Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Principal component”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources
PubMed2005

On the slow convergence of EM and VBEM in low-noise linear models.

We analyze convergence of the expectation maximization (EM) and variational Bayes EM (VBEM) schemes for parameter estimation in noisy linear models. The analysis shows that both schemes are inefficient in the low-noise limit. The linear model with additive noise includes as special cases independent component analysis, probabilistic principal component analysis, factor analysis, and Kalman filtering. Hence, the results are relevant for many practical applications.

Algorithms↗
PubMed2004

Application of ab initio theory to QSAR study of 1,4-dihydropyridine-based calcium channel blockers using GA-MLR and PC-GA-ANN procedures.

The usefulness of the quantum chemical descriptors, calculated at the level of the RHF theory using 6-31G basis set for QSAR study of 1,4-dihydropyridine-based calcium channel antagonist was examined. A data set containing 45 dihydropyridine derivatives with known activity was used. Multiple linear regressions combined with genetic algorithm for variable selection and an artificial neural network model combined with principal component analysis for dimension reduction and genetic algorithm for factor selection (PC-GA-ANN) were employed. Some multiparametric MLR equations with good statistical quality were obtained for different classes of dihydropyridine derivatives. The resulting equations suggest that the electronic properties of the atoms belonging to the backbone of the molecules as well as the conformation of the molecules affect the binding of these molecules with their receptor. In the PC-GA-ANN, The principal components of the descriptors data matrix were used as the input of the neural network and then genetic algorithm was applied to select the most relevant set of principal components. Two ANN models with five selected principal components were obtained. These models, which have high statistical qualities, can predict the activity of the molecules with prediction errors lower than +/-5%.

Algorithms↗
PubMed1989

Components of the responses of a population of DSCT neurons determined from single-unit recordings.

1. Impulse activity of single units belonging to the dorsal spinocerebella tract (DSCT) was recorded in response to electrical stimulation of peripheral muscle nerves at group I intensities. The responses for 187 units were determined using a spike train analysis technique that facilitates the comparison of poststimulus response time course across units (response probability function, RPF; 16). 2. The poststimulus changes in impulse activity were represented in the waveform of the RPF. Principal component analysis was used to determine the component waveforms that were common to the responses across units. The analysis showed that there were a few waveforms that dominated the majority of the responses (85% of the total variability was accounted for by five principal component waveforms). 3. A cluster analysis based on three principal component waveforms revealed seven major groups of responses according to the patterns of their poststimulus activity. These response types were composed of different combinations of short- or long-latency excitation and inhibition. The same clusters were formed regardless of response amplitude or the source of the stimulus. 4. The responses were characterized by three general features, revealed by the first three principal components. The primary feature was the sign of the response, either mostly excitatory or inhibitory. The second feature was a distinction between a short- (up to 15 ms) and long- (approximately 30 ms) latency to peak response, and the third feature was the appearance of two separate phases of opposite sign in some of the responses.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2007

Multi-model statistical process monitoring and diagnosis of a sequencing batch reactor.

Biological processes exhibit different behavior depending on the influent loads, temperature, microorganism activity, and so on. It has been shown that a combination of several models can provide a suitable approach to model such processes. In the present study, we developed a multiple statistical model approach for the monitoring of biological batch processes. The proposed method consists of four main components: (1) multiway principal component analysis (MPCA) to reduce the dimensionality of data and to remove collinearity; (2) multiple models with a posterior probability for modeling different operating regions; (3) local batch monitoring by the T(2)- and Q-statistics of the specific local model; and (4) a new discrimination measure (DM) to identify when the system has shifted to a new operating condition. Under this approach, local monitoring by multiple models divides the entire historical data set into separate regions, which are then modeled separately. Then, these local regions can be supervised separately, leading to more effective batch monitoring. The proposed method is applied to a pilot-scale 80-L sequencing batch reactor (SBR) for biological wastewater treatment. This SBR is characterized by nonstationary, batchwise, and multiple operation modes. The results obtained for the pilot-scale SBR indicate that the proposed method has the ability to model multiple operating conditions, to identify various operating regions, and also to determine whether the biosystem has shifted to a new operating condition. Our findings show that the local monitoring approach can give more reliable and higher resolution monitoring results than the global model.

