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PubMed2005

Environmentally stratified sampling design for the development of Great Lakes environmental indicators.

Understanding the relationship between human disturbance and ecological response is essential to the process of indicator development. For large-scale observational studies, sites should be selected across gradients of anthropogenic stress, but such gradients are often unknown for apopulation of sites prior to site selection. Stress data available from public sources can be used in a geographic information system (GIS) to partially characterize environmental conditions for large geographic areas without visiting the sites. We divided the U.S. Great Lakes coastal region into 762 units consisting of a shoreline reach and drainage-shed and then summarized over 200 environmental variables in seven categories for the units using a GIS. Redundancy within the categories of environmental variables was reduced using principal components analysis. Environmental strata were generated from cluster analysis using principal component scores as input. To protect against site selection bias, sites were selected in random order from clusters. The site selection process allowed us to exclude sites that were inaccessible and was shown to successfully distribute sites across the range of environmental variation in our GIS data. This design has broad applicability when the goal is to develop ecological indicators using observational data from large-scale surveys.

Animals↗
PubMed2005

A directed essential dynamics simulation of peptide folding.

We present a directed essential dynamics (DED) method for peptide and protein folding. DED is a molecular dynamics method based on the essential dynamics sampling and the principal component analysis. The main idea of DED is to use principal component analysis to determine the direction of the most active collective motion of peptides at short intervals of time (20 fs) during the folding process and then add an additional force along it to adjust the folding direction. This method can make the peptides avoid being trapped in the local minima for a long time and enhance the sampling efficiency in conformational space during the simulation. An S-peptide with 15 amino acids is used to demonstrate the DED method. The results show that DED can lead the S-peptide to fold quickly into the native state, whereas traditional molecular dynamics needs more time to do this.

Biophysics↗
PubMed1984

Blood pressure in patients with four different primary glomerulopathies.

It is well known that patients with different kidney diseases have different prevalence of hypertension, independent of renal function. To investigate whether a lesion of some portion of the glomerular tuft, without renal insufficiency, is associated more frequently with high blood pressure, we undertook a retrospective study on 189 patients analyzing by means of multiple regression analysis as independent variables : type of glomerulopathy (IgA Nephropathy, Acute Glomerulonephritis, Membranous Glomerulonephritis and Focal Glomerulosclerosis), sex, age, body weight, plasma creatinine, plasma and urinary proteins, plasma urate, time interval first symptom-renal biopsy and steroid therapy. The dependent variable was a Principal Component formed by Mean Blood Pressure and an Antihypertensive Therapy score, calculated with a computer program. Focal Glomerulosclerosis patients had a higher prevalence of hypertension and a higher Principal Component value than patients of the other 3 groups. Plasma urate was correlated and time interval first symptom-renal biopsy was inversely correlated to Principal Component. These observations suggest that sclerosis of the glomeruli is the lesion most often associated with hypertension. On the other hand, since plasma urate is correlated with blood pressure also in "essential" hypertensives, it seems likely that hyperuricemia is a phenomenon secondary to hypertension.

Adult↗
PubMed1997

Geographical variation of persistent organochlorine concentrations in blubber of ringed seal (Phoca hispida) from the Canadian Arctic: univariate and multivariate approaches.

Geographical variation of organochlorine (OC) concentrations in ringed seal (Phoca hispida) in the Canadian Arctic was studied using univariate and multivariate statistical techniques. The dataset consisted of 80 individual OC components (58 PCB congeners plus DDT- and chlordane (CHL)-related compounds, toxaphene, hexachlorocyclohexanes (HCH), chlorobenzenes (CBz), and dieldrin) determined in 221 ringed seal blubber samples from 13 locations throughout the Canadian Arctic from the period 1983 to 1989. Mean concentrations of the major OC groups in ringed seal blubber (SigmaPCBs, SigmaDDT, SigmaCHL and toxaphene), adjusted for the age and sex of the seals, showed few significant geographical differences. Principal components analysis was used to examine geographical trends. Significant differences in mean factor scores for three of four principal components were found between sampling locations. Locations in the western and high Arctic could be distinguished from those in Hudson Bay by highest scores along principal component two which was associated principally with CBz. PCB congeners with six or more chlorine substitutions declined with increasing north latitude, whereas more volatile OCs (CBz, HCH, less chlorinated PCBs) increased in the proportion of total OCs with latitude. Proportions of less chlorinated PCBs also decreased with increasing longitude, whereas slopes of regressions for more highly chlorinated PCBs increased significantly. The results were generally consistent with the 'cold condensation' hypothesis of increasing proportions of more volatile OCs with increasing latitude and distance from sources.

