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Comparative analysis of dermatoglyphic traits in Hungarian and Gypsy populations.

We examined dermatoglyphic prints of children in 11 Hungarian and 5 Gypsy population samples (collected from 1,998 children). We compared Hungarian and Gypsy populations based on 22 finger and 24 palmar traits. In univariate comparisons the two ethnic groups differed significantly in half of the studied variables (9 finger and 14 palmar traits). We used several types of multivariate analyses of the studied traits to separate the population samples. Homogeneity analysis and discriminant analysis proved to be the most appropriate method to distinguish the populations, whereas a principal components analysis was less adequate. Multivariate analyses were conducted separately for both finger and palmar traits. Although the differences between the populations were more pronounced for palmar traits, in our study Hungarian and Gypsy populations showed the best separation when finger and palmar traits were combined for analysis, except in the principal components analysis. As expected, the Hungarian and Gypsy populations separated definitely in most statistical analyses; the main reason for this is the different origins of the two ethnic groups. The existence of the difference also shows that admixture between Hungarians and Gypsies has been small despite their living beside one another for several centuries.

Adolescent↗

[Community succession patterns of pests and natural enemies in jujube orchard ecosystem].

Through investigation and by the methods of optimal partitioning, principal component analysis, and one-or two-dimensional ordination, this paper analyzed the main groups and succession trends of the pest and natural enemy communities at a jujube orchard of Taigu area. The results showed that the communities had more obvious dominant factors and temporal succession pattern. The first three principal components of the communities had a bigger variation, with an obvious follow effects. The community succession was temporally divided into four stages, i. e., in the periods of pre-budding, leaf expanding and blooming, fruiting, and maturing. The dominant species of pests and their natural enemies were demonstrated.

Animals↗

Quantitative taste evaluation of total enteral nutrients.

The purpose of this study was to evaluate quantitatively the taste of the various total enteral nutrients marketed in Japan using human gustatory sensation tests and an artificial taste sensor. In the human gustatory sensation test, four basic taste intensities (sweetness, saltiness, sourness, and bitterness), as well as 15 kinds of palatability scales, were evaluated according to the semantic differential (SD) method. Among 15 palatability items, the item; difficult to drink/easy to drink, was adopted as an overall palatability since it shows the highest factor loading by factor analysis. The overall palatability was found to be highly positively correlated with sweetness and sourness, but negatively correlated with bitterness and saltiness. Addition of a flavour to the amino acid-based enteral nutrient AminolebanEN significantly improved its palatability. This effect is presumably due to sour components of the flavour, such as citric acid, which reduce the bitterness intensity of branched-chain amino acids in the product. The sweetness and sourness intensities predicted by the taste sensor showed a high correlation with the results obtained in the human gustatory sensation tests. The taste sensor was able to predict the overall palatability of the total enteral nutrients with high accuracy. The products could be classified into three groups (peptide-based, amino-acid-based, and protein-based) by principal component analysis using sensor output of 8 channels. The products could be also classified into four groups; peptide-based, amino-acid-based, and protein-based and flavor addition group by principal component analysis using sensor output of channels 1, 3, 4 and 7, which are specific to basic tastes. The taste sensor could therefore be useful in predicting the taste or palatability of total enteral nutrients, and could contribute to attempts to improve compliance for such products and for enteral nutrients.

Biosensing Techniques↗

Quantitative kinetics of damage and recovery of cytoskeletal structure by means of image analysis.

The cytoskeleton is a network of proteins which structurally and dynamically organise the cytoplasm of living cells. Microtubules are among its constituents. Morphological alterations of microtubules are related to functional impairment. Therefore cytoskeletal morphology is a valuable indicator of cell injury and functionality. This paper focuses on the comparison between normal and altered cytoskeletal microtubules by means of image analysis and classification with the aim of replacing visual assessment. Morphology has been quantified by the extraction of some descriptors yielded by spatial differentiation, fractal analysis and Fourier analysis followed by non-linear filtering. The principal component analysis of these descriptors has led to image recognition and has been applied to hepatocytes and fibroblasts exposed to some xenobiotics. In the case of hepatocytes, images have been ranked according to the severity of cytoskeletal damage, a dose-response relation has been derived from the regression of the first principal component and the percentage of structural recovery after exposure has been estimated.

