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PubMed2006

Structure-activity relationship study of flavone compounds with anti-HIV-1 integrase activity: a density functional theory study.

Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Flavone compounds have been very much studied due to their activity during the inhibition process of HIV-1 IN. In this study, we employed density functional theory (DFT) using the B3LYP hybrid functional to calculate a set of molecular properties for 32 flavonoid compounds with anti-HIV-1 IN activity. The stepwise discriminant analysis (SDA), principal component analysis (PCA) and hierarchical cluster analysis (HCA) methods were employed to reduce dimensionality and investigate possible relationship between the calculated properties and the anti-HIV-1 IN activity. These analyses showed that the molecular hydrophobicity (ClogP), charge on atom 11 and electrophilic index (omega) are responsible for the separation between anti-HIV-1 IN active and inactive compounds.

Cluster Analysis↗
PubMed1998

Correlations between condylar characteristics and facial morphology in Class II preadolescent patients.

The aim of this retrospective study was to determine correlations between condylar characteristics measured from preorthodontic tomograms of preadolescents and their facial morphologic characteristics. The sample consisted of 136 patients displaying a Class II malocclusion, a vertical or horizontal skeletal growth tendency, and ranging in age between 10 years 0 months and 12 years 6 months for males and 9 years 0 months and 11 years 6 months for females. Two groups were established: the vertical group had 68 patients, 36 males and 32 females, (average pretreatment age, 11 years 0 months); the horizontal group also had 68 patients, 29 males and 39 females, their average pretreatment age was 10 years 9 months. The central cut of axially corrected lateral tomograms of the left and right temporomandibular joints for each group was randomized, blinded, and traced for condyle/fossa measurements including: anterior, superior and posterior joint space; condylar head and posterior condylar ramus inclination; condylar neck width; and condylar shape and condylar surface area. A logistic discriminant analysis with significance values set at p < 0.05 was used to determine the most reliable condylar characteristics to predict facial morphology. A cluster analysis was completed on the significant variables to form three clusters. Numeric ranges separating these clusters were then calculated. Chi-square tests measures of association were computed for significant variables and tested for associations between facial morphologic characteristics. Condylar head inclination and superior joint space proved to be significantly correlated to facial morphology (p values ranged from 0.010 to 0.018). Patients with vertical facial morphologic characteristics displayed decreased superior joint spaces and posteriorly angled condyles. Increased superior joint spaces and anteriorly angled condyles were significantly correlated to patients with a horizontal facial morphology. No significant correlations between the other condylar characteristics and facial morphology were determined.

Analysis of Variance↗
PubMed2004

Sperm subpopulations in Iberian red deer epididymal sperm and their changes through the cryopreservation process.

We have applied a statistical protocol based on principal component analysis, clustering methods, and discriminant analysis for the identification of sperm subpopulations in computer-assisted sperm analysis (CASA) data. Samples were obtained from the cauda epididymis of 11 Iberian red deer and cryopreserved following a standard protocol. Motility by CASA was analyzed just after sperm recovery, just before freezing, and after thawing, and eight motility descriptors for each individual spermatozoon were recorded. Sperm viability and acrosomal status were also assessed. Subpopulation analysis was performed in four sequential steps: principal component analysis using the eight motility descriptors; nonhierarchical clustering analysis (k-means) using the first two principal components; hierarchical clustering analysis (UPGMA); and selection of the final number of clusters. Three clusters were obtained for each motility analysis: slow and nonlinear; rapid and linear; and rapid, high ALH, nonlinear. We detected variations in the clusters between treatments (initial, prefreezing and postthawed). Indeed, motility increased and linearity decreased in the prefreezing analysis. A discriminant analysis isolated three descriptors that were used again in the same statistical analysis, giving four clusters that resembled the pattern found in the first classification. We also performed a clustering analysis of the males according to prefreezing/postthawed variation of total motility, viability, and acrosomal status. The proportion of the linear subpopulations in the prefreezing treatment, in both clustering analyses, correlated positively with postthawed viability recovery. Our results show that clustering analysis of CASA data gives useful and practical information that is not obtained by conventional sperm analysis.

