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PubMed2004

The application of independent component analysis to the multi-channel surface electromyographic signals for separation of motor unit action potential trains: part II-modelling interpretation.

The purpose of this article was to investigate whether or not FastICA can separate identical motor unit action potential trains (MUAPTs) of the 8-channel surface electromyographic (sEMG) signals constructed by an sEMG model into the independent components. Firstly, we have examined how much the increase of motor units (MUs) in the simulated sEMG signals influenced the performance on the separation of MUAPTs by kurtosis. The decreased trend of mean kurtosis on both sEMG signals and their independent components were observed as MUs were increased. These data suggested that the separation performance decayed when MUs were increased. Secondary, the differences between the independent components and the principal components have been also applied to the simulated sEMG signals with or without time delay between the sEMG channels. FastICA could successfully separate identical MUAPTs with no time delay but principal component analysis (PCA) could not do so. Against it, both FastICA and PCA could not separate MUAPTs with some time delay. In conclusion, our results suggested that FastICA could separate identical MUAPTs with no time delay into the independent components by FastICA, which might offer a new technique for the separation of interfered MUAP waveforms based on statistical properties of sEMG signal distributions.

Action Potentials↗
PubMed1997

Asymptomatic HIV-infected women: preliminary study of quantitative EEG activity and performance on a continuous performance test.

Several studies have examined the electrophysiological correlates of human immunodeficiency virus (HIV) infection in medically asymptomatic men. Although the rates of HIV infection are increasing at a greater rate in women than men, there have been no publications to date of electrophysiological functioning in HIV-infected women. In the present study, quantitative electroencephalographic (qEEG) activity was measured in 22 women (11 asymptomatic HIV-seropositive and 11 HIV-seronegative) utilizing a procedure comprised of three auditory continuous performance tests and a set of qEEG components derived from principal components analysis. No significant group differences were found in qEEG or in performance on the continuous performance tests; however, task-related differences were detected across groups between simple and complex language tasks in EEG fast beta power, delta power, and a left-hemisphere principal components analysis-derived EEG component. In examining the electrophysiological correlates of HIV infection, researchers might employ a similar methodology while increasing the sample size and varying the task modality or difficulty.

Adult↗
PubMed2003

Coping strategies in male and female rats exposed to multiple stressors.

Because of the pathogenic effects of chronic stress exposure, it is important to identify factors, such as effective coping strategies, that mitigate stress-induced pathology. Of interest in the present study was the consistency of behavioral responses across a diverse array of stressors. Sixteen male and 16 female Long-Evans rats were assigned to either a stress or control group. The stressed animals were subsequently exposed to a battery of ecologically relevant stressors (e.g., predator odor, novel stimuli, and immunological challenge) to determine trends in coping strategies. Blood was collected for corticosterone (CORT) assay and brains were harvested for assessment of fos immunoreactivity in the paraventricular hypothalamus (PVH) and central amygdala (CEA) following exposure to the final stressor of fox urine. A correlational analysis indicated that certain response strategies (e.g., latency to respond in different stress tests such as the open-field and novel item tests) persist across several behavioral tests, especially those tests involving exploratory components. A subsequent principal component factor analysis revealed the following four components: initiative to explore, low reactivity, variable reactivity, and high reactivity. Females exhibited higher recovery CORT levels than males; however, sex only affected one behavioral response measure (i.e., females demonstrated more attempts to climb the wall in the forced-swim test than their male counterparts). In conclusion, these results support the importance and prevalence of initiative to explore as a common factor in many stress tests; additionally, the principal component analysis indicated that physiological correlates of stress are more closely associated with more challenging environments and stimuli such as forced swimming, immunological challenges, and exposure to predator odors.

Adaptation, Psychological↗
PubMed2003

New approach to generalized two-dimensional correlation spectroscopy. IV: eigenvalue manipulation transformation (EMT) for partial attenuation of dominant factors.

