A combination of fuzzy set ordination with detrended correspondence analysis: One way to combine multi-environmental variables with vegetation data

This paper examines one possible way of Fuzzy Set Ordination by using multi-environmental variables. FSO's function is improved through combination with Detrended Correspondence Analysis which is used to summarize environmental information. It can be used to analyse the relationships between vegetation and environment no matter how many environmental variables are involved. An example with vegetation and environmental data collected from upland grasslands in Northern Snowdonia, Wales, is presented. Its results are consistent with that of CCA and DCCA.Abbreviations FSO Fuzzy set ordination - DCA Detrended correspondence analysis - CCA Canonical correspondence analysis - DCCA Detrended canonical correspondence analysis     

数据点选择与参数估计方法对杉木人工林自疏边界线的影响

自疏边界线是指植物种群发生密度依赖死亡时种群最大收获量的上边界线。已有研究由于在拟合自疏边界线的过程中对数据点的选择和参数估计的方法存在诸多的差异,进而导致产生对自疏法则的争议。该研究采用26年生杉木(Cunninghamia lanceolata)人工林的定位观测数据,对视觉法、死亡率法、等距区间法和相对密度法等4种数据点选择方法以及最小二乘法、降维分析法、分位数回归法和随机边界方程等4种参数拟合方法进行对比分析,以探寻客观选择自疏拟合数据和正确拟合方法的途径。比较4种不同的数据选择方法得出:视觉法具有较强的主观性;对于没有发生非密度依赖死亡的林分,死亡率法可以准确地确定林分自疏的起始点;等距区间法可以减少非密度依赖死亡的影响,得到的数据点能充分反映林分的自疏过程;相对密度法可以保证临界密度阈值以上的数据点拟合林分自疏边界线的有效性,并能排除非密度依赖死亡的影响。比较分析4种不同的拟合方法发现:最小二乘法和降维分析法拟合的林分自疏边界线均从实测数据"中心"穿过,与林分自疏边界线为林分收获量上边界线的涵义不相符合,无法真实反映林分的自疏进程;分位数回归和随机边界方程的拟合结果均与实测数据一致,能够较为准确地反映林分自疏的真实过程,但二者的统计推断要求都比较严格。分位数值的正确选取和残差足够小且趋于0,是分位数回归法和随机边界方程能否正确反映林分自疏动态的前提。     

A comparison of two different approaches to inventory analysis of dairies

Two different methods for Life Cycle Inventory (LCI) applied to the dairy industry was performed at two dairies. In the simplified method, total environmental loads from a dairy was registred and allocated to liquid milk. Energy and emissions are measured for each process step for the detailed method. Both methods have advantages and disadvantages. The simplified method captures all energy and emissions of dairy processing, but treats the dairy as a “black box”. The energy consumption was found to be 1, 27 MJ/1 and 2,55 MJ/1 for the two dairies. By use of the detailed method it is easy to “loose” information, and it is very time consuming. The energy consumption was lower than for the simplified method. The environmental loads can on the other hand be divided on the different process steps. The main conclusion is that choice of method depends on the purpose of the LCA-study.     

Towards unification of national vegetation classifications: A comparison of two methods for analysis of large data sets

Abstract. In European phytosociology, national classifications of corresponding vegetation types show considerable differences even between neighbouring countries. Therefore, the European Vegetation Survey project urgently needs numerical classification methods for large data sets that are able to produce compatible classifications using data sets from different countries. We tested the ability of two methods, TWINSPAN and COCKTAIL, to produce similar classifications of wet meadows (Calthion, incl. Filipendulenion) for Germany (7909 relevés) and the Czech Republic (1287 relevés) in this respect. In TWINSPAN, the indicator ordination option was used for classification of two national data sets, and the extracted assignment criteria (indicator species) were applied crosswise from one to the other national data set. Although the data sets presumably contained similar community types, TWINSPAN revealed almost no correspondence between the groups derived from the proper classification of the national data set and the groups defined by the assignment criteria taken from the other national data set. The reason is probably the difference in structure between the national data sets, which is a typical, but hardly avoidable, feature of any pair of phytosociological data sets. As a result, the first axis of the correspondence analysis, and consequently the first TWINSPAN division, are associated with different environmental gradients; the difference in the first division is transferred and multiplied further down the hierarchy. COCKTAIL is a method which produces relevé groups on the basis of statistically formed species groups. The user determines the starting points for the formation of species groups, and groups already found in one data set can be tested for existence in the other data set. The correspondence between the national classifications produced by COCKTAIL was fairly good. For some relevé groups, the lack of correspondence to groups in the other national data set could be explained by the absence of the corresponding vegetation types in one of the countries, rather than by methodological problems.     

