PCA

Distribution by Scientific Domains
Distribution within Medical Sciences

Terms modified by PCA

  • pca analysis
  • pca cell
  • pca cell line
  • pca method
  • pca patient
  • pca tissue
  • pca treatment

  • Selected Abstracts


    Interactive low-dimensional human motion synthesis by combining motion models and PIK

    COMPUTER ANIMATION AND VIRTUAL WORLDS (PREV: JNL OF VISUALISATION & COMPUTER ANIMATION), Issue 4-5 2007
    Schubert R. Carvalho
    Abstract This paper explores the issue of interactive low-dimensional human motion synthesis. We compare the performances of two motion models, i.e. Principal Components Analysis (PCA) or Probabilistic PCA (PPCA), for solving a constrained optimization problem within a low-dimensional latent space. We use PCA or PPCA as a first step of preprocessing to reduce the dimensionality of the database to make it tractable, and to encapsulate only the essential aspects of a specific motion pattern. Interactive user control is provided by formulating a low-dimensional optimization framework that uses a Prioritized Inverse Kinematics (PIK) strategy. The key insight of PIK is that the user can adjust a motion by adding constraints with different priorities. We demonstrate the robustness of our approach by synthesizing various styles of golf swing. This movement is challenging in the sense that it is highly coordinated and requires a great precision while moving with high speeds. Hence, any artifact is clearly noticeable in the solution movement. We simultaneously show results comparing local and global motion models regarding synthesis realism and performance. Finally, the quality of the synthesized animations is assessed by comparing our results against a per-frame PIK technique. Copyright © 2007 John Wiley & Sons, Ltd. [source]


    Geometry-Driven Local Neighbourhood Based Predictors for Dynamic Mesh Compression

    COMPUTER GRAPHICS FORUM, Issue 6 2010
    Libor Vá
    Computer Graphics [I.3.7]: Animation Abstract The task of dynamic mesh compression seeks to find a compact representation of a surface animation, while the artifacts introduced by the representation are as small as possible. In this paper, we present two geometric predictors, which are suitable for PCA-based compression schemes. The predictors exploit the knowledge about the geometrical meaning of the data, which allows a more accurate prediction, and thus a more compact representation. We also provide rate/distortion curves showing that our approach outperforms the current PCA-based compression methods by more than 20%. [source]


    Evaluation of a single-platform microcapillary flow cytometer for enumeration of absolute CD4+ T-lymphocyte counts in HIV-1 infected Thai patients,,

    CYTOMETRY, Issue 5 2007
    Kovit Pattanapanyasat
    Abstract Background: Various assays are used to enumerate peripheral blood absolute CD4+ T-lymphocytes. Flow cytometry is considered the gold standard for this purpose. However, the high cost of available flow cytometers and monoclonal antibody reagents make it difficult to implement such methods in the resource-poor settings. In this study, we evaluated a cheaper, recently developed single-platform microcapillary cytometer for CD4+ T-lymphocyte enumeration, the personal cell analyzer (PCA), from Guava® Technologies. Methods: CD4+ and CD8+ T-lymphocyte counts in whole blood samples from 250 HIV-1 infected Thais were determined, using a two-color reagent kit and the Guava PCA, and compared with the results obtained with two reference microbead-based methods from Becton Dickinson Biosciences: the three-color TruCOUNTÔ tube method and the two-color FACSCountÔ method. Statistical correlations and agreements were determined using linear correlation and Bland,Altman analysis. Results: Absolute CD4+ T-lymphocyte counts obtained using the Guava PCA method highly correlated with those obtained using TruCOUNT method (R2 = 0.95, mean bias +13.1 cells/,l, limit of agreement [LOA] ,101.8 to +168.3 cells/,l). Absolute CD8+ T-lymphocyte counts obtained using the Guava PCA method also highly correlated with those obtained with the two reference methods (R2 = 0.92 and 0.88, respectively). Conclusion: This study shows that the enumeration of CD4+ T-lymphocytes using the Guava microcapillary cytometer PCA method performed well when compared with the two reference bead-based methods. However, like the two reference methods, this new method needs substantial technical expertise. © 2007 Clinical Cytometry Society. [source]


    Pattern-reversal visual evoked potentials in infants: gender differences during early visual maturation

    DEVELOPMENTAL MEDICINE & CHILD NEUROLOGY, Issue 5 2002
    CA Malcolm BScN RN RGN
    This paper investigates gender differences in the peak latency and amplitude of the P1 component of the pattern-reversal visual evoked potential (pattern-reversal VEP) recorded in healthy term infants. Pattern-reversal VEPs in response to a series of high contrast black and white checks (check widths 120,, 60,, 30,, 24,, 12,, 6,) were recorded in 50 infants (20 males, 30 females) at 50 weeks post-conceptional age (PCA) and in 49 infants (22 males, 27 females) at 66 weeks PCA. Peak latency of the major component, P1, was considerably shorter in female compared with male infants. Differences in head circumference do not entirely account for the gender differences in peak latency reported here. A gender difference in P1 amplitude was not detected. These findings stress the importance of considering gender norms as well as age-matched norms when utilizing the pattern-reversal VEP in clinical investigations. Studies including a wider range of ages are clearly necessary in order to establish whether the earlier peak latencies in female infants represents a difference in the onset or rate of visual maturation. [source]


