Systematic misregistration and the statistical analysis of surface data.

Spatial normalisation is a key element of statistical parametric mapping and related techniques for analysing cohort statistics on voxel arrays and surfaces. The normalisation process involves aligning each individual specimen to a template using some sort of registration algorithm. Any misregistration will result in data being mapped onto the template at the wrong location. At best, this will introduce spatial imprecision into the subsequent statistical analysis. At worst, when the misregistration varies systematically with a covariate of interest, it may lead to false statistical inference. Since misregistration generally depends on the specimen's shape, we investigate here the effect of allowing for shape as a confound in the statistical analysis, with shape represented by the dominant modes of variation observed in the cohort. In a series of experiments on synthetic surface data, we demonstrate how allowing for shape can reveal true effects that were previously masked by systematic misregistration, and also guard against misinterpreting systematic misregistration as a true effect. We introduce some heuristics for disentangling misregistration effects from true effects, and demonstrate the approach's practical utility in a case study of the cortical bone distribution in 268 human femurs.

Species identification of Chinese sturgeon using acoustic descriptors and ascertaining their spatial distribution in the spawning ground of Gezhouba Dam

This study has developed an improved subjective approach of classification in conjunction with Step wise DFA analysis to discriminate Chinese sturgeon signals from other targets. The results showed that all together 25 Chinese sturgeon echo-signals were detected in the spawning ground of Gezhouba Dam during the last 3 years, and the identification accuracy reached 90.9%. In Stepwise DFA, 24 out of 67 variables were applied in discrimination and identification. PCA combined with DFA was then used to ensure the significance of the 24 variables and detailed the identification pattern. The results indicated that we can discriminate Chinese sturgeon from other fish species and noise using certain descriptors such as the behaviour variables, echo characteristics and acoustic cross-section characteristics. However, identification of Chinese sturgeon from sediments is more difficult and needs a total of 24 variables. This is due to the limited knowledge about the acoustic-scattering properties of the substrate regions. Based on identified Chinese sturgeon individuals, 18 individuals were distributed in the region between the site of Gezhouba Dam and Miaozui reach, with a surface area of about 3.4 km(2). Seven individuals were distributed in the region between Miaozui and Yanshouba reach, with a surface area of about 13 km(2).

Spatial distribution of benthic algae in the Gangqu River, Shangrila, China

This study consisted of sampling benthic algae at 32 sites in the Gangqu River, an important upstream tributary of the Yangtze River. Our aims were to characterize the benthic algae communities and relationships with environmental variables. Among the 162 taxa observed, Achnanthes linearis and Achnanthes lanceolata var. elliptica were the dominant species (17.10% and 14.30% of the total relative abundance, respectively). Major gradients and principal patterns of variation within the environmental variables were detected by principal component analysis (PCA). Then non-metric multidimensional scaling (NMS) divided all the sites into three groups, which were validated by multi-response permutation procedures (MRPP). Canonical correspondence analysis (CCA) indicated that three environmental variables (TN, TDS, and TP) significantly affected the distribution of benthic algae. Weighted averaging regression and cross-calibration produced strong models for predicting TN and TDS concentration, which enabled selection of algae taxa as potentially sensitive indicators of certain TN and TDS levels: for TN, Achnanthes lanceolata, Achnanthes lanceolata var. elliptica, and Cymbella ventricosa var. semicircularis; for TDS, Cocconeis placentula, Cymbella alpina var. minuta, and Fragilaria virescens. The present study represents an early step in establishing baseline conditions. Further monitoring is suggested to gain a better understanding of this region.

Temporal and spatial variations in the species composition, distribution, and abundance of protozoa in East Dongting lake, China

Investigations of protozoa were carried out during four surveys of East Dongting Lake, China. A total of 160 protozoan species belonging to 71 genera was identified, of which 53 were flagellates, 37 sarcodines, and 70 ciliates. Among them, Peritrichida (32.6% of frequency), Arcellinida (16.2%), Volvocales (13.61/6), Peridiniales (13.1%), and Chrysomonadales (9.1%) were the main groups and contributed to 84.5% of the overall species. Ciliates were mainly composed of sessile species and small species. The total protozoan abundance varied from 2,400 cells L-1 to 20,250 cells L-1. The highest protozoan abundance occurred in spring; the lowest number was in autumn. The highest abundance of ciliates occurred in spring and winter, whereas flagellates developed the highest abundance in,summer and autumn. Pearson correlation analysis and linear regressions indicated that chlorophyll a and water velocity were the main factors affecting ternporal and spatial variations of the protozoan abundance.

Geostatistical analysis of chlorophyll a in freshwater ecosystems

Horizontal spatial patterns of chlorophyll a in Meiziya Reservoir, Hubei Province, China were analyzed once each month during May, June and July 1997. Two geostatistical techniques, semivariance and fractal analysis, were used to determine variation in chlorophyll a over the whole study area (isotropic) and in different directions (anisotropic). Both techniques provided useful information for detecting and assessing spatial pattern changes of chlorophyll a in freshwater environments. Based on our case study, the distribution of chlorophyll a shifted from aggregated to random distribution in the case of small rainfall event, and then returned to the aggregated distribution after a large rainfall event. On the other hand, the distribution of chlorophyll a became more heterogeneous or random in the direction of water flow (S-N direction) when rainfall events occurred, which was enhanced by rainfall intensity. In contrast, the influence of water flow on the spatial patterns was weak in the E-W direction, and thus the distribution of chlorophyll a remained aggregate with a moderate spatial heterogeneity.

