Using multiviriate analyses for separating spatial and temporal effects within species-environment relationships

We present a multiviriate approach for the analysis of contigency tables involved in the study of species-environment relationships. The first table (species x sample) contains the abundance of p species collected in n samples. The second table (environment variables x sample) contains values for q environmental variables measured in the n samples. The third table contains the indication of where and when samples were taken.In this paper we demonstrate: (1) how to match an environmental table and a faunistic table using co-inertia analysis; (2) how to take into account a spatial effect using between-class analyses; and (3) how to combine point (1) and (2) to determine the spatial structure shared by fauna and habitat.We illustrate such an approach by using a set of hydrobiological data concerning 13 Ephemeroptera species and ten physical and chemical variables which were collected in the same site at the same dates in a small river of the Prealps.     

Examining the relative importance of spatial and nonspatial coexistence mechanisms

Much of the work on species coexistence has focused on the presence or absence of single mechanisms. Most theoretical frameworks, however, do not allow one to measure the strength of coexistence mechanisms, and so it has been difficult to determine the relative importance of each mechanism when multiple mechanisms are present. We present a model inspired by the California red scale system, in which two parasitoids coexist on a single, tree-dwelling host-scale insect. Previous work suggests that coexistence may be promoted both by intraguild predation (IGP) and by differing preferences for hosts on stems versus hosts on leaves (habitat preference). By applying an analytic framework that quantifies the strengths of spatial coexistence mechanisms, we are able to measure the individual contributions of IGP, habitat preference, and their interaction to maintaining coexistence. We find that habitat preference is much more effective at promoting coexistence in this model than in IGP. Furthermore, the effects of habitat preference and IGP are not independent. When the two parasitoids prefer different habitats, the coexistence-promoting effects of habitat preference are strengthened by IGP if IGP gives a moderate advantage to the inferior competitor. If IGP either confers an excessive advantage or favors the superior competitor, it can diminish the coexistence region.     

Coherent optical spatial filtering of diatoms in water pollution monitoring

Summary The use of Fourier transform coherent optical techniques in the pattern recognition of microscopic algae, i.e., diatoms, is described. The results of the construction of complex-valued filters for diatoms and their usefulness in algal identification are presented. Some general applications to water pollution monitoring and control are discussed.     

Environmental filtering and spatial effects on metacommunity organisation differ among littoral macroinvertebrate groups deconstructed by biological traits

We examined spatial and environmental effects on the deconstructed assemblages of littoral macroinvertebrates within a large lake. We deconstructed assemblages by three biological trait groups: body size, dispersal mode and oviposition behaviour. We expected that spatial effects on assemblage structuring decrease and environmental effects increase with increasing body size. We also expected stronger environmental filtering and weaker spatial effect on the assemblages of flying species compared with assemblages of non-flying species. Stronger effect of environmental filtering was expected on the assemblages with species attaching eggs compared with assemblages of species with free eggs. We used redundancy analysis with variation partitioning to examine spatial and environmental effects on the deconstructed assemblages. As expected, the importance of environmental filtering increased and that of spatial effects decreased with increasing body size. Opposite to our expectations, assemblages of non-flying species were more affected by environmental conditions compared to assemblages of flying species. Concurring with our expectations, the importance of environmental filtering was higher in structuring assemblages of species attaching eggs than in structuring those with freely laid eggs. The amount of unexplained variation was higher for assemblages with small-sized to medium-sized species, flying species and species with free eggs than those with large-sized species, non-flying species and species with attached eggs. Our observations of decreasing spatial and increasing environmental effects with increasing body size of assemblages deviated from the results of previous studies. These results suggest differing metacommunity dynamics between within-lake and among-lake levels and between studies covering contrasting taxonomic groups and body size ranges.     