Algorithms↗

Serum concentration of human alpha 2 HS glycoprotein during the inflammatory process: evidence that alpha 2 HS glycoprotein is a negative acute-phase reactant.

A nonspecific opsonin function has been ascribed to human alpha 2 HS glycoprotein. Its serum level has been shown to be decreased in trauma patients. Recent studies from this laboratory revealed a heterogeneity among the products obtained in the course of the preparation of the protein. To date, no definitive agreement existed with regard to a molecular homogeneous entity of alpha 2 HS glycoprotein (Ba-alpha 2 glycoproteins). The purpose of the current work was to study the variations in serum level of alpha 2 HS in patients suffering from an acute inflammatory process of bacterial etiology and to determine whether a decrease in alpha 2 HS was accompanied by the appearance of fragments of this protein in the serum. A method of preparing alpha 2 HS was thus developed, using an immune absorbent as a final purification step. In an intermediary step of the preparation, alpha 2 HS was found to bind zinc when metal chelate affinity chromatography was employed. Immunologically and physico-chemically pure alpha 2 HS was obtained. The protein consists of a unique polypeptide chain of about 50,000 daltons and has a unique amino-terminal residue, alanine. However, the protein maintained its molecular integrity with difficulty, and spontaneous fragments ranging from 30,000 to less than 10,000 daltons were produced in some of the preparations. No major modification in the molecular structure of the protein was noted in the sera of subjects suffering from an acute inflammatory process. Serum level of alpha 2 HS and alpha 1 antitrypsin (AT)was determined in 23 patients. When the acute-phase (AP-)reactant alpha 1 AT was increased (difference with normal mean greater than +2 or +3 SD), the sera showed a large decrease in alpha 2 HS (difference with normal mean less than -2 or -3 SD). The serum level of alpha 2 HS, albumin, alpha 2 macroglobulin, and of positive AP-reactants, orosomucoidinal study of seven patients. The results were submitted to a principal components analysis. Alpha 2 HS showed a negative correlation with the AP-reactants alpha 1 AT, orosomucoid, and haptoglobin (P less than 0.05) and a positive correlation with albumin (P less than 0.05); these findings indicate that alpha 2 HS is a negative AP-reactant. In addition, analysis of the principal components confirms thestrong analogy between alpha 2 HS and albumin and indicates that serum level behavior of the AP-reactants during the course of the disease closely depends on the protein studied.

Blood Proteins↗

Spatial working memory deficits in schizophrenia: relationship with tardive dyskinesia and negative symptoms.

OBJECTIVE: This study examined the interrelationship between negative symptoms, orofacial tardive dyskinesia, and specific neurocognitive processes, particularly those involved in memory and executive function, in patients with schizophrenia. METHOD: A set of computerized neurocognitive tasks, the Cambridge Neuropsychological Test Automated Battery, was used to assess executive and memory function in 54 hospitalized patients with chronic schizophrenia. Analysis of covariance was used to examine differences between groups with or without the topographical syndromes of orofacial tardive dyskinesia and between groups with high or low negative symptom scores. Principal-components and path analyses were used to examine further the influence of negative symptoms and orofacial tardive dyskinesia on performance on tests of memory and executive function. RESULTS: Both orofacial tardive dyskinesia and negative symptoms were significantly and independently associated with deficits on measures of spatial working memory span derived from principal-components analysis, but only orofacial tardive dyskinesia was associated with deficits on measures of spatial working memory strategy. Both were also associated with impairment on the delayed-matching-to-sample task, a test of memory. These associations were not explained by deficits in global intellectual function. Path analysis suggested that the relationships between the clinical symptoms and performance on the delayed-matching-to-sample task were mediated entirely through their relationship with the spatial working memory measures. CONCLUSIONS: In schizophrenia, orofacial tardive dyskinesia and evident negative symptoms are relatively independent markers of compromise of the cerebral systems that mediate spatial working memory. Candidate neural circuits include the frontal-striatal-thalamic systems, particularly those involving the dorsolateral prefrontal cortex.

Adult↗

Further evidence linking urolithiasis and blood coagulation: urinary prothrombin fragment 1 is present in stone matrix.