    Complex visual hallucination and mirror sign in posterior cortical atrophy

    ACTA PSYCHIATRICA SCANDINAVICA, Issue 1 2006
    T. Yoshida
    Objective:, In posterior cortical atrophy (PCA), visual hallucinations are rare symptoms and mirror sign has not been described. Method:, Single case report. Results:, We reported a 60-year-old woman with PCA who reported complex visual hallucinations, such as a man walking in her room, and mirror sign, which was the perception of a stranger staring at her when she looked into a mirror. She could not recognize images of herself in the mirror correctly, although she could recognize that a person standing next to her and the images of that person reflected in the mirror were the same person. Conclusion:, Early complex visual hallucinations in this patient appeared to be more characteristic of dementia with Lewy body than Alzheimer's disease (AD). It is hard to explain mirror sign in this patient as being because of either prosopagnosia, Balint's syndrome or advanced AD. This patient may have other underlying cognitive dysfunction. [source]


    Gastric parietal cell antibodies are associated with glutamic acid decarboxylase-65 antibodies and the HLA DQA1*0501-DQB1*0301 haplotype in Type 1 diabetes mellitus

    DIABETIC MEDICINE, Issue 8 2000
    C. E. M. De Block
    SUMMARY Aims To assess the prevalence of thyrogastric autoimmunity in relation to age, sex, ,-cell antibody status and HLA DQ haplotypes in Type 1 diabetes mellitus. Methods One hundred and seventy-one patients with Type 1 diabetes mellitus were studied (male/female 86/85; mean age 19 ± 11 years; duration of diabetes 5 ± 4 years). Islet cell antibodies (ICA) and parietal cell antibodies (PCA) were measured using indirect immunofluorescence; glutamic acid decarboxylase-65 antibodies (GADA) by radiobinding assay and thyroid peroxidase antibodies (TPO) with an immunoradiometric assay (IRMA). Results The majority of subjects (81.3%) showed one or more autoantibodies. The prevalence rates were: GADA 64.9%, ICA 46.2%, PCA 19.9% and TPO 19.3%. Patients with ICA+ , 3 years after diagnosis had a higher prevalence of GADA (P = 0.03, odds ratio (OR) 2.66) and thyrogastric antibodies (P = 0.05, OR 2.23) than subjects ICA, after 3 years. PCA+ patients were older (P = 0.04), had a higher prevalence of GADA (P = 0.005, OR 3.89) and TPO (P = 0.05, OR 2.50) than PCA, subjects. Logistic regression analysis showed that PCA status was determined by the HLA DQA1*0501-DQB1*0301 haplotype (, = 2.94, P = 0.04) and GADA status (, = 2.44, P = 0.041). Conclusions Thyrogastric antibodies are highly prevalent in Type 1 diabetes mellitus, especially in patients with persisting ICA. Screening for gastric autoimmunity is particularly advised in patients who are positive for GADA and for the HLA DQA1*0501-DQB1*0301 haplotype. [source]


    A PCA-based modelling technique for predicting environmental suitability for organisms from presence records

    DIVERSITY AND DISTRIBUTIONS, Issue 1-2 2001
    M. P. Robertson
    We present a correlative modelling technique that uses locality records (associated with species presence) and a set of predictor variables to produce a statistically justifiable probability response surface for a target species. The probability response surface indicates the suitability of each grid cell in a map for the target species in terms of the suite of predictor variables. The technique constructs a hyperspace for the target species using principal component axes derived from a principal components analysis performed on a training dataset. The training dataset comprises the values of the predictor variables associated with the localities where the species has been recorded as present. The origin of this hyperspace is taken to characterize the centre of the niche of the organism. All the localities (grid-cells) in the map region are then fitted into this hyperspace using the values of the predictor variables at these localities (the prediction dataset). The Euclidean distance from any locality to the origin of the hyperspace gives a measure of the ,centrality' of that locality in the hyperspace. These distances are used to derive probability values for each grid cell in the map region. The modelling technique was applied to bioclimatic data to predict bioclimatic suitability for three alien invasive plant species (Lantana camara L., Ricinus communis L. and Solanum mauritianum Scop.) in South Africa, Lesotho and Swaziland. The models were tested against independent test records by calculating area under the curve (AUC) values of receiver operator characteristic (ROC) curves and kappa statistics. There was good agreement between the models and the independent test records. The pre-processing of climatic variable data to reduce the deleterious effects of multicollinearity, and the use of stopping rules to prevent overfitting of the models are important aspects of the modelling process. [source]


    Comparison of LiDAR waveform processing methods for very shallow water bathymetry using Raman, near-infrared and green signals