Journal Article↗
PubMed1995

Subcutaneous adipose tissue distribution in adolescent girls of four ethnic groups.

OBJECTIVE: To compare the distribution of subcutaneous adipose tissue (SAT) in adolescent girls from four ethnic groups. SUBJECTS: The cross-sectional sample included 498 American adolescent girls from four ethnic groups: Mexican (n = 327), European (White, n = 81), Asian (n = 63, all except two Filipino), and African (Black, n = 27). Ages ranged from 11 to 18 years, but 98% of the sample was 12 to 17 years of age. MEASUREMENTS: Body mass, stature and four skinfolds were measured on each girl by a single observer. Three ratios of SAT distribution were derived: the ratio of the sum of the two T (subscapular + suprailiac) to the sum of the two E (triceps + medial calf) skinfolds (T/E ratio); the ratio of the two T to the sum of four skinfolds (T/SUM ratio); and the ratio of the subscapular to the triceps skinfolds (S/T ratio). Principal components analysis was also used to evaluate SAT distribution. RESULTS: Adolescent girls in the four ethnic groups differed significantly in the three skinfold ratios and in the first principal component, which contrasted trunk and extremity skinfolds. The sequence from proportionally more to proportionally less trunk SAT was as follows: Asian > Mexican > White > Black. Two other principal components were identified, one contrasting the upper and lower extremity skinfolds and the other contrasting the upper and lower trunk skinfolds, but ethnic differences in these two components were not significant.

Adipose Tissue↗
PubMed2026

jsPCA: fast, scalable, and interpretable identification of spatial domains and variable genes across multi-slice and multi-sample spatial transcriptomics data.

MOTIVATION: Spatial transcriptomics technologies record genome-wide measurements of gene expression with high spatial resolution. These technologies generate large and high-dimensional datasets requiring efficient automated methods for their analysis. We introduce joint spatial PCA (jsPCA), a novel, fast, scalable and interpretable method for the automatic identification of spatial domains and variable genes in multi-slice and multi-sample spatial transcriptomics data. RESULTS: jsPCA relies on a simple mathematical formulation of a spatial covariance defined as the product of the gene expression covariance with the spatial autocorrelation. The principal components of this spatial covariance yield a biologically meaningful low-dimensional representation. From this representation, spatial domains are derived by simple clustering and spatially variable genes are identified directly from the principal component coefficients. A joint representation of multiple slices and samples without spatial alignment is obtained by computing common principal components via joint diagonalization. By leveraging data sparsity and non-convex manifold optimization, jsPCA leads to computing time in the order of seconds to minutes, substantially outperforming state-of-the-art approaches. We benchmarked jsPCA against 10 state-of-the-art methods on two reference databases. Our approach demonstrated excellent performance, comparable or better than state-of-the-art methods, while being much faster, interpretable, and scalable to very large datasets.

Journal Article↗
PubMed2006

Detection of atherosclerosis using autoregressive modelling and principles component analysis to carotid artery Doppler signals.

The purpose of this study was to evaluate principal component analysis method to power spectral density acquired with autoregressive modeling (AR) of carotid artery Doppler signals. Carotid artery Doppler signals from patient with atherosclerosis and healthy subjects were recorded. Afterwards, power spectral densities of these signals were obtained using AR method. The basic differences between the healthy and patients were obtained with 1st principal component obviously. These results could be extrapolated to situations involving noninvasive measurement where PCA can be extremely time saving. As a result the patient and healthy groups are separated clearly from each other via an arbitrary power function y=ax with perfect accuracy resulting in a precision sensitivity and specificity of 100 percent and the use of PCA of physiological waveform is presented as a powerful method likely to be incorporated in future medical signal processing.