Biodegradation, Environmental↗
PubMed1986

Effects of delta 9-THC, the principal psychoactive component of marijuana, during pregnancy in the rhesus monkey.

The effect of delta 9-tetrahydrocannabinol (THC), the principal psychoactive component in marijuana, was studied in pregnant and lactating rhesus monkeys. THC (2.5 mg/kg/d) or vehicle was administered during different periods of gestation, and effects on pregnancy outcome and hormone concentrations during pregnancy were studied. The most obvious effects were observed with administration early in pregnancy; three of five pregnancies aborted within days after the drug injections began, and one pregnancy resulted in a stillbirth at term. The three abortions were associated with a rapid decrease in chorionic gonadotropin and a subsequent fall in progesterone concentrations to nondetectable levels. In the two pregnancies that continued until term, estradiol concentrations were significantly higher than in vehicle control pregnancies. Daily THC administration during the middle or third portion of gestation resulted in lesser pregnancy loss (one premature birth and four live births at term with THC treatment during the middle portion; two premature births and three live births at term with THC treatment during the third portion). All the premature infants died within two weeks of birth. The weights of the infants at birth and weaning were not significantly different for the infants from vehicle control pregnancies and for full-term infants exposed to THC during gestation. Also, no effects on intrauterine growth and development were detected with ultrasound in the drug-treated pregnancies. With acute administration, THC readily crossed the placenta at term in rhesus monkeys and was transferred into the milk of nursing mothers. Significant blood levels of THC and depressant effects were observed in both mothers and neonates when the drug was administered to the mothers one hour before birth or during lactation.

Abortion, Spontaneous↗
PubMed1981

A multivariate analysis of temporal change in Arikara craniometrics: a methodological approach.

We have examined temporal changes in the cranial architecture of Arikara Amerindians from five archaeological sites in South Dakota which span a time period of approximately 230 years (ca. A.D. 1600-1830). We have utilized a multivariate statistical method based on a principal components analysis of the pooled within-groups correlation matrix rather than the more traditional methods of ascertaining morphological relationships, e.g., discriminant functions, Mahalanobis' D2, or Penrose's Size and Shape. Our component structure, based on a regional sample and the mathematically simpler principal components analysis, is very similar to the factor structure obtained by Howells (1973) using a world-wide sample and factor analysis proper. This supports the notion of the "universality" of cranial structure. An axis of temporal variation was introduced into the component space by means of multiple regression. This analysis indicates that a substantial portion of the intergroup variation is temporal in nature and the systematic temporal changes occur along the facial height, transverse frontal flatness, and frontal profile flatness components. Earlier analyses of the same material by more conventional methods either did not detect the temporal trends at all or failed to isolate the specific nature of the temporal changes. The success of the present analysis attests to the value of examining morphological relationships be means of principal components.

Cephalometry↗
PubMed2005

Group I and II metabotropic glutamate receptors alter brain cortical metabolic and glutamate/glutamine cycle activity: a 13C NMR spectroscopy and metabolomic study.