Acrosome↗
PubMed2004

Classification of normal and dysphagic swallows by acoustical means.

This paper proposes a noninvasive, acoustic-based method to differentiate between individuals with and without dysphagia or swallowing dysfunction. Swallowing sound signals, both normal and abnormal (i.e., at risk of some degree of dysphagia) were recorded with accelerometers over the trachea. Segmentation based on waveform dimension trajectory (a distance-based technique) was developed to segment the nonstationary swallowing sound signals. Two characteristic sections emerged, Opening and Transmission, and 24 characteristic features were extracted and subsequently reduced via discriminant analysis. A discriminant algorithm was also employed for classification, with the system trained and tested using the leave-one-out approach. Overall, 350 signals were used from three bolus consistencies (semisolid, thick and thin liquids). A final screening algorithm correctly classified 13 of 15 control subjects and 11 of 11 subjects with some degree of dysphagia and/or neurological impairments. The proposed method has great potential to reduce the need for videofluoroscopic swallowing studies (the current gold standard method for swallowing assessment, which is invasive and nonportable) and to assist in the overall clinical assessment of swallowing sound signals.

Adolescent↗
PubMed2002

Breed variations in histopathologic features of chronic severe otitis externa in dogs: 80 cases (1995-2001).

OBJECTIVE: To compare pathologic changes of the horizontal ear canal associated with chronic severe otitis externa between Cocker Spaniels and dogs of other breeds. DESIGN: Retrospective study. ANIMALS: 80 dogs with severe otitis externa that required total ear canal ablation with lateral bulla osteotomy. PROCEDURE: Medical records were reviewed for breed, sex, and age at time of surgery. Histologic specimens from the horizontal ear canal were evaluated by a single examiner for overall tissue response pattern and scored for sebaceous gland hyperplasia, ceruminous gland hyperplasia, ceruminous gland ectasia, fibrosis, pigment-laden macrophages, and osseous metaplasia. RESULTS: 48 of 80 (60%) dogs were Cocker Spaniels. Thirty-five of 48 (72.9%) Cocker Spaniels had a predominately ceruminous tissue response pattern; only 9 of 32 (28.1 %) dogs of other breeds had the same pattern. Other breeds most commonly had a pattern dominated by fibrosis (n = 13 [40.6%]); fibrosis was the predominant pattern in only 4 of 48 (8.3%) Cocker Spaniels. Discriminant analysis and K-means clustering of 4 histopathologic criteria correctly classified 75% of the dogs as Cocker Spaniels or all other breeds. CONCLUSIONS AND CLINICAL RELEVANCE: Cocker Spaniels are at increased risk for chronic severe otitis externa requiring total ear canal ablation with lateral bulla osteotomy, indicating that earlier and more aggressive management of the primary otitis externa and secondary inflammation is warranted in this breed. Cocker Spaniels with chronic severe otitis externa have distinct differences in pathologic characteristics of the horizontal ear canal, compared with other breeds.

Animals↗
PubMed2000

Image analysis of mesothelioma. II. Discrimination of mesothelioma from metastatic serous ovarian adenocarcinoma.

OBJECTIVE: To examine the utility of karyometric measurements in the differentiation of mesothelioma from metastatic serous ovarian adenocarcinoma. STUDY DESIGN: High-resolution images of 1,631 nuclei from 32 cases of mesothelioma and 742 nuclei from 15 cases of ovarian adenocarcinoma were recorded. A stepwise discriminant analysis and nonparametric classifier were applied. RESULTS: Nuclei from these two diagnostic categories appear very similar and occupy feature space with significant overlap. A nonparametric classification procedure provided acceptable correct classification. CONCLUSION: For certain regions in feature space, cases could be unequivocally classified.

Cell Nucleus↗
PubMed2003

[Imaging of dopamine transporter with Tc99m-Trodat-SPECT in movement disorders].

