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PubMed1998

Nuclear magnetic resonance spectroscopic and principal components analysis investigations into biochemical effects of three model hepatotoxins.

1H NMR spectroscopy of urine combined with pattern recognition (PR) methods of data analysis has been used to investigate the time-related biochemical changes induced in Sprague-Dawley rats by three model hepatotoxins: alpha-naphthyl isothiocyanate (ANIT), d-(+)-galactosamine (GalN), and butylated hydroxytoluene (BHT). The development of hepatic lesions was monitored by conventional plasma analysis and liver histopathology. Urine was collected continuously postdosing up to 144 h and analyzed by 600-MHz 1H NMR spectroscopy. NMR spectra of the urine samples showed a number of time-dependent perturbations of endogenous metabolite levels that were characteristic for each hepatotoxin. Biochemical changes common to all three hepatotoxins included a reduction in the urinary excretion of citrate and 2-oxoglutarate and an increased excretion of taurine and creatine. Increased urinary excretion of betaine, urocanic acid, tyrosine, threonine, and glutamate was characteristic of GalN toxicity. Both GalN and ANIT caused increased urinary excretion of bile acids, while glycosuria was evident in BHT- and ANIT-treated rats. Data reduction of the NMR spectra into 256 integrated regions was used to further analyze the data. Mean values of each integrated region were analyzed by principal components analysis (PCA). Each toxin gave a unique time-related metabolic trajectory that could be visualized in two-dimensional PCA maps and in which the maximum distance from the control point corresponded to the time of greatest cellular injury (confirmed by conventional toxicological tests). Thereafter, the metabolic trajectories changed direction and moved back toward the control region of the PR map during the postdose recovery phase. The combination of urinary metabolites which were significantly altered at various time points allowed for differentiation between biliary and parenchymal injury. This NMR-PR approach to the noninvasive detection of liver lesions will be of value in furthering the understanding of hepatotoxic mechanisms and assisting in the discovery of novel biomarkers of hepatotoxicity.

1-Naphthylisothiocyanate↗
PubMed1989

[Metrical study on teeth and mandible in Macaca fuscata fuscata. 2. Principal component analysis].

Metrical investigation on teeth and mandible together was performed to understand the morphological relationship between these two components in Macaca fuscata fuscata. Measurements are 9 items from the mandible, 2 items from dental arch, and 8 mesiodistal diameters from teeth. Correlation matrix composed of 19 items, in total, was examined in males and females, respectively. Significant correlation coefficients were frequently seen among mandibular measurements and also among tooth measurements, but rarely seen between mandibular and tooth measurements. The only exception was a mesiodistal diameter of P3 which has a few significant correlations with mandibular measurements. Principal component analysis was also carried out based on the correlation matrix of 19 measurements. The first component was a size factor in which factor loadings were all positive. The second component was thought to be a factor of the mandibular size in which factor loadings were highly positive on the mandibular measurements and contrarily low on the dental measurements. It is concluded that there is no obvious correlation between general sizes of the mandible and the teeth in Macaca fuscata fuscata.

Animals↗
PubMed2005

Principal component analysis calibration method for dual-luminophore oxygen and temperature sensor films: application to luminescence imaging.

Oxygen sensor films are frequently used to image air-pressure distributions on surfaces in aerodynamic wind tunnels. In this application, the sensor film is referred to as a pressure-sensitive paint (PSP). A Stern-Volmer calibration is used to relate the emission intensity ratio of a long-lifetime luminescent dye (the pressure-sensitive luminophore, PSL) to surface air pressure. A major problem in PSP measurements arises because the Stern-Volmer calibration of the PSL's emission varies with temperature. To correct for the temperature dependence, a second luminescent dye that has an emission that varies with temperature (the temperature-sensitive luminophore, TSL) is incorporated into the sensor film. With such a dual-luminophore PSP (DL-PSP), it is possible to measure the surface-temperature distribution with the TSL emission, and this information is then used to correct the temperature dependence of the PSL's pressure response. In the present article, we report the application of a DL-PSP to obtain high-resolution air-pressure distributions on a surface that is subjected to a 20 degrees C temperature gradient. Two different calibration methods are used to generate surface-temperature and air-pressure distributions from the luminescence imaging data, and a quantitative comparison of the results obtained from the two methods is provided. The first method is based on an intensity-ratio calibration that uses luminescence images collected at two wavelengths, one corresponding to the TSL emission and the second corresponding to the PSL emission. The second method is based on principal component analysis (PCA) of luminescence images obtained at four wavelengths throughout the spectral region of the TSL and PSL emission (hyperspectral imaging, 550-750 nm). The results demonstrate that the PCA method allows the measurement of surface air pressure with higher accuracy and precision compared to those of the intensity-ratio method. The improvement is especially significant at pressures near 1 atm, where the temperature interference is most pronounced. Surface-pressure distributions are measured with comparable accuracy and precision with the two methods.