Metabotropic glutamate receptors (mGluR) modulate neuronal function. Here, we tested the effect on metabolism of a range of Group I and II mGluR ligands in Guinea pig brain cortical tissue slices, applying 13C NMR spectroscopy and metabolomic analysis using multivariate statistics. The effects of Group I agonists (S)-3,5-dihydroxyphenylglycine (DHPG) and (RS)-2-chloro-5-hydroxyphenylglycine (CHPG) depended upon concentration and were mostly stimulatory, increasing both net metabolic flux through the Krebs cycle and glutamate/glutamine cycle activity. Only the higher (50 microm) concentrations of CHPG had the opposite effect. The Group I antagonist (RS)-1-aminoindan-1,5-dicarboxylic acid (AIDA), consistent with its neuroprotective role, caused significant decreases in metabolism. With principal components analysis of the metabolic profiles generated by these ligands, the effects could be separated by two principal components. Agonists at Group II mGluR [(2S,2'R,3'R)-2-(2',3'-dicarboxycyclopropyl)glycine (DCG IV) and 2R,4R-4-aminopyrrolidine-2,4-dicarboxylate (APDC)] generally stimulated metabolism, including glutamate/glutamine cycling, although this varied with concentration. The antagonist (2S)-alpha-ethylglutamic acid (EGLU) stimulated astrocyte metabolism with minimal impact on glutamate/glutamine cycling. (RS)-1-Aminophosphoindan-1-carboxylic acid (APICA) decreased metabolism at 5 microm but had a stimulatory effect at 50 microm. All ligand effects were separated from control and from each other using two principal components. The ramifications of these findings are discussed.

Animals↗
PubMed2006

The development of a standardized neighborhood deprivation index.

Census data are widely used for assessing neighborhood socioeconomic context. Research using census data has been inconsistent in variable choice and usually limited to single geographic areas. This paper seeks to a) outline a process for developing a neighborhood deprivation index using principal components analysis and b) demonstrate an example of its utility for identifying contextual variables that are associated with perinatal health outcomes across diverse geographic areas. Year 2000 U.S. Census and vital records birth data (1998-2001) were merged at the census tract level for 19 cities (located in three states) and five suburban counties (located in three states), which were used to create eight study areas within four states. Census variables representing five socio-demographic domains previously associated with health outcomes, including income/poverty, education, employment, housing, and occupation, were empirically summarized using principal components analysis. The resulting first principal component, hereafter referred to as neighborhood deprivation, accounted for 51 to 73% of the total variability across eight study areas. Component loadings were consistent both within and across study areas (0.2-0.4), suggesting that each variable contributes approximately equally to "deprivation" across diverse geographies. The deprivation index was associated with the unadjusted prevalence of preterm birth and low birth weight for white non-Hispanic and to a lesser extent for black non-Hispanic women across the eight sites. The high correlations between census variables, the inherent multidimensionality of constructs like neighborhood deprivation, and the observed associations with birth outcomes suggest the utility of using a deprivation, index for research into neighborhood effects on adverse birth outcomes.

Censuses↗
PubMed2001

Determination of the rotational diffusion tensor of macromolecules in solution from nmr relaxation data with a combination of exact and approximate methods--application to the determination of interdomain orientation in multidomain proteins.

In this paper we present a method for determining the rotational diffusion tensor from NMR relaxation data using a combination of approximate and exact methods. The approximate method, which is computationally less intensive, computes values of the principal components of the diffusion tensor and estimates the Euler angles, which relate the principal axis frame of the diffusion tensor to the molecular frame. The approximate values of the principal components are then used as starting points for an exact calculation by a downhill simplex search for the principal components of the tensor over a grid of the space of Euler angles relating the diffusion tensor frame to the molecular frame. The search space of Euler angles is restricted using the tensor orientations calculated using the approximate method. The utility of this approach is demonstrated using both simulated and experimental relaxation data. A quality factor that determines the extent of the agreement between the measured and predicted relaxation data is provided. This approach is then used to estimate the relative orientation of SH3 and SH2 domains in the SH(32) dual-domain construct of Abelson kinase complexed with a consolidated ligand.

Computer Simulation↗
PubMedDate not supplied

Fermentation diagnosis by multivariate statistical analysis.

