an often-used large system of interconnected processes. Most of the approaches perform quite well: computation time on a moderate PC is between a few seconds a few minutes. Only Monte Carlo analyses may require much longer, but even then it appears that most questions can be answered within a few hours. Moreover, analytical expressions for error propagation are much faster than Monte Carlo analyses, while giving almost identical results. Despite the fact that many processes are connected to each other, leading to the possibility of a very unstable system and very sensitive coefficients, the overall results show that most results are not extremely uncertain. There are, however, some exceptions to this positive message.     

甲醇对酵母过氧化氢酶活性的影响机理研究

将酵母过氧化氢酶加入一定比例的甲醇,测定其活性变化。结果表明:在含2%甲醇时酶活比对照提高4026%。将粗酶液用70%饱和度的硫酸铵盐析后离心所得的上清液再加入硫酸铵至80%饱和度,离心的沉淀溶解在缓冲液中,上SephadexG75柱,分离出的有酶活性的蛋白峰经电泳得一条蛋白带,说明过氧化氢酶已经被提纯到电泳纯。光谱分析发现,甲醇处理后过氧化氢酶纯酶的吸收光谱和荧光发射光谱与未经处理的比较基本不变,而差示光谱出现明显的正峰和负峰。由动力学分析可知,在甲醇中,过氧化氢酶的Vmax和Km值均有不同程度提高 。     

Pathway analysis for genome-wide genetic variation data: Analytic principles,latest developments,and new opportunities

Pathway analysis, also known as gene-set enrichment analysis, is a multilocus analytic strategy that integrates a priori, biological knowledge into the statistical analysis of high-throughput genetics data. Originally developed for the studies of gene expression data, it has become a powerful analytic procedure for indepth mining of genome-wide genetic variation data. Astonishing discoveries were made in the past years,uncovering genes and biological mechanisms underlying common and complex disorders. However, as massive amounts of diverse functional genomics data accrue, there is a pressing need for newer generations of pathway analysis methods that can utilize multiple layers of high-throughput genomics data. In this review, we provide an intellectual foundation of this powerful analytic strategy, as well as an update of the state-of-the-art in recent method developments. The goal of this review is threefold:(1) introduce the motivation and basic steps of pathway analysis for genome-wide genetic variation data;(2) review the merits and the shortcomings of classic and newly emerging integrative pathway analysis tools; and(3)discuss remaining challenges and future directions for further method developments.     

A novel method to evaluate error in anatomical marker placement using a modified generalized Procrustes analysis

As biomechanical research evolves, a continuing challenge is the standardization of data collection and analysis techniques. In gait analysis, placement of markers to construct an anatomical model has been identified as the single greatest source of error; however, there is currently no standardized approach to quantifying these errors. The current study applies morphometric methods, including a generalized Procrustes analysis (GPA) and a nearest neighbour comparison to quantify discrepancies in marker placement, with the goal of improving reliability in gait analysis. An extensive data-set collected by an Expert (n = 340) was used to evaluate marker placements performed by a Novice (n = 55). Variances identified through principal component analysis were used to create a modified GPA to transform anatomical data, and scaled coordinates from the Novice data-set were then scored against the Expert subset. The results showed quantitative differences in marker placement, suggesting that, although training improved consistency, systematic biases remained.     

引水后杭州西湖主要水质参数的因子分析

利用2000年西湖常规监测数据,通过聚类分析选取三个具有代表性的采样点,用因子分析方法探讨了西湖水质各个参数之间的相互影响,结果表明,西湖水质主要受水温和营养盐的影响,各水域由于所处的地理位置和受到钱塘江引水影响程度的不同又有各自的主要水质影响因子,说明引水工程对改善西湖水质具有一定的作用。     

Microsatellite inheritance and multiple paternity in the deep-sea octopus Graneledone boreopacifica (Mollusca: Cephalopoda)

Abstract. Octopodids are a globally distributed group of marine molluscs. Despite this, our knowledge of their reproductive biology rests heavily on inference, as all phases of copulation, beginning with sperm transfer, occur within the mantle cavity. Male octopuses insert a spermatophore into the female's oviduct, which is predicted to release a sperm-filled sac that either bursts to release sperm for storage or to itself be stored in a gland in the middle of the oviduct. To test whether female octopuses use sperm from multiple males to fertilize their eggs, as may be predicted from anatomy and anecdotal accounts, we apply microsatellite analysis to a partial clutch of Graneledone boreopacifica collected at 1600-m depth to test for multiple paternity. At least two genetically distinct sires contributed sperm to the hatchlings analyzed, demonstrating for the first time multiple paternity in octopodids.     