Optical analysis of dislocation-related physical processes in GaN-based epilayers

In this paper, recent progresses in optical analysis of dislocation-related physical properties in GaN-based epilayers are surveyed with a brief review. The influence of dislocations on both near-band edge emission and yellow luminescence (YL) is examined either in a statistical way as a function of dislocation density or focused on individual dislocation lines with a high spatial resolution. Threading dislocations may introduce non-radiative recombination centers and enhance YL, but their effects are affected by the structural and chemical environment. The minority carrier diffusion length may be dependent on either dislocation density or impurity doping as confirmed by the result of photovoltaic spectra. The in situ optical monitoring of the strain evolution process is employed during GaN heteroepitaxy using an AIN interlayer. A typical transition of strain from compression to tension is observed and its correlation with the reduction and inclination of threading dislocation lines is revealed. (c) 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatial Mode Selection by the Phase Modulation of Subwavelength Plasmonic Grating

The extraordinary transmission of the subwavelength gold grating has been investigated by the rigorous coupled-wave analysis and verified by the metal-insulator-metal plasmonic waveguide method. The physical mechanisms of the extraordinary transmission are characterized as the excitation of the surface plasmon polariton modes. The subwavelength grating integrated with the distributed Bragg reflector is proposed to modulate the phase to realize spatial mode selection, which is prospected to be applied for transverse mode selection in the vertical cavity surface-emitting laser.

Analysis of current induced by long internal solitary waves in stratified ocean

An approximate theoretical expression for the current induced by long internal solitary waves is presented when the ocean is continuously or two-layer stratified. Particular attention is paid to characterizing velocity fields in terms of magnitude, flow components, and their temporal evolution/spatial distribution. For the two-layer case, the effects of the upper/lower layer depths and the relative layer density difference upon the induced current are further studied. The results show that the horizontal components are basically uniform in each layer with a shear at the interface. In contrast, the vertical counterparts vary monotonically in the direction of the water depth in each layer while they change sign across the interface or when the wave peak passes through. In addition, though the vertical components are generally one order of magnitude smaller than the horizontal ones, they can never be neglected in predicting the heave response of floating platforms in gravitationally neutral balance. Comparisons are made between the partial theoretical results and the observational field data. Future research directions regarding the internal wave induced flow field are also indicated.

Soil microbial community analysis using denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment.

Introduction to Molecular Analysis of Ectomycorrhizal Communities

A number of methods are available for those researchers considering the addition of molecular analyses of ectomycorrhizal (EcM) fungi to their research projects and weighing the various approaches they might take. Analyzing natural EcM fungal communities has traditionally been a highly skilled, time-consuming process relying heavily on exacting morphological characterization of EcM root tips. Increasingly powerful molecular methods for analyzing EcM communities make this area of research available to a much wider range of researchers. Ecologists can gain from the body of work characterizing EcM while avoiding the requirement for exceptional expertise by carefully combining elements of traditional methods with the more recent molecular approaches. A cursory morphological analysis can yield a traditional quantification of EcM fungi based on tip numbers, a unit with functional and historical significance. Ectomycorrhizal root DNA extracts may then be analyzed with molecular methods widely used for characterizing microbiota. These range from methods applicable only to the simple mixes resulting from careful morphotyping, to community-oriented methods that identify many types in mixed samples as well as provide an estimate of their relative abundances. Extramatrical hyphae in bulk soil can also be more effectively studied, extending characterization of EcM fungal communities beyond the rhizoplane. The trend toward techniques permitting larger sample sets without prohibitive labor and time requirements will also permit us to more frequently address the issues of spatial and temporal variability and better characterize the roles of EcM fungi at multiple scales.

Spatial variability in water quality and surface sediment diatom assemblages in a complex lake basin,lake of the woods,ontario,canada

Lake of the Woods (LOW) is an international waterbody spanning the Canadian provinces of Ontario and Manitoba, and the U.S. state of Minnesota. In recent years, there has been a perception that water quality has deteriorated in northern regions of the lake, with all increase in the frequency and intensity of toxin-producing cyanobacterial blooms. However, given the lack of long-term data these trends are difficult to verify. As a first step, we examine spatial and seasonal patterns in water quality in this highly complex lake on the Canadian Shield. Further, we examine surface sediment diatom assemblages across multiple sites to determine if they track within-take differences in environmental conditions. Our results show that there are significant spatial patterns in water quality in LOW. Principal Component Analysis divides the lake into three geographic zones based primarily on algal nutrients (i.e., total phosphorus, TP), with the highest concentrations at sites proximal to Rainy River. This variation is closely tracked by sedimentary diatom assemblages, with [TP] explaining 43% of the variation in diatom assemblages across sites. The close correlation between water quality and the surface sediment diatom record indicate that paleoecological models could be used to provide data on the relative importance of natural and anthropogenic sources of nutrients to the lake.

