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PubMed1988

Relationship between serum lipoproteins and hemostatic parameters in men with prostatic cancer.

Serum lipoprotein concentrations were related to hemostatic parameters in a group of 31 men before and during three different hormone treatment regimens for prostate cancer in an attempt to analyse to what extent the changes in these two systems correlate. In a correlation matrix the number of significant relationships at the 5% and 1% level corresponded to what could be expected by chance. The study thus failed to demonstrate any consistent relationship between any lipoprotein lipid concentration and the hemostatic parameters in men treated for prostate cancer. Most significant relationships were found for HDL-TG versus plasminogen, but the clinical significance of this observation is not clear.

Estradiol Congeners↗

PubMed1990

13-year clinical assessment of 10 amalgam alloys.

The first commercial high-copper amalgam was developed in the mid-1960's. In 1975, a study to evaluate in vivo/in vitro performance of nine of these new alloys was initiated at Indiana University. These nine high-copper amalgams plus a traditional amalgam were tested for four laboratory properties and their gamma-2 content, and were clinically assessed for fracture at the margins. Originally, 60 restorations of each material were placed in patients and then recalled at six, 12, and 24 months. Recently, 13 years post-operatively, approximately one-third of the original patients were located. These patients were given a clinical exam, and photographs were taken of their restorations. From these recall data, the mean loss of all restorations at 13 years was 11.3%. The alloys Cupralloy, Tytin, and Dispersalloy had the lowest loss rates. The evaluation of the fracture at the margins (ridit means) indicates that there are five groups of alloys with some overlap between groups. The alloys Cupralloy, Indiloy, Dispersalloy, and Phasealloy exhibited the least fracture at the margins. The gamma-2-containing alloys--Optaloy II, Micro II, Velvalloy, and Aristaloy CR--showed the greatest rate of fracture at the margins. A correlation matrix of the ridit means at different years, the loss of restorations at 13 years, and the mechanical properties indicate that the early (one- and two-year) fracture at the margins predicts the 13-year results. Mechanical properties, however, do not predict the clinical performance of the materials at 13 years.

Copper↗

PubMed1987

Isolation and two-dimensional 1H-NMR of peptide [1-24] of dog serum albumin and studies of its complexation with copper and nickel by NMR and CD spectroscopy.

The NH2-terminal peptide fragment [1-24] of dog serum albumin was obtained by controlled peptic digestion of the protein. The peptide was purified to homogeneity by gel filtration and ion-exchange chromatography. The NMR assignments of the protons of the individual amino acid residues were made by using two-dimensional correlation matrix, spin-decoupling experiments and analysis of the titration curves. The polypeptide itself has a random-coil conformation. There is a conformational change as a function of pH, but it does not arise from any direct involvement of the amino acid side chains. Complexation of the peptide fragment with Ni(II) and Cu(II) has been investigated by NMR and CD. The Ni(II) complex is in slow exchange with the free ligand on the NMR time scale. The complexation involves the alpha-NH2, three deprotonated amide nitrogens of Ala-2, Tyr-3 and Lys-4 residues. The phenolate oxygen of Tyr-3 is not involved in the metal binding; however, an interaction between the aromatic ring and the metal ion is likely. The CD results of Cu(II)-binding to this peptide suggest that the complexation takes place from the terminal NH2 and step by step to three deprotonated amide nitrogens. There is no major conformational change of the peptide fragment upon complexation.

Animals↗

PubMed1994

Which nutritional measurements assess protein-energy nutritional status in patients receiving home parenteral nutrition?

Weight, midarm circumference, triceps skinfold thickness, arm muscle circumference, albumin, prealbumin, transferrin and total lymphocyte count were measured at each outpatient visit in patients reveiving home parenteral nutrition from September 1987 to November 1991. Each nutritional variable was analysed for individuals and for the whole group. Group data were expressed using the actual values obtained and successive differences (the change between clinic attendances). Nutritional variables were evaluated using a correlation matrix. Identical analysis of individual and group data demonstrates that laboratory investigations are of little value in the assessment of nutritional status in patients receiving home parenteral nutrition. Anthropometry detected changes in body weight secondary to changes in muscle and/or fat in 80% of patients. Pooling anthropometric data distors the relationship between variables owing to inter-individual variability when actual values are used. The method of successive differences is the preferred method of analysis for group anthropometric data.