The fact that organic material is always present and distributed throughout each renal calculus suggests that it may play a role in stone formation. The organic matrix of calcium oxalate (CaOx) crystals freshly generated in urine in vitro contains urinary prothrombin fragment 1 (UPTF1) as the principal protein. In this initial study, matrix was extracted from 12 renal calculi and evaluated for the presence of UPTF1 using Western blotting. UPTF1 was present in all eight stones whose principal component was CaOx, and in one of two stones which consisted mainly of calcium phosphate (CaP). UPTF1 was absent from the two struvite calculi examined. The relationship between CaP and UPTF1 was explored further. Matrix harvested from CaP crystals freshly generated in urine in vitro was also shown to contain UPTF1 as its principal component. Our inability to detect UPTF1 in one mixed CaOx/CaP stone may be related to our methods of matrix retrieval, while its absence from two struvite stones argues against it being present in the other stones merely as a consequence of passive inclusion. This absence may be related to the alkaline environment typical of struvite stone growth. The finding that UPTF1 is present in some renal stones provides the first direct evidence that links blood coagulation proteins with urolithiasis.

Adult↗

Spatial variation of anthropometric traits in Ireland.

To further elucidate the relationship between geography and genetics in Ireland, we considered variation in anthropometric traits of adult males by town using spatial autocorrelation methods. By describing and distinguishing significant patterns of anthropometric variation, we determined whether the anthropometric traits display a simple pattern of spatial variation, as predicted by the isolation by distance model, or other patterns of spatial variation. Several hypotheses were examined, including (1) whether there was spatial patterning of 20 anthropometric phenotypic distributions and 7 principal components of Irish males and (2) if there was, whether these phenotypic distributions could be explained by a simple isolation by distance model. The results of this study can be summarized by several key findings: (1) There is significant spatial patterning among towns, as detected in correlograms of 14 anthropometric traits and 2 principal component factor scores (values of Moran's I ranging from 0.7510 to -0.3616, p < or = 0.0071); (2) 4 spatial patterns were detected, including clinical patterns, long-distance differentiation, distance distinction, and regional patchiness. These results suggest several likely causes of the observed spatial patterns. First, in Ireland patterns of anthropometric variation could not be explained by a single spatial pattern (i.e., isolation by distance). Second, through an examination of the various combinations of statistical homogeneity or heterogeneity, spatial patterning or nonpatterning, and similarity or dissimilarity of spatial patterns, we conclude that several migrational events structured the genetic landscape of Ireland.

Adult↗

Chemical study of triterpenoid resinous materials in archaeological findings by means of direct exposure electron ionisation mass spectrometry and gas chromatography/mass spectrometry.

A systematic study of standard triterpenes (alpha-amyrine, oleanolic acid, betulin, lupeol, betulinic acid and lupenone) and of raw resinous materials (frankincense resin, mastic resin and birch bark pitch) was performed using direct exposure electron ionisation mass spectrometry (DE-MS) and gas chromatography/mass spectrometry (GC/MS). DE-MS provides a mass spectral fingerprint of organic materials in a few minutes which highlights the compounds that are the main components in the sample. The application of principal component analysis (PCA) on DE-MS data in the mass ranges m/z 181-260 and m/z 331-500, corresponding to the fragmentation of triterpenoid molecules, enabled us to distinguish between different triterpenoid materials such as mastic resin, frankincense resin and birch bark pitch, and to graphically plot the resinous substances in three separate clusters, retaining 89% of the total variance. GC/MS analysis of the same materials has permitted us to elucidate in detail the molecular composition and to identify minor components and species that act as markers of the degradation undergone by the materials. The paper also reports the results for the organic residues contained in an Egyptian censer (5th-7th century AD) which was recovered in the excavation of the Necropolis of Antinoe (Egypt), and for the hafting material found on a Palaeolithic tool recovered at the site of Campitello (Arezzo, Tuscany), dating back to the Mid-Pleistocene period. Although DE-MS was found to be a fast analytical tool, it failed to give any information on the presence of less abundant compounds when applied to mixtures of different materials: only mastic resin was found in the residues from the Roman censer, whereas GC/MS analysis identified the presence of a vegetable oil from Brassicaceae seeds and Pinaceae resin. Birch bark pitch as a pure material was identified in the sample from the Palaeolithic flint flake using both procedures.