Considerable effects of diversity indices and spatial scales on conclusions relating to ecological diversity

The relationships between ecological diversity and ecosystem functions such as stability and productivity have long been debated and have no final conclusion until now. It is ignored that the debate should be firstly based on the same diversity index, which should be theoretically complete, and on same observation scale. For the issue on the scale of ecotope observation, ecosystems should be distinguished according to intensity of human disturbance. For the issue on the scale of species observation, either number diversity or biomass diversity should be identified. This paper takes grassland ecosystems located within the Bayin Xile grassland of Xilin Gol League of Inner Mongolia Autonomous Region as an example to analyze effects of different diversity indices and spatial scales on the conclusions of ecological diversity and its relationships with ecosystem functions. The analysis results both on the scale of ecotope observation and on the scale of species observation show that different diversity indices might give different conclusions and spatial resolution has a great effect on the relative conclusions. (c) 2005 Elsevier B.V. All rights reserved.

Land-cover classification of China: integrated analysis of AVHRR imagery and geophysical data

Over last two decades, numerous studies have used remotely sensed data from the Advanced Very High Resolution Radiometer (AVHRR) sensors to map land use and land cover at large spatial scales, but achieved only limited success. In this paper, we employed an approach that combines both AVHRR images and geophysical datasets (e.g. climate, elevation). Three geophysical datasets are used in this study: annual mean temperature, annual precipitation, and elevation. We first divide China into nine bio-climatic regions, using the long-term mean climate data. For each of nine regions, the three geophysical data layers are stacked together with AVHRR data and AVHRR-derived vegetation index (Normalized Difference Vegetation Index) data, and the resultant multi-source datasets were then analysed to generate land-cover maps for individual regions, using supervised classification algorithms. The nine land-cover maps for individual regions were assembled together for China. The existing land-cover dataset derived from Landsat Thematic Mapper (TM) images was used to assess the accuracy of the classification that is based on AVHRR and geophysical data. Accuracy of individual regions varies from 73% to 89%, with an overall accuracy of 81% for China. The results showed that the methodology used in this study is, in general, feasible for large-scale land-cover mapping in China.

STUDY ON THE SPATIAL PATTERNS OF LAND-USE CHANGE AND ANALYSES OF DRIVING FORCES IN NORTHEASTERN CHINA DURING 1990-2000

Land-use change is an important aspect of global environment change. It is, in a sense, the direct result of human activities influencing our physical environment. Supported by the dynamic serving system of national resources, including both the environment database and GIS technology, this paper analyzed the land-use change in northeastern China in the past ten years (1990 - 2000). It divides northeastern China into five land-use zones based on the dynamic degree (DD) of land-use: woodland/grassland - arable land conversion zone, dry land - paddy field conversion zone, urban expansion zone, interlocked zone of farming and pasturing, and reclamation and abandoned zone. In the past ten years, land-use change of northeastern China can be generalized as follows: increase of cropland area was obvious, paddy field and dry land increased by 74. 9 and 276. 0 thousand ha respectively; urban area expanded rapidly, area of town and rural residence increased by 76. 8 thousand ha; area of forest and grassland decreased sharply with the amount of 1399. 0 and 1521. 3 thousand ha respectively; area of water body and unused land increased by 148. 4 and 513. 9 thousand ha respectively. Besides a comprehensive analysis of the spatial patterns of land use, this paper also discusses the driving forces in each land-use dynamic zones. The study shows that some key biophysical factors affect conspicuously the conversion of different land- use types. In this paper, the relationships between land- use conversion and DEM, accnmlated temperature(>= 10 degrees C) and precipitation were analysed and represented. We conclude that the land- use changes in northeast China resulted from the change of macro social and economic factors and local physical elements. Rapid population growth and management changes, in some sense, can explain the shaping of woodland/grassland - cropland conversion zone. The conversion from dry land to paddy field in the dry land - paddy field conversion zone, apart from the physical elements change promoting the expansion of paddy field, results from two reasons: one is that the implementation of market-economy in China has given farmers the right to decide what they plant and how they plant their crops, the other factor is originated partially from the change of dietary habit with the social and economic development. The conversion from paddy field to dry land is caused primarily by the shortfall of irrigation water, which in turn is caused by poor water allocation managed by local governments. The shaping of the reclamation and abandoned zone is partially due to the lack of environment protection consciousness among pioneer settlers. The reason for the conversion from grassland to cropland is the relatively higher profits of fanning than that of pasturing in the interlocked zone of farming and pasturing. In northeastern China, the rapid expansion of built-up areas results from two factors: the first is its small number of towns; the second comes from the huge potential for expansion of existing towns and cities. It is noticeable that urban expansion in the northeastern China is characterized by gentle topographic relief and low population density. Physiognomy, transportation and economy exert great influences on the urban expansion.