    EARTH SURFACE PROCESSES AND LANDFORMS, Issue 6 2010
    Tristan Allouis
    Abstract Airborne light detection and ranging (LiDAR) bathymetry appears to be a useful technology for bed topography mapping of non-navigable areas, offering high data density and a high acquisition rate. However, few studies have focused on continental waters, in particular, on very shallow waters (<2,m) where it is difficult to extract the surface and bottom positions that are typically mixed in the green LiDAR signal. This paper proposes two new processing methods for depth extraction based on the use of different LiDAR signals [green, near-infrared (NIR), Raman] of the SHOALS-1000T sensor. They have been tested on a very shallow coastal area (Golfe du Morbihan, France) as an analogy to very shallow rivers. The first method is based on a combination of mathematical and heuristic methods using the green and the NIR LiDAR signals to cross validate the information delivered by each signal. The second method extracts water depths from the Raman signal using statistical methods such as principal components analysis (PCA) and classification and regression tree (CART) analysis. The obtained results are then compared to the reference depths, and the performances of the different methods, as well as their advantages/disadvantages are evaluated. The green/NIR method supplies 42% more points compared to the operator process, with an equivalent mean error (,4·2,cm verusu ,4·5,cm) and a smaller standard deviation (25·3,cm verusu 33·5,cm). The Raman processing method provides very scattered results (standard deviation of 40·3,cm) with the lowest mean error (,3·1,cm) and 40% more points. The minimum detectable depth is also improved by the two presented methods, being around 1,m for the green/NIR approach and 0·5,m for the statistical approach, compared to 1·5,m for the data processed by the operator. Despite its ability to measure other parameters like water temperature, the Raman method needed a large amount of reference data to provide reliable depth measurements, as opposed to the green/NIR method. Copyright © 2010 John Wiley & Sons, Ltd. [source]


    Soil erosion assessment using geomorphological remote sensing techniques: an example from southern Italy

    EARTH SURFACE PROCESSES AND LANDFORMS, Issue 3 2010
    Sergio Lo Curzio
    Abstract The aim of this study is to assess of the distribution and map the geomorphological effects of soil erosion at the basin scale identifying newly-formed erosional landsurfaces (NeFELs), by means of an integration of Landsat ETM 7+ remotely sensed data and field-surveyed geomorphological data. The study was performed on a 228·6,km2 -wide area, located in southern Italy. The study area was first characterized from a lithological, pedological, land-use and morpho-topographic point of view and thematic maps were created. Then, the georeferenced Landsat ETM 7+ satellite imagery was processed using the RSI ENVI 4.0 software. The processing consisted of contrast stretching, principal component analysis (PCA), decorrelation stretching and RGB false colour compositing. A field survey was conducted to characterize the features detected on the imagery. Particular attention was given to the NeFELs, which were located using a global positioning system (GPS). We then delimited the Regions of Interest (ROI) on the Landsat ETM 7+ imagery, i.e. polygons representing the ,ground-truth', discriminating the NeFELs from the other features occurring in the imagery. A simple statistical analysis was conducted on the digital number (DN) values of the pixels enclosed in the ROI of the NeFELs, with the aim to determine the spectral response pattern of such landsurfaces. The NeFELs were then classified in the entire image using a maximum likelihood classification algorithm. The results of the classification process were checked in the field. Finally, a spatial analysis was performed by converting the detected landsurfaces into vectorial format and importing them into the ESRI ArcViewGIS 9.0 software. Application of these procedures, together with the results of the field survey, highlighted that some ,objects' in the classified imagery, even if displaying the same spectral response of NeFELs, were not landsurfaces subject to intense soil erosion, thus confirming the strategic importance of the field-checking for the automatically produced data. During the production of the map of the NeFELs, which is the final result of the study, these ,objects' were eliminated by means of simple, geomorphologically-coherent intersection procedures in a geographic information system (GIS) environment. The overall surface of the NeFELs had an area of 22·9,km2, which was 10% of the total. The spatial analysis showed that the highest frequency of the NeFELs occurred on both south-facing and southwest-facing slopes, cut on clayey-marly deposits, on which fine-textured and carbonate-rich Inceptisols were present and displaying slope angle values ranging from 12° to 20°. The comparison of two satellite imageries of different periods highlighted that the NeFELs were most clearly evident immediately after summer tillage operations and not so evident before them, suggesting that these practices could have played an important role in inducing the erosional processes. Copyright © 2009 John Wiley & Sons, Ltd. [source]


    Energy input and zooplankton species richness

    ECOGRAPHY, Issue 6 2007
    Dag O. Hessen
    What are the relative contribution of temperature and solar irradiance as types of energy deliveries for species richness at the ecosystem level? In order to reveal this question in lake ecosystems, we assessed zooplankton species richness in 1891 Norwegian lakes covering a wide range in latitude, altitude, and lake area. Geographical variables could largely be replaced by temperature-related variables, e.g. annual monthly maximum temperature or growth season. Multivariate analysis (PCA) revealed that not only maximum monthly temperature, but also energy input in terms of solar radiation were closely associated with species richness. This was confirmed by stepwise, linear regression analysis in which lake area was also found to be significant. We tested the predictive power of the "metabolic scaling laws" for species richness by regressing Ln of species richness over the inverse of the air temperature (in Kelvin), corrected for the activation energy (eV) as predicted by the Boltzmann constant. A significant, negative slope of 0.78 for ln richness over temperature, given as 1/kT, was found, thus slightly higher than the range of slopes predicted from the scaling law (0.60,0.70). Temperature basically constrained the upper bound of species number, but it was only a modest predictor of actual richness. Both PCA-analysis and linear regression models left a large unexplained variance probably due to lake-specific properties such as catchment influence, lake productivity, food-web structure, immigration constraints or more stochastic effects. [source]


    Parental care in response to natural variation in nest predation pressure in six sunfish (Centrarchidae: Teleostei) species