泡桐属七种植物的RAPD分析

利用 1 3个 1 0 mer的随机引物对中国泡桐属的 7个种进行了 RAPD分析 ,对扩增形成的谱带进行了对比 ,发现 7个种间存在较丰富的多态性带纹。经用 UPGMA法聚类结果说明可把研究的 7个种分成 2个类群。其中白花泡桐与川泡桐亲缘关系最近 ,二者与揪叶泡桐、南方泡桐、山明泡桐归为 1个类群。毛泡桐与兰考泡桐亲缘关系也较近 ,二者在系统演化上比较原始 ,归为 1个类群。     

New Zealand Demersal Fish Assemblages

Demersal fish assemblages in the New Zealand Exclusive Economic Zone were identified using presence–absence data from 19215 bottom trawl tows made over a 37-year period. The dataset spanned latitudes 34–54°S and depths of 4–1500m. A total of 123 taxa occurred in more than 1% of the tows (121 fish and 2 squid). Multivariate ordination and classification (correspondence analysis and Ward's cluster analysis) identified four primary species assemblages that were associated with the inner continental shelf, mid–outer continental shelf and shelf edge, upper continental slope and mid continental slope. The most frequently occurring species (> 40% of tows) in each assemblage were (in descending order): inshore – Chelidonichthys kumu, Pagrus auratus and Zeus faber; shelf – Nototodarus spp., Squalus acanthias and Thyrsites atun; upper slope – Macruronus novaezelandiae, Lepidorhynchus denticulatus, Genypterus blacodes and Hydrolagus sp.; mid slope – Hoplostethus atlanticus, Etmopterus baxteri, Halargyreus johnsonii, Coryphaenoides subserrulatus, Deania calcea, Coryphaenoides serrulatus, Pseudocyttus maculatus, Mora moro, Diastobranchus capensis and Centroscymnus crepidater. Further species associations were also identified within each primary assemblage. Canonical correspondence analysis revealed that most of the explainable variation in species composition was associated with depth and latitude; longitude and season explained little extra variance. The usefulness of our results is limited by the use of presence–absence rather than abundance data, and by the uneven spatial distribution of trawl tows. However, the present study provides a large-scale framework within which to interpret the results of studies using abundance data over smaller spatial and temporal scales.     

Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds

Background

Traditionally, Chinese indigenous sheep were classified geographically and morphologically into three groups: Mongolian, Kazakh and Tibetan. Herein, we aimed to evaluate the population structure and genome selection among 140 individuals from ten representative Chinese indigenous sheep breeds: Ujimqin, Hu, Tong, Large-Tailed Han and Lop breed (Mongolian group); Duolang and Kazakh (Kazakh group); and Diqing, Plateau-type Tibetan, and Valley-type Tibetan breed (Tibetan group).

Results

We analyzed the population using principal component analysis (PCA), STRUCTURE and a Neighbor-Joining (NJ)-tree. In PCA plot, the Tibetan and Mongolian groups were clustered as expected; however, Duolang and Kazakh (Kazakh group) were segregated. STRUCTURE analyses suggested two subpopulations: one from North China (Kazakh and Mongolian groups) and the other from the Southwest (Tibetan group). In the NJ-tree, the Tibetan group formed an independent branch and the Kazakh and Mongolian groups were mixed. We then used the d_i statistic approach to reveal selection in Chinese indigenous sheep breeds. Among the 599 genome sequence windows analyzed, sixteen (2.7%) exhibited signatures of selection in four or more breeds. We detected three strong selection windows involving three functional genes: RXFP2, PPP1CC and PDGFD. PDGFD, one of the four subfamilies of PDGF, which promotes proliferation and inhibits differentiation of preadipocytes, was significantly selected in fat type breeds by the Rsb (across pairs of populations) approach. Two consecutive selection regions in Duolang sheep were obviously different to other breeds. One region was in OAR2 including three genes (NPR2, SPAG8 and HINT2) the influence growth traits. The other region was in OAR 6 including four genes (PKD2, SPP1, MEPE, and IBSP) associated with a milk production quantitative trait locus. We also identified known candidate genes such as BMPR1B, MSRB3, and three genes (KIT, MC1R, and FRY) that influence lambing percentage, ear size and coat phenotypes, respectively.

Conclusions

Based on the results presented here, we propose that Chinese native sheep can be divided into two genetic groups: the thin type (Tibetan group), and the fat type (Mongolian and Kazakh group). We also identified important genes that drive valuable phenotypes in Chinese indigenous sheep, especially PDGFD, which may influence fat deposition in fat type sheep.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1384-9) contains supplementary material, which is available to authorized users.