This paper extends our previous work on the potential of eigenvalue manipulating transformation (EMT) of a data matrix for spectral selectivity enhancement in two-dimensional (2D) correlation analysis. EMT operation by uniformly lowering the power of a set of eigenvalues associated with the original data exaggerates the information content of minor principal components and reduces that of major principal components. Thus, much more subtle differences of spectral behavior for each component are now highlighted. Similarly, the selective truncation of dominant principal component (PC) factors to bring up the subtle contributions of minor factors is also considered. The EMT-reconstructed data matrix where power parameter m is negative greatly reduces the contribution of the first PC. Hybrid models for the attenuation of the contribution of the first PC are discussed. Synchronous 2D correlation spectra from PC1-attenuated data matrix A** obtained by varying the value of the attenuation parameter k show a much more profound effect than asynchronous 2D correlation spectra. As the value of k is increased, features of 2D correlation spectra start looking very much like those from the principle component analysis (PCA)-reconstructed data with only the second and third PCs and from the EMT-reconstructed data matrix where the power parameter m is negative.

Artifacts↗
PubMed1990

Structure of ischemic heart disease risk factors in the North Khanty population of western Siberia.

The relationships between serum lipids, blood pressures, anthropometric traits, age, and ischemic changes of the electrocardiogram (ECG) in the North Khanty population were studied. To this end, eight morphophysiological variables--presumably risk factors for ischemic heart disease--have been subjected to a principal components analysis. Two principal components were extracted. The first revealed age dependency of the traits not associated with ischemic changes of myocardium in both sexes. A comparative analysis of the second component has shown that the chosen traits correlated with ischemic heart disease in males but not in females. Interpretation is given of the components obtained.

Age Factors↗
PubMedDate not supplied

An automatic color segmentation algorithm with application to identification of skin tumor borders.

A principal components transform algorithm for automatic color segmentation of images is described. This color segmentation algorithm was used to find tumor borders in six different color spaces including the original red, green, and blue (RGB) color space of the digitized image, the intensity/hue/saturation (IHS) transform, the spherical transform, chromaticity coordinates, the CIE transform and the uniform color transform designated CIE-LUV. Five hundred skin tumor images were separated into a training set and a test set for comparison of the different color spaces. Automatic induction was applied to dynamically determine the number of colors for segmentation. Ninety-one percent of image variance was contained in the image component along the principal axis (also containing the most image information). When compared to a luminance radial search method, the principal components color segmentation border method performed equally well by one measure and 10% better by another measure, including more near border points outside the tumor. The spherical transform provides the highest success rate and the chromaticity transform the lowest error rate, although large variances in the data preclude definitive statistical comparisons.

Algorithms↗
PubMed2000

The use of lichen (Cetraria nivalis) and moss (Rhacomitrium lanuginosum) as monitors for atmospheric deposition in Greenland.

Concentrations of Pb, Cd, Hg, Zn, Cu, Cr, Ni, As, V, Al and Fe are reported from soil, humus, moss (Rhacomitrium lanuginosum) and lichen (Cetraria nivalis) sampled at four locations in Greenland. For Al, Fe, Cr and V the levels in soil were highest followed by humus and R. lanuginosum and with the lowest levels in C. nivalis. The same was true for Pb, Cu and Ni but without as great a difference between medias. For Cd and Hg, the lowest levels were found in soil. For Zn and As, the media with highest levels differed between locality. Data were examined by a principal component analysis. Three principal components explained 87% of the total variation. The dominant elements in the first component were Fe, Al, V, Ni, Cr, Cu and Pb. This component is interpreted as a soil dust factor. The concentrations in R. lanuginosum and C. nivalis of these elements are believed to be highly influenced by soil dust. Pb concentrations in moss and lichen may also be influenced by other sources as Pb also had some correlation's with the third component. Zn and Cd and to a lesser extent. As were the dominant elements in the second component. The third component was highly dominated by Hg with a lesser influence of Pb and As, Zn, Cd and Hg concentrations in R. lanuginosum and C. nivalis are believed to be influenced by other sources than soil dust which may be long-range atmospheric transport. In general, both the within locality and the between locality variability in the values of the three components decreased in the order soil, humus, R. lanuginosum and C. nivalis. The lichen C. nivalis is looked at as an indicator with greater potential for monitoring atmospheric deposition of elements than the moss R. lanuginosum.