Journal Article↗
PubMedDate not supplied

Application of three-way principal component analysis to the evaluation of two-dimensional maps in proteomics.

Three-way PCA has been applied to proteomic pattern images to identify the classes of samples present in the dataset. The developed method has been applied to two different datasets: a rat sera dataset, constituted by five samples of healthy Wistar rat sera and five samples of nicotine-treated Wistar rat sera; a human lymph-node dataset constituted by four healthy lymph-nodes and four lymph-nodes affected by a non-Hodgkin's lymphoma. The method proved to be successful in the identification of the classes of samples present in both of the groups of 2D-PAGE images, and it allowed us to identify the regions of the two-dimensional maps responsible for the differences occurring between the classes for both rat sera and human lymph-nodes datasets.

Algorithms↗
PubMed1981

Principal component analysis of slow brain potentials during six second anticipation intervals.

The comparison of principal component analyses between seven experimental studies demonstrates a remarkable similarity of the extracted components. Slow scalp-recorded potentials of the brain (SPs) during a constant 6 sec foreperiod can be described by an early frontal, and a late preparatory component. Furthermore, an additional intermediate component may be retained by the PCA. This component seems to reduce the between-subject variance and often describes processes dependent on stimulus repetition. There is evidence favoring the varimaxed solution of the PCA for the parametrization of most of the experimental data.

Biofeedback, Psychology↗
PubMed1977

Principal component analysis of the elongation of metacarpal and phalangeal bones.

A hypothesis that the first principal component computed from the covariance matrix of logarithms reflected the specific growth rates of corresponding bones was taken to analyze the growth pattern of the tubular bones of the hand. The total length of 19 tubular bones of the right hand was measured on standardized radiographs of Japanese children (33 boys, 33 girls). Metacarpals in boys and bones of the fifth digit in girls showed higher growth coefficients. The second, third and fourth proximal, and the third and fourth middle phalanges showed lower coefficients for both sexes. These observations suggest the signs of proximal row dominance in boys and of fifth ray dominance in girls in the elongation of the hand bones. A marked sex difference was found in the fifth middle phalanx. In girls the growth coefficients of this bone was much larger than any other bones, but was moderate in boys.

Adolescent↗
PubMed2004

Discrimination of normal and malignant gastric tissues with FTIR spectroscopy and principal component analysis.

In this paper, the identification of normal and malignant gastric tissues, including 11 cases of cancerous tissues and 10 cases of normal tissues, was investigated using mid-IR spectroscopy and principal componentanalysis (PCA). The results indicated that the difference between cancerous and normal tissues was found in the first principal component. The IR detection and PCA results are in agreement with the biopsy results. The combination of these two methods might provide a new opportunity for clinical application.

Algorithms↗
PubMed2004

[Adopting the method of principal components analysis combined with correlation coefficient to increase the predicted concentration's accuracy of benzene and its homology mixture].

The concentrations of benzene and its homology mixture were measured by near infrared spectra, and the emphasis was put on the character of the principal component and its physical significance. It is pointed out that the anterior principal components are very similar to the correlation coefficient of the multi-component solution and the theoretical proof for the right condition is given. The high frequency noise of the system can be checked out by principal component combined with the correlation coefficient. Removing the noise can greatly increase the accuracy of the prediction model.

Benzene↗
PubMed1998

[Method of simulation and choice of factors in the analysis of principal components].

OBJECTIVE: There are many methods to determine how many components should be retained in principal components analysis. This choice can be made on the basis of arbitrary (Kaiser) or subjective (Interpretable factors) criteria. This work presents the simulation criteria of Lébart e Dreyfus. The method create a matrix of randomized numbers and a principal component analysis is performed on the basis of this matrix. The components extracted from this data represent the cut off values. Those that exceed this cut off value should be retained. As an example, a principal component analysis is performed with the Hamilton depression rating scale (17 items) on a sample of 130 subjects. RESULTS AND CONCLUSION: The Simulation method is compared with the Kaiser method and is shown that the Simulation method maintains the components clinically significant.

Depression↗
PubMed2005

Principal components analysis of Laplacian waveforms as a generic method for identifying ERP generator patterns: II. Adequacy of low-density estimates.

