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PubMed1986

Carotid artery blood flow: single factor classification of Doppler waveforms.

The usefulness of principal components factor analysis as a way of classifying Doppler waveforms from the carotid artery has been established. The waveform is first reduced to a small set of coefficients which capture, via their associated principal components, the essential shape of the waveform. The vector of these coefficients can be used to classify the waveform by finding the position of this vector in a classification space relative to one or more classifying surfaces. This short communication will show how these two steps may be combined to produce a single factor for classification.

Carotid Arteries↗
PubMed2003

Measuring outcomes of undergraduate medical education: residency directors' ratings of first-year residents.

PURPOSE: There is a growing recognition of the need to show the relationship between undergraduate medical education (UME) and achievements during residency. This study provides reliability and validity evidence for a residency rating scale as well as a method for gathering comparison information about first-year residents. METHOD: A 25-item rating scale measuring important areas of physician functioning was mailed to residency directors of 485 graduates of the 1998-2000 classes of the University of Kansas School of Medicine. The same rating scale was sent to residency directors for a comparison sample of 251 graduates of other U.S. medical schools who were residents at the University of Kansas Medical Center. Each item on the rating scale was rated on a five-point Likert scale. Principal-components analysis, correlational analyses, internal consistency reliability analysis, and mean comparisons were used to provide evidence of reliability and validity. RESULTS: A total of 382 (82%) usable rating scales were returned. A principal-components analysis extracted five factors that accounted for 86% of the variance. The final factors were (1) interpersonal communication, (2) clinical skills, (3) population-based health care, (4) record-keeping skills, and (5) critical appraisal skills. The internal consistency of the entire scale was.98, with coefficients for the five factors ranging from.92 to.97. The correlations between the five factors and measures of undergraduate performance ranged from.21 to.49. Group analyses revealed that residents with high GPAs and USMLE Step 1 and Step 2 scores tended to be rated higher than those with lower scores. CONCLUSIONS: The rating scale demonstrated adequate reliability and validity and showed that residency directors' ratings are a useful outcome measure for UME performance.

Academic Medical Centers↗
PubMed1996

Representation of olfactory information in the primate orbitofrontal cortex.

1. To analyze the information represented about individual odor stimuli in the responses of single olfactory neurons in the primate orbitofrontal area, neuronal responses were measured to a set of seven to nine odorants in macaques performing an olfactory discrimination task. The population of neurons analyzed had responses that were significantly differential to the odorants. 2. Information theoretic analyses were applied to the responses of the neurons, and information measures were calculated from the firing rate of the responses and from the principal components of the responses. The information reflected by the firing rate of the response accounted for the majority of the information present (86%) when compared with the information derived from the first three principal components of the spike train. This indicated that temporal encoding had a very minor role in the encoding of olfactory information by single orbitofrontal olfactory cells. 3. The average information about which odorant was presented, averaged across the 38 neurons, was 0.09 bits, a figure that is low when compared with the information values previously published for the responses of temporal lobe face-selective neurons. 4. Application of information theoretic analyses to the responses of these neurons showed how much information about which stimulus was delivered was present in the responses of individual neurons. It was found that for the majority of the neurons significant amounts of information were reflected about one or two of the odorants presented. 5. For each neuron, the information reflected in the responses of that neuron about the reinforcement value and the information about the identity of the odorants were calculated. It is shown that many neurons carry information about which of the odorants was presented; in addition, some neurons reflect information only about the taste association of the stimuli and not about odorant identity. 6. Measurements of the sparseness of the representation indicated that a broadly distributed representation of the identity of odorants was present in this population of neurons.

Animals↗
PubMed2025

Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.

BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings. METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types. RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings. CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.

Animals↗
PubMed1998

Postural hand synergies for tool use.

Subjects were asked to shape the right hand as if to grasp and use a large number of familiar objects. The chosen objects typically are held with a variety of grips, including "precision" and "power" grips. Static hand posture was measured by recording the angular position of 15 joint angles of the fingers and of the thumb. Although subjects adopted distinct hand shapes for the various objects, the joint angles of the digits did not vary independently. Principal components analysis showed that the first two components could account for >80% of the variance, implying a substantial reduction from the 15 degrees of freedom that were recorded. However, even though they were small, higher-order (more than three) principal components did not represent random variability but instead provided additional information about the object. These results suggest that the control of hand posture involves a few postural synergies, regulating the general shape of the hand, coupled with a finer control mechanism providing for small, subtle adjustments. Because the postural synergies did not coincide with grip taxonomies, the results suggest that hand posture may be regulated independently from the control of the contact forces that are used to grasp an object.