Air Pollution↗
PubMed2000

Behavioural evaluation of methods for assessing fear responses in weaned pigs.

Models of anxiety and fear of novelty were evaluated using correlations and principal component analysis. A total of 84 pigs (LandracexYorkshire) from nine different litters were subjected to a tonic immobility (TI) test at the age of 2.5 weeks, an elevated plus-maze (EPM) at the age of 6 weeks, a light/dark (L/D) exploration test at the age of 7 weeks and an open-field (OF) test at the age of 8 weeks.The first component from the principal component analysis had the highest correlation with number of entries into open arms in the EPM but was also highly correlated to variables from the other three tests confirming a common aversion-related element in the four experimental tests. The second component was negatively correlated with percent entries into and time spent on open arms in the EPM, but positively correlated with the number of entries into closed arms in the same test, number of lines crossed in the OF and time spent in the lit compartment of the L/D test. The last point illustrates a negative relationship between "anxiety" and "activity" in the EPM and OF. To achieve purer measures of fear of novelty and activity in the tests, the components were rotated using the Varimax criterion. The rotated factor pattern demonstrated a simple structure where variables related to "anxiety" or "fear of novelty" (i.e., percent entries into open arms and time spent on open arms of the EPM) had the highest loading on factor 1, whereas variables related to activity (i.e., number of entries into the closed arms in the EPM, number of lines crossed in the OF and time spent in the lit compartment of the L/D test) had the highest loading on factor 2. TI duration loaded more strongly on factor 1 ("fear of novelty") than on factor 2 ("activity"), but did not represent any pure measure of either fear of novelty or activity.In conclusion, all of the test variables were related to one another. Open-arm avoidance represented the purest measure of fear of novelty, whereas entries into closed arms and number of lines crossed in the OF were the purest measures of activity. The EPM appeared to provide the best way to separate the fear of novelty and activity-related elements, indicating that the EPM may be a useful behavioural model of fear of novelty or avoidance in pigs.

Journal Article↗
PubMed2000

Are baseline frequencies of SCEs, CAs, and MN in human lymphocytes related to hematological values?

In the present study, the correlation among several hematic values and the baseline frequencies of sister chromatid exchanges (SCEs), chromosome aberrations (CAs), and micronucleus (MN) were evaluated in human peripheral blood lymphocytes from a group of 1429 volunteers. Donors were selected to be representative of the general population of people living in the city of Pisa (Italy). By the use of the principal component analysis (PCA), principal components (PCs) were extracted from the complex pattern of correlations intrinsic in the hematic values (for example such as those among hemoglobin content, hematocrit, and erythrocyte count), and were tested for correlation on SCE, CA and MN frequencies. The seven PCs extracted (among 20 hematic values) were either positively or negatively correlated with the three cytogenetic endpoints. However, after correction by independent confounding factors (such as the age), with the use of the coefficient of partial correlation (CPC) analysis, only one PC significantly held the correlation with MN frequencies. This PC had the main contribution from the correlation between the concentration of potassium and the activity of alkaline phosphatase. These variables are known to be markers for bone (calcium) metabolism and are negatively correlated with MN frequencies. Because MN can arise from aneuploidy, the hematic concentrations of calcium may be important for stabilizing the mitotic process in stimulated lymphocytes. Finally, our study shows that the analysis of the hematic values adds very little information and removes a meaningless part of variance of the total variability observed for SCEs, CAs and MN.

Adult↗
PubMed2003

Feasibility study on the use of visible and near-infrared spectroscopy together with chemometrics to discriminate between commercial white wines of different varietal origins.