    ECOLOGY OF FRESHWATER FISH, Issue 4 2008
    S. J. Cooke
    Abstract,,, Parental care is an important, energetically costly component of the life history of many fishes. Despite this importance, little is known about how different species of fish vary parental care in response to natural nest predator burdens. In this study, underwater videography was used to quantify parental care activity of six species of syntopic nesting male centrarchid fishes in Lake Opinicon, Ontario, in response to natural predators. This approach was used to test the hypothesis that as offspring develop from eggs to wrigglers, parental care activity should decrease or remain static for fish guarding nests with low predator burden and increase for those with high predator burden, reflecting different external risks. Principal components analysis (PCA) was used to derive common aeration and nest defence variables. Aeration and predator defence activity of the fish varied extensively among species. Parental care behaviours indicative of defence and vigilance (e.g., turning, departures, time away from nest, displays) tended to be highest for species that had the most predation attempts, although this was not entirely consistent. There was also a positive relationship between the defence PCA metric and attempted predation. Defence did not vary with stage of offspring development, although interactions between defence and developmental stage were noted for several species. A trade-off between aeration and defence was not observed. In fact, species that provide high levels of aeration also simultaneously provide high levels of defence. Stage-specific patterns of defence in this study were less apparent than those documented by studies using responses to staged predator intrusions making it unclear as to the extent that fish were responding to the level of the risk to offspring than to the value of the brood. Therefore, combined use of observational and experimental assessments of parental care investment may be most appropriate for refining current theoretical paradigms. [source]


    Effects of size and morphology on swimming performance in juvenile brown trout (Salmo trutta L.)

    ECOLOGY OF FRESHWATER FISH, Issue 4 2003
    A. F. Ojanguren
    Abstract,,, Our study assesses swimming capacity (speed and stamina) and possible morphometric determinants of locomotor performance of juvenile brown trout (Salmo trutta L.). We addressed these issues at the individual level to have an approach of the functional significance of intraspecific variation in morphological design. Both swimming speed and endurance time showed significant positive relationships with fish length. Size-corrected values of speed and endurance time were negatively correlated suggesting a phenotypic trade-off between burst and prolonged swimming. Size was also highly correlated with all the morphological variables measured. Therefore, we used the residuals of the regressions of those variables on fish length to remove the effect of body size. A principal components analysis (PCA) summarised the 12 morphological variables into two factors, which accounted for 44.3% of the variance. PC1 combined several measures of body depth and width, whereas PC2 represented mainly postanal length relative to abdomen length. Relationships between the scores of the two factors and size-corrected values of maximum swimming speed and endurance time were weak. PC2 showed a significant positive relationship with endurance time; that is, individuals with longer caudal regions were able to swim against water flow for longer periods of time. Stoutness (PC1) showed a marginally significant negative correlation with endurance time. The lack of stronger relationships could be because of the low morphometric variability among the test individuals, all proceeding from the same population, reared in a common environment, and measured at the same ontogenetic stage. [source]


    Use of a Voltammetric Electronic Tongue for Detection and Classification of Nerve Agent Mimics

    ELECTROANALYSIS, Issue 14 2010
    Inmaculada Campos
    Abstract An electronic tongue (ET) based on pulse voltammetry has been used to predict the presence of nerve agent mimics in aqueous environments. The electronic tongue array consists of eight working electrodes (Au, Pt, Ir, Rh, Cu, Co, Ni and Ag) encapsulated on a stainless steel cylinder. Studies including principal component analysis (PCA), artificial neural networks (fuzzy ARTMAP) and partial least square techniques (PLS) have been applied for data management and prediction models. For instance the electronic tongue is able to discriminate the presence of the nerve agent simulants diethyl chlorophosphate (DCP) and diethyl cyanophosphate (DCNP) from the presence of other organophosphorous derivatives in water. Finally, PLS data analysis using a system of 3 compounds and 3 concentration levels shows a good accuracy in concentration prediction for DCP and DCNP in aqueous environments. [source]


    Electroanalytical Approach to Evaluate Antioxidant Capacity in Honeys: Proposal of an Antioxidant Index

    ELECTROANALYSIS, Issue 18 2006
    Mónica Ávila
    Abstract A novel electrochemical route to estimate the antioxidant capacity in honey samples is proposed just using flow injection analysis. The analytical strategy involved the selective oxidation of polyphenolic compounds using two different target potentials, +0.8 and +0.5,V, at two different pHs. An oxidation current obtained at the fixed potential was used as an analytical guide of the antioxidant activity of the target honeys. Chemometrics (correlation and principal component analysis, PCA) demonstrated the significance of the electrochemical protocol versus the traditional spectrophotometric ones in the evaluation of antioxidant capacity and revealed the role of detection potential as a screening variable. The proposed protocol is very simple and fast. However, the most relevant merit of the electrochemical procedure is its inherent versatility which allows the evaluation of the antioxidant activity under predesigned controlled oxidation conditions. In addition, since intercept was statistically zero, its corresponding antioxidant content using just a calibration factor is proposed thus simplifying the calibration-analysis process. As a result, an electrochemical antioxidant index (EAI) is proposed. [source]


    Evaluation of different warping methods for the analysis of CE profiles of urinary nucleosides

