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Multidimensional Scaling (multidimensional + scaling)
Kinds of Multidimensional Scaling Terms modified by Multidimensional Scaling Selected AbstractsLand-cover and land-use change and its contribution to the large-scale organization of Puerto Rico's bird assemblagesDIVERSITY AND DISTRIBUTIONS, Issue 1 2008Miguel A. Acevedo ABSTRACT Global biodiversity is changing rapidly driven by human alteration of habitat, and nowhere this is more dramatic than in insular habitats. Yet land-cover change is a complex phenomenon that not only involves habitat destruction but also forest recovery over different time scales. Therefore, we might expect species to respond in diverse ways with likely consequences for the reorganization of regional assemblages. These changes, however, may be different in tropical islands because of their low species richness, generalist habits and high proportion of endemics. Here, we focus on the island of Puerto Rico and ask how island-wide changes in land cover and land use has influenced the large-scale organization of bird assemblages. To address this question, we combined in a Geographical Information System (GIS) the first 6 years (1997,2002) of the Puerto Rican Breeding Bird Survey (PR-BBS) with land-cover and land-use data extracted from a published digital map derived from the classification of Landsat images. A Non-metric Multidimensional Scaling (NMS) ordination based on the composition and abundance of birds, and percentage land-use types showed that land use followed by climate could explain most of the variation observed among routes in terms of species composition and abundance. Moreover, endemic and exotic species were widely distributed throughout the island, but the proportion of endemic species is higher in closed forests while exotic species are more abundant in open habitats. However, historical accounts from the early 1900s indicate that endemic species were distributed across the entire island. Today, most of the land cover transformation in Puerto Rico occurs in the lowlands which may explain the high abundance of endemic species in cloud forests and the high abundance of exotic species in open habitats in the lowlands. [source] Moist lower montane rainforest classification: a case study from Bwindi Impenetrable National Park, UgandaAFRICAN JOURNAL OF ECOLOGY, Issue 3 2010Tomas Chaigneau Abstract Moist lower montane vegetation has rarely been classified beyond broad zonational belts over large altitudinal ranges due to highly diverse species composition and structure. This study shows it is possible to further classify such forest types within Bwindi-Impenetrable National Park (BINP), and that these assemblages can be explained by a combination of environmental conditions and past management. Botanical and environmental data were collected along some 4000 m of linear transects from the area surrounding Mubwindi Swamp, BINP. Ordination using Nonmetric Multidimensional Scaling (NMDS) and classification using Two-way Indicator Species Analysis (TWINSPAN) successfully identified four different species assemblages. These forest types were then named on the basis of the ecological characteristics of the species within the group, and the environmental conditions influencing the distribution and past disturbance of the forest. The techniques used were in agreement for three out of the four forest types identified. Analysis using an environmental overlay showed a significant association between forest type and altitude. The results of this study indicate that a regional classification of forest types within moist lower montane forest belt using only tree species is possible, and that the forest types identified can be explained by environmental conditions and past management. Résumé La végétation humide de basse montagne a rarement été classée au-delà de larges ceintures de zonage portant sur des étendues de grandes amplitudes altitudinales, en raison de compositions et de structures d'espèces extrêmement diverses. Cette étude montre qu'il est possible de classer plus précisément de tels types forestiers dans le Parc National de la Forêt Impénétrable de Bwindi (BINP), et que l'on peut expliquer ces assemblages par une combinaison de conditions environnementales et de gestion passée. Des données botaniques et environnementales ont été collectées le long de quelque 4,000 m de transects linéaires à partir de la zone entourant le Marais de Mubwindi, au BINP. L'ordination par la Gradation non métrique multidimensionnelle et la classification utilisant l'Analyse TWINSPAN (Two-way Indicator Species Analysis) ont réussi à identifier quatre assemblages d'espèces différents. Ces types forestiers furent alors nommés en se basant sur les caractéristiques écologiques des espèces au sein du groupe ainsi que sur les conditions environnementales qui influencent la distribution et des perturbations anciennes des forêts. Les techniques utilisées se sont montrées cohérentes pour trois des quatre types de forêt identifiés. L'analyse utilisant une superposition environnementale a révélé une association significative entre type forestier et altitude. Les résultats de cette étude indiquent qu'une classification régionale des types forestiers dans la ceinture forestière humide qui entoure la basse montagne est possible en n'utilisant que trois espèces d'arbres, et que les types forestiers identifiés peuvent s'expliquer par les conditions environnementales et par la gestion antérieure. [source] Projected Alcohol Dose Influences on the Activation of Alcohol Expectancies in College DrinkersALCOHOLISM, Issue 7 2009Jennifer P. Read Background:, Alcohol expectancies have been linked to drinking behavior in college students, and vary according to a number of factors, including projected dose of alcohol. Research using Multidimensional Scaling (MDS) suggests that drinking may be influenced by activation of differing expectancy dimensions in memory, yet studies have not examined expectancy activation according to projected alcohol doses. Methods:, The present study used Individual Differences Scaling (INDSCAL) to map expectancy networks of college students (n = 334) who imagined varied drinking at high and low alcohol doses. Expectancy activation was modeled by dose, as well as by gender and by drinking patterns (typical quantity, blood alcohol content, heavy episodic drinking, and alcohol consequences). Expectancies were organized along positive,negative and arousal,sedation dimensions. Anticipation of a high dose of alcohol was associated with greater emphasis on the arousal,sedation dimension, whereas anticipation of a lower dose was associated with greater emphasis on the positive,negative dimension. Results:, Across heavy, medium, and light drinkers, expectancy dimensions were most distinguishable at higher doses; activation patterns were more similar across drinking