Adult↗
PubMed2004

How rheumatologists and patients with rheumatoid arthritis discuss exercise and the influence of discussions on exercise prescriptions.

OBJECTIVE: To describe how patients and their rheumatologists discuss exercise, and to identify predictors of exercise prescriptions. METHODS: Twenty-five rheumatologists and 132 patients with rheumatoid arthritis completed questionnaires and were audiotaped during a subsequent clinic visit. Chi-square and t-tests assessed associations between variables. Principal components analysis identified patterns of talk about exercise. Multivariate logistic regression identified predictors of an exercise prescription. RESULTS: Seventy of the 132 patients (53%) discussed exercise. Of these, 18 (26%) received an exercise prescription. Principal components analysis identified 3 patterns of talk about exercise. Aerobic exercise discussions contained more information about drawbacks, side effects, pain, and bargaining than did discussions about general exercises, and referral to physical therapy for exercise. Significant predictors of a prescription included rheumatologist-initiated discussion about exercise (odds ratio [OR] 4.6; P = 0.03); talk about exercise in improving function, exercise instructions, opinions about the usefulness of exercise (OR 3.1; P = 0.01); and discussions about non-exercise treatments (OR 1.6; P = 0.01). CONCLUSION: Exercise and referral to physical therapy for exercise are discussed differently and are 4 times more likely to occur when the rheumatologist initiates the discussion. These discussions strongly impact on the likelihood a patient receives an exercise prescription.

Adult↗
PubMed2002

Comparison of methods for characterization of reversed-phase liquid chromatographic selectivity.

The goal of the present work is to obtain a better understanding of the chemical factors affecting liquid chromatographic retention. One of the most commonly used formats for liquid chromatographic separations is based on a nonpolar stationary phase, typically an octadecyl-derivatized silica material. A wide variety of these reversed-phase columns are commercially available that differ significantly in their chromatographic retention and selectivity. We seek to quantitatively characterize these differences. Retention data for a range of compounds with many diverse characteristics have been measured on several different octadecyl silica columns (J. Chromatogr. A, submitted for publication). Principal components analysis is used to characterize the different properties of these stationary phases and predict retention factors. The key set factor analysis method and the typical solute method are used in conjunction with the principal components analysis to identify small subsets of solutes that can be used to quantitatively describe the retention of a broad range of compounds. In addition, a quantitative comparison to alternative data analysis methods is made, including linear solvation energy relationships and an iterative subtraction method based on linear regression techniques. Although many earlier studies have reported the application of these methods, this study is the first to make a quantitative comparison of these methods using a highly precise and structurally variable set of test compounds.

Chromatography, Liquid↗
PubMed1993

Recent advances in structure and function of food proteins: QSAR approach.

QSAR (quantitative structure-activity relationship), widely used in chemistry with hydrophobic, electronic, and steric parameters as structural factors, was found to be appropriate for use with food proteins, despite the difficulty, due to the complexity in macromolecular structure, in defining the steric terms. Emulsifying ability was closely related to hydrophobicity, and incorporation of solubility to hydrophobicity as factors improved the R2 of regression analysis. Foaming activity required both hydrophobicity and other factors pertaining to the adsorption of proteins at the interface in order to obtain adequate foam lamella strength. Hydrophobicity as well as other factors relating to the intermolecular interactions, for example, Ca and SH are involved in thermally induced gelation. For breadmaking, although no extensive QSAR work had been carried out, the important function of high molecular glutenin subunits was confirmed, and, notably, the critical function of hydrophobicity in breadmaking also was demonstrated. PLS (partial least-squares regression) and neural networks classify more correctly than other multivariate techniques, thereby yielding higher r2 values in modeling and prediction. However, multiple regression analysis and PCR (principal component regression) also were found to be effective for modeling because the information useful in elucidating the mechanism of protein function could be readily obtained. A characteristic property of unsupervised learning techniques, especially PCS (principal component similarity analysis), in identifying influential factors in the function mechanisms was demonstrated.

Bread↗
PubMed2000

Magnetoencephalographic characterization of sleep spindles in humans.