    ELECTROPHORESIS, Issue 16 2007
    Ewa Szyma
    Abstract Nowadays, numerous metabolite concentrations can readily be determined in a given biological sample by high-throughput analytical methods. However, such raw analytical data comprise noninformative components due to many disturbances normally occurring in the analyses of biological material. To eliminate those unwanted original analytical data components, advanced chemometric data preprocessing methods might be of help. Here, such methods are applied to electrophoretic nucleoside profiles in urine samples of cancer patients and healthy volunteers. In this study, three warping methods: dynamic time warping (DTW), correlation optimized warping (COW), and parametric time warping (PTW) were examined on two sets of electrophoretic data by means of quality of peaks alignment, time of preprocessing, and way of customization. The application of warping methods helped to limit shifting of peaks and enabled differentiation between whole electropherograms of healthy and cancer patients objectively by a principal component analysis (PCA). The evaluation of preprocessed data and raw data by PC analysis confirms differences between the applied warping tools and proves their suitability in metabonomic data interpretation. [source]


    Growth-induced changes in the proteome of Helicobacter pylori

    ELECTROPHORESIS, Issue 5-6 2006
    Christina Uwins
    Abstract Helicobacter pylori is a major human pathogen that is responsible for a number of gastrointestinal infections. We have used 2-DE to characterise protein synthesis in bacteria grown either on solid agar-based media or in each of two broth culture media (Brucella and brain heart infusion (BHI) broth). Significant differences were observed in the proteomes of bacteria grown either on agar-based or in broth media. Major changes in protein abundance were identified using principal component analysis (PCA), which delineated the profiles derived for the three key growth conditions (i.e. agar plates, Brucella and BHI broth). Proteins detected across the gel series were identified by peptide mass mapping and Edman sequencing. A number of proteins associated with protein synthesis in general as well as specific amino acid synthesis were depressed in broth-grown bacteria compared to plate-grown bacteria. A similar reduction was also observed in the abundance of proteins involved in detoxification. Two of the most abundant spots, identified as UreB and GroEL, in plate-grown bacteria showed a >140-fold drop in abundance in bacteria grown in Brucella broth compared to bacteria grown on agar plates. Two protein spots induced in bacteria grown in broth culture were both identified as glyceraldehyde 3-phosphate dehydrogenase based on their N -terminal amino acid sequences derived by Edman degradation. The underlying causes of the changes in the proteins abundance were not clear, but it was likely that a significant proportion of the changes were due to the alkaline pH of the broth culture media. [source]


    Ascomycete communities in the rhizosphere of field-grown wheat are not affected by introductions of genetically modified Pseudomonas putida WCS358r

    ENVIRONMENTAL MICROBIOLOGY, Issue 11 2005
    Mareike Viebahn
    Summary A long-term field experiment (1999,2002) was conducted to monitor effects on the indigenous microflora of Pseudomonas putida WCS358r and two transgenic derivatives constitutively producing phenazine-1-carboxylic acid (PCA) or 2,4-diacetylphloroglucinol (DAPG). The strains were introduced as seed coating on wheat into the same field plots each year. Rhizosphere populations of ascomycetes were analysed using denaturing gradient gel electrophoresis (DGGE). To evaluate the significance of changes caused by the genetically modified microorganisms (GMMs), they were compared with effects caused by a crop rotation from wheat to potato. In the first year, only the combination of both GMMs caused a significant shift in the ascomycete community. After the repeated introductions this effect was no longer evident. However, cropping potato significantly affected the ascomycete community. This effect persisted into the next year when wheat was grown. Clone libraries were constructed from samples taken in 1999 and 2000, and sequence analysis indicated ascomycetes of common genera to be present. Most species occurred in low frequencies, distributed almost evenly in all treatments. However, in 1999 Microdochium occurred in relatively high frequencies, whereas in the following year no Microdochium species were detected. On the other hand, Fusarium -like organisms were low in 1999, and increased in 2000. Both the DGGE and the sequence analysis revealed that repeated introduction of P. putida WCS358r had no major effects on the ascomycete community in the wheat rhizosphere, but demonstrated a persistent difference between the rhizospheres of potato and wheat. [source]


    Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater

    ENVIRONMENTAL MICROBIOLOGY, Issue 1 2003
    Tingfen Yan
    Summary Nitrate-contaminated groundwater samples were analysed for nirK and nirS gene diversity. The samples differed with respect to nitrate, uranium, heavy metals, organic carbon content, pH and dissolved oxygen levels. A total of 958 nirK and 1162 nirS clones were screened by restriction fragment length polymorphism (RFLP) analysis: 48 and 143 distinct nirK and nirS clones, respectively, were obtained. A single dominant nirK restriction pattern was observed for all six samples and was 83% identical to the Hyphomicrobium zavarzinii nirK gene. A dominant nirS pattern was observed for four of the samples, including the background sample, and was 95% identical to the nirS of Alcaligenes faecalis. Diversity indices for nirK and nirS sequences were not related to any single geochemical characteristic, but results suggested that the diversity of nirK genes was inversely proportional to the diversity of nirS. Principal component analysis (PCA) of the sites based on geochemistry grouped the samples by low, moderate and high nitrate but PCA of the unique operational taxonomic units (OTUs) distributions grouped the samples differently. Many of the sequences were not closely related to previously observed genes and some phylogenetically related sequences were obtained from similar samples. The results indicated that the contaminated groundwater contained novel nirK and nirS sequences, functional diversity of both genes changed in relation to the contaminant gradient, but the nirK and nirS functional diversity was affected differently. [source]


    Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes

    ENVIRONMENTAL MICROBIOLOGY, Issue 11 2001
    K. Van der Gucht
    We characterized the bacterioplankton community and its seasonal dynamics in two neighbouring hypertrophic lakes by denaturing gradient gel electrophoresis (DGGE) analysis of short (193 bp) 16S ribosomal DNA polymerase chain reaction (PCR) products obtained with primers specific for the domain Bacteria. Lake Blankaart is turbid and has a high phytoplankton biomass and episodic cyanobacterial blooms, whereas biomanipulated Lake Visvijver is characterized by clearwater conditions and the establishment of a dense charophyte vegetation. Both lakes were dominated by bacterial groups commonly found in freshwater habitats (e.g. ACK4 cluster of Actinomycetes; ACK stands for clones isolated from the Adirondack mountain lakes). Yet, cluster analysis and principal components analysis (PCA) revealed that taxon composition of the bacterioplankton community of the two lakes differs substantially and consistently throughout the season. During the study year (1998), the bacterioplankton community of both lakes showed a distinct seasonal pattern. Lake Blankaart showed a clear differentiation between winter, spring, summer and autumn. In Lake Visvijver, summer samples differed greatly from spring, autumn and winter samples. We hypothesize that the contrasting bacterioplankton in the two neighbouring shallow lakes is determined largely by the presence or absence of macrophytes. [source]


    Prediction of municipal solid waste generation with combination of support vector machine and principal component analysis: A case study of Mashhad

    ENVIRONMENTAL PROGRESS & SUSTAINABLE ENERGY, Issue 2 2009
    R. Noori
    Abstract Quantity prediction of municipal solid waste (MSW) is crucial for design and programming municipal solid waste management system (MSWMS). Because effect of various parameters on MSW quantity and its high fluctuation, prediction of generated MSW is a difficult task that can lead to enormous error. The works presented here involve developing an improved support vector machine (SVM) model, which combines the principal component analysis (PCA) technique with the SVM to forecast the weekly generated waste of Mashhad city. In this study, the PCA technique was first used to reduce and orthogonalize the original input variables (data). Then these treated data were used as new input variables in SVM model. This improved model was evaluated by using weekly time series of waste generation (WG) and the number of trucks that carry waste in week of t. These data have been collected from 2005 to 2008. By comparing the predicted WG with the observed data, the effectiveness of the proposed model was verified. Therefore, in authors' opinion, the model presented in this article is a potential tool for predicting WG and has advantages over the traditional SVM model. © 2008 American Institute of Chemical Engineers Environ Prog, 2009 [source]


    PCA- and PMF-based methodology for air pollution sources identification and apportionment

    ENVIRONMETRICS, Issue 8 2009
    Marie Chavent
    Abstract Air pollution is a wide concern for human health and requires the development of air quality control strategies. In order to achieve this goal pollution sources have to be accurately identified and quantified. The case study presented in this paper is part of a scientific project initiated by the French Ministry of Ecology and Sustainable Development. For the following study measurements of chemical composition data for particles have been conducted on a French urban site. The first step of the study consists in the identification of the sources profiles which is achieved through principal component analysis (PCA) completed by a rotation technique. Then the apportionment of the sources is evaluated with a receptor modeling using positive matrix factorization (PMF) as estimation method. Finally the joint use of these two statistical methods enables to characterize and apportion five different sources of fine particulate emission. Copyright © 2008 John Wiley & Sons, Ltd. [source]


    Hourly surface wind monitor consistency checking over an extended observation period

    ENVIRONMETRICS, Issue 4 2009
    Scott Beaver
    Abstract A consistency checking methodology is presented to aid in identifying biased values in extended historical records of hourly surface wind measurements obtained from a single station. The method is intended for screening extended observation periods for values which do not fail physical consistency checks (i.e., standard or complex quality assurance methods), yet nonetheless exhibit statistical properties which differ from the bulk of the record. Several specific types of inconsistencies common in surface wind monitoring datasets are considered: annual biases, unexpected values, and discontinuities. The purely empirical method checks for self-consistency in the temporal distribution of the wind measurements by explicitly modeling the diurnal variability. Each year of data is modeled using principal component analysis (PCA) (or empirical orthogonal functions, EOF), then hierarchical clustering with nearest neighbor linkage is used to visualize any annual biases existing in the measurements. The diurnal distributions for wind speed and direction are additionally estimated and visualized to determine any periods of time which are inconsistent with the typical diurnal cycle for a given monitor. The robust consistency checking method is applied to a set of 44 monitors operating in the San Joaquin Valley (SJV) of Central California over a 9-year period. Monitors from the SLAMS, CIMIS, and RAWS networks are considered. Similar inconsistencies are detected in all three networks; however, network-specific types of inconsistencies are found as well. Copyright © 2008 John Wiley & Sons, Ltd. [source]


    Assessment of high density of onsite wastewater treatment systems on a shallow groundwater coastal aquifer using PCA