The use of visible (vis) and near-infrared spectroscopy (NIR) was explored as a tool to discriminate between samples of Australian commercial white wines of different varietal origins (Chardonnay and Riesling). Discriminant models were developed using principal component analysis (PCA), principal component regression (PCR), and discriminant partial least-squares (DPLS) regression. The samples were randomly split into two sets, one used as a calibration set (n = 136) and the remaining samples as a validation set (n = 133). When used to predict the variety of the validation set samples, the DPLS models correctly classified 100% of Riesling and up to 96% of Chardonnay wines. These results showed that vis-NIR might be a suitable and alternative technology that can be easily implemented by the wine industry to discriminate Riesling and Chardonnay commercial wine varieties. However, the relatively limited number of samples and varieties involved in the present work suggests caution in extending the potential of such a technique to other wine varieties.

Discriminant Analysis↗
PubMed2005

Bioactive compounds in cod (Gadus morhua) products and suitability of 1H NMR metabolite profiling for classification of the products using multivariate data analyses.

This work investigates the suitability of (1)H NMR spectroscopy to identify the fate of some bioactive compounds in seafood submitted to several processing conditions and examines the possibility of using (1)H NMR spectroscopy profiling to classify such products. Perchloric acid extracts of cod white muscle from newly killed and (i) unprocessed, (ii) boiled, and (iii) fried fillets and from (iv) frozen fillets, (v) the frozen fillets after thawing, and (vi) their drip loss and from (vii) rehydrated cod klippfish (n = 5) were analyzed by 500 MHz (1)H NMR spectroscopy. It was possible to identify taurine, betaine, anserine, creatine, and trimethylamine oxide (TMAO) in all extracts examined, and frozen fish was recognizable by the presence of dimethylamine (DMA). None of the heating procedures seemed to induce the loss of bioactive compounds from the fillet, but freezing and thawing did: the compounds were lost in what is known as drip loss. About 80% of the samples were correctly classified using a probabilistic neural network procedure having as inputs the scores of the first 20 principal components of the principal component analysis of a selected region of the NMR spectra.

Animals↗
PubMed2002

QTL analysis of a red junglefowl x White Leghorn intercross reveals trade-off in resource allocation between behavior and production traits.

Behaviors with high energetic costs may decrease in frequency in domestic animals as a response to selection for increased production. The aim of this study was to quantify production traits, foraging behavior, and social motivation in F2 progeny from a White Leghorn x red junglefowl intercross (n = 751-1046) and to perform QTL analyses on the behavioral traits. A foraging-social maze was used for behavioral testing, which consisted of four identical arms and a central box. In two arms there was ad libitum access to the birds' usual food, and in the other two there was novel food (sunflower seeds) mixed with cat litter. In one arm with each of the two food sources, social stimuli were simulated by the presence of a mirror. Each bird could therefore feed on novel or well known food either alone or in the perceived company of a conspecific. Egg production, sexual maturity (females), food intake, and growth were measured individually, and residual food intake and metabolic body weight were estimated using standard methods. A genome scan using 104 microsatellite markers was carried out to identify QTLs affecting behavioral traits. Phenotypic growth rates at different ages showed weak associations in both sexes. Sexual maturity and egg weight were not strongly correlated to growth, indicating that these traits are not genetically linked. Time spent in each arm and in the central part of the maze was analyzed using principal component analyses. Four principal components (PC) were extracted, each reflecting a pattern of behavior in the maze. Females with early onset of sexual maturity scored higher on the PC1 reflecting preference for free food without social stimuli, and females with higher egg production scored higher on the PC2 reflecting exploration. Males with an overall higher growth rate and higher residual food intake scored higher on the PC3, which possibly reflected fear of the test situation, and tended to score higher on the PC4 reflecting low contrafreeloading. Significant QTLs were found for PC1 and PC4 scores on chromosomes 27 and 7, respectively. The location of the QTLs coincided with known QTLs for growth rate and body weight. The results suggest a trade-off between energy-demanding behavior and high production and that some of this may be caused by genetic linkage or pleiotropic gene effects.