groups at lighter doses. Modest evidence for the influence of gender on activation patterns was observed. Findings were consistent across alcohol involvement indices. Conclusions:, These data suggest that both dimensionality and context should be considered in the refinement of interventions designed to alter expectancies in order to decrease hazardous drinking. [source] Pluralism and diversity: trends in the use and application of ordination methods 1990-2007JOURNAL OF VEGETATION SCIENCE, Issue 4 2009Henrik Von Wehrden Abstract Question: What are the trends and patterns in the application of ordination techniques in vegetation science since 1990? Location: Worldwide literature analysis. Methods: Evaluation of five major journals of vegetation science; search of all ISI-listed ecological journals. Data were analysed with ANCOVAs, Spearman rank correlations, GLMs, biodiversity indices and simple graphs. Results: The ISI search retrieved fewer papers that used ordinations than the manual evaluation of five selected journals. Both retrieval methods revealed a clear trend in increasing frequency of ordination applications from 1990 to the present. Canonical Correspondence Analysis was far more frequently detected by the ISI search than any other method. Applications such as Correspondence Analysis/Reciprocal Averaging and Detrended Correspondence Analysis have increasingly been used in studies published in "applied" journals, while Canonical Correspondence Analysis, Redundancy Analysis and Non-Metric Multidimensional Scaling were more frequently used in journals focusing on more "basic" research. Overall, Detrended Correspondence Analysis was the most commonly applied method within the five major journals, although the number of publications slightly decreased over time. Use of Non-Metric Multidimensional Scaling has increased over the last 10 years. Conclusion: The availability of suitable software packages has facilitated the application of certain techniques such as Non-Metric Multidimensional Scaling. However, choices of ordination techniques are currently less driven by the constraints imposed by the software; there is also limited evidence that the choice of methods follows social considerations such as the need to use fashionable methods. Methodological diversity has been maintained or has even increased over time and reflects the researcher's need for diverse analytical tools suitable to address a wide range of questions. [source] The mental adjustment to cancer (MAC) scale: French replication and assessment of positive and negative adjustment dimensionsPSYCHO-ONCOLOGY, Issue 1 2003Sandrine Cayrou The Mental Adjustment to Cancer (MAC) scale was validated on a heterogeneous French sample of 317 cancer patients. Internal consistency was satisfactory for the original subscales (, coefficients=0.62,0.80), except for the Fatalism subscale (,=0.40). The intercorrelations of the subscales and the correlations between the subscales and Anxiety and Depression criteria were congruent with the values reported in the literature. Multidimensional Scaling revealed three positive and three negative subsets of items revealing adjustment to cancer. Congeneric factor analysis of the subsets was performed with LISREL 8.3 and only three of them (after discarding certain items) were retained: Fighting Spirit (FS) Hopelessness/Helplessness (HH) and Anxious Preoccupation (AP). A confirmatory hierarchical factor analysis on the 21 items included showed that FS measured positive adjustment to cancer and HH and AP measured negative adjustment. A differential adjustment hypothesis was proposed in order to explain the stability and instability of the measures of the diverse constructs. The three revised subscales showed the same validity pattern as the corresponding original scales, but the magnitude of the correlations was considerably improved with respect to the original subscales. The practical and the theoretical importance of FS, HH and AP are emphasized. Copyright © 2003 John Wiley & Sons, Ltd. [source] Conflicts between traditional pastoralism and conservation of Himalayan ibex (Capra sibirica) in the Trans-Himalayan mountainsANIMAL CONSERVATION, Issue 2 2004Sumanta Bagchi There is recent evidence to suggest that domestic livestock deplete the density and diversity of wild herbivores in the cold deserts of the Trans-Himalaya by imposing resource limitations. To ascertain the degree and nature of threats faced by Himalayan ibex (Capra sibirica) from seven livestock species, we studied their resource use patterns over space, habitat and food dimensions in the pastures of Pin Valley National Park in the Spiti region of the Indian Himalaya. Species diet profiles were obtained by direct observations. We assessed the similarity in habitat use and diets of ibex and livestock using Non-Metric Multidimensional Scaling. We estimated the influence of the spatial distribution of livestock on habitat and diet choice of ibex by examining their co-occurrence patterns in cells overlaid on the pastures. The observed co-occurrence of ibex and livestock in cells was compared with null-models generated through Monte Carlo simulations. The results suggest that goats and sheep impose resource limitations on ibex and exclude them from certain pastures. In the remaining suitable habitat, ibex share forage with horses. Ibex remained relatively unaffected by other livestock such as yaks, donkeys and cattle. However, most livestock removed large amounts of forage from the pastures (nearly 250 kg of dry matter/day by certain species), thereby reducing forage availability for ibex. Pertinent conservation issues are discussed in the light of multiple-use of parks and current socio-economic transitions in the region, which call for integrating social and ecological feedback into management planning. [source] Prediction of herbage yield in grassland: How well do Ellenberg N-values perform?APPLIED VEGETATION SCIENCE, Issue 1 2007Markus Wagner Wisskirchen & Haeupler (1998) Abstract Question: How useful are Ellenberg N-values for predicting the herbage yield of Central European grasslands in comparison to approaches based on ordination scores of plant species composition or on soil parameters? Location: Central Germany (11°00,-11°37'E, 50°21-50°34'N, 500,840 m a.s.l.). Methods: Based on data from a field survey in 2001, the following models were constructed for predicting herbage yield in montane Central European grasslands: (1) Linear regression of mean Ellenberg N-, R- and F-values; (2) Linear regression of ordination scores derived from Non-metric Multidimensional Scaling (NMDS) of vegetation data; and (3) Multiple linear regression (MLR) of soil variables. Models were evaluated by cross-validation and validation with additional data collected in 2002. Results: Best predictions were obtained with models based on species composition. Ellenberg N-values and NMDS