The effects of one- and two-legged exercise on the lactate and ventilatory threshold

The purpose of this investigation was to compare differences between one- and two-legged exercise on the lactate (LT) and ventilation (VT) threshold. On four separate occasions, eight male volunteer subjects (1-leg VO2max = 3.36 l X min-1; 2-leg VO2max = 4.27 l X min-1) performed 1- and 2-legged submaximal and maximal exercise. Submaximal threshold tests for 1- and 2-legs, began with a warm-up at 50 W and then increased every 3 minutes by 16 W and 50 W, respectively. Similar increments occurred every minute for the maximal tests. Venous blood samples were collected during the last 30 s of each work load, whereas noninvasive gas measures were calculated every 30 s. No differences in VO2 (l X min-1) were found between 1- and 2-legs at LT or VT, but significant differences (p less than 0.05) were recorded at a given power output. Lactate concentration ([LA]) was different (p less than 0.05) between 1- and 2-legs (2.52 vs. 1.97 mmol X l-1) at LT. This suggests it is VO2 rather than muscle mass which affects LT and VT. VO2max for 1-leg exercise was 79% of the 2-leg value. This implies the central circulation rather than the peripheral muscle is limiting to VO2max.     

Evaluation of experimental designs and spatial analyses in wheat breeding trials

Thirty-three wheat breeding trials were conducted from 1994 to 1996 in the Northern Grains Region (QLD and Northern NSW) of Australia to evaluate the influence of experimental designs and spatial analyses on the estimation of genotype effects for yield and their impact on selection decisions. The relative efficiency of the alternative designs and analyses was best measured by the average standard error of difference between line means. Both more effective designs and spatial analyses significantly improved the efficiency relative to the randomised complete block model, with the preferred model (which combined the design information and spatial trends) giving an average relative efficiency of 138% over all 33 trials. When the Czekanowski similarity coefficient was used, none of the studied models were in full agreement with the randomised complete block model in the selection of the top lines. The agreement was influenced by selection proportions. Hence, the use of these methodologies can impact on the selection decisions in plant breeding. Received: 17 December 1998 / Accepted: 29 July 1999     

Examining how the spatial organization of chromatin signals influences metaphase spindle assembly

During cell division, the proper assembly of a microtubule-based bipolar spindle depends on signals from chromatin. However, it is unknown how the spatial organization of chromatin signals affects spindle morphology. Here, we use paramagnetic chromatin beads, and magnetic fields for their alignment in cell-free extracts, to examine the spatial components of signals that regulate spindle assembly. We find that for linear chromatin-bead arrays that vary by eightfold in length, metaphase spindle size and shape are constant. Our findings indicate that, although chromatin provides cues for microtubule formation, metaphase spindle organization, which is controlled by microtubule-based motors, is robust to changes in the shape of chromatin signals.     

Metacommunity ecology meets biogeography: effects of geographical region,spatial dynamics and environmental filtering on community structure in aquatic organisms

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the “elements of metacommunity structure” analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.     

Examining the spatial distribution of flower thrips in southern highbush blueberries by utilizing geostatistical methods

Flower thrips (Frankliniella spp.) are one of the key pests of southern highbush blueberries (Vaccinium corymbosum L. x V. darrowii Camp), a high-value crop in Florida. Thrips' feeding and oviposition injury to flowers can result in fruit scarring that renders the fruit unmarketable. Flower thrips often form areas of high population, termed "hot spots", in blueberry plantings. The objective of this study was to model thrips spatial distribution patterns with geostatistical techniques. Semivariogram models were used to determine optimum trap spacing and two commonly used interpolation methods, inverse distance weighting (IDW) and ordinary kriging (OK), were compared for their ability to model thrips spatial patterns. The experimental design consisted of a grid of 100 white sticky traps spaced at 15.24-m and 7.61-m intervals in 2008 and 2009, respectively. Thirty additional traps were placed randomly throughout the sampling area to collect information on distances shorter than the grid spacing. The semivariogram analysis indicated that, in most cases, spacing traps at least 28.8 m apart would result in spatially independent samples. Also, the 7.61-m grid spacing captured more of the thrips spatial variability than the 15.24-m grid spacing. IDW and OK produced maps with similar accuracy in both years, which indicates that thrips spatial distribution patterns, including "hot spots," can be modeled using either interpolation method. Future studies can use this information to determine if the formation of "hot spots" can be predicted using flower density, temperature, and other environmental factors. If so, this development would allow growers to spot treat the "hot spots" rather than their entire field.     