Archaeology↗

MALDI-TOF serum protein profiling for the detection of breast cancer.

BACKGROUND: Proteomic expression profiling has been suggested as a potential tool for the early diagnosis of cancer and other diseases. The objective of our study was to assess the feasibility of this approach for the detection of breast cancer. MATERIALS AND METHODS: In a randomized block design pre-operative serum samples obtained from 78 breast cancer patients and 29 controls were used to generate high-resolution MALDI-TOF protein profiles. The spectra generated using C8 magnetic beads assisted mass spectrometry were smoothed, binned and normalized after baseline correction. Linear discriminant analysis with double cross-validation, based on principal component analysis, was used to classify the protein profiles. RESULTS: A total recognition rate of 99%, a sensitivity of 100%, and a specificity of 97.0% for the detection of breast cancer were shown. The area under the curve of the classifier was 98.3%, which demonstrates the separation power of the classifier. The first 2 principal components account for most of the between- group separation. CONCLUSIONS: Double cross-validation showed that classification could be attributed to actual information in the protein profiles rather than to chance. Although preliminary, the high sensitivity and specificity indicate the potential usefulness of serum protein profiles for the detection of breast cancer.

Adult↗

Relations among self-talk, self-consciousness, and self-knowledge.

The aim of this study was to examine the relations among self-talk, self-consciousness, and self-knowledge through an exploratory principal component analysis and to test the hypothesis that only the functional and reflective aspects of self-consciousness contribute to self-knowledge. A self-report questionnaire including 6 scales assessing different aspects of self-talk, self-consciousness, and self-knowledge was administered to 203 German undergraduate university students. A principal component analysis of the scales yielded a two-factor solution, supporting the distinction between functional and dysfunctional self-consciousness. In a stepwise multiple regression analysis, only functional self-consciousness was a significant predictor of self-knowledge. Limitations of the present measures of inner speech are addressed.

Adult↗

Assessment of similarities of pairs and groups of proteins using transformed amino-acid-residue data.

Using as a primary standard a representative set of 208 proteins whose amino-acid-residue mole frequencies have been accurately established, a set of standard distributions of mole frequencies is defined for each amino acids, in terms of which percentile values for the observed mole frequencies of the amino-acid residues in any other protein can be determined. Data so transformed have a distribution much closer to Gaussian than untransformed values, and allow meaningful determinations of correlations between the amino-acid-residue compositions of two proteins as well as between pairs of amino-acid-residues within groups of proteins. Of the 153 possible pairs of amino acids (Asx and Glx are used) 39 are significantly correlated at p less than or equal to 0.01 and 22 at p less than or equal to 0.001. A percentile table is included for those wishing to use the method with programmable calculators. The transformed data for amino-acid compositions have been used to perform principal components analyses on groups of proteins in order to determine if meaningful sub-groupings (observable clusters in scatter diagrams) were detectable. Such analyses are shown for the representative set of proteins and for a group of 184 globins. With regard to the globin chains, a correlation is observed for alpha chains in the first principal component projection (PCP), (accounting for 22% of the variance) with respect to the evolutionary time-scale while beta chains show such a correlation in the first and second PCPs (22% and 18% of the variance respectively). Thus, alpha and beta chains appear to diverge from a common progenitor, similar in position to globin chains from "primitive" forms. Furthermore, globins from "primitive" forms are nearer to one another than they are to globins from the vertebrates, a finding without a priori reason, suggesting perhaps that once a chain has reached a stable relationship with its environment, strong constrains are placed on the co-existing globin chains so that they maintain appropriate interaction with one another. In addition, positions of the epsilon, gamma and delta chains are in the order: epsilon (embryonal) more primitive than gamma (foetal) more primitive than delta equal to beta (adult).

Amino Acids↗

Evaluation of pyridine-3-carboxylic acid as a drug carrier by utilizing multivariate methods, structure property correlations, and pattern recognition techniques.