Journal Article↗

PubMed1995

Methods for displaying macromolecular structural uncertainty: application to the globins.

Most molecular graphics programs ignore any uncertainty in the atomic coordinates being displayed. Structures are displayed in terms of perfect points, spheres, and lines with no uncertainty. However, all experimental methods for defining structures, and many methods for predicting and comparing structures, associate uncertainties with each atomic coordinate. We have developed graphical representations that highlight these uncertainties. These representations are encapsulated in a new interactive display program, PROTEAND. PROTEAND represents structural uncertainty in three ways: (1) The traditional way: The program shows a collection of structures as superposed and overlapped stick-figure models. (2) Ellipsoids: At each atom position, the program shows an ellipsoid derived from a three-dimensional Gaussian model of uncertainty. This probabilistic model provides additional information about the relationship between atoms that can be displayed as a correlation matrix. (3) Rigid-body volumes: Using clouds of dots, the program can show the range of rigid-body motion of selected substructures, such as individual alpha helices. We illustrate the utility of these display modalities by the applying PROTEAND to the globin family of proteins, and show that certain types of structural variation are best illustrated with different methods of display.

Animals↗

PubMed1993

Evidence from the rat for a general factor that underlies cognitive performance and that relates to brain size: intelligence?

The data on a group of 22 rats, each measured for their speed of reasoning, accuracy of reasoning, response flexibility, and attention for novelty, were subjected to two different methods of factor analysis. By both methods, the correlation matrix of their performance was consistent with a single-factor model. In a second cohort of rats, where brain size was known, the score for this 'general factor' was computed. The regression for brain weight and the general factor was significant.

Animals↗

PubMed1990

Psychometric properties of the Drug Abuse Screening Test in a psychiatric patient population.

The Drug Abuse Screening Test (DAST) is a 28-item screening instrument developed by Skinner for clinical screening and treatment evaluation research in the substance abuse field. In a sample of 250 psychiatric patients drawn from four treatment programs, the DAST evidenced high internal consistency reliability and good item-total score correlations. A factor analysis of the DAST item correlation matrix revealed a predominantly unidimensional scale with the possibility of rotating five additional factors reflecting a continuum of drug abuse. The five factors were interpreted as (a) self-recognition of a drug problem, (b) serious social consequences of drug use, (c) help-seeking for drug abuse, (d) illegal drug-related activities, and (e) inability to control drug use. The diagnostic validity of the DAST in discriminating patients according to DSM-III Substance Abuse diagnostic criteria was high and a range of valid clinical DAST cutoff scores from 5/6 through 10/11 was identified. The DAST appears to be a valid measure of drug involvement and abuse in a psychiatric patient population, a finding of increasing clinical relevance.

Adult↗

PubMed1990

Prediction of stature from hand measurements.

A sample of 166 normal adult males and females was taken from different colleges of Assiut representing those living in upper Egypt. Each subject has been studied for measurements of stature (S), hand length (HL) and hand breadth (HB). The data were statistically analysed in order to assess the relationship between stature and hand measurements. The correlation matrix of the study indicates close similarity of the relationship between stature and hand measurements in both sexes and in both sides. A generalized multiple regression equation has been designed to estimate stature from values of hand length and hand breadth regardless of sex or side in the form: S = 34.5 + 5.77 HL + 2.7 HB +/- 5.1. This equation may be helpful to obtain approximate stature when there is difficulty in obtaining a direct measurement or where there is a chance print of a criminal or an amputated hand or arm.

Adult↗

PubMed1991

Development of a behavioral measure of mouth pain, nausea, and wellness for patients receiving radiation and chemotherapy.