OBJECTIVE: To evaluate the comparability of high- and low-density surface Laplacian estimates for determining ERP generator patterns of group data derived from a typical ERP sample size and paradigm. METHODS: High-density ERP data (129 sites) recorded from 17 adults during tonal and phonetic oddball tasks were converted to a 10-20-system EEG montage (31 sites) using spherical spline interpolations. Current source density (CSD) waveforms were computed from the high- and low-density, but otherwise identical, ERPs, and correlated at corresponding locations. CSD data were submitted to separate covariance-based, unrestricted temporal PCAs (Varimax of covariance loadings) to identify and effectively summarize temporally and spatially overlapping CSD components. Solutions were compared by correlating factor loadings and scores, and by plotting ANOVA F statistics derived from corresponding high- and low-resolution factor scores using representative sites. RESULTS: High- and low-density CSD waveforms, PCA solutions, and F statistics were remarkably similar, yielding correlations of .9 < or = r < or = .999 between waveforms, loadings, and scores for almost all comparisons at low-density locations except for low-signal CSD waveforms at occipital sites. Each of the first 10 high-density factors corresponded precisely to one factor of the first 10 low-density factors, with each 10-factor set accounting for the meaningful CSD variance (> 91.6%). CONCLUSIONS: Low-density surface Laplacian estimates were shown to be accurate approximations of high-density CSDs at these locations, which adequately and quite sufficiently summarized group data. Moreover, reasonable approximations of many high-density scalp locations were obtained for group data from interpolations of low-density data. If group findings are the primary objective, as typical for cognitive ERP research, low-resolution CSD topographies may be as efficient, given the effective spatial smoothing when averaging across subjects and/or conditions. SIGNIFICANCE: Conservative recommendations for restricting surface Laplacians to high-density recordings may not be appropriate for all ERP research applications, and should be re-evaluated considering objective, costs and benefits.

Acoustic Stimulation↗
PubMed1994

Principal component analysis of gene frequencies and the origin of Basques.

The genetic peculiarity of the Basque population has long been noted. We aim to describe Basque distinctiveness in space and assess the internal Basque heterogeneity. All these aspects are relevant to the question of the origin of Basques. After a thorough literature search, a data base was created containing all the available data on gene frequencies in the Iberian Peninsula and France. Twenty-nine systems, comprising 71 alleles, were used to carry out a principal component (PC) analysis. The results show a sharp peak in the first PC in the Basque area, which remains even when the geographic scope is widened to include western Europe. As demonstrated by "wombling" analysis, the steeper slope in the first PC is found to the east of the Basque area, along the Pyrenees. Measures of genetic heterogeneity (such as FST values) within the Basque country, as compared to those for non-Basques, do not show a particular internal substructuration in the Basque population. The genetic results support a scenario in which the Basques are the product of in situ differentiation around the time of the Last Glacial Maximum (18,000 B.P.), in agreement with archaeological and linguistic data. Isolation from the surrounding populations has allowed the differentiation to last for millennia, but has erased the differences existing among Basques.

Alleles↗
PubMed2001

Facial expression of children receiving immunizations: a principal components analysis of the child facial coding system.

OBJECTIVE: To identify the structure of facial reaction to procedural pain and to determine the subset of facial actions that best describe the response. DESIGN: Observational. SETTING: Five rural and five urban physicians' offices. PATIENTS: One hundred twenty-three children aged 4 to 5 years undergoing routine diphtheria, pertussis, tetanus, and polio immunization. OUTCOME MEASURES: The Child Facial Coding System, comprising 13 discrete facial actions, was used to code each second of five 10-second phases from videotape: baseline, preneedle, needle, postneedle, and posthandling. Parents and a technician provided visual analog scale ratings of children's pain. Children provided a self-report using a Faces Pain Scale, and parents and nurses rated the children's pain and anxiety using visual analog scales. RESULTS: A "pain face" similar to that reported in adults emerged with the onset of pain. Principal component analyses revealed the frequency and intensity of facial action during the needle phase could be represented by components reflecting pain sensation, a "brave face," and the children's expectations for pain. Children's Faces Pain Scale and adult visual analog scale ratings were best predicted by components reflecting pain sensation and expectations of high pain. CONCLUSIONS: These results provide a preliminary indication that the Child Facial Coding System can be reduced to components that reflect several aspects of children's acute pain experience and predict self-reports and observer reports of children's pain.