scores performed equally well and better than models based on Ellenberg R- or F-values. Predictions based on soil variables were least accurate. When tested with data from 2002, models based on Ellenberg N-values or on NMDS scores accurately predicted productivity rank order of sites, but not the actual herbage yield of particular sites. Conclusions: Mean Ellenberg N-values, which are easy to calculate, are as accurate as ordination scores in predicting herbage yield from plant species composition. In contrast, models based on soil variables may be useful for generating hypotheses about the factors limiting herbage yield, but not for prediction. We support the view that Ellenberg N-values should be called productivity values rather than nitrogen values. [source] Unofficial international conflict resolution: Is there a Track 1½?CONFLICT RESOLUTION QUARTERLY, Issue 1 2009Are there best practices? Analysis of twenty-four cases of unofficial international conflict resolution initiatives, done according to similarities across seven variables, shows that the practice of "Track 1½" diplomacy is distinct from Track 2 diplomacy. Furthermore, these initiatives are distinguished by their focus on process or diverse goals. Multidimensional scaling organized the cases into four groupings of similar initiatives: Track 1½ process-focused, Track 1½ diversified, Track 2 process-focused, and Track 2 diversified. The variety of approaches used in these twenty-four cases of high-quality international conflict resolution initiatives suggests best practices. These practices should be considered sensitive to context rather than a standard set of procedures used regardless of conflict environment. [source] Sourcing Research as an Intellectual Network of Ideas,DECISION SCIENCES, Issue 3 2008G. Tomas M. Hult ABSTRACT What are the current intellectual clusters in the sourcing literature? How do these clusters relate to each other? How has sourcing-related research changed over the last 10 years? We respond to these questions by examining the intellectual structure of research in the sourcing literature across 21 journals during the last decade (1998,2007). Multidimensional scaling is used to analyze cocitation data involving 72,003 citations from 1,960 sourcing articles. The results indicate that 10 different sourcing clusters emerged in the 1998,2002 period and 6 sourcing clusters surfaced in the 2003,2007 period. Five of the intellectual clusters in 1998,2002 disappeared in 2003,2007, five clusters remained, and one new cluster materialized in 2003,2007 that did not exist in the earlier period (Managerial Behavior and Upstream Decision Making). [source] The major- and trace-element whole-rock fingerprints of Egyptian basalts and the provenance of Egyptian artefactsGEOARCHAEOLOGY: AN INTERNATIONAL JOURNAL, Issue 7 2001John D. Greenough Discrimination diagrams have been developed that source Egyptian basaltic artefacts using whole-rock major element geochemistry. These include K2O versus SiO2, TiO2 and P2O5 against MgO/Fe2O3t (total Fe as Fe2O3), and a discriminant analysis diagram using SiO2, Fe2O3t, CaO, and MnO. A complementary set of diagrams uses easily obtained trace element data (Nb/Y versus Zr/Nb; Zr [ppm] versus Rb/Sr; TiO2 [wt % volatile free] versus V; and Cr [ppm] versus Zr/Y) to determine the bedrock sources. These diagrams have been applied to seven First Dynasty basalt vessels (Abydos), two Fourth Dynasty basalt paving stones (Khufu's funerary temple, Giza), and two Fifth Dynasty paving stones (Sahure's complex, Abu Sir). They show that the bedrock source for all the artefacts was the Haddadin flow in northern Egypt. Multidimensional scaling and cluster analysis applied to the whole-rock data (major elements and trace elements together) and previously published mineral fingerprinting studies confirm these results. Comparing mineral versus whole-rock fingerprinting techniques, a major advantage of the former is the small sample size required (0.001 g compared to , 0.1 g). Analytical costs are similar for both methods assuming that a comparison (bedrock) database can be assembled from the literature. For most archaeological problems, a whole-rock bedrock database is more likely to exist than a mineral database, and whole-rock analyses on artefacts will generally be easier to obtain than mineral analyses. Whole-rock fingerprinting may be more sensitive than mineral-based fingerprinting. Thus, if sample quantity is not an issue, whole-rock analysis may have a slight cost, convenience, and technical advantage over mineral-based methods. Our results also emphasize that the Egyptians cherished their Haddadin basalt flow and used it extensively and exclusively for manufacturing basalt vessels and paving stones for at least 600 years (,3150 B.C. to 2500 B.C., approximate ages of the vessels and Abu Sir paving stones, respectively). © 2001 John Wiley & Sons, Inc. [source] Multidimensional scaling of fragrances: A comparison between the verbal and non-verbal methods of classifying fragrances1JAPANESE PSYCHOLOGICAL RESEARCH, Issue 1 2004Takahiro Higuchi Abstract:,Higuchi, Shoji, and Hatayama (2002) selected nine sense-descriptive adjectives (e.g., sweet, clear) to describe the olfactory properties of fragrances. In order to clarify the ability of these adjectives to classify fragrances, the present study used a non-verbal sorting of fragrances that has been widely accepted in previous studies as a method of classifying fragrance. Interfragrance similarities obtained from the non-verbal sorting were then compared with those obtained from the adjective rating based on a two-dimensional spatial configuration of fragrances created by a multidimensional scaling (MDS) analysis. The similarities of the two MDS configurations, obtained from the verbal and non-verbal sorting, were estimated by the correlation of interfragrance distances on the spatial configuration. The correlation coefficient was 0.61, indicating that the ability of the sense-descriptive adjectives to classify fragrances is nearly the same as that of the non-verbal sorting. [source] Discrimination between worry and anxiety among cancer patients: development of a brief cancer-related worry inventoryPSYCHO-ONCOLOGY, Issue 12 2008Kei Hirai Abstract Objectives: A psychometric scale for assessing cancer-related worry among cancer patients, called the Brief Cancer-Related Worry Inventory (BCWI), was developed. Methods: A cross-sectional questionnaire survey for item development was conducted of 112 Japanese patients diagnosed with breast cancer, and test,retest validation analysis was conducted using the data from another prospective study of 20 lung cancer patients. The questionnaire contained 15 newly developed items for cancer-related worry, the Hospital Anxiety and Depression Scale, The Impact of Event Scale Revised, and the Medical Outcomes Study Short Form-8. Results: Exploratory factor