UNLABELLED: 99mTc-TRODAT-1 is a new, technetium based radiopharmaceutical that selectively binds to the dopamine transporters. The aim of the study was to evaluate the dopamine transporter status in movement disorders. METHODS: In eight healthy volunteers (age range 22-58 years), 28 patients with Parkinson's disease (age range 42-80 years), 10 patients with Parkinsonian syndrome (age range 51-79 years) and 13 patients with essential tremor (age range 43-71 years) were 99mTc-TRODAT-SPECT tests performed. The results were evaluated visually and semiquantitatively. RESULTS: The visual assessments were concordant with those of the semiquantitative in each case. The 99mTc-TRODAT uptake of the striatum was referenced to the cerebellum, the frontal and occipital cortex. The best deviation was found in aspect of the occipital cortex. The striatum/occipital ratio was the following: healthy volunteers: 2.12 +/- 0.27; Parkinson's disease: 1.52 +/- 0.27; Parkinsonian syndrome: 1.57 +/- 0.26; essential tremor: 2.06 +/- 0.69. The striatal dopamine transporter availability was significantly lower in subjects with Parkinson's disease or Parkinsonian syndrome compared to the control subjects. There was no difference between healthy volunteers and patients with essential tremor. Using discriminant analysis, the discriminant function had significantly different values in the group of Parkinson's disease than in Parkinsonian syndrome: f = -3.675 x caud/occipit + 6.293 x put/occipit -2.548. CONCLUSION: 99mTc-TRODAT-SPECT is able to visualise the presynaptic dopaminergic degeneration. This method itself can be useful in differential diagnosis in some type of movement disorders.

Aged↗
PubMed2003

A map of angular tuning preference in thalamic barreloids.

A double-labeling protocol was used to determine how cells with different angular preferences to whisker motion distribute across the dimensions of a barreloid in the ventral posterior medial nucleus of the rat thalamus. Individual barreloids were labeled retrogradely by injecting Fluoro-Gold in identified barrel columns, and single relay cells (n = 30) pertaining to the labeled barreloids were stained juxtacellularly with Neurobiotin after determination of their angular tuning preference to controlled whisker deflection. Results show that cells with like angular preference are clustered within the barreloids. Those best tuned to forward and upward directions are located principally in the dorsal sector of the barreloid, whereas those best tuned to backward and downward motion are located principally in the central and ventral sectors, respectively. The relationship between cell location and angular preference was assessed by regression, cluster, and discriminant analysis. Together, these tests indicate that barreloids contain a map of shifting angular preference that transposes along the length of a barreloid directional property imposed at the periphery by the circumferential distribution of receptors around the vibrissa follicles.

Action Potentials↗
PubMedDate not supplied

[Pathogenetic criteria of nephroptosis].

The aim of the study was to specify treatment policy in nephroptosis on the basis of characteristics of the onset, development and course of the disease. A total of 83 patients with nephroptosis were examined. The rotation angles of the kidney were summed using standard excretory urograms in clino- and orthostasis. Radionuclide nephroscintigraphy, rheorenography were made in 72 patients. Statistical processing employed correlation, cluster, discriminant analysis of the program Statistica. The method of estimation of the angles of rotation of the movable kidney in three planes was introduced. Grouping of patients by the sum of the rotation angles appeared more precise in reflecting disorders of intraorganic circulation in the kidney than skeletotopic distribution by the nephroptosis degree. Standard excretory urograms allow determination of the sum of the angle of rotation of the movable kidney and, finally, adequate conservative or surgical treatment method. Surgery can correct disorders of intraorganic blood flow by creating physiological position for the kidney raising to the due level and eliminating rotation.

Adolescent↗
PubMed1991

Toward an empirically derived typology of obese persons.