Animals↗
PubMed2006

Phytogeographical analysis of seed plant genera in China.

BACKGROUND AND AIMS: A central goal of biogeography and ecology is to uncover and understand distributional patterns of organisms. China has long been a focus of attention because of its rich biota, especially with respect to plants. Using 290 floras from across China, this paper quantitatively characterizes the composition of floristic elements at multiple scales (i.e. national, provincial and local), and explores the extent to which climatic and geographical factors associated with each flora can jointly and independently explain the variation in floristic elements in local floras. METHODS: A study was made of 261 local floras, 28 province-level floras and one national-level flora across China. Genera of seed plants in each flora were assigned to 14 floristic elements according to their worldwide geographical distributions. The composition of floristic elements was related to climatic and geographical factors. KEY RESULTS AND CONCLUSIONS: Variations in percentages of cosmopolitan, tropical and temperate genera among local floras tend to be greater at higher latitudes than at lower latitudes. Latitude is strongly correlated with the proportions of 13 of the 14 floristic elements. Correlations of the proportions of floristic elements with longitude are much weaker than those with latitude. Climate represented by the first principal component of a principal component analysis was strongly correlated with the proportions of floristic elements in local floras (|r| = 0.75 +/- 0.18). Geographical coordinates independently explained about four times as much variation in floristic elements as did climate. Further research is necessary to examine the roles of water-energy dynamics, geology, soils, biotic interactions, and historical factors such as land connections between continents in the past and at present in creating observed floristic patterns.

China↗
PubMed2004

Diversity and distribution of Microcystis (Cyanobacteria) oligopeptide chemotypes from natural communities studied by single-colony mass spectrometry.

Microcystis sp. has been recognized in recent years as a producer of a high number of secondary metabolites. Among these, peptides that are produced by the non-ribosomal peptide synthetase pathway often show bioactivity or are toxic to humans. The production of particular peptides is specific for individual Microcystis clones, allowing their characterization as chemotypes by analysing the peptidome. The authors studied the in situ diversity of peptides and chemotypes in Microcystis communities from lakes in and around Berlin, Germany, by direct analysis of individual colonies by MALDI-TOF mass spectrometry. From 165 colonies analysed a total of 46 individual peptides could be identified, 21 of which have not been described previously. For six of the new peptides the structures could be elucidated from fragment patterns, while for others only a preliminary classification could be achieved. In most colonies, two to ten individual peptides were detected. In 19 colonies, 16 of which were identified as M. wesenbergii, no peptide metabolites could be detected. The peptide data of 146 colonies were subjected to an ordination (principal components analysis). The principal components were clearly formed by the microcystin variants Mcyst-LR, -RR and -YR, anabaenopeptins B and E/F, a putative microviridin, and a new cyanopeptolin. In the resulting ordination plots most colonies were grouped into five distinct groups, while 40 colonies scattered widely outside these groups. In some cases colonies from different lakes clustered closely, indicating the presence of similar chemotypes in the respective samples. With respect to colony morphology no clear correlation between a chemotype and a morphospecies could be established, but M. aeruginosa, for example, was found to produce predominantly microcystins. In contrast, M. ichthyoblabe colonies were mostly negative for microcystins and instead produced anabaenopeptins. The number of peptides detected in a limited number of samples and the various combinations of peptides in individual Microcystis colonies highlights the immense metabolic potential and diversity of this genus.

Fresh Water↗
PubMed2004

Refinement and validation of a French in-patient experience questionnaire.

The objective of this study was to check psychometric properties of a French-language in-patient experience questionnaire in a test sample different from the development sample. The questionnaire was sent out to 5,736 in-patients, within two to four weeks of discharge from a teaching hospital of 2,200 beds. Overall 4,095 questionnaires (71.4 per cent) were returned. Of these, 3,879 questionnaires were analyzed. In principal component analysis, seven principal components accounted for 62.4 per cent of the total variance. Cronbach's alpha coefficient ranged from 0.62 to 0.90, with the exception of the seventh scale (convenience scale, two items, Cronbach = 0.39). The overall patient experience score increased with increasing patient age (except for patients older than 65), male sex, low education level, use of a single room, and prior stay in the department. It also differed with respect to patients' behavioral intentions, answers to an overall satisfaction item, and open-ended comments.