analysis of the 15 items yielded a 3-factor structure including (1) future prospects, (2) physical and symptomatic problems and (3) social and interpersonal problems. A second-order confirmatory factor analysis identified a second-order factor called cancer-related worry and confirmed the factor structure with an acceptable fit (chi-square (df=87)=160.16, P=0.001; GFI=0.83; CFI=0.92; RMSEA=0.09). The internal consistency and test,retest reliability were confirmed with the lung cancer sample. Multidimensional scaling found that cancer-related worry is separate from anxiety, depression, and posttraumatic stress disorder (PTSD) symptoms. Conclusion: Our study succeeded in developing and confirming the validity and reliability of a BCWI. The study also confirmed the discriminable aspects of cancer-related worry from anxiety, depression, and PTSD symptoms. Copyright © 2008 John Wiley & Sons, Ltd. [source] Implications of spatial variability of fish assemblages for monitoring of Australia's tropical estuariesAQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 3 2010Marcus Sheaves Abstract 1. Although often seen as ideal targets for monitoring environmental change because of their high public profile, fish assemblages rarely appear as indicators in monitoring and reporting. 2. Published data were evaluated to develop a simple approach to quantifying the temporal consistency in assemblage structure suitable for routine monitoring and assessment. Data were examined as catch per unit effort (CPUE) and probability of encounter (PoE), and compared using three approaches with the potential to produce simple indices quantifying the patterns of similarity within an estuary over time: species richness, Bray-Curtis Similarities and a new approach, DeltaPoE. Indices derived from published data were then tested against a time series of data from two estuarine lakes with a history of fish kills. 3. Multidimensional scaling based on PoE emphasizes the temporal consistency of fish assemblages within estuaries at least as well as one based on mean CPUE while providing operational advantages. Similarities based on PoE were more sensitive to change from ,natural' assemblage structure than the simpler indices and showed comparable results with Similarities from (log) CPUE data. The one drawback to Similarities is that their complex statistical formulation often makes them less effective vehicles for reporting and communication. Where this is the case the conceptual simplicity of DeltaPoE and its performance relative to Similarities suggests it is a good candidate from which to develop monitoring indices suitable for routine reporting. 4. The performance of each of the indices were considered against the known fish kills. Species richness tracked the observed changes, an expected outcome in this case because a major impact directly removed species. Both indices based on Similarities also tracked the changes faithfully. Of the two, Similarities based on PoE seemed to react more strongly to assemblage changes. Copyright © 2010 John Wiley & Sons, Ltd. [source] Identification of neutrophil gelatinase-associated lipocalin (NGAL) as a discriminatory marker of the hepatocyte-secreted protein response to IL-1,: a proteomic analysisBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2005Arul Jayaraman Abstract The liver is the major source of proteins used throughout the body for various functions. Upon injury or infection, an acute phase response (APR) is initiated in the liver that is primarily mediated by inflammatory cytokines such as interleukin-1, (IL-1,) and interleukin-6. Among others, the APR is characterized by an altered protein synthetic profile. We used two-dimensional gel electrophoresis to study the dynamics of changes in protein synthesis in hepatocytes exposed to these inflammatory cytokines. Protein profiles were quantified using image analysis and further analyzed using multivariate statistical methods. Our results indicate that IL-1, and IL-6 each induces secreted protein responses with distinct dynamics and dose-dependence. Parallel stimulation by IL-1, and IL-6 results in a protein pattern indistinguishable from the IL-1, pattern, indicating a dominant effect of IL-1, over IL-6 at the doses tested. Multidimensional scaling (MDS) of correlation distances between protein secretion levels revealed two protein pairs that are robustly co-secreted across the various cytokine stimulation conditions, suggesting shared regulatory pathways. Finally, we also used multivariate alternating conditional expectation (MACE) to identify transformation functions that discriminated the cytokine-stimulated and untreated hepatocyte-secreted protein profiles. Our analysis indicates that the expression of neutrophil gelatinase-associated lipocalin (NGAL) was sufficient to discriminate between IL-1, and IL-6 stimulation. The combination of proteomics and multivariate analysis is expected to provide new information on the cellular regulatory networks involved in generating specific cellular responses. © 2005 Wiley Periodicals, Inc. [source] Diversity and composition of Arctiidae moth ensembles along a successional gradient in the Ecuadorian AndesDIVERSITY AND DISTRIBUTIONS, Issue 5 2005Nadine Hilt ABSTRACT Andean montane rain forests are among the most species-rich terrestrial habitats. Little is known about their insect communities and how these respond to anthropogenic habitat alteration. We investigated exceptionally speciose ensembles of nocturnal tiger moths (Arctiidae) at 15 anthropogenically disturbed sites, which together depict a gradient of forest recovery and six closed-forest understorey sites in southern Ecuador. At weak light traps we sampled 9211 arctiids, representing 287 species. Arctiid abundance and diversity were highest at advanced succession sites, where secondary scrub or young forest had re-established, followed by early succession sites, and were lowest, but still high, in mature forest understorey. The proportion of rare species showed the reverse pattern. We ordinated moth samples by non-metric multidimensional scaling using the chord-normalized expected species shared index (CNESS) index at various levels of the sample size parameter m. A distinct segregation of arctiid ensembles at succession sites from those in mature forest consistently emerged only at high m -values. Segregation between ensembles of early vs. late succession stages was also clear at high m values only, and was rather weak. Rare species were responsible for much of the faunal difference along the succession gradient, whereas many common arctiid species occurred in all sites. Matrix correlation tests as well as exploration of relationships between ordination axes and environmental variables revealed the degree of habitat openness, and to a lesser extent, elevation, as best predictors of faunal dissimilarity. Faunal differences were not related to