During the course of fermentation, online measuring procedures able to estimate the performance of the current operation are highly desired. Unfortunately, the poor mechanistic understanding of most biologic systems hampers attempts at direct online evaluation of the bioprocess, which is further complicated by the lack of appropriate online sensors and the long lag time associated with offline assays. Quite often available data lack sufficient detail to be directly used, and after a cursory evaluation are stored away. However, these historic databases of process measurements may still retain some useful information. A multivariate statistical procedure has been applied for analyzing the measurement profiles acquired during the monitoring of several fed-batch fermentations for the production of erythromycin. Multivariate principal component analysis has been used to extract information from the multivariate historic database by projecting the process variables onto a low-dimensional space defined by the principal components. Thus, each fermentation is identified by a temporal profile in the principal component plane. The projections represent monitoring charts, consistent with the concept of statistical process control, which are useful for tracking the progress of each fermentation batch and identifying anomalous behaviors (process diagnosis and fault detection).

Biotechnology↗
PubMed2005

Comparative analysis of morphological diversity: does disparity accumulate at the same rate in two lineages of centrarchid fishes?

Evolutionary lineages differ with regard to the variety of forms they exhibit. We investigated whether comparisons of morphological diversity can be used to identify differences in ecological diversity in two sister clades of centrarchid fishes. Species in the Lepomis clade (sunfishes) feed on a wider range of prey items than species in the Micropterus clade (black basses). We quantified disparity in morphology of the feeding apparatus as within-clade variance on principal components and found that Lepomis exhibits 4.4 and 7.4 times more variance than Micropterus on the first two principal components. However, lineages are expected to diversify morphologically and ecologically given enough time, and this pattern could have arisen due to differences in the amount of time each clade has had to accumulate variance. Despite being sister groups, the age of the most recent common ancestor of Lepomis is approximately 14.6 million years ago and its lineages have a total length of 86.4 million years while the age of the most recent common ancestor of Micropterus is only about 8.4 million years ago, and it has a total branch length of 42.9 million years. We used the Brownian motion model of character evolution to test the hypothesis that time of independent evolution of each clade's lineages accounts for differences in morphological disparity and determined that the rates of evolution of the first two principal components are 4.4 and 7.7 times greater in Lepomis. Thus, time and phylogeny do not account for the differences in morphological disparity observed in Lepomis and Micropterus, and other diversity-promoting mechanisms should be investigated.

Adaptation, Biological↗
PubMed1994

[Multi-functional dementia rating scale: reliability and clinical validity].

A new rating method was designed to evaluate five symptoms of dementia; disorders of memory, cognition, language, visuospatial functions, and personality, which are defined as recent neuropsychological criteria for dementias by Cummings and Benson. Thirty-two items were made from the items of the Hasegawa dementia scale and neuropsychological tests. Scales for the five symptoms of dementia were then constituted of the items. In semi-structured interview, 113 demented patients and 16 normal elderly volunteers were rated. Interrater reliability of the five symptom scales were tested by ANOVA ICC and all the symptoms had a significant reliability. The scores of the five symptoms were correlated with each other and with the scores of the Hasegawa dementia scale. A Principal Component Analysis was applied to the scores of the five symptoms. The largest principal component had correlations with the scores of the Hasegawa dementia scale and the scores of the all five symptoms and was interpreted as a factor for severity of dementia. This component explains about 70% of total variance of the data. The other 30% of the variance were explained by four principal components which were interpreted as factors of the differences of the scores of the symptom scales. Relations between the scores of the symptoms and regional cerebral blood flow (rCBF) measured using SPECT were investigated in 25 moderately demented patients which met the criteria of probable Alzheimer's disease of NINCDS-ADRDA. rCBF was calculated as a ratio of 123I-IMP uptake of the areas to the mean uptake of right and left cerebellum. Significant correlations were found between the scores of memory symptom and the rCBF of the left temporal lobe (r = 0.59: p < 0.01) and between the scores of personality changes and the rCBF of the both frontal lobes (r = 0.58, 0.54: p < 0.01). Results suggest the possibility that the distribution of brain damage reflects symptoms in dementia and also supports the validity of analytic evaluation of dementia symptoms by this scale.

Aged↗
PubMed1993

Coplanar polychlorinated biphenyl congener levels and patterns and the identification of separate populations of harbor seals (Phoca vitulina) in Denmark.