Adult↗
PubMed1992

Relationships between the chromatographic retention data and the effects of nucleoside derivatives in highly metastatic 3LL cells.

The effect of 21 nucleoside derivatives on the [3H]-thymidine cellular uptake and on the incorporation into DNA of highly metastatic 3LL (Lewis lung carcinoma) cells has been measured. Hydrophobic and hydrophilic molecular parameters (the adsorption capacity, specific adsorption surface, lipophilicity and specific hydrophobic surface area) have been determined by using thin-layer chromatography. Stepwise linear regression analysis and principal component analysis have been applied in order to reveal the relationships between the molecular parameters and the effect of the nucleoside derivatives on highly metastatic 3LL cells. The first principal component obtained from the measured activity data could be attributed to the change of [3H]-thymidine cellular uptake caused by the nucleoside, while the second principal component could be regarded as the measure of the effect on the DNA incorporation of [3H]-thymidine. The effect of the nucleosides on the [3H]-thymidine uptake could be explained by the specific hydrophobic and adsorption surface area of the nucleoside, on the other hand the effect on the DNA incorporation could be described by the adsorption characteristics (specific hydrophilic surface area and adsorption capacity) of the derivatives.

Animals↗
PubMed1998

Patterns of dietary intake and serum lipids interact with proteinuria as risk factors for progression of chronic renal failure.

UNLABELLED: This prospective study assessed the interactions between patterns of nutrient intake and serum lipids with other risk factors for progression of chronic renal failure. The study cohort consisted of 52 individuals with documented chronic renal failure, 18 women and 34 men, with a mean age of 65 +/- 11 years at the time of recruitment. The dependent variable was the rate of progression of chronic renal failure, which was determined by the slope of the curve generated from five or more values of the reciprocal of serum creatinine (SCr-1) and divided by time (in months of follow-up) for each patient, and recorded in dung/month. The independent variables included dietary factors (phosphorus, protein); serum lipids (total cholesterol, LDL-cholesterol, HDL-cholesterol, triglycerides); proteinuria; serum phosphorus; serum albumin; serum glucose; and blood pressure. Serum creatinine was drawn in a fasting state and determined using the picric acid technique on five or more occasions for each patient. The mean monthly rate of decline in dL/mg/month was calculated for each patient. The cohort was followed for 1.5 years. Descriptive statistics were determined for all variables. Analysis of principal components was used to generate variables representing patterns of nutrient intake and serum lipids. The outcome variable was modeled using stepwise linear regression which included principal components representing dietary and serum lipid patterns. The Student's t test and the F test were used for hypothesis testing. All tests were significant at p < 0.05. RESULTS AND CONCLUSIONS: Multicolinearity prevented the inclusion of more than one individual dietary or serum lipid variable into the multiple linear regression model of rate of decline in kidney function. Principal components representing patterns of dietary intake and serum lipids, contributed to the prediction of rate of decline in renal function together with proteinuria.

Adolescent↗
PubMed2006

Peptide 17O chemical shielding and electric field gradient tensors.

Complete (17)O chemical shielding (CS) and quadrupole coupling (QC) tensors and their molecular orientations were determined for the central residues in two tripeptides Gly-Gly-Val (GGV) and Ala-Gly-Gly (AGG) by single-crystal NMR methods. Tensor orientations in the two peptides are very similar, however, principal components are different. The most shielded CS and smallest magnitude QC components are normal to the peptide plane, while the most deshielded CS and largest QC components are in the peptide plane either at an angle of 17 degrees (CS) or perpendicular (QC) to the C=O bond. Comparisons of principal components from experiment and DFT calculations indicate that the smaller shielding tensor span in GGV (549 ppm) compared to AGG (606 ppm) is likely due to two factors: a shorter "direct" H-bond distance to the peptide carbonyl oxygen and an "indirect" H bond of the peptide NH to a carboxylate rather than a carbonyl. We anticipate that (17)O NMR should be generally useful for probing H-bonding and local electrostatic interactions in proteins and polypeptides. Using the single-crystal data as an accurate reference, we show that a useful subset of the NMR parameters, QC and CS principal components and their relative orientation, can be obtained with reasonable accuracy from a very high-field (21.2 T), stationary sample powder spectrum.