geographical distances between sampling sites. Our results suggest that many of the more common tiger moths of Neotropical montane forests have a substantial recolonization potential at the small spatial scale of our study and accordingly occur also in landscape mosaics surrounding nature reserves. These species contribute to the unexpectedly high diversity of arctiid ensembles at disturbed sites, whereas the proportion of rare species declines outside mature forest. [source] Beta diversity of geometrid moths (Lepidoptera: Geometridae) in an Andean montane rainforestDIVERSITY AND DISTRIBUTIONS, Issue 5 2003Gunnar Brehm Abstract. Turnover in species composition of the extremely species-rich family Geometridae (Lepidoptera) was investigated along an elevational gradient ranging from 1040 m to 2677 m above sea level. Moths were sampled using weak light traps (30 W) in three field periods in 1999 and 2000 in an Andean montane rainforest in the province of Zamora-Chinchipe in southern Ecuador. A total of 13 938 specimens representing 1010 species were analysed. Similarities of ensembles of all geometrid moths and of the subfamilies Ennominae and Larentiinae were calculated using the NESS index (with mmax). Ordinations performed using nonmetric multidimensional scaling (NMDS) and correspondence analysis depicted a gradual change of the ensembles along the altitudinal gradient. Extracted ordination scores significantly correlate with altitude (,0.97 , r , ,0.95, P < 0.001) and with ambient air temperature (0.93 , r , 0.97, P < 0.001). Temperature is therefore assumed to be the most important abiotic determinant responsible for the species turnover among the moths. Matrix correlation tests were performed in order to compare faunal matrices with matrices derived from available environmental factors. Both tree diversity and vegetation structure significantly correlate with faunal data, but tree diversity explains considerably more of the data variability (range: Mantel r = 0.81,0.83, P < 0.001) than vegetation structure (range: Mantel r = 0.35, P < 0.005 to r = 0.43, P < 0.001). Tree diversity also changes gradually and scores of the first NMDS dimension are highly significantly correlated with altitude (r = 0.98, P < 0.001). A common underlying factor such as ambient temperature might also be responsible for such vegetation changes. Additionally, simulated model data was developed that assumed a constant turnover of moth species and equal elevational ranges of all species involved. Despite the simplicity of the models, they fit empirical data very well (Mantel r > 0.80 and P < 0.001 in all models). [source] Microsite-dependent changes in methanogenic populations in a boreal oligotrophic fenENVIRONMENTAL MICROBIOLOGY, Issue 11 2003Pierre E. Galand Summary Wetlands, including peatlands, are the main source of natural methane emission. Well-defined fen microsites have different methane emissions rates, but it is not known whether the methane-producing Archaea communities vary at these sites. Possible horizontal variations of communities, in a natural oligotrophic fen, were analysed by characterizing the methanogens from two well-defined microsites: Eriophorum lawn and Hummock. Community structures were studied at two different layers of the fen, showing, respectively, high and low methane production. The structure of methanogen populations was determined using molecular techniques targeting the 16SrRNA gene and combined denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) analysis. Results subjected to non-metric multidimensional scaling (MDS), diversity indices calculation and phylogenetic analysis revealed that upper layer communities changed with site while deeper layer communities remained the same. Phylogenetic analyses revealed six different clusters of sequences grouping with only two known orders of methanogens. Upper layers of Hummock were dominated by sequences clustering with members of Methanomicrobiales and sequences dominating the upper part of the Eriophorum lawn were related to members of the order Methanosarcinales. Novel methanogenic sequences were found at both sites at both depths. Vegetation characterizing the microsites probably influences the microbial communities in the layers of the fen where methane is produced. [source] Discovering hidden knowledge in data classification via multivariate analysisEXPERT SYSTEMS, Issue 2 2010Yisong Chen Abstract: A new classification algorithm based on multivariate analysis is proposed to discover and simulate the grading policy on school transcript data sets. The framework comprises three major steps. First, factor analysis is adopted to separate the scores of several different subjects into grading-related ones and grading-unrelated ones. Second, multidimensional scaling is employed for dimensionality reduction to facilitate subsequent data visualization and interpretation. Finally, a support vector machine is trained to classify the filtered data into different grades. This work provides an attractive framework for intelligent data analysis and decision making. It also exhibits the advantages of high classification accuracy and supports intuitive data interpretation. [source] Spatial and temporal heterogeneity of the bacterial communities in stream epilithic biofilmsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Gavin Lear Abstract The spatial and temporal variability in bacterial communities within freshwater systems is poorly understood. The bacterial composition of stream epilithic biofilms across a range of different spatial and temporal scales both within and between streams and across the profile of individual stream rocks was characterised using a community DNA-fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA). The differences in bacterial community structure between two different streams were found to be greater than the spatial variability within each stream site, and were larger than the weekly temporal variation measured over a 10-week study period. Greater variations in bacterial community profiles were detected on different faces of individual stream rocks than between whole rocks sampled within a 9-m stream section. Stream temperature was found to be the most important determinant of bacterial community variability using distance-based redundancy analysis (dbRDA) of ARISA data, which may have broad implications for riparian zone management and ecological change as a consequence of global warming. The combination of ARISA with multivariate statistical methods and ordination, such as multidimensional scaling (MDS), permutational manova and RDA, provided rapid and effective methods for quantifying and visualising variation in bacterial community structure, and to identify potential drivers of ecological change. [source] Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structureFEMS MICROBIOLOGY ECOLOGY, Issue 2 2005Katleen van der Gucht Abstract