Toxicities from the chemotherapy and irradiation preparative regimen for bone marrow transplantation include nausea, emesis, and oral pain. Behavioral measures were developed as alternatives to paper and pencil measures of these symptoms because patients are sometimes too ill, unavailable, or unwilling to complete self-report scales. Behavioral observations also provide supplements to self-report for these multidimensional symptoms. For 24 days during the acute phase of transplantation, nurses rated the behavior of adult patients on: (a) oral pain (for example, requests pain medication or refuses mouth examination), (b) nausea (for instance, retches or keeps emesis basin near), (c) wellness (for example, talks voluntarily or smiles), (d) verbal complaints of pain, and (e) verbal complaints of nausea. The behavioral measures demonstrated good interday reliability (range, 0.70-0.86) and construct validity as demonstrated by a multitrait, multimethod correlation matrix.

Adult↗

PubMed1988

Growth changes in the nasal profile from 7 to 18 years of age.

Lateral head cephalograms of 17 male and 23 female subjects, aged 7 to 18 years, were evaluated for age changes in morphology and position of the nose with reference to the pterygomaxillary vertical plane. The study was confined to persons with normal facial profiles, normal overjets, and Class I molar relationships. Four linear and two angular dimensions were measured. Statistical analysis included the calculation of medians, Q ranges, proportion of growth completed at each age expressed as a percentage of the size of the variable at 18 years, and a pairwise correlation matrix. The results indicated that (1) increments in nose height, depth, and inclination are essentially complete in girls by 16 years of age, while continuing to increase in males up to and beyond 18 years; (2) the ratio of upper to lower nose heights remains at approximately 3:1 from 7 to 18 years in both sexes; (3) the ratio of nose depth to sagittal depth of the underlying skeleton changed from 1:2 at 7 years in both sexes to 1:1.5 in male subjects and 1:1.6 in female subjects at 18 years; (4) although upper nose inclination was similar for the two sexes, lower nose inclination was slightly larger in female subjects, especially after the age of 10 years; (5) persons with greater increments in nose depth than in nose height, or in nose depth than in the sagittal depth of the underlying skeleton, develop larger upper nose inclinations. The impact of nasal growth changes on orthodontic diagnosis and treatment planning was emphasized.

Adolescent↗

PubMedDate not supplied

Measuring stress in the mildly intellectually handicapped: the factorial structure of the Subjective Stress Scale.

The Subjective Stress Scale (SSS) was developed by Bramston and Bostock (1994) to provide a sensitive measure of stress for people with intellectual disabilities. This study examined the underlying structure of the SSS by analysing responses of 221 intellectually disabled people to the questionnaire. Exploratory factor analysis of the interitem correlation matrix yielded at least three solutions that were quite interpretable: a one-factor, a two-factor, and a four-factor solution. Factors in all three solutions bore a strong resemblance to stress dimensions reported for the general population using other stress measures. The results suggest that although the actual stressors vary, persons with mild intellectual disability are affected by the same major stress dimensions as the general population. The results also suggest that the SSS can be used as a much needed measure of subjective stress levels in people with mild intellectual disabilities.

Adult↗

PubMedDate not supplied

Response to Mathias and Nettelbeck on the structure of competence: need for theory-based methods to test theory-based questions.

In this paper, we respond to a 1992 study by Mathias and Nettelbeck in which, using exploratory factor analysis, they argued that the structure of intelligence in persons with mental retardation deviates from the model previously proposed by Greenspan. Applying the LISREL method of confirmatory factor analysis to Mathias and Nettelbeck's original correlation matrix, we found the Greenspan model (in which social and practical intelligence form separate factors) to be an equally plausible interpretation of their data as the single (Interpersonal Competence) factor found by Mathias and Nettelbeck. The fundings are discussed with respect to (a) the importance of using theory-based methods when addressing theory-based questions and (b) the role of social intelligence in the ongoing controversy over the meaning of mental retardation.

Factor Analysis, Statistical↗

PubMed1996

Using Features for the Storage of Patterns in a Fully Connected Net.