Amides↗
PubMed2003

H1-histamine receptor affinity predicts short-term weight gain for typical and atypical antipsychotic drugs.

As a result of superior efficacy and overall tolerability, atypical antipsychotic drugs have become the treatment of choice for schizophrenia and related disorders, despite their side effects. Weight gain is a common and potentially serious complication of some antipsychotic drug therapy, and may be accompanied by hyperlipidemia, hypertension and hyperglycemia and, in some extreme cases, diabetic ketoacidosis. The molecular mechanism(s) responsible for antipsychotic drug-induced weight gain are unknown, but have been hypothesized to be because of interactions of antipsychotic drugs with several neurotransmitter receptors, including 5-HT(2A) and 5-HT(2C) serotonin receptors, H(1)-histamine receptors, alpha(1)- and alpha(2)-adrenergic receptors, and m3-muscarinic receptors. To determine the receptor(s) likely to be responsible for antipsychotic-drug-induced weight gain, we screened 17 typical and atypical antipsychotic drugs for binding to 12 neurotransmitter receptors. H(1)-histamine receptor affinities for this group of typical and atypical antipsychotic drugs were significantly correlated with weight gain (Spearman rho=-0.72; p<0.01), as were affinities for alpha(1A) adrenergic (rho=-0.54; p<0.05), 5-HT(2C) (rho=-0.49; p<0.05) and 5-HT(6) receptors (rho=-0.54; p<0.05), whereas eight other receptors' affinities were not. A principal components analysis showed that affinities at the H(1), alpha(2A), alpha(2B), 5-HT(2A), 5-HT(2C), and 5-HT(6) receptors were most highly correlated with the first principal component, and affinities for the D(2), 5-HT(1A), and 5-HT(7) receptors were most highly correlated with the second principal component. A discriminant functions analysis showed that affinities for the H(1) and alpha(1A) receptors were most highly correlated with the discriminant function axis. The discriminant function analysis, as well as the affinity for the H(1)-histamine receptor alone, correctly classified 15 of the 17 drugs into two groups; those that induce weight gain and those that do not. Because centrally acting H(1)-histamine receptor antagonists are known to induce weight gain with chronic use, and because H(1)-histamine receptor affinities are positively correlated with weight gain among typical and atypical antipsychotic drugs, it is recommended that the next generation of atypical antipsychotic drugs be screened to avoid H(1)-histamine receptors.

Animals↗
PubMed1976

Application of factor analytic procedures to complex evoked potential measurements in psychiatric research.

Several factor analytic procedures were applied to data gathered with a modified somatosensory evoked potential (SEP) recovery function prodecure in 56 non-patients and 224 psychiatric inpatients. The data were analyzed for each option reflected in three main issues. (1) Which group should be used for calculating the basic factor structure--normals only or all subjects? (2) Should measurements be preadjusted for covariance with variables known to obscure events of interest? (3) Should varimax rotation be used, or are principal components sufficient? Using two criteria, interpretability of factors in relation to experimental design, and their ability to discriminate clinical groups, it appeared that: (1) choice of either population yielded similar results; (2) when measurements were pre-adjusted for covariance more interpretable factors, which also yielded clinical discriminations, were obtained by varimax rotations than by principal components, and (3) when data were not adjusted by covariance, principal component analysis produced a factor which, although less interpretable in relation to experimental design than the varimax factors, provided equivalent clinical discriminations.

Brain↗
PubMed1988

[Morphometrical study of physical growth in infant cynomolgus monkeys using multivariate analysis].