The MMPI, medical, anthropomorphic, and laboratory evaluations were completed by 260 obese patients (211 females, 49 males) at a New York hospital. Biological and psychological variables were separately subjected to principal components analyses. Fifteen biological and five psychological components were extracted. A three-cluster solution was selected from a K-means clustering on biological components, replicated via Ward's method, and validated via a discriminant analysis on psychological components. Cluster 1, 'android obesity', contained 75 percent of the males and was characterized by 'masculine phenotypy', 'poor conditioning' and 'adverse serum lipids', and less 'feminine' responding on the MMPI. Cluster 2, 'gynoid obesity', was low on components measuring physical stress and masculine phenotypy, was 95 percent female, moderately obese compared to clusters 1 and 3, and had a relatively healthy profile. Cluster 3 had elevations on overall fatness and physiological and psychological stress, and low scores on a 'healthy blood synthesis' component. This cluster, labeled 'morbidly obese', was the most obese and had profiles suggesting adverse effects of obesity.

Adult↗
PubMed1990

Discriminant function analysis: a case study of some socioeconomic constraints on child nutrition.

Discriminant function analysis was used to understand the combination of socioeconomic variables in various forms of malnutrition in preschool children. Data available (1976) from two sets viz., 4000 children of rural and urban areas of Hyderabad (in south India) and 215 children of urban and rural areas of Jaipur (in north India) were used for the study. The prevalence rates of various forms of malnutrition in children were different by variations in socioeconomic status and sex (P less than 0.05). Discriminant function analysis of all socioeconomic indicators showed that educational levels and occupational status of parents and percaput income were most important for differentiation of children who were normals and undernourished. Occupational status of the father and the child's calorie intake or duration of lactation improved the differentiation of normals from those who were under-nourished. Higher prevalence of malnutrition in female children than in the male children was found due to variations in per capita income and levels of maternal education. Closely associated best set of factors could be traced using the discriminant function analysis.

Child Nutrition Disorders↗
PubMed2001

Comparison of the performance of different discriminant algorithms in analyte discrimination tasks using an array of carbon black--polymer composite vapor detectors.

An array of 20 compositionally different carbon black--polymer composite chemiresistor vapor detectors was challenged under laboratory conditions to discriminate between a pair of extremely similar pure analytes (H2O and D2O), compositionally similar mixtures of pairs of compounds, and low concentrations of vapors of similar chemicals. Several discriminant algorithms were utilized, including k nearest neighbors (kNN, with k = 1), linear discriminant analysis (LDA, or Fisher's linear discriminant), quadratic discriminant analysis (QDA), regularized discriminant analysis (RDA, a hybrid of LDA and QDA), partial least squares, and soft independent modeling of class analogy (SIMCA). H2O and D2O were perfectly classified by most of the discriminants when a separate training and test set was used. As expected, discrimination performance decreased as the analyte concentration decreased, and performance decreased as the composition of the analyte mixtures became more similar. RDA was the overall best-performing discriminant, and LDA was the best-performing discriminant that did not require several cross-validations for optimization.

Journal Article↗
PubMed1982

Determination of sex of white femora by discriminant function analysis: forensic science applications.

Stepwise multiple discriminant function analysis is used to establish classification functions for sex assessment of North American white femora. The functions correctly assign sex for 82% of a sample consisting of 85 femora of verified age, sex, and race, and for a similarly verified test sample of 30. The objectives are to provide criteria for sexing poorly preserved and fragmentary unknown specimens and a statement of the probable accuracy of such assessments in individual cases. The application of the method to forensic casework is illustrated by a sample case.

Anthropometry↗
PubMed2002

Characterization of selected Spanish table wine samples according to their biogenic amine content from liquid chromatographic determination.

Pattern recognition techniques, such as principal component analysis, cluster analysis, and linear discriminant analysis, have been applied to samples of red, white, and rosé wines to determine whether some biogenic amines could be considered as chemical descriptors. Eight amines (tryptamine, phenylethylamine, putrescine, cadaverine, histamine, tyramine, spermidine, and spermine) were determined by RP-HPLC, after derivatization with dabsyl chloride. However, only putrescine, cadaverine, histamine, tyramine, spermidine, and spermine were found in the wines analyzed. From the association between variables obtained by principal component analysis and clustering and from the relationship found by linear discriminant analysis, it can be deduced that the amines generated during malolactic fermentation (putrescine, histamine, and tyramine) could be used as chemical descriptors to characterize table wine samples.