    ENVIRONMETRICS, Issue 3 2005
    Steven Carroll
    Abstract Onsite wastewater treatment systems are common throughout the world, including Australia, with approximately 17% of the Australian population relying on these systems to treat and ultimately dispose of wastewater. Systems which are properly sited, designed and managed are an effective way of providing the necessary treatment of wastewater. However, incidence of onsite system failure is common, and this is further compounded in areas where high densities of systems are established. The density of systems is not appropriately assessed in the siting and design stage. Various factors, such as site and soil characteristics and climate, can influence the treatment efficiency, and this is more critical in high density areas. Principal component analysis was used for assessing chemical and microbiological data from shallow groundwater below a high density of onsite treatment systems. The results of this study confirmed that high system densities can significantly impact shallow groundwater systems. Additionally, changes in spatial and climatic conditions, as well as the type of onsite system, can also influence the quality of groundwater. Copyright © 2004 John Wiley & Sons, Ltd. [source]


    Data analysis of environmental air pollutant monitoring systems in Europe

    ENVIRONMETRICS, Issue 6 2004
    Kristina Voigt
    Abstract Public access to information about the environment is being strengthened across Europe. The concept of public's right to information gives the basis for the access to environmental information. In this paper the quality of air pollutant monitoring systems in the 15 European member states is analyzed. For pragmatic reasons only the capitals are looked upon. Comprehensive data on environmental monitoring programs concerning air pollutants like ozone (O3), nitrogen dioxide (NO2), nitrogen oxide (NO), carbon dioxide (CO2) and carbon monoxide (CO), and sometimes suspended dust, benzene and other environmental chemicals are available on the free Internet. As different monitoring information systems exist in the European member states a comparison of these systems with their pros and cons is of great interest to the public. Environmental air pollutant monitoring systems in the capitals of the 15 EEC member countries (objects) are evaluated by applying 5 evaluation criteria for the differentiation of these systems. The scores run from 0,=,insufficient, 1,=,medium, to 2,=,excellent. Different data-analysis methods will be applied. As order theory is still not sufficiently presented in the scientific literature, a short overview about the so-called Hasse diagram technique and POSAC method is outlined. In several steps the data-matrix is analyzed coming to the conclusion that all methods (additionally PCA is used) identify one criterion as specifically important. Not unexpected, each method has its own advantage. The aim of this data-analysis is the evaluation of the publicly available air quality monitoring systems in Europe with their pros and cons. This might help the interested public to find and understand the information given on the Internet. Furthermore our evaluation approach might give some recommendations for an improvement of the air quality monitoring systems. Copyright © 2004 John Wiley & Sons, Ltd. [source]


    Vasoconstriction as the Etiology of Hypercalcemia-induced Seizures

    EPILEPSIA, Issue 5 2004
    Tsung-Hua Chen
    Summary: Purpose: Reversible cerebral vasoconstriction has been hypothesized to be the etiology of seizures due to hypercalcemia, but angiographic studies documenting vasoconstriction have not previously been available. Methods: We present a 43-year-old woman who had frequent seizures that later evolved to status epilepticus with marked hypercalcemia at the time of the seizures. Results: Magnetic resonance imaging (MRI) of the patient's brain revealed high signal changes in T2 -weighted imaging, fluorescence-attenuated inversion recovery (FLAIR), and diffusion-weighted imaging (DWI) over the bilateral occipital and thalamic areas. Cerebral angiography showed blood vessels narrowing, disappearing altogether over the right posterior cerebral artery (PCA) branch, which is compatible with vasoconstriction. Vasoconstriction caused the MRI high signal in the occipital area, which was associated with subsequent periodic lateralized epileptic discharges. The patient's clinical condition improved with management of seizures and hypercalcemia. A second brain MRI 2 weeks later revealed complete resolution of the high-signal lesions. Follow-up cerebral angiography study also showed total recovery of vasoconstriction. Conclusions: The sequence of events suggests the hypothesis that reversible cerebral vasoconstriction may play a role in hypercalcemia-induced seizures. [source]


    Components of Relationship Quality in Chimpanzees

    ETHOLOGY, Issue 9 2008
    Orlaith N. Fraser
    A novel approach to studying social relationships in captive adult chimpanzees (Pan troglodytes) was taken by using principal components analysis (PCA) to extract three key components of relationship quality from nine behavioural variables. Based on the loadings of the behavioural variables, the components appeared to match previously hypothesized critical aspects of social relationships and were therefore labelled Value, Compatibility and Security. The effects of kinship, sex combination, age difference and time spent together on each of the relationship quality components were analysed. As expected, kin were found to have more valuable, compatible and secure relationships than non-kin. Female,female dyads were found to be more compatible than male,male or mixed-sex dyads, whereas the latter were found to be most secure. Partners of a similar age were found to have more secure and more valuable relationships than those with a larger age gap. Individuals that were together in the group for longer were more valuable and more compatible, but their relationships were found to be less secure than individuals that were together in the group for a shorter time. Although some of the results may be unexpected based on chimpanzee socio-ecology, they fit well overall with the history and social dynamics of the study group. The methods used confer a significant advantage in producing quantitative composite measures of each component of relationship quality, obtained in an objective manner. These findings therefore promote the use of such measures in future studies requiring an assessment of the qualities of dyadic social relationships. [source]