Comparison of bioclogging effects in saturated porous media within one- and two-dimensional flow systems

The accumulation of microbial biomass in a porous medium can lead to a reduction of pore space and an associated decrease in the hydraulic conductivity of the medium – an effect called bioclogging. This phenomenon may occur in several natural and engineered subsurface systems and can be relevant in fields ranging from contaminant hydrology to civil and environmental engineering, as well as for enhanced oil recovery. During the last decades bioclogging has been studied in various laboratory and theoretical studies. Most of these studies considered only one-dimensional flow fields inside a porous medium. Although these studies provided valuable information on bioclogging and factors controlling it, recent studies showed that an extrapolation of these results to multi-dimensional flow fields is not straight forward. This paper reviews the experimental results obtained for one- and two-dimensional flow fields and compares the modeling results obtained using different conceptualizations of the pore space.     

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

Background  

We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of C _α traces for short proteins (up to 200 amino acids).     

Disentangling the role of connectivity,environmental filtering,and spatial structure on metacommunity dynamics

Dispersal is a key process in metacommunity dynamics, allowing the maintenance of diversity in complex community networks. Geographic distance is usually used as a surrogate for connectivity implying that communities that are closely located are considered more prone to exchange individuals than distant communities. However, in some natural systems, organisms may be subjected to directional dispersal (air or water flows, particular landscape configuration), possibly leading close communities to be isolated from each other and distant communities to be connected. Using geographic distance as a proxy for realised connectivity may then yield misleading results regarding the role of dispersal in structuring communities in such systems. Here, we quantified the relative importance of flow connectivity, geographic distance, and environmental gradients to explain polychaete metacommunity structure along the coasts of the Gulf of Lions (northwest Mediterranean Sea). Flow connectivity was estimated by Lagrangian particle dispersal simulations. Our results revealed that this metacommunity is strongly structured by the environment at large spatial scales, and that both flow connectivity and geographic distance play an important role within homogeneous environments at smaller spatial scales. We thus strongly advocate for a wider use of connectivity measures, in addition to geographic distance, to study spatial patterns of biological diversity (e.g. distance decay) and to infer the processes behind these patterns at different spatial scales. Synthesis Everything is connected, but connections are seldom accurately quantified. Biological communities are often studied separately, using observations, experiments and models to unravel local dynamics of organisms interacting with each other. However, regional processes such as dispersal through ocean and air circulation, likely to connect distant communities and influence their local dynamics, are not always accounted for, or, at best, used as an homogeneous and distance‐related factor. Ocean models have being extensively developed and validated during the past decades with the increasing availability of accurate meteorological data. Using such model outputs, precise quantifi cation of exchange rates of organisms between communities was performed in a marine Mediterranean coastal area. Jointly with local environmental and biological data, these results were used to quantify the effects of realistic connectivity on local and regional polychaete community structure, and revealed that the environmental gradient, geographic distance, and connectivity were responsible for community structure at different spatial scales.     