Sleep spindles in EEG recordings of adults are most prominent over the central and frontal midline regions. Early magnetoencephalographic recordings agreed with conventional EEG findings. However, more recent small-array magnetoencephalography and quantitative EEG studies suggest that the source areas for spindles are more widespread. We used a whole-head 122-channel biomagnetometer to characterize the sources of sleep spindles in four normal volunteers. Parallel interactive and automated multiple dipole spatiotemporal source modeling was conducted on the data sets of 10 spindles from each subject. Principal component analysis was used to estimate the number of sources in interactive source modeling, and singular value decomposition was used in automated dipole modeling. Spectral analysis of the epochs containing sleep spindles was performed. Principal component analysis and singular value decomposition suggested that all sleep spindles were made up of activity from multiple sources. Similarly, interactive and automated multiple dipole source modeling showed that three or more sources were present in 75% of spindle bursts. The sources for sleep spindles localized to all four cerebral lobes. Parietal and frontal lobes were the areas most frequently involved. Interactive source modeling resulted in more frequent temporal lobe than occipital dipole localizations; automated source modeling showed more frequent occipital than temporal sources. Spindle source localizations varied across subjects and across different spindles within subjects. Our results indicate that individual sleep spindles are generated by multiple cortical sources that are widespread within and across individuals.

Adolescent↗
PubMed1995

Expressive timing in Schumann's "Träumerei:" an analysis of performances by graduate student pianists.

Statistical analyses were conducted on the expressive timing patterns of performances of Schumann's "Träumerei" by ten graduate student pianists who played from the score on a Yamaha Disclavier after a brief rehearsal. A previous study of acoustic recordings of "Träumerei" by 24 famous pianists [B. H. Repp, J. Acoust. Soc. Am. 92, 2546-2568 (1992)] provided "expert" timing data for comparison. In terms of group average timing pattern, individual shaping of ritardandi, and within-performance consistency, the students turned out to be quite comparable to the experts. This demonstrates that precision in expressive timing does not require extensive study and practice of the music at hand, only general musical and technical competence. Subsequent principal components analyses on the students' timing patterns revealed that they were much more homogeneous than the experts'. Individual differences among student pianists seemed to represent mainly variations around a common performance standard (the first principal component), whereas expert performances exhibited a variety of underlying timing patterns, especially at a detailed level of analysis. Experienced concert artists evidently feel less constrained by a performance norm, which makes their performances more interesting and original, hence less typical. Since the norm may represent the most natural or prototypical timing pattern, relatively spontaneous performances by young professionals may be a better starting point for modeling expressive timing than distinguished artists' performances.

Adult↗
PubMed1991

Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization.

The BLOLOG redox technology based on tetrazolium dye reduction as an indicator of sole-carbon-source utilization was evaluated as a rapid, community-level method to characterize and classify heterotrophic microbial communities. Direct incubation of whole environmental samples (aquatic, soil, and rhizosphere) in BIOLOG plates containing 95 separate carbon sources produced community-dependent patterns of sole-carbon-source utilization. Principal-component analysis of color responses quantified from digitized images of plates revealed distinctive patterns among microbial habitats and spatial gradients within soil and estuarine sites. Correlation of the original carbon source variables to the principal components gives a functional basis to distinctions among communities. Intensive spatial and temporal analysis of microbial communities with this technique can produce ecologically relevant classifications of heterotrophic microbial communities.

Journal Article↗
PubMed1985

Methods of analysis of large numbers of audiograms.

The analysis of large numbers of audiograms raises the question if and how we can reduce the amount of data without discarding essential information. The present paper compares two ways of data reduction: principal-component analysis and curve fitting. The methods are tested on the audiograms of a large family suffering from a dominant hereditary, progressive hearing loss, beginning in the high frequencies. It is shown that principal-component analysis rejects information on the shape of the audiogram, as do all methods generally referred to as factor analysis. The information concerned is essential for our understanding of the patient's ability to discriminate speech. Curve-fitting procedures are shown to be effective in data reduction.

Audiometry↗
PubMed2026

Pilot study identifying distinct circulating proteomic profiles associated with longitudinal CT-defined fibrotic and inflammatory sarcoidosis.