We describe the relative growth in infant cynomolgus monkeys (Macaca fascicularis). The multivariate analyses using the principal component analysis and multivariate allometric analysis were applied to biometrical data of laboratory-bred cynomolgus monkeys aged from birth to 12 weeks. All the animals had been bred and reared under uniform environmental conditions at Tsukuba Primate Center for Medical Science, N. I. H., Japan. As the result of the principal component analysis, the cumulative contribution ratio of the 1st and 2nd principal components (PC1 and PC2) accounted for 88.2% and 85.7% in males and females, respectively. This indicates that the morphologic traits (15 traits) grow normally in size, but the analysis did not detect any differences in growth rate among the traits. So, the multivariate allometric analysis was applied to the same data. The traits concerning the face and truck showed relatively high growth rates compared to head breadth, whereas the limbs and arms grew slowly.

Analysis of Variance↗
PubMed2002

Fluorescence-guided laser removal of chemically damaged cornea.

PURPOSE: To correlate the observed fluorescence spectrum with the depth of ablation during 193 nm argon-fluoride excimer laser ablation of chemically damaged corneas. SETTING: Laser facility, Cedars-Sinai Medical Center, Los Angeles, California, USA. METHODS: Three cadaver New Zealand white rabbit corneas were exposed to 1 N hydrogen chloride for 10 seconds. The resultant opaque corneas were ablated to perforation using the excimer laser. Laser-induced fluorescence was collected at 45 degrees from incidence and channeled into an ultraviolet-visible spectrometer coupled to an optical multichannel analyzer reading a diode array detector. The detector recorded single-shot fluorescence spectra. The data were examined by principal component analysis, and the evolution of eigenvectors and their weighting coefficients were used to compare data among corneas. The results were correlated with histopathological sections. RESULTS: The eigenvalues of 3 principal components corresponded to 88.9%, 10.0%, and 0.4% of the data in acid-burned corneas. Compared to that in undamaged corneas, more information was stored in the first principal component and the third eigenvector was distinctly altered. Acid-scarred tissue blue shifted the dominant fluorescence peak compared to that in normal corneal tissue. CONCLUSIONS: After severe hydrogen chloride burn to the rabbit corneal surface, monitoring the dominant peak wavelength shift of excimer-laser-induced fluorescence can detect the transition between severely acid-damaged and underlying tissue.

Animals↗
PubMed1997

Evaluation of the spatial aspects of T-wave complexity in the long-QT syndrome.

BACKGROUND: The duration of the QT interval is only a gross estimate of repolarization. Besides its limited accuracy and reproducibility, it does not provide information on the morphology of the T wave; thus, morphologic alterations such as notches can be only qualitatively described but not objectively quantified. METHODS AND RESULTS: To measure the complexity of repolarization in the long-QT syndrome (LQTS) patients, we previously applied principal component analysis to body surface mapping and found it useful in distinguishing normal from abnormal repolarization patterns (sensitivity, 87%). In the present study, we applied principal component analysis to 12-lead Holter recordings. The index of complexity of repolarization that we have developed (CR24h) reflects the average 24-hour complexity of repolarization and is mathematically defined as the average ratio between the second and the first eigenvalue. We studied 36 LQTS patients and 40 control subjects. A mean of 22+/-1.3 ECG recordings at 1-hour intervals was used in each patient, and a total of 1655 recordings were analyzed. CR24h was significantly higher in LQTS than in control subjects (34+/-12% versus 13+/-3%; P<.0001). A CR24h exceeding 2 SD above the mean of the control group (>20%) was present in 32 of 36 patients (88%). The negative predictive value of CR24h in LQTS was 88%, and the combination of prolonged QT and abnormal CR24h identified all LQTS patients from normal subjects, including 4 affected symptomatic individuals with a normal QT interval duration, suggesting that CR24h provides information independent of QT duration. CONCLUSIONS: Our data suggest that principal component analysis applied to 24-hour, 12-lead Holter recording adequately quantifies the complexity of ventricular repolarization and may become a useful noninvasive diagnostic tool in LQTS.

Adolescent↗
PubMed2006

Dietary patterns and survival in older Dutch women.