Adult↗
PubMed2005

Feature selection and nearest centroid classification for protein mass spectrometry.

BACKGROUND: The use of mass spectrometry as a proteomics tool is poised to revolutionize early disease diagnosis and biomarker identification. Unfortunately, before standard supervised classification algorithms can be employed, the "curse of dimensionality" needs to be solved. Due to the sheer amount of information contained within the mass spectra, most standard machine learning techniques cannot be directly applied. Instead, feature selection techniques are used to first reduce the dimensionality of the input space and thus enable the subsequent use of classification algorithms. This paper examines feature selection techniques for proteomic mass spectrometry. RESULTS: This study examines the performance of the nearest centroid classifier coupled with the following feature selection algorithms. Student-t test, Kolmogorov-Smirnov test, and the P-test are univariate statistics used for filter-based feature ranking. From the wrapper approaches we tested sequential forward selection and a modified version of sequential backward selection. Embedded approaches included shrunken nearest centroid and a novel version of boosting based feature selection we developed. In addition, we tested several dimensionality reduction approaches, namely principal component analysis and principal component analysis coupled with linear discriminant analysis. To fairly assess each algorithm, evaluation was done using stratified cross validation with an internal leave-one-out cross-validation loop for automated feature selection. Comprehensive experiments, conducted on five popular cancer data sets, revealed that the less advocated sequential forward selection and boosted feature selection algorithms produce the most consistent results across all data sets. In contrast, the state-of-the-art performance reported on isolated data sets for several of the studied algorithms, does not hold across all data sets. CONCLUSION: This study tested a number of popular feature selection methods using the nearest centroid classifier and found that several reportedly state-of-the-art algorithms in fact perform rather poorly when tested via stratified cross-validation. The revealed inconsistencies provide clear evidence that algorithm evaluation should be performed on several data sets using a consistent (i.e., non-randomized, stratified) cross-validation procedure in order for the conclusions to be statistically sound.

Algorithms↗
PubMed1994

Alcohol dependence and cue reactivity.

A group of 35 severely dependent male alcoholic patients undergoing cue exposure treatment were studied. Thirty-one subjects had complete data and their physiological and subjective responses to drink cues on the first day of the cue exposure program were subjected to a principal components analysis. The principal component loadings were then used to construct a single measure of responsivity and this responsivity measure was found to correlate significantly with Severity of Alcohol Dependence Questionnaire (SADQ) scores. Further analysis of the relationship between responsivity and the subscales of the SADQ showed that the experience of affective withdrawal symptoms, craving for alcohol and drinking to relieve withdrawal symptoms were the most strongly correlated with responsivity.

Adult↗
PubMed2004

Reliability and validity of a Swedish language version of the Resilience Scale.

The purpose of this study was to test the reliability and validity of the Swedish language version of the Resilience Scale (RS). Participants were 142 adults between 19-85 years of age. Internal consistency reliability, stability over time, and construct validity were evaluated using Cronbach's alpha, principal components analysis with varimax rotation and correlations with scores on the Sense of Coherence Scale (SOC) and the Rosenberg Self-Esteem Scale (RSE). The mean score on the RS was 142 (SD = 15). The possible scores on the RS range from 25 to 175, and scores higher than 146 are considered high. The test-retest correlation was .78. Correlations with the SOC and the RSE were .41 (p < 0.01) and .37 (p < 0.01), respectively. Personal Assurance and Acceptance of Self and Life emerged as components from the principal components analysis. These findings provide evidence for the reliability and validity of the Swedish language version of the RS.

Adaptation, Psychological↗