Multivariate methods and molecular properties are utilized to show similarity of pyridine-3-carboxylic acid (nicotinic acid) to seven drugs that penetrate the central nervous system. Multivariate methods applied include cluster analysis, discriminant analysis, correspondence analysis, self organizing tree algorithm (SOTA) analysis, factor analysis, and principal component analysis. Numerical values of properties for nicotinic acid showed very high correlation with the values from dihydropyridine, barbital, metharbital, phenobarbital, methohexital, 4-aminohex-5-enoic acid, and (4-chlorophenyl)(5-fluoro-2-hydroxyphenyl)methanone. Descriptive statistics of property values for these drugs showed overlapping numerical values for partition coefficients, index of refraction, and nOnN. Principal component analysis and factor analysis of molecular properties showed that nicotinic acid is highly similar to dihydropyridine as well as to other members of this group of drugs. Applying cluster analysis utilizing standard euclidean distance with single linkage and centroid linkage showed that nicotinic acid is highly similar to dihydropyridine and both are consistently grouped into the identical cluster (indicating high similarity). Both nicotinic acid and dihydropyridine show zero violations of the Rule of 5, which indicates good bioavailability characteristics. Discriminant analysis of molecular properties for these eight compounds could not demonstrate differentiation between nicotinic acid and dihydropyridine within the properties applied, this indicating high level of similarity. Neural cluster analysis of molecular properties showed that nicotinic acid and dihydropyridine are included into the same cluster (indicating very strong similarity). SOTA analysis also placed nicotinic acid and dihydropyridine into the same cluster unit. SOTA analysis of molecular properties indicates high similarity between nicotinic acid and dihydropyridine. Correspondence analysis was performed on the molecular properties and showed that there exists considerable association between dihydropyridine and nicotinic acid. Multiple regression analysis of these molecular properties produced a mathematical equation to predict the formula weight of similar compounds for use as drug carriers.

Algorithms↗

Construct validity of the abbreviated mental test in older medical inpatients.

OBJECTIVES: To evaluate validity and internal structure of the Abbreviated Mental Test (AMT), and to assess the dependence of the internal structure upon the characteristics of the patients examined. DESIGN: Cross-sectional examination using data from the Italian Group of Pharmacoepidemiology in the Elderly (GIFA) database. SETTING: Twenty-four acute care wards of Geriatrics or General Medicine. PARTICIPANTS: Two thousand eight hundred and eight patients consecutively admitted over a 4-month period. MEASUREMENTS: Demographic characteristics, functional status, medical conditions and performance on AMT were collected at discharge. Sensitivity, specificity and predictive values of the AMT <7 versus a diagnosis of dementia made according to DSM-III-R criteria were computed. The internal structure of AMT was assessed by principal component analysis. The analysis was performed on the whole population and stratified for age (<65, 65-80 and >80 years), gender, education (<6 or >5 years) and presence of congestive heart failure (CHF). RESULTS: AMT achieved high sensitivity (81%), specificity (84%) and negative predictive value (99%), but a low positive predictive value of 25%. The principal component analysis isolated two components: the former component represents the orientation to time and space and explains 45% of AMT variance; the latter is linked to memory and attention and explains 13% of variance. Comparable results were obtained after stratification by age, gender or education. In patients with CHF, only 48.3% of the cumulative variance was explained; the factor accounting for most (34.6%) of the variance explained was mainly related to the three items assessing memory. CONCLUSION: AMT >6 rules out dementia very reliably, whereas AMT <7 requires a second level cognitive assessment to confirm dementia. AMT is bidimensional and maintains the same internal structure across classes defined by selected social and demographic characteristics, but not in CHF patients. It is likely that its internal structure depends on the type of patients. The use of a sum-score could conceal some part of the information provided by the AMT.

Aged↗

Context of maternal lineages in the Greater Southwest.

We present mitochondrial haplogroup characterizations of the prehistoric Anasazi of the United States (US) Southwest. These data are part of a long-term project to characterize ancient Great Basin and US Southwest samples for mitochondrial DNA (mtDNA) diversity. Three restriction site polymorphisms (RSPs) and one length polymorphism identify four common Native American matrilines (A, B, C, and D). The Anasazi (n = 27) are shown to have a moderate frequency of haplogroup A (22%), a high frequency of haplogroup B (56%), and a low frequency of C (15%). Haplogroup D has not yet been detected among the Anasazi. In comparison to modern Native American groups from the US Southwest, the Anasazi are shown to have a distribution of haplogroups similar to the frequency pattern exhibited by modern Pueblo groups. A principal component analysis also clusters the Anasazi with some modern (Pueblo) Southwestern populations, and away from other modern (Athapaskan speaking) Southwestern populations. The Anasazi are also shown to have a significantly different distribution of the four haplogroups as compared to the eastern Great Basin Great Salt Lake Fremont (n = 32), although both groups cluster together in a principal component analysis. The context of our data suggests substantial stability within the US Southwest, even in the face of the serious cultural and biological disruption caused by colonization of the region by European settlers. We conclude that although sample numbers are fairly low, ancient DNA (aDNA) data are useful for assessing long-term populational affinities and for discerning regional population structure.