Analysis of Variance↗
PubMed1989

Classification of lung cancer patients and controls by chromatography of modified nucleosides in serum.

A wide spectrum of modified nucleosides has been quantified by high-performance liquid chromatography in serum of 49 male lung cancer patients, 35 patients with other cancers, and 48 patients hospitalized for nonneoplastic diseases. Data for 29 modified nucleoside peaks were normalized to an internal standard and analyzed by discriminant analysis and stepwise discriminant analysis. A model based on peaks selected by a stepwise discriminant procedure correctly classified 79% of the cancer and 75% of the noncancer subjects. It also demonstrated 84% sensitivity and 79% specificity when comparing lung cancer to noncancer subjects, and 80% sensitivity and 55% specificity in comparing lung cancer to other cancers. The nucleoside peaks having the greatest influence on the models varied dependent on the subgroups compared, confirming the importance of quantifying a wide array of nucleosides. These data support and expand previous studies which reported the utility of measuring modified nucleoside levels in serum and show that precise measurement of an array of 29 modified nucleosides in serum by high-performance liquid chromatography with UV scanning with subsequent data modeling may provide a clinically useful approach to patient classification in diagnosis and subsequent therapeutic monitoring.

Biomarkers, Tumor↗
PubMed2004

Intensity and the ratios of compounds in the scent of snapdragon flowers affect scent discrimination by honeybees (Apis mellifera).

Floral scent is used by pollinators during foraging to identify and discriminate among flowers. The ability to discriminate among scents may depend on both scent intensity and the ratios of the concentrations of the volatile compounds of a complex mixture rather than on the presence of a few compounds. We used four scent-emitting cultivars of snapdragon (Antirrhinum majus) to test this hypothesis by examining the ability of honeybees to differentiate among their scents. Each cultivar produced three monoterpenes (myrcene, E-beta-ocimene, and linalool) and five phenylpropanoids (methylbenzoate, acetophenone, dimethoxytoluene, cis-methylcinnamate, and trans-methylcinnamate). Cultivars were reliably classified by their scents in a canonical discriminant analysis. Honeybees were unable to discriminate among the scents of flowers of the same cultivar in our assay. The ability of honeybees to discriminate among the scents of different cultivars was a function of the intensity of the floral scent. Discrimination was also correlated to the distance among the scents described by the discriminant analysis; the cultivars that had the greatest differences observed in the discriminant analysis were the easiest to discriminate. Our results show that honeybees are capable of using all of the floral volatiles to discriminate subtle differences in scent.

Animals↗
PubMed1998

Vision-guided navigation using SHOSLIF.

This paper presents an unconventional approach to vision-guided autonomous navigation. The system recalls information about scenes and navigational experience using content-based retrieval from a visual database. To achieve a high applicability to various road types, we do not impose a priori scene features, such as road edges, that the system must use, but rather, the system automatically derives features from images during supervised learning. To accomplish this, the system uses principle component analysis and linear discriminant analysis to automatically derive the most expressive features (MEF) for scene reconstruction or the most discriminating features (MDF) for scene classification. These features best describe or classify the population of the scenes and approximate complex decision regions using piecewise linear boundaries up to a desired accuracy. A new self-organizing scheme called recursive partition tree (RPT) is used for automatic construction of a vision-and-control database, which quickly prunes the data set in the content-based search and results in a low time complexity of O(log(n)) for retrieval from a database of size n. The system combines principle component and linear discriminant analysis networks with a decision tree network. It has been tested on a mobile robot, Rome, in an unknown indoor environment to learn scenes and the associated navigation experience. In the performing phase, the mobile robot navigates autonomously in similar environments, while allowing the presence of scene perturbations such as the presence of passersby.

Journal Article↗