Non-centred component analysis of vegetation data: A comparison of orthogonal and oblique rotation

Summary Non-centred principal components analyses followed by varimax rotation and ortho-oblique rotation are applied to 4 test data tables of known structure. These methods are also applied to a set of boreal forest understorey vegetation data. The effectiveness of varimax and ortho-oblique rotation techniques at generating unipolar components is considered and the ortho-oblique method with =0.5 appears optimal. Efficiency of cluster seeking, through the emergence of unipolar components, is assessed in terms of test data table recapture. The ortho-oblique method is superior at all levels of data structure considered.Stability of clusters at different levels of component rotation is examined. Beyond a level of fundamental structure, oblique-roatation produces fortuitous unipolar components whereas varimax rotation is very conservative. The use of both rotation techniques is advocated as complementary aspects of nodal component analysis. The advantages of nodal component analysis in vegetation study are briefly diseussed, especially with respect to large collections of stand data.This work was conducted with the assistance of N.S.E.R.C. of Canada Grant No. A6234 and computer funding by the Department of Botany, University of Toronto.     

Analysing spectral data: comparison and application of two techniques

This study compares two different methods of condensing complex spectral data into interpretable indices or metrics of colour. Colour spectra were measured on standardized Munsell colour paint chips and estimates of the three fundamental components of colour (brightness, chroma and hue) were generated using principal component analysis (PCA) and segment classification (SC). We tested the accuracy of these techniques for generating colour component estimates from spectral data in four different 'colour classes' (red/orange, yellow/ green, green/blue, and blue/purple) and in an aggregate data set containing all measured spectra. We conclude that both analysis techniques will generally provide more information than more conventional colour assessment techniques. Neither technique was superior under all conditions; appropriateness of each technique depends on the system under study. Efficacy of both techniques depends on the variability present in the data set; greater variance in colour tends to reduce overall resolution. An application of tfiese techniques is also presented in which we characterize sex-specific differences in colour between different populations of the poecilliid fish, Limia perugia.     

Limiting the sedimentation coefficient for sedimentation velocity data analysis: partial boundary modeling and g(s) approaches revisited

Brown and coworkers (Eur. Biophys. J. 38 (2009) 1079–1099) introduced partial boundary modeling (PBM) to simplify sedimentation velocity data analysis by excluding species outside the range of interest (e.g., aggregates, impurities) via restricting the sedimentation coefficient range being fitted. They strongly criticized the alternate approach of fitting g(s^∗) distributions using similar range limits, arguing that (i) it produces “nonoptimal fits in the original data space” and (ii) the g(s^∗) data transformations lead to gross underestimates of the parameter confidence intervals. It is shown here that neither of those criticisms is valid. These two approaches are not truly fitting the same data or in equivalent ways; thus, they should not actually give the same best-fit parameters. The confidence limits for g(s^∗) fits derived using F statistics, bootstrap, or a new Monte Carlo algorithm are in good agreement and show no evidence for significant statistical distortion. Here 15 g(s^∗) measurements on monoclonal antibody samples gave monomer mass estimates with experimental standard deviations of less than 1%, close to the confidence limit estimates. Tests on both real and simulated data help to clarify the strengths and drawbacks of both approaches. New algorithms for computing g(s^∗) and a scan-differencing approach for PBM are introduced.     

A comparison of the folding of two knotted proteins: YbeA and YibK

The extraordinary topology of proteins belonging to the alpha/beta-knot superfamily of proteins is unexpected, due to the apparent complexities involved in the formation of a deep trefoil knot in a polypeptide backbone. Despite this, an increasing number of knotted structures are being identified; how such proteins fold remains a mystery. Studies on the dimeric protein YibK from Haemophilus influenzae have led to the characterisation of its folding pathway in some detail. To complement research into the folding of YibK, and to address whether folding pathways are conserved for members of the alpha/beta-knot superfamily, the structurally similar knotted protein YbeA from Escherichia coli has been studied. A comprehensive thermodynamic and kinetic analysis of the folding of YbeA is presented here, and compared to that of YibK. Both fold via an intermediate state populated under equilibrium conditions that is monomeric and considerably structured. The unfolding/refolding kinetics of YbeA are simpler than those found for YibK and involve two phases attributed to the formation of a monomeric intermediate state and a dimerisation step. In contrast to YibK, a change in the rate-determining step on the unfolding pathway for YbeA is observed with a changing concentration of urea. Despite this difference, both proteins fold by a mechanism involving at least one sequential monomeric intermediate that has properties similar to that observed during the equilibrium unfolding. The rate of dimerisation observed for YbeA and YibK is very similar, as is the rate constant for formation of the kinetic monomeric intermediate that precedes dimerisation. The findings suggest that relatively slow folding and dimerisation may be common attributes of knotted proteins.     