INTRODUCTION: Pulmonary sarcoidosis exhibits heterogeneous clinical trajectories ranging from self-limited disease resolution to chronic progressive fibrosis, yet reliable biomarkers capable of distinguishing these disease patterns remain lacking. Whether longitudinal CT-defined sarcoidosis phenotypes are associated with distinct circulating molecular signatures remains unknown. METHODS: We performed high-throughput plasma proteomics (SomaScan 11K) in participants with pulmonary sarcoidosis classified into longitudinal chest CT-defined progressive fibrosis, progressive nodular inflammatory disease, or resolving disease trajectories, along with healthy controls. CT phenotypes were assigned based on predefined longitudinal changes in reticulation, traction bronchiectasis, nodular involvement, and mediastinal lymphadenopathy across serial CT scans. One plasma sample per participant was selected from the study visit corresponding to the CT time point at which criteria for the assigned longitudinal phenotype were met. Principal component analysis, hierarchical clustering, pathway enrichment, and correlation-based analyses linking protein expression to quantitative CT features were used to evaluate whether distinct longitudinal CT phenotypes were associated with divergent proteomic signatures. RESULTS: Principal component analysis and hierarchical clustering suggested partial segregation by CT-defined phenotype. Longitudinal CT phenotypes were associated with distinct pathway-level proteomic signatures, with progressive fibrosis enriched for epithelial-mesenchymal transition signaling, and progressive nodular inflammatory disease enriched for mTORC1, MYC, oxidative phosphorylation, adipogenesis, and fatty acid metabolism pathways. Correlation analyses showed coordinated protein-expression patterns associated with fibrotic CT features and mediastinal lymph node enlargement. DISCUSSION: These findings suggest that longitudinal CT-defined fibrotic and inflammatory sarcoidosis phenotypes are associated with distinct pathway-level proteomic signatures. This pilot study provides preliminary proof-of-concept evidence that integrating longitudinal CT imaging phenotypes with plasma proteomics may serve as a framework for future mechanistic studies and biomarker discovery in pulmonary sarcoidosis.

Humans↗
PubMed1996

Muscle biopsy as a tool for assessing muscular adaptation to training in horses.

OBJECTIVE: To describe an applied method for quantitative estimation of training condition in horses. ANIMALS: 17 sedentary adult (5 to 14 years old) stallions of several breeds endurance trained for 3 months. PROCEDURE: Muscle biopsy specimens from 2 depths (20 and 60 mm) of the gluteus medius muscle were obtained before and after training and were analyzed for fiber type distribution, mean cross-sectional area, relative fiber area, and mean number of capillaries in contact with each fiber type relative to their mean area. Fiber types were designated as types 1, 2A, and 2B (high, low, and moderate myosin ATPase activities at pH 4.5, respectively). Data were subjected to discriminant and principal component analyses. RESULTS: 77% of the observations were correctly discriminated according to training condition of horses by use of discriminant analyses when histochemical and morphometric data from the 2 muscle biopsy specimens were used. Principal component analysis indicated that the most efficient variables describing muscular adaptation to training are fiber area and number of capillaries in contact with type-1 and type-2A fibers, particularly from the deepest sampling site of the muscle. CONCLUSION: It is possible to satisfactorily classify an individual horse in a given training category on the basis of a physiologic muscle index. CLINICAL RELEVANCE: These methods could become a useful aid for evaluation of the individual horse's response to training.

Acclimatization↗
PubMed1983

Middle and long latency auditory evoked potentials in cat. I. Component definition and dependence on behavioral factors.

Middle (10-50 ms) and long (50-600 ms) latency auditory evoked potentials (AEPs) were investigated in artificially respired, muscle-paralyzed cats. Similarity to human potentials of comparable latencies was examined in two ways: (1) the similarity of waveform features such as peak amplitude, polarity and latency, and (2) the effects of task-related variables on these various waveform features. Four behavioral variations of a classical pupillary conditioning paradigm were used to vary attention and arousal. Twelve peaks and troughs were identified in the AEP: P10, N13, P17, N22, P31, N41, P55, N70, N100, N140, P260 and N520. Principal components analysis (PCA) defined 7 AEP components, some of which spanned several peaks. Analysis both of peak latencies and amplitudes, and of principal component scores, revealed differential effects of the behavioral manipulations on these components: those with latencies longer than 50 ms were strongly influenced by behavioral variations, while earlier components were relatively immune to these effects. On the basis of these findings, several relationships between cat and human AEP components were suggested. Specifically, peaks P10-P41 in the cat were thought related to human middle latency components, cat P55 to human P50, cat N140 to human N300, and cat P260 to human P300. Cat N520 was comparable to several long latency components in humans. No obvious correspondences between cat AEP components and human N90 and P170 were identified.

Acoustic Stimulation↗
PubMedDate not supplied

Genetics of human body size and shape: complex segregation analysis.