Acute Disease↗
PubMed2005

Principal components analysis of Laplacian waveforms as a generic method for identifying ERP generator patterns: I. Evaluation with auditory oddball tasks.

OBJECTIVE: To evaluate the effectiveness and comparability of PCA-based simplifications of ERP waveforms versus their reference-free Laplacian transformations for separating task- and response-related ERP generator patterns during auditory oddball tasks. METHODS: Nose-referenced ERPs (31 sites total) were recorded from 66 right-handed adults during oddball tasks using syllables or tones. Response mode (left press, right press, silent count) and task was varied within subjects. Spherical spline current source density (CSD) waveforms were computed to sharpen ERP scalp topographies and eliminate volume-conducted contributions. ERP and CSD data were submitted to separate covariance-based, unrestricted temporal PCAs (Varimax) to disentangle temporally and spatially overlapping ERP and CSD components. RESULTS: Corresponding ERP and CSD factors were unambiguously related to known ERP components. For example, the dipolar organization of a central N1 was evident from factorized anterior sinks and posterior sources encompassing the Sylvian fissure. Factors associated with N2 were characterized by asymmetric frontolateral (tonal: frontotemporal R > L) and parietotemporal (phonetic: parietotemporal L > R) sinks for targets. A single ERP factor summarized parietal P3 activity, along with an anterior negativity. In contrast, two CSD factors peaking at 360 and 560 ms distinguished a parietal P3 source with an anterior sink from a centroparietal P3 source with a sharply localized Fz sink. A smaller parietal but larger left temporal P3 source was found for silent count compared to button press. Left or right press produced opposite, region-specific asymmetries originating from central sites, modulating the N2/P3 complex. CONCLUSIONS: CSD transformation is shown to be a valuable preprocessing step for PCA of ERP data, providing a unique, physiologically meaningful solution to the ubiquitous reference problem. By reducing ERP redundancy and producing sharper, simpler topographies, and without losing or distorting any effects of interest, the CSD-PCA solution replicated and extended previous task- and response-related findings. SIGNIFICANCE: Eliminating ambiguities of the recording reference, the combined CSD-PCA approach systematically bridges between montage-dependent scalp potentials and distinct, anatomically-relevant current generators, and shows promise as a comprehensive, generic strategy for ERP analysis.

Acoustic Stimulation↗
PubMed2003

A robust subspace algorithm for principal component analysis.

We present a noise robust PCA algorithm which is an extension of the Oja subspace algorithm and allows tuning the noise sensitivity. We derive a loss function which is minimized by this algorithm and interpret it in a noisy PCA setting. Results on the local stability analysis of this algorithm are given and it is shown that the locally stable equilibria are those which minimize the loss function.

Algorithms↗
PubMed2025

WinPCA: a package for windowed principal component analysis.

SUMMARY: With chromosomal reference genomes and population-scale whole genome-sequencing becoming increasingly accessible, contemporary studies often include characterizations of the genomic landscape as it varies along chromosomes, commonly termed genome scans. While traditional summary statistics like FST and dXY between pre-assigned populations remain integral to characterizing the genomic divergence profile, PCA differs by providing single-sample resolution, thereby supporting the identification of polymorphic inversions, introgression and other types of divergent sequence that may not be fully aligned with global population structure. Here, we introduce WinPCA, a user-friendly package to compute, polarize and visualize genetic principal components in windows along the genome. To accommodate low-coverage whole genome-sequencing datasets, WinPCA can optionally make use of PCAngsd methods to compute principal components in a genotype likelihood framework. WinPCA accepts variant data in either VCF or BEAGLE format and can generate rich plots for interactive data exploration and downstream presentation. AVAILABILITY AND IMPLEMENTATION: WinPCA is implemented in Python and freely available at https://github.com/MoritzBlumer/winpca and https://doi.org/10.5281/zenodo.15614979.

Software↗
PubMedDate not supplied

Comparison between neural networks (NN) and principal component analysis (PCA): structure activity relationships of 1,4-dihydropyridine calcium channel antagonists (nifedipine analogues).

The applicability of the neural network computer package PSDD (Perceptron Simulator for Drug Design/Perceptron-type Neural Network Simulator) in structure-activity relationship (SAR) studies was investigated. A group of 1,4-dihydropyridine derivatives was used in order to compare the PSDD results with those obtained previously with PCA. Calculated atomic and molecular descriptors using the semiempirical AM1 method were mainly used. It was shown that the predictive capability demonstrated by PSDD in SAR analysis were almost equivalent to that of PCA.

Algorithms↗