BACKGROUND: The need to gain insight into prevailing eating patterns and their health effects is evident. OBJECTIVE: This study aimed to identify dietary patterns and their relation to total mortality in older Dutch women. DESIGN: A principal component analysis of 22 food groups was used to identify dietary patterns in 5427 women aged 60-69 y who were included in the Dutch European Prospective Investigation into Cancer and Nutrition-Elderly cohort (follow-up: approximately 8.2 y). Mortality ratios for 3 major principal components were assessed by using Cox proportional hazard analysis. RESULTS: The most relevant principal components were a Mediterranean-like dietary pattern (high intakes of vegetable oils, pasta and rice, sauces, fish, and wine), a Traditional Dutch dinner dietary pattern (high intakes of meat, potatoes, vegetables, and alcoholic beverages), and a Healthy Traditional Dutch dietary pattern (healthy variant of the Traditional Dutch dinner dietary pattern; high intakes of vegetables, fruit, nonalcoholic drinks, dairy products, and potatoes). Differences in mean intakes between the highest and lowest tertiles of the 3 patterns were greatest for fruit, dairy products, potatoes, and alcoholic beverages. Consumption of Mediterranean foods, such as fish and oils, was relatively low overall. Two hundred seventy-seven deaths occurred in 44,667 person-years. Independent of age, education, and other lifestyle factors, only the Healthy Traditional dietary pattern score was associated with a lower mortality rate. Women in the highest tertile of this pattern experienced a 30% reduction in mortality risk. CONCLUSION: A Healthy Traditional Dutch diet, rather than a Mediterranean diet, appears beneficial for longevity and feasible for health promotion in older Dutch women. This diet is comparable with other reported healthy or prudent diets that have been shown to be protective against morbidity or mortality.

Aged↗
PubMed2002

Age-related dedifferentiation of visuospatial abilities.

Forty-eight older adults were tested on a battery of seven speeded visuospatial tasks that were developed by Chen et al. to measure the functions of the ventral and dorsal neural processing streams. Principal components analysis revealed only one factor with an eigenvalue greater than 1.0, and all of the tasks loaded heavily on this general factor. These results are in contrast to those reported in a previous study of young adults in which principal components analysis revealed two factors with eigenvalues greater than 1.0. Importantly, for young adults the second principal component was a bipolar factor which grouped the tasks based on the neural processing stream (i.e. ventral versus dorsal) whose function they had been designed to assess. The age-related difference in the factor structure of visuospatial abilities apparent from the present results may be interpreted as reflecting an age-related dedifferentiation of the neural processing streams consistent with the results of recent neuroimaging studies.

Aged↗
PubMed2003

Multivariate chemometrics for the forensic discrimination of blue ball-point pen inks based on their Vis spectra.

Fifty blue ball-point pen inks of five different brands were examined on the basis of the Vis spectrum of their ethanolic solutions with a view to achieving good discrimination between them. Samples were dissolved in absolute ethanol and their absorbance values in the range of 400-750 nm, after appropriate transformations, were used as variables in the multivariate statistical techniques of cluster analysis (CA), principal component analysis (PCA) and discriminant analysis (DA). These techniques were used successively so that an effective and meaningful discriminant model was calculated in the final step. The initial 351 variables (log10 transformed ink absorption values at each wavelength) were subjected to a K-means CA over the objects (samples) and only 20 variables were retained. Principal component analysis was used to detect any outliers (four samples were removed) and the remaining samples were re-subjected to PCA to decide how many variables to enter into DA and whether original variables or components should be used. It was found that the first three principal components (in accordance with the Kaiser criterion) were good descriptors of the 20 original variables (96.97% of the data variance was explained) and their use as latent variables in DA lead to low average variable redundancy (33.6%) in the discriminant model. The calculated model had a Wilks' lambda of 8.98 x 10(-5) and was statistically significant at the P = 0.05 level. The post hoc classification of the training dataset was 100% correct. From the DA results and the component loadings it was found that discrimination was achieved on the basis of differences in the shape of the absorption bands as well as their relative intensities. The method was therefore deemed appropriate for supporting exclusionary forensic purposes.

Journal Article↗