The genetic component in a mixed heritability model, including major gene, multifactorial and sibling environment transmissible components, was studied for some 20 anthropometric traits in two ethnically different samples. The first sample comprised 305 Mexican nuclear families, and the second comprised 83 Ashkenazi Jewish nuclear families living in Israel. All variables, after adjustment for age and sex, were subjected to principal-components analysis (PCA) in each sample separately. The mixed model of inheritance as implemented in the computer program POINTER was used in the present study. An attempt was made to evaluate genetic effects in the variation of the first principal components (PCs). PCA showed a clear separation of variables and was easily interpretable. The PC1 was a credibly general size factor. This factor alone accounted for about 30% of the total variance. Other components are rather shape factors for various combinations of traits. The testing of several genetic hypothesis showed the following: (1) For all factor scores the genetic component was high and statistically significant. (2) In a Mexican sample, for PC1 and PC2, both major gene and polygenes contributed significantly to the total variation of these variables; in the major locus the alleles were most probably codominant. (3) For all other PCs the major gene effect hypothesis was rejected, with more than 50% of the variation attributable to the polygenes contribution. (4) No evidence was found for sibling environmental resemblance in either sample.

Adolescent↗
PubMed1995

Determination of body heat storage in clothing: calorimetry versus thermometry.

Two methods of estimating body heat storage were compared under differing conditions of clothing, training, and acclimation to heat. Six male subjects underwent 8 weeks of physical training [60-80% of maximal aerobic power (VO2max) for 30-45 min.day-1, 3-4 days.week-1 at < 25 degrees C dry bulb (db)] followed by 6 consecutive days of heat acclimation (45-55% VO2max for 60 min.day-1 at 40 degrees C db, 30% relative humidity)]. Nine other male subjects underwent corresponding periods of control observation followed by heat acclimation. Before and after each treatment, subjects walked continuously on a treadmill (1.34 m.s-1, 2% grade) in a climatic chamber (40 degrees C db, 30% relative humidity) for an average of 118 min (range 92-120 min) when wearing normal light combat clothing and for an average of 50 min (range 32-68 min) when wearing protective clothing resistant to nuclear, biological, and chemical agents. The heat storage was determined calorimetrically (by the balance of heat gains and losses) and thermometrically [by the conventional equations, using one or two set(s) of relative weightings for the rectal temperature (Tre) to mean skin temperature (Tsk) of 4:1 and 4:1, 2:1 and 4:1, or 2:1 and 9:1 in thermoneutral and hot environments, respectively]. Tsk was calculated from 12-site measurements, weighted according to the regional distribution of body surface area and the first eigenvectors of principal component analysis. There were only minor differences (< 5%) between the heat storage values calculated by given weighting factors for Tre and Tsk, whether the individual coefficients were derived from estimates of regional surface area or principal component methodologies. When wearing normal clothing, no significant differences were found between the two estimates of heat storage (calorimetry vs thermometry with an invariant relative weighting of 4:1) in any experimental condition, with one specific exception: when wearing protective clothing, thermometry underestimated the heat storage by 24-31%. This under-estimation was attenuated by using two sets of relative weightings of 2:1 and 4:1 or 2:1 and 9:1. The results suggest that when subjects wearing protective clothing are transferred from thermoneutral to hot environments, the accuracy of thermometric estimates of heat storage can be improved by using two sets of weighting factors for Tre and Tsk.

Adult↗
PubMed1989

Relationships between human parotid saliva lysozyme lactoferrin, salivary peroxidase and secretory immunoglobulin A in a large sample population.

Saliva antimicrobial proteins may interact in a common system for host defence. This study applied multivariate analysis as a means of describing inter-person variation in that system. Samples of stimulated parotid saliva were obtained from 198 subjects. Flow rate was determined, and assays run for total protein, lysozyme, lactoferrin, salivary peroxidase and secretory IgA. Correlation and principal components analysis were used to define the relationships between proteins; cluster analysis was used to identify persons with similar protein concentration profiles. All proteins were significantly correlated at p less than 0.002 (r = 0.20-0.52). Principal components analysis identified a major axis of common variation, defined by lysozyme and salivary peroxidase, and a second axis, defined by secretory IgA. Lactoferrin was associated with both axes. Seven major groupings were obtained by cluster analysis; these were significantly different at p less than 0.001. Such groupings may prove useful in comparing the antimicrobial properties of saliva samples.

Adolescent↗