Blubber samples from 21 harbor seals (Phoca vitulina), found dead on Danish beaches during the morbilli virus epidemic in 1988, have been analyzed for toxic coplanar chlorinated biphenyl (CB) congeners. The 21 samples consist of seven samples from 1-2-year-old animals (both males and females) from each of three geographical separate locations: The Limfjord, the Kattegat, and the Wadden Sea. The level of the CBs, defined as the sum of all the measured CB congeners, were highest in the samples from the Wadden Sea and lowest in the Limfjord samples. The quotient between highest level and lowest level was 4. Toxic equivalency factors given by Safe (1990) was used for calculation of the contribution to dioxin-like toxicity from the coplanar CB congeners, and the result was compared to literature data on polychlorinated dibenzo-p-dioxins and -dibenzofurans in harbor seal. CB congeners CB-118, CB-156, CB-157, and CB-105 were major contributors to sigma TEQ in all samples. The patterns of polychlorinated biphenyl congeners in harbor seals from the three locations were compared by principal component analysis. The two first principal components could separate the samples in groups corresponding to each of the three geographical locations. The geographical and biological variations were estimated from the data. It was shown, that the geographical variation was the largest. Possible reasons behind the geographical variation in CB congener patterns are discussed.

Adipose Tissue↗
PubMed1992

Growth of the cranial bones in human fetuses (2nd and 3rd trimesters).

The increase of the weight of some cranial bones was studied in 30 human fetuses (from 17 to 41 weeks of gestation, both sexes together) by multivariate allometry. The study was performed with a covariance matrix of the log-transformed bony weights and the Principal Components Analysis (PCA). The first principal component in PCA accounted for 92.12% of the total variance, and all characters were positively correlated with this component. PCA scaled the growth of the bones in the following sequence: a) with negative allometry: vomer, palatine, mandible and maxillae; b) with isometry (p less than 0.05): zygomatic bone; c) with positive allometry: sphenoid, ethmoid, frontal, occipital, temporal and parietal. During the 2nd and 3rd trimesters of gestation the skull exhibited two different growth rates, i.e., the bony group of the facial skeleton presented lower eigenvalues than the bony group of the calvaria, including the base of the skull. These bones of the calvaria certainly are affected by the high increase in volume of the fetal brain during the prenatal life. The knowledge of the cranial growth is a useful information for the anatomy, anthropology, orthodontics, and several medical specialties: radiology, obstetrics, pediatrics, orthopedics and reconstructive surgery.

Cephalometry↗
PubMed1985

A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids.

The 20 naturally occurring amino acids are characterized by 20 variables: pKNH2, pKCOOH, pI, molecular weight, substituent van der Waals volume, seven 1H and 13C nuclear magnetic resonance shift variables, and eight hydrophobicity-hydrophilicity scales. The 20-dimensional data set is reduced to a few new dimensions by principal components analysis. The three first principal components reveal relationships between the properties of the amino acids and the genetic code. Thus the amino acids coded for by adenosine (A), uracil (U), or cytosine (C) in their second codon position (corresponding to U, A, or G in the second anticodon position) are grouped in these components. No grouping was detected for the amino acids coded for by guanine (G) in the second codon position (corresponding to C in the second anticodon position). The results show that a relationship exists between the physical-chemical properties of the amino acids and which of the A (U), U (A), or C (G) nucleotide is used in the second codon (anticodon) position. The amino acids coded for by G (C) in the second codon (anticodon) position do not participate in this relationship.

Amino Acids↗
PubMed2006

Interfollicular fibrosis in the thyroid of the harbour porpoise: an endocrine disruption?