One of the many possible conditions for pattern storage in a Hopfield net is to demand that the local field vector be a pattern reconstruction. We use this criterion to derive a set of weights for the storage of correlated biased patterns in a fully connected net. The connections are built from the eigenvectors or principal components of the pattern correlation matrix. Since these are often identified with the features of a pattern set we have named this particular set of weights as the feature matrix. We present simulation results that show the feature matrix to be capable of storing up to N random patterns in a network of N spins. Basins of attraction are also investigated via simulation and we compare them with both our theoretical analysis and those of the pseudo-inverse rule. A statistical mechanical investigation using the replica trick confirms the result for storage capacity. Finally we discuss a biologicaly plausible learning rule capable of realising the feature matrix in a fully connected net. Copyright 1996 Elsevier Science Ltd

Journal Article↗

PubMed2005

Influence of the very polluted inputs of the Tinto-Odiel system on the adjacent littoral sediments of southwestern Spain: a statistical approach.

A spatial and temporal analysis (period 1990-2003) of 15 sampling points distributed along the southwestern Spanish coast permits to delimitate the influence area of the extremely polluted discharges coming from the Tinto-Odiel system in the bottom sediments of the adjacent littoral area. As, Cu, Pb and Zn are the main heavy metals transported by the freshwater runoffs toward the shallow shelf and present very high negative (r < -0.7) and significant (p < 0.001) correlations with the distance to the estuarine mouth. The statistical analysis (index of geoaccumulation, Pearson correlation matrix, cluster analysis) of their concentrations in the littoral sediments located between the Guadiana and Guadalquivir mouths delimitates three zones: (a) Zone 1 (from the estuarine mouth to 6 km to the east), characterized by moderate to strongly polluted bottom sediments and main responsible of the mean annual variations of the former heavy metals in the area studied; (b) Zone 2 (from 21.2 km to the west to 29 km to the east), characterized by moderate pollution levels; and (c) Zone 3, located near the Guadiana and Guadalquivir mouths, with very low As-Cu-Pb contents and unpolluted to moderately levels of Zn due to urban sewages or the presence of local low mobility areas for this element.

Data Interpretation, Statistical↗

PubMed2005

Lead, cadmium and arsenic bioavailability in the abandoned mine site of Cabezo Rajao (Murcia, SE Spain).

An in vitro method that simulated the physiological conditions of the digestive process was applied to samples taken from an old mining site, providing information on the levels of metals (Cd, Pb and As) that can be ingested and assimilated by humans. Samples were first characterized by determining pH, texture, mineralogical composition and total metal contents. The mean pH value was 5.4, ranging from 3.1 to 8.4. The mean total metal content for Pb was 2,632+/-59 mg kg(-1), 65+/-1.5 mg kg(-1) for Cd and 279.9+/-9.9 mg kg(-1) for As. Cadmium was the most bioavailable metal both in the stomach and intestinal phases (mean value of 47% and 27.8%, respectively), followed by lead (25.3% and 11.5%) and arsenic (4.9% and 0.5%). A Pearson correlation matrix suggested that pH and mineralogical composition were important factors controlling metal bioavailability from materials in abandoned mining sites.

Arsenic↗

PubMed2006

Distribution-insensitive cluster analysis in SAS on real-time PCR gene expression data of steadily expressed genes.

Cluster analysis is a tool often employed in the micro-array techniques but used less in the real-time PCR. Herein we present core SAS code that instead of the Euclidian distances takes correlation coefficient as a dissimilarity measure. The dissimilarity measure is made robust using a rank-order correlation coefficient rather than a parametric one. There is no need for an overall probability adjustment like in scoring methods based on repeated pair-wise comparisons. The rank-order correlation matrix gives a good base for the clustering procedure of gene expression data obtained by real-time RT-PCR as it disregards the different expression levels. Associated with each cluster is a linear combination of the variables in the cluster, which is the first principal component. Large set of variables can then be replaced by the set of cluster components with little loss of information. In this way, distinct clusters containing unregulated housekeeping genes along with other steadily expressed genes can be disclosed and utilized for standardization purposes. Simulated data in parallel with the data from a biological experiment were taken to validate the SAS macro. For both cases, good intuitive results were obtained.