The phylogenetic composition of bacterioplankton communities in the water column of four shallow eutrophic lakes was analyzed by partially sequencing cloned 16S rRNA genes and by PCR-DGGE analysis. The four lakes differed in nutrient load and food web structure: two were in a clearwater state and had dense stands of submerged macrophytes, while two others were in a turbid state characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had very high nutrient levels (total phosphorus > 100 ,g/l), while the other lakes were less nutrient rich (total phosphorus < 100,g/l). Cluster analysis, multidimensional scaling and ANOSIM (analysis of similarity) were used to investigate differences among the bacterial community composition in the four lakes. Our results show that each lake has its own distinct bacterioplankton community. The samples of lake Blankaart differed substantially from those of the other lakes; this pattern was consistent throughout the year of study. The bacterioplankton community composition in lake Blankaart seems to be less diverse and less stable than in the other three lakes. Clone library results reveal that Actinobacteria strongly dominated the bacterial community in lake Blankaart. The relative abundance of Betaproteobacteria was low, whereas this group was dominant in the other three lakes. Turbid lakes had a higher representation of Cyanobacteria, while clearwater lakes were characterized by more representatives of the Bacteroidetes. Correlating our DGGE data with environmental parameters, using the BIOENV procedure, suggests that differences are partly related to the equilibrium state of the lake. [source] Geomorphology and fish assemblages in a Piedmont river basin, U.S.A.FRESHWATER BIOLOGY, Issue 11 2003D. M. Walters Summary 1.,We investigated linkages between fishes and fluvial geomorphology in 31 wadeable streams in the Etowah River basin in northern Georgia, U.S.A. Streams were stratified into three catchment sizes of approximately 15, 50 and 100 km2, and fishes and geomorphology were sampled at the reach scale (i.e. 20,40 times stream width). 2.,Non-metric multidimensional scaling (NMDS) identified 85% of the among-site variation in fish assemblage structure and identified strong patterns in species composition across sites. Assemblages shifted from domination by centrarchids, and other pool species that spawn in fine sediments and have generalised food preferences, to darter-cyprinid-redhorse sucker complexes that inhabit riffles and runs, feed primarily on invertebrates, and spawn on coarser stream beds. 3.,Richness and density were correlated with basin area, a measure of stream size, but species composition was best predicted (i.e. |r| between 0.60,0.82) by reach-level geomorphic variables (stream slope, bed texture, bed mobility and tractive force) that were unrelated to stream size. Stream slope was the dominant factor controlling stream habitat. Low slope streams had smaller bed particles, more fines in riffles, lower tractive force and greater bed mobility compared with high slope streams. 4.,Our results contrast with the ,River Continuum Concept' which argues that stream assemblages vary predictably along stream size gradients. Our findings support the ,Process Domains Concept', which argues that local-scale geomorphic processes determine the stream habitat and disturbance regimes that influence stream communities. [source] A propensity score approach to correction for bias due to population stratification using genetic and non-genetic factorsGENETIC EPIDEMIOLOGY, Issue 8 2009Huaqing Zhao Abstract Confounding due to population stratification (PS) arises when differences in both allele and disease frequencies exist in a population of mixed racial/ethnic subpopulations. Genomic control, structured association, principal components analysis (PCA), and multidimensional scaling (MDS) approaches have been proposed to address this bias using genetic markers. However, confounding due to PS can also be due to non-genetic factors. Propensity scores are widely used to address confounding in observational studies but have not been adapted to deal with PS in genetic association studies. We propose a genomic propensity score (GPS) approach to correct for bias due to PS that considers both genetic and non-genetic factors. We compare the GPS method with PCA and MDS using simulation studies. Our results show that GPS can adequately adjust and consistently correct for bias due to PS. Under no/mild, moderate, and severe PS, GPS yielded estimated with bias close to 0 (mean=,0.0044, standard error=0.0087). Under moderate or severe PS, the GPS method consistently outperforms the PCA method in terms of bias, coverage probability (CP), and type I error. Under moderate PS, the GPS method consistently outperforms the MDS method in terms of CP. PCA maintains relatively high power compared to both MDS and GPS methods under the simulated situations. GPS and MDS are comparable in terms of statistical properties such as bias, type I error, and power. The GPS method provides a novel and robust tool for obtaining less-biased estimates of genetic associations that can consider both genetic and non-genetic factors. Genet. Epidemiol. 33:679,690, 2009. © 2009 Wiley-Liss, Inc. [source] SNP selection and multidimensional scaling to quantify population structureGENETIC EPIDEMIOLOGY, Issue 6 2009Kelci Miclaus Abstract In the new era of large-scale collaborative Genome Wide Association Studies (GWAS), population stratification has become a critical issue that must be addressed. In order to build upon the methods developed to control the confounding effect of a structured population, it is extremely important to visualize and quantify that effect. In this work, we develop methodology for single nucleotide polymorphism (SNP) selection and subsequent population stratification visualization based on deviation from Hardy-Weinberg equilibrium in conjunction with non-metric multidimensional scaling (MDS); a distance-based multivariate technique. Through simulation, it is shown that SNP selection based on Hardy-Weinberg disequilibrium (HWD) is robust against confounding linkage disequilibrium patterns that have been problematic in past studies and methods as well as producing a differentiated SNP set. Non-metric MDS is shown to be a multivariate visualization tool preferable to principal components in conjunction with HWD SNP selection through theoretical and empirical study from HapMap samples. The proposed selection tool offers a simple and effective way to select appropriate substructure-informative markers for use in exploring the effect that population stratification may have in association studies. Genet. Epidemiol. 