Mitochondrial swelling measurement in situ by optimized spatial filtering: astrocyte-neuron differences

Mitochondrial swelling is a hallmark of mitochondrial dysfunction, and is an indicator of the opening of the mitochondrial permeability transition pore. We introduce here a novel quantitative in situ single-cell assay of mitochondrial swelling based on standard wide-field or confocal fluorescence microscopy. This morphometric technique quantifies the relative diameter of mitochondria labeled by targeted fluorescent proteins. Fluorescence micrographs are spatial bandpass filtered transmitting either high or low spatial frequencies. Mitochondrial swelling is measured by the fluorescence intensity ratio of the high- to low-frequency filtered copy of the same image. We have termed this fraction the “thinness ratio”. The filters are designed by numeric optimization for sensitivity. We characterized the thinness ratio technique by modeling microscopic image formation and by experimentation in cultured cortical neurons and astrocytes. The frequency domain image processing endows robustness and subresolution sensitivity to the thinness ratio technique, overcoming the limitations of shape measurement approaches. The thinness ratio proved to be highly sensitive to mitochondrial swelling, but insensitive to fission or fusion of mitochondria. We found that in situ astrocytic mitochondria swell upon short-term uncoupling or inhibition of oxidative phosphorylation, whereas such responses are absent in cultured cortical neurons.     

不同空间尺度三维建筑景观变化

以沈阳市铁西区建筑物三维信息为基础数据,从建筑高度、密度、体积与体形、分布均匀度与空间拥挤度等方面构建了三维建筑景观评价指标,分别从区域、功能分区和梯度带3个角度分析了三维建筑景观的变化特征.结果表明:从1997年到2008年,铁西区建筑向垂直方向扩张,建筑空间分布越来越不均匀,空间拥挤度、建筑平均体积与容积率逐渐增大;居住区平均高度、平均体积、覆盖率、容积率、空间拥挤程度最小,建筑分布最均匀;商业区除建筑高度变异系数和平均体形系数最小外,其余指标值最大;工业区高度变异系数和平均体形系数最大,空间分布最不均匀;从梯度带上看,建筑使用类型的差异决定了三维建筑景观的变化特征.     

Identification of movement-related cortical potentials with optimized spatial filtering and principal component analysis

We present a method for detecting movement intention from multichannel electroencephalographic (EEG) recordings. Movement intention is expressed as a slow negative deflection in amplitude of the EEG signal recorded above the motor cortex. This deflection is known as a movement-related cortical potential (MRCP). Detection of movement intention implies discrimination between MRCPs and noise. The signal-to-noise ratio of MRCPs was improved by an optimized spatial filter. Features were extracted with principal component analysis or locality preserving projections from the spatially filtered signals and classification between MRCPs and noise was performed with a k-nearest neighbors algorithm, modified by adjusting the decision rule to improve specificity, and a support vector machine approach. In one representative subject the sensitivity and specificity in detection were in the range 80–90% and 98–99.5%, respectively. The method seems promising for the development of asynchronous brain–computer interfaces (BCIs) based on MRCPs.     

Confocal microscopy-based three-dimensional cell-specific modeling for large deformation analyses in cellular mechanics

This study introduces a new confocal microscopy-based three-dimensional cell-specific finite element (FE) modeling methodology for simulating cellular mechanics experiments involving large cell deformations. Three-dimensional FE models of undifferentiated skeletal muscle cells were developed by scanning C2C12 myoblasts using a confocal microscope, and then building FE model geometries from the z-stack images. Strain magnitudes and distributions in two cells were studied when the cells were subjected to compression and stretching, which are used in pressure ulcer and deep tissue injury research to induce large cell deformations. Localized plasma membrane and nuclear surface area (NSA) stretches were observed for both the cell compression and stretching simulation configurations. It was found that in order to induce large tensile strains (>5%) in the plasma membrane and NSA, one needs to apply more than ～15% of global cell deformation in cell compression tests, or more than ～3% of tensile strains in the elastic plate substrate in cell stretching experiments. Utilization of our modeling can substantially enrich experimental cellular mechanics studies in classic cell loading designs that typically involve large cell deformations, such as static and cyclic stretching, cell compression, micropipette aspiration, shear flow and hydrostatic pressure, by providing magnitudes and distributions of the localized cellular strains specific to each setup and cell type, which could then be associated with the applied stimuli.