Cluster Analysis↗

PubMed2006

An S-Plus function to calculate relative risks and adjusted means for regression models using natural splines.

We provide for generalized linear regression models that use natural cubic splines to model predictors an S-Plus function to calculate relative risks (RR), log relative risk (logRR), mean percent change (MPC) for continuous covariates modeled using a logarithmic link as well as adjusted means differences (MD) for the identity link. The function makes explicit use of the natural spline basis functions, the estimated coefficients for each natural spline basis function, and the fitted correlation matrix for the estimated coefficients and can thus accommodate any number of degrees of freedom. The main function produces a publication-quality graph of all of these quantities as compared to a user-specified reference value as well as the associated confidence limits. In another function, specific values of these statistics comparing a vector of values of the independent variable to the reference value can be calculated rather than plotted.

Regression Analysis↗

PubMed2005

Fast 3D-EM reconstruction using Planograms for stationary planar positron emission mammography camera.

At the University of Pisa we are building a PEM prototype, the YAP-PEM camera, consisting of two opposite 6 x 6 x 3 cm3 detector heads of 30 x 30 YAP:Ce finger crystals, 2 x 2 x 30 mm3 each. The camera will be equipped with breast compressors. The acquisition will be stationary. Compared with a whole body PET scanner, a planar Positron Emission Mammography (PEM) camera allows a better, easier and more flexible positioning around the breast in the vicinity of the tumor: this increases the sensitivity and solid angle coverage, and reduces cost. To avoid software rejection of data during the reconstruction, resulting in a reduced sensitivity, we adopted a 3D-EM reconstruction which uses all of the collected Lines Of Response (LORs). This skips the PSF distortion given by data rebinning procedures and/or Fourier methods. The traditional 3D-EM reconstruction requires several times the computation of the LOR-voxel correlation matrix, or probability matrix {p(ij)}; therefore is highly time-consuming. We use the sparse and symmetry properties of the matrix {p(ij)} to perform fast 3D-EM reconstruction. Geometrically, a 3D grid of cubic voxels (FOV) is crossed by several divergent 3D line sets (LORs). The symmetries occur when tracing different LORs produces the same p(ij) value. Parallel LORs of different sets cross the FOV in the same way, and the repetition of p(ij) values depends on the ratio between the tube and voxel sizes. By optimizing this ratio, the occurrence of symmetries is increased. We identify a nucleus of symmetry of LORs: for each set of symmetrical LORs we choose just one LOR to be put in the nucleus, while the others lie outside. All of the possible p(ij) values are obtainable by tracking only the LORs of this nucleus. The coordinates of the voxels of all of the other LORs are given by means of simple translation rules. Before making the reconstruction, we trace the LORs of the nucleus to find the intersecting voxels, whose p(ij) values are computed and stored with their voxel coordinates on a hard disk. Only the non-zero p(ij) are considered and their computation is performed just once. During the reconstruction, the stored values are loaded and are available in the random access memory for all of the operations of normalization, backprojection and projection: these are now performed rapidly, because the application of the translation rules is much faster than the probability computations. We tested the algorithm on Monte Carlo data fully simulating the typical YAP-PEM clinical condition. The adopted algorithm gives an excellent positioning capability for hot spots in the camera FOV. To use all of the possible skew LORs in the FOV avoids the software rejection of collected data. Reconstructed images indicate that a 5mm diameter tumor of 37 kBq/cm3, in an active breast with a 10:1 Tissue to Background ratio (T/B), with a 10 min acquisition, for a head distance of 5 cm, can be detected by the YAP-PEM with a SNR of 8.7+/-1.0. The obtained SNR values depend linearly on the tumor volume. The algorithm allows one to discriminate between two hot sources of 5.0 mm diameter if they do not lie on the same axis. The YAP-PEM is now in the assembly stage.

Algorithms↗