33:488,496, 2009. © 2009 Wiley-Liss, Inc. [source] Influence of Potsdam sandstone on the trace element signatures of some 19th-century American and Canadian glass: Redwood, Redford, Mallorytown, and Como,HudsonGEOARCHAEOLOGY: AN INTERNATIONAL JOURNAL, Issue 5 2008J. Victor Owen Potsdam sandstone from quarries and outcrops near 19th-century glassworks sites in Redwood, NY, and Saranac, NY, Mallorytown, ON, and Como and Hudson, QC, commonly contains _97% silica, so in terms of its purity can compete with other historical producers of silica sand (e.g., Cheshire quartzite, MA; southern New Jersey sand). Exploratory analysis of trace element data using multidimensional scaling (MDS) shows that geographically distinct sources of Potsdam sandstone can be distinguished from one another and from competing sources of silica sand, particularly in terms of high field strength elements (e.g., Nb, Y, Ti, Zr), the rare earth elements, and radioactive elements (U, Th), and this geochemical signature is carried through to the glass it was used to manufacture. Other trace elements (e.g., Ba, Sr, Rb) are concentrated in various batch ingredients (e.g., limestone, alkali fluxes). The Hf/Nb, La/Ce, Nb/Th, and La/Zr ratios for each type of glass and nearby Potsdam sandstone sources cluster together in distinct fields on MDS plots. These data confirm the use of Potsdam sandstone in these important historical glassworks, and show that except for material sampled from neighboring communities (Mallorytown and Redwood), trace elements can be used to identify specific sources of silica historically used by the glassmaking industry. © 2008 Wiley Periodicals, Inc. [source] Elevated air temperature alters an old-field insect community in a multifactor climate change experimentGLOBAL CHANGE BIOLOGY, Issue 4 2009SHAWN N. VILLALPANDO Abstract To address how multiple, interacting climate drivers may affect plant,insect community associations, we sampled insects that naturally colonized a constructed old-field plant community grown for over 2 years under simultaneous CO2, temperature, and water manipulation. Insects were sampled using a combination of sticky traps and vacuum sampling, identified to morphospecies and the insect community with respect to abundance, richness, and evenness quantified. Individuals were assigned to four broad feeding guilds in order to examine potential trophic level effects. Although there were occasional effects of CO2 and water treatment, the effects of warming on the insect community were large and consistent. Warming significantly increased Order Thysanoptera abundance and reduced overall morphospecies richness and evenness. Nonmetric multidimensional scaling found that only temperature affected insect community composition, while a Sørensen similarity index showed less correspondence in the insect community between temperature treatments compared with CO2 or soil water treatments. Within the herbivore guild, elevated temperature significantly reduced richness and evenness. Corresponding reductions of diversity measures at higher trophic levels (i.e. parasitoids), along with the finding that herbivore richness was a significant predictor of parasitoid richness, suggest trophic-level effects within the insect community. When the most abundant species were considered in temperature treatments, a small number of species increased in abundance at elevated temperature, while others declined compared with ambient temperature. Effects of temperature in the dominant insects demonstrated that treatment effects were limited to a relatively small number of morphospecies. Observed effects of elevated CO2 concentration on whole-community foliar N concentration did not result in any effect on herbivores, which are probably the most susceptible guild to changes in plant nutritional quality. These results demonstrate that climatic warming may alter certain insect communities via effects on insect species most responsive to a higher temperature, contributing to a change in community structure. [source] Representation of place by monkey hippocampal neurons in real and virtual translocationHIPPOCAMPUS, Issue 2 2003Etsuro Hori Abstract The hippocampal formation (HF) is hypothesized as a neuronal substrate of a cognitive map, which represents environmental spatial information by an ensemble of neural activity. However, the relationships between the hippocampal place cells and the cognitive map have not been clarified in monkeys. The present study was designed to investigate how activity patterns of place-selective neurons encode spatial relationships of various environmental stimuli; to do this, we used multidimensional scaling (MDS) for hippocampal neuronal activity in the monkey during the performance of real and virtual translocation. Of 389 neurons recorded from the monkey HF and parahippocampal gyrus (PH), 166 had place fields that displayed increased activity in a specific area of an experimental field and/or on a monitor (place-selective neurons). The MDS transformed relationships among the 16 places in the experimental field and the monitor, expressed as correlation coefficients between all possible pairs of two places based on the 166 place-selective responses, into geometric relationships in a two-dimensional MDS space. In the real translocation tasks, the 16 places were distributed throughout the MDS space, and their relative positions were well correlated to real positions in the experimental laboratory. However, the correlation between the MDS space and real arrangements was significantly smaller in virtual than real translocation tasks. The present results strongly suggest that activity patterns of the HF and PH neurons represent spatial information and might provide a neurophysiological basis for a cognitive map. Hippocampus 2003;13:190,196. © 2003 Wiley-Liss, Inc. [source] Whining as mother-directed speechINFANT AND CHILD DEVELOPMENT, Issue 5 2005Rosemarie I. Sokol Abstract Although little studied, whining is a vocal pattern that is both familiar and irritating to parents of preschool- and early school-age children. The current study employed multidimensional scaling to identify the crucial acoustic characteristics of whining speech by analysing participants' perceptions of its similarity to other types of speech (question, neutral speech, angry statement, demand, and boasting). We discovered not only that participants find whining speech more annoying than other forms of speech, but that it shares the salient acoustic characteristics found in motherese, namely increased pitch, slowed production, and exaggerated pitch contours. We think that this relationship is not random but may reflect the fact that the two forms of vocalization are the result of a similar accommodation to a universal human auditory sensitivity to the prosody of both forms of speech. Copyright © 2005 John Wiley & Sons, Ltd. [source] Chronic Pain: Nursing Diagnosis or Syndrome?INTERNATIONAL JOURNAL OF NURSING TERMINOLOGIES AND CLASSIFICATION, Issue 4 2001Diná Almeida Lopes Monteiro Cruz PhD PROBLEM. To explore the existence of a pattern of nursing diagnoses that