Correction to: Early detection monitoring for non-indigenous fishes; comparison of survey approaches during two species introductions in a Great Lakes port

Biological Invasions -     

A comparison of two different techniques for the detection of blood parasite, Theileria annulata, in cattle from two districts in Khyber Pukhtoon Khwa Province (Pakistan)

The present study was carried out to determine the prevalence of Theileria annulata in large ruminants from two districts, Peshawar and Kohat, in Khyber Pukhtoon Khwa (Pakistan). Blood samples were collected from 95 cattle. Data on the characteristics of animals and herds were collected through questionnaires. No significant risk factors were found associated with the spread of tropical theileriosis in the study area. Two different parasite detection techniques, PCR amplification and screening of Giemsa stained slides, were compared and it was found that PCR amplification is a more sensitive tool (33.7% parasite detection), as compared to smear scanning (5.2% parasite detection) for the detection of Theileria annulata. 32 out of 95 animals, from both districts, produced the 721-bp fragment specific for Theileria annulata.     

From Survey to Ecology: The Role of the British Vegetation Committee, 1904–1913

This article focuses on early British vegetation science, in particular on the British Vegetation Committee. In earlier histories of (plant) ecology, the period of the Committee's life, 1904–1913, renowned for its surveys and its maps, was depicted as a brief prelude to British plant ecology. This article traces the course of ``survey' and ``ecology' within the Committee, demonstrating that survey and ecology were both distinct and intertwined within the Committee.The Committee adhered to two lines of research, one analyzing relatively large areas of vegetation on a small scale (few details), and the other, relatively small areas on a large scale (great detail). When the Committee was founded, vegetation research of relatively large areas dominated, but the balance gradually swung towards research on small areas. Two prominent Committee members, Smith and Tansley, furthermore advocated two research plans, a national survey plan and an ecological research plan. These diverging ideals however co‐existed peacefully and uncontroversially, in contrast to a survey and ecology dichotomy suggested in earlier accounts.An analysis demonstrates the intertwinement of survey and ecology in the period of the Committee's existence. The ``ecological expeditions' also mapped vegetation, and the scale of the ``survey work' moreover increased in the Committee's early years. Only by acknowledging their intertwinement can the fate of a particular kind of ``survey-research' be understood. My analysis shows that this kind of vegetation research did not survive the Committee because of its ecological orientation. This conclusion contradicts the impression prevailing from earlier historical accounts, viz. that British survey work failed because it was insufficiently ecological. This revised version was published online in July 2006 with corrections to the Cover Date.     

鄂尔多斯高原北缘水分梯度下天然植被分布格局初探

以鄂尔多斯高原杭锦旗北部独贵塔拉镇的过渡带为研究对象,通过样线调查,研究了水分梯度下天然植被的空间分布规律.TWINSPAN的分类结果表明,群落以中生和旱生为主,一些耐盐的植物散布其中;相邻样方间相似性指数的变化反映了不同类型群落在研究区内的镶嵌分布,从而形成了该区域内群落的多样性和复杂性.对植被样方与地形地貌因子的CCA排序结果显示,植被群落空间格局的形成更多地取决于区域内的水分变化梯度.在本文的研究尺度上,这种水分变化梯度主要由微地形地貌的变化来决定,而不是由与黄河的距离因子来决定.因此,在本区域的土地开发利用过程中,应充分考虑目前已经形成的相对稳定的地形地貌单元特点,在缺乏完善的风沙防护措施和排水除盐措施的情况下,不宜采取大规模平整土地进行综合开发.     

The mid‐domain effect and habitat complexity applied to elevational gradients: Moss species richness in a temperate semihumid monsoon climate mountain of China

The utility of elevational gradients as tools to test either ecological hypotheses and delineate elevation‐associated environmental factors that explain the species diversity patterns is critical for moss species conservation. We examined the elevational patterns of species richness and evaluated the effects of spatial and environmental factors on moss species predicted a priori by alternative hypotheses, including mid‐domain effect (MDE), habitat complexity, energy, and environment proposed to explain the variation of diversity. Last, we assessed the contribution of elevation toward explaining the heterogeneity among sampling sites. We observed the hump‐shaped distribution pattern of species richness along elevational gradient. The MDE and the habitat complexity hypothesis were supported with MDE being the primary driver for richness patterns, whereas little support was found for the energy and the environmental factors.     