Previous studies have described high levels of polychlorobiphenyls (PCB), polybrominated diphenylether (PBDE), toxaphene, p,p'-dichlorodiphenyltrichloroethane (DDT), and p,p'-dichlorodiphenyldichloroethylene (DDE) in the blubber of the harbour porpoise from the North Sea raising the question of a potential endocrine disruption in this species. In the present study, the thyroids of 57 harbour porpoises from the German and Danish (North and Baltic Seas), Norwegian, and Icelandic coasts have been collected for histological and immunohistological investigations. The number of follicles and the relative distribution of follicles, connective, and solid tissues (%) were quantified in the thyroid of each individual. Then, the potential relationship between the thyroid morphometry data and previously described organic compounds (namely, PCB, PBDE, toxaphene, DDT, and DDE) was investigated using factor analysis and multiple regressions. Thyroid morphology differed strongly between sampling sites. Porpoises from the German (North and Baltic Seas) and Norwegian coasts displayed a high percentage of connective tissues between 30 and 38% revealing severe interfollicular fibrosis and a high number of large follicles (diameter>200 microm). A correlation-based principal component analysis (PCA) revealed two principal components explaining 85.9% of the total variance. The variables PCB, PBDE, DDT, and DDE compounds loaded highest on PC1 whereas toxaphene compound loaded most on PC2. Our results pointed out a relationship between PC1 (PCBs, PBDE, DDE, and DDT compounds) and interfollicular fibrosis in the harbour porpoise thyroids. Such an association is not alone sufficient for a cause-effect relationship but supports the hypothesis of a contaminant-induced thyroid fibrosis in harbour porpoises raising the question of the long-term viability in highly polluted areas.

Animals↗
PubMed2005

Pollution topography of chlorobenzenes and hexachlorobutadiene in sediments along the Kaohsiung coast, Taiwan--a comparison of two consecutive years' survey with statistical interpretation.

Forty sediments were analyzed for chlorobenzenes (CBs) and hexachlorobutadiene (HCBD) to investigate their pollution topography along the Kaohsiung coast, Taiwan. Maximum CB concentrations found, varied from 15.4ng/gdw for 1,2,3-TCB to 56.8ng/gdw for 1,2,4-TCB, while higher HCBD concentrations were detected among north-bound stations (around the exit of the Tsoying outfall pipe) and its concentration decreases from north to south. Compared to a previous survey executed a year before, there is no statistically significant difference in CB and HCBD congeners between these two surveys (p = 0.68-0.87, two-tailed paired t-test). The spatial distribution of toxic index reveals that biological effects might occur near Tsoying and Dalinpu outfall pipe outlets which dispose of petro-chemical wastewater. Evidence found in this study also shows distinct CB patterns from the two nearby sources, the Dalinpu outfall pipe outlet and the Kaoping estuary. Principal component analysis shows that four principal components conducting CBs and HCBD distribution were extracted. Both the first two components (accounted for 58.8% of the total variance), comprised all of the CBs except HCB (DCBs to PeCB), were found not capable of differentiating any distinct pollution source. On the other hand, HCBD and HCB were extracted as third and fourth components, respectively, pointing out their distinct sources in this area.

Butadienes↗
PubMed2002

UV-VIS spectroscopy of 2,4,6-trinitrotoluene-hydroxide reaction.

Contamination of groundwater, surface water and soil by explosives has occurred at military sites throughout the world as a result of manufacture of explosive compounds, assembly of munitions, and deployment of explosives containing devices. Due to the adverse effects of explosives on humans and other natural receptors, a low cost means of decontaminating these areas of contamination is needed. Base-induced transformation of explosives has shown promise as a rapid, low cost, and minimally resource-intensive technology for detoxifying explosives in soil and water. In order to understand the reaction mechanism, a reaction mixture of 2:1:1 (water:2,4,6-trinitrotoluene (TNT):1 N KOH) was analyzed by UV/VIS spectrometry from 190 to 1,100 nm. Time course measurements were conducted at 25, 20, 15, and 12 degrees C. A factor analysis program was used to analyze the spectral data. Principal component analysis indicated that six principal components explained the spectra to within experimental error, with four factors explaining the majority of the variance. Test spectral vectors for four components were developed, including TNT, two intermediates, and the final product, and were tested against the abstract vectors. Two possible reaction mechanisms were suggested and tested to explain the spectral data.

Hydroxides↗