DNA, Mitochondrial↗

Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns.

Understanding X-ray crystallographic diffuse scattering is likely to improve our comprehension of equilibrium collective protein dynamics. Here, using molecular dynamics (MD) simulation, a detailed analysis is performed of the origins of diffuse scattering in crystalline Staphylococcal nuclease, for which the complete diffuse scattering pattern has been determined experimentally. The hydrogen-atom contribution and the scattering range over which the scattering can be considered to be a sum of solvent and protein scattering are determined. Two models of correlated protein motion are investigated by calculating the model-derived diffuse scattering and comparing with the scattering calculated directly from MD trajectories. In one model, previously used in diffuse scattering interpretation, the atomic displacement correlations decay isotropically with increasing separation. Model correlation lengths are obtained by refining the model scattering against the simulation-derived scattering pattern, and are found to be significantly different from those correlation lengths derived directly from the MD trajectories. Furthermore, the convergence between the model-derived and MD-derived scattering is poor. The second model, in which the displacement correlations are calculated from the principal components of the MD trajectories, is capable of fully reproducing the MD-derived diffuse scattering if the approximately 50% lowest-frequency modes are included. However, a small number ( approximately 10) of lowest-frequency and largest-amplitude modes dominates the diffuse scattering and thus the correlated protein motions. A detailed analysis of the principal components is performed. In particular, the effective free energy profile associated with each principle mode is analyzed and the eigenfrequency and damping coefficient computed using a model of Brownian dynamics. Those collective modes with effective frequencies below approximately 0.5 THz, including those that determine the diffuse scattering, are overdamped.

Anisotropy↗

Smelling renal dysfunction via electronic nose.

The human body odor plays an important role in social communication in various situations, like the olfactory identification of partners and relatives as well as in parents-child interactions. In patients with renal dysfunction the compound of sweat and volatile gases is changed because of the limited ability for removing metabolic products from the blood. The regulation of electrolyte composition and acid-base balance are also altered so that the body odor of these patients may be significantly influenced by these disorders. We show the ability of an electronic nose to detect changes in the human body odor in consequence of renal dysfunction by reducing multivariate sensor signals with principal component analysis to its first and second principal odor component (POC). All healthy subjects could clearly be distinguished from patients with renal failure using quadratic discriminant analysis, whereas a correct classification of 95.2% (98.4% using 1st-3rd POC) of patients between end stage renal failure and chronic renal failure was found. This methodology of analyzing human body odor may also provide new approaches for investigating symptoms of renal failure and for diagnosing other diseases of internal or cutaneous origin.

Biomarkers↗

Determination of hydrophobicity of non-homologous series of anticancer drugs by reversed-phase high-performance liquid chromatography.

The hydrophobicity and specific hydrophobic surface area of 21 commercial anticancer drugs were determined by reversed-phase high-performance liquid chromatography on an octadecyl-silica column using methanol-water mixtures as eluents. Linear correlations were calculated between the log k' values and the methanol concentration of the eluent, the intercept and slope were considered as the best estimation of the hydrophobicity and specific hydrophobic surface area. The relationship between retention characteristics and physicochemical parameters of drugs was evaluated by multivariate mathematical statistical methods, such as principal component analysis followed by two-dimensional non-linear mapping, varimax rotation and by cluster analysis. Anticancer drugs can be well separated by reversed-phase HPLC. Various multivariate mathematical statistical calculations indicate that the retention of the investigated drugs is mainly governed by hydrophobic and steric parameters. The results suggest that the use of principal component analysis followed by two-dimensional non-linear mapping is superior to cluster analysis for the evaluation of large retention data matrices.

Antineoplastic Agents↗