represents a chronic pain syndrome. METHODS. The nursing diagnoses of 68 oncologic and 46 nononcologic patients with chronic pain were submitted to univariate and multivariate analyses. Diagnoses ranked above the 75th percentile, without association with pain etiology, and presenting a pattern in cluster analyses and multidimensional scaling was accepted as possible components of chronic pain syndrome. FINDINGS. The possible components of chronic pain syndrome were disturbed sleep pattern,a constipation or risk for constipation, deficient knowledge,a impaired physical mobility, and anxiety/fear. CONCLUSIONS. Although a pattern of diagnoses has been proposed, confirmation will require further studies and the exploration of the clinical usefulness of the concept of chronic pain as a syndrome. PRACTICE IMPLICATIONS. Increased skill in the assessment and understanding of chronic pain can result in improved relief strategies. Douleur chronique: Diagnostic infirmier ou syndrome? PROBLÈME. Explorer l'existence d'un regroupement de diagnostics infirmiers représentant le syndrome de douleur chronique (SDC). MÉTHODES. Les diagnostics infirmiers présents chez 68 patients cancéreux et 46 patients non-cancéreux, souffrant de douleur chronique furent soumis à des analyses unidimensionnelles et multidimensionnelles. Les diagnostics qui furent retenus comme composantes possibles du SDC se situaient au dessus du 75e percentile, n'étaient pas associés à l'étiologie et représentaient un ensemble dans les analyses de regroupement et l'échelle multidimensionnelle. RÉSULTATS. Les composantes possibles du SDC furent perturbation des habitudes de sommeil, constipation ou risque de constipation, manque de connaissances, altération de la mobilité et anxiété/peur. CONCLUSIONS. Même si un schéma de diagnostics infirmiers a été proposé, il faudrait encore entreprendre plusieurs recherches et explorer l'utilité clinique du concept syndrome de douleur chronique, avant de confirmer la pertinence de ce syndrome. IMPLICATIONS PRATIQUES. L'amélioration de l'évaluation et de la compréhension de la douleur chronique peut conduire à de meilleures stratégies pour soulager la douleur. PROBLEMA. Explorar a existência de um padrão de diagnósticos de enfermagem que represente uma síndrome de dor crônica. MÉTODOS. Diagnóstics de enfermagem de 68 pacientes com dor crônica oncológica e 46 pacientes com dor crônica não oncológica foram submetidos a análises univariadas e multivariadas. Os diagnóstics posicionados acima do Percentil 75, sem associação com a etiologia da dor e que apresentaram um padrão na Análise de Cluster e no Escalonamento Multidimensional foram aceitos como possíveis componentes da síndrome de dor crónica. RESULTADOS. Os possíveis componentes da síndrome de dor crônica foram: distúrbio do padrão de sono, cnstipação ou risco para constipação, déficit de conhecimento, mobilidade física prejudicada e ansiedade/medo. CONCLUSÕES. Apesar de um padrão de diagnósticos ter sido proposto, a sua confirmação requer outros estudos e a exploração da utilidade clínica de se conceituar a dor crônica como uma síndrome. IMPLIAÇÕES PRÁTICAS. Melhorar a compreensão e as habilidades na avaliação da dor crônica pode resultar em melhores estratégias de alívio. Dolor crónico: Diagnóstico enfermero o síndrome? PROBLEMA. Explorar la existencia de un patrón diagnóstico de enfermería que represente el síndrome de dolor crónico (SDC). MÉTODOS. Los diagnósticos enfermeros de 68 pacientes oncológicos y 46 no-oncológicos con dolor crónico, se sometieron a análisis variable y multivariable. Se aceptaron como posibles componentes del SDC, los diagnósticos que estaban sobre el percentil 75, sin asociación con etiología de dolor y que presentaban un patrón agrupado al hacer el análisis y en la escala multidimensional. RESULTADOS. Los posibles componentes de SDC fueron alteración del patrón del sueño, estreñimiento o riesgo de estreñimiento, déficit de conocimientos, trastorno de la movilidad física y ansiedad/temor. CONCLUSIONES. Aunque un patrón de diagnósticos ha sido propuesto, la confirmación requerirá que se llevan más allá los estudios y la exploración de la utilidad clínica del concepto del dolor crónico, como un síndrome. IMPLICACIONES PARA LA PRÁCTICA. Mejorar la habilidad en la valoración y comprensión del dolor crónico pueden producir mejoras en las estrategias de alivio. [source] Development of psychophysics in Japan,JAPANESE PSYCHOLOGICAL RESEARCH, Issue 4 2008TADASU OYAMA Abstract:, In Japan, psychophysics began as early as 1888 with the first lecture on it given by Yujiro Motora at the Imperial University (the University of Tokyo), following the completion of his PhD, at the laboratory of G. S. Hall. In 1910, A Photographic Album of Experimental Psychology was published, which included many photographs of psychophysical experiments. In 1933, Sadaji Takagi conducted the first experiment on animal psychophysics to investigate shape constancy in small birds. In 1949, the first experiment on infant psychophysics was conducted by Jyuji Misumi to study the early development of size constancy. And, in 1955, Tadasu Oyama proposed a new psychophysical technique, naming the method of transposition to measure perceived size ratios without using numerical expressions. This method has been successfully applied to the measurement of illusions, figural after-effects, and size constancy. In 1960, Tarow Indow and his collaborators published their first systematic application of multidimensional scaling to color perception. They also applied it to study the perceptual structure of visual space. Recent developments in those topics in Japan are also reviewed. [source] Multidimensional scaling of fragrances: A comparison between the verbal and non-verbal methods of classifying fragrances1JAPANESE PSYCHOLOGICAL RESEARCH, Issue 1 2004Takahiro Higuchi Abstract:,Higuchi, Shoji, and Hatayama (2002) selected nine sense-descriptive adjectives (e.g., sweet, clear) to describe the olfactory properties of fragrances. In order to clarify the ability of these adjectives to classify fragrances, the present study used a non-verbal sorting of fragrances that has been widely accepted in previous studies as a method of classifying fragrance. Interfragrance similarities obtained from the non-verbal sorting were then compared with those obtained from the adjective rating based on a two-dimensional spatial configuration of fragrances created by a multidimensional scaling (MDS) analysis. The similarities of the two MDS configurations, obtained from the verbal and non-verbal sorting, were estimated by the correlation of interfragrance distances on the spatial configuration. The correlation coefficient was 0.61, indicating that the ability of the sense-descriptive adjectives to classify fragrances is nearly the same as that of the non-verbal sorting. [source] | ||||||||||||||||||||||||||||||||||||||||||||||