A field guide to the proteomics of post-translational modifications in DNA repair

All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.     

Enzyme specificity under dynamic control II: Principal component analysis of α-lytic protease using global and local solvent boundary conditions

The contributions of conformational dynamics to substrate specificity have been examined by the application of principal component analysis to molecular dynamics trajectories of alpha-lytic protease. The wild-type alpha-lytic protease is highly specific for substrates with small hydrophobic side chains at the specificity pocket, while the Met190-->Ala binding pocket mutant has a much broader specificity, actively hydrolyzing substrates ranging from Ala to Phe. Based on a combination of multiconformation analysis of cryo-X-ray crystallographic data, solution nuclear magnetic resonance (NMR), and normal mode calculations, we had hypothesized that the large alteration in specificity of the mutant enzyme is mainly attributable to changes in the dynamic movement of the two walls of the specificity pocket. To test this hypothesis, we performed a principal component analysis using 1-nanosecond molecular dynamics simulations using either a global or local solvent boundary condition. The results of this analysis strongly support our hypothesis and verify the results previously obtained by in vacuo normal mode analysis. We found that the walls of the wild-type substrate binding pocket move in tandem with one another, causing the pocket size to remain fixed so that only small substrates are recognized. In contrast, the M190A mutant shows uncoupled movement of the binding pocket walls, allowing the pocket to sample both smaller and larger sizes, which appears to be the cause of the observed broad specificity. The results suggest that the protein dynamics of alpha-lytic protease may play a significant role in defining the patterns of substrate specificity. As shown here, concerted local movements within proteins can be efficiently analyzed through a combination of principal component analysis and molecular dynamics trajectories using a local solvent boundary condition to reduce computational time and matrix size.     

An analysis of species response curves and of competition from field data: Some results from heath vegetation

The variation in species composition of plant communities has been described by means of the Gaussian distribution (relations between plant populations and environmental variables) and by linear equations (mutual interference between mixed populations). An important presupposition is the existence of a theoretical population, covering 100% of the soil surface. A numerical approximation of the parameters can be obtained by means of an iterative procedure. This technique has been applied to heath vegetation. A small sample has been used to demonstrate the algorithm. The cover ofCalluna vulgaris, Erica tetralix andMolinia caerulea could be explained to a large extent from phosphate and ground water table. A comparison of the results with those of experiments by other authors showed a reasonable similarity. The linear coefficients of interference as means to describe relations between mixed plant populations in a local area have been evaluated by means of dynamic simulation.     

Vegetation mapping and multivariate approach to indicator species of a forest ecosystem: A case study from the Thandiani sub Forests Division (TsFD) in the Western Himalayas

QuestionsDoes the plant species composition of Thandiani sub Forests Division (TsFD) correlate with edaphic, topographic and climatic variables? Is it possible to identify different plant communities in relation to environmental gradients with special emphasis on indicator species? Can this approach to vegetation classification support conservation planning?LocationThandiani sub Forests Division, Western Himalayas.MethodsQuantitative and qualitative characteristics of species along with environmental variables were measured using a randomly stratified design to identify the major plant communities and indicator species of the Thandiani sub Forests Division. Species composition was recorded in 10 × 2.5 × 2 and 0.5 × 0.5 m square plots for trees, shrubs and herbs, respectively. GPS, edaphic and topographic data were also recorded for each sample plot. A total of 1500 quadrats were established in 50 sampling stations along eight altitudinal transects encompassing eastern, western, northern and southern aspects (slopes). The altitudinal range of the study area was 1290 m to 2626 m above sea level using. The relationships between species composition and environmental variables were analyzed using Two Way Cluster Analysis (TWCA) and Indicator Species Analysis (ISA) via PCORD version 5.ResultsA total of 252 plant species belonging to 97 families were identified. TWCA and ISA recognized five plant communities. ISA additionally revealed that mountain slope aspect, soil pH and soil electrical conductivity were the strongest environmental factors (p ≤ 0.05) determining plant community composition and indicator species in each habitat. The results also show the strength of the environment-species relationship using Monte Carlo procedures.ConclusionsAn analysis of vegetation along an environmental gradient in the Thandiani sub Forests Division using the Braun-Blanquet approach confirmed by robust tools of multivariate statistics identified indicators of each sort of microclimatic zones/vegetation communities which could further be used in conservation planning and management not only in the area studied but in the adjacent regions exhibit similar sort of environmental conditions.