    Near-nerve needle sensory and medial plantar nerve conduction studies in patients with small-fiber sensory neuropathy

    EUROPEAN JOURNAL OF NEUROLOGY, Issue 9 2008
    K. Uluc
    Background and purpose:, The aim of this prospective study was to show and compare the rate of large-fiber involvement with near-nerve needle sensory (NNNS) nerve conduction study (NCS) and with medial plantar NCS recorded with surface electrodes in a group of patients who had clinically pure small-fiber sensory neuropathy (SFSN) with reduced intra-epidermal nerve fiber density in skin biopsy and with normal routine NCS. Methods and results:, The study included 19 patients with clinically pure SFSN with normal routine NCS results and 17 healthy volunteers. Routine NCS, skin biopsy, medial plantar NCS and NNNS NCS were performed. NNNS NCS data were evaluated both by using univariate analysis methods and by using a multivariate analysis method, principal components analysis (PCA). Eight patients (42%) had abnormal results for medial plantar NCS with surface electrodes. Seven patients (37%) had abnormal results for NNNS NCS with PCA, whilst only four patients with univariate analysis. We found a significant correlation between intra-epidermal nerve fiber densities, medial plantar NCS and PCA results of NNNS NCS. Conclusions:, This study showed that large-nerve fibers are also involved in some patients with pure SFSN and medial plantar NCS can accurately diagnose neuropathy without a need for NNNS NCS in patients with normal routine NCS. [source]


    Effect of neurotrophin-3 on reinnervation of the larynx using the phrenic nerve transfer technique

    EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 2 2007
    Paul J. Kingham
    Abstract Current techniques for reinnervation of the larynx following recurrent laryngeal nerve (RLN) injury are limited by synkinesis, which prevents functional recovery. Treatment with neurotrophins (NT) may enhance nerve regeneration and encourage more accurate reinnervation. This study presents the results of using the phrenic nerve transfer method, combined with NT-3 treatment, to selectively reinnervate the posterior cricoarytenoid (PCA) abductor muscle in a pig nerve injury model. RLN transection altered the phenotype and morphology of laryngeal muscles. In both the PCA and thyroarytenoid (TA) adductor muscle, fast type myosin heavy chain (MyHC) protein was decreased while slow type MyHC was increased. These changes were accompanied with a significant reduction in muscle fibre diameter. Following nerve repair there was a progressive normalization of MyHC phenotype and increased muscle fibre diameter in the PCA but not the TA muscle. This correlated with enhanced abductor function indicating the phrenic nerve accurately reinnervated the PCA muscle. Treatment with NT-3 significantly enhanced phrenic nerve regeneration but led to only a small increase in the number of reinnervated PCA muscle fibres and minimal effect on abductor muscle phenotype and morphology. Therefore, work exploring other growth factors, either alone or in combination with NT-3, is required. [source]


    Dental beliefs: factor structure of the revised dental beliefs survey in a group of regular dental patients

    EUROPEAN JOURNAL OF ORAL SCIENCES, Issue 6 2009
    Kajsa H. Abrahamsson
    The aim of this study was to investigate the factor structure of the revised dental beliefs survey (DBS-R) in a group of regular dental patients. The study group consisted of 278 patients (mean age 54 yr), 61% of whom were women. The DBS-R item mean value was 1.6. Principal component analysis (PCA) and confirmatory factor analysis (CFA) were performed. The initial PCA among the 28 DBS-R items showed four factors with eigenvalues of > 1 explaining 67% of the total variance. Five different CFA models were tested. The final model revealed a four-factor solution with one second-order factor (i.e. a hierarchical CFA). Thus, the latent second-order variable, ,dental beliefs', explains the variance from all DBS-R items through the four first-order factors labeled ,ethics', ,belittlement', ,communication and empathy', and ,control and anxiety'. The results suggest a somewhat different factor structure of DBS-R than previously reported for dental-fear patients. Hence, the underlying factor structure of the DBS-R may differ between different patient groups. The results point towards the use of the original 28-item DBS-R and interpreting the scale as measuring an overall construct of ,dental beliefs' and thus patients' attitudes and feelings related to dentists and dentistry. [source]


    Effect of residual vanadyl ions on the spectroscopic analysis of humic acids: a multivariate approach

    EUROPEAN JOURNAL OF SOIL SCIENCE, Issue 3 2008
    E. H. Novotny
    Summary In a study of the vanadyl (VO2+)-humic acids system, the residual vanadyl ion suppressed fluorescence and specific electron paramagnetic resonance (EPR) and NMR signals. In the case of NMR, the proton rotating frame relaxation times (T1,H) indicate that this suppression is due to an inefficient H-C cross polarization, which is a consequence of a shortening of T1,H. Principal components analysis (PCA) facilitated the isolation of the effect of the VO2+ ion and indicated that the organic free radical signal was due to at least two paramagnetic centres and that the VO2+ ion preferentially suppressed the species whose electronic density is delocalized over O atoms (greater g -factor). Additionally, the newly obtained variables (principal components , PC) indicated that, as the result of the more intense tillage a relative increase occurred in the accumulation of: (i) recalcitrant structures; (ii) lignin and long-chain alkyl structures; and (iii) organic free radicals with smaller g -factors. [source]