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PubMed1987

The utility of principal component analysis for the image display of brain lesions. A preliminary, comparative study.

Principal component analysis (PCA), a common tool from multivariate statistical analysis, has been implemented into the computer display system of a MR imaging device. PCA allows the calculation of images in which the information in a defined region of interest inherent in the basic acquired images is condensed. PCA image calculation has been applied to acquired MR studies of 13 patients with brain lesions. The appearance of the brain lesions on the resultant PCA images was scored in comparison to the acquired images before and after administration of Gd-DTPA as well as to other calculated images including T1, T2, hydrogen density, and contrast-optimized images. The conspicuity of a lesion and the number of distinguishable components within a lesion were slightly superior on PCA than on the acquired images. PCA is an analytical tool for MR imaging that should be helpful in revealing information that is inherent in, but not readily visible on, standard acquired MR images.

Brain Neoplasms↗
PubMed2004

Improving the spatial specificity of canonical correlation analysis in fMRI.

The contrast-to-noise ratio (CNR) is often very low in fMRI data, and standard univariate methods suffer from a loss of sensitivity in the context of noise. The increased power of a multivariate statistical analysis method known as canonical correlation analysis (CCA) in fMRI studies with low CNR was established previously. However, CCA in its conventional form has weak spatial specificity. In this work we propose a new assignment scheme to rectify this problem. It is shown that the new method has improved spatial specificity as well as sensitivity compared to conventional CCA for detecting activation patterns in fMRI.

Adult↗
PubMedDate not supplied

Acetylcholine receptor antibodies in myasthenia gravis.

A multivariate statistical analysis of levels of serum acetylcholine receptor antibody (AChR Ab) obtained from 197 patients with various clinical forms of myasthenia gravis (MG) was performed. Elevated AChR Ab levels are specific for MG, but normal AChR Ab levels do not rule out MG. Patients in remission or with purely ocular MG had the lowest incidence of elevation of serum AChR Ab levels, while patients with generalized, severe MG, particularly in the presence of thymoma, tended to have the greatest antibody elevations. Corticosteroids depressed AChR Ab levels, but thymectomy did not exert a consistent effect on antibody levels within a 24- to 30-month postoperative period. The relatively low 55% positivity of antibody elevations in all 197 patients probably reflects the use of heterologous (rat) AChR.

Adrenal Cortex Hormones↗
PubMed2003

Analysis of complex autoantibody repertoires by surface-enhanced laser desorption/ionization-time of flight mass spectrometry.

Normal sera contain a large number of naturally occurring autoantibodies which can mask important disease-associated ones. Western blotting has evolved as the most important tool to demonstrate autoantibodies in autoimmune diseases, because of its ability to simultaneous screening for a wide spectrum of different antigens. In previous studies we have shown the diagnostic potential of the analysis of autoantibodies in autoimmune diseases by means of multivariate statistics and artificial neural networks. However, the Western blotting procedure remains very time-consuming and is also limited in sensitivity. Therefore, we used an on-chip approach for the analysis of autoantibodies. This ProteinChip system uses ProteinChip arrays and SELDI-TOF MS (surface-enhanced laser desorption/ionization-time of flight mass spectrometry) technology for capturing, detection, and analysis of proteins without labelling or without the need of chemical modification. The microscale design of the arrays allows the analysis of very small quantities of proteins. In the present study, we used arrays with biologically activated surfaces that permit antibody capture studies. Protein-A-Chips were incubated with sera of patients (n = 12). After washing, the chips were incubated with a complex solution of autoantigens and subsequently washed again. If the Protein-A bound autoantibodies recognized their antigens, these proteins could be separated by their molecular masses and were to be detected by mass spectrometry. Previous studies using monoclonal antibodies have demonstrated that the detection limit is in the attomole level. Furthermore, all sera were analyzed by conventional Western blotting for direct comparison. In the present study, we have shown complex on-chip antibody-antigen reactions. At higher molecular weights (> 30 kDa) the detection sensitivity of this on-chip method was comparable to conventional Western blotting. At lower molecular mass, the Western blot technique is easily exceeded by the on-chip method. Considering that this on-chip procedure is quite easy to use, is much less time-consuming than Western blotting, and is much more sensitive at least in the low molecular weight range, the SELDI-TOF technology is a very promising approach for the screening of autoantibodies in autoimmune diseases. Due to its versatility, this on-chip technology could allow the large-scale screening for complex autoantibody distributions for diagnostic purposes and early detection of autoimmune diseases might be possible.

Autoantibodies↗
PubMed2004

In vitro and in silico processes to identify differentially expressed proteins.

We present an integrated proteomics platform designed for performing differential analyses. Since reproducible results are essential for comparative studies, we explain how we improved reproducibility at every step of our laboratory processes, e.g. by taking advantage of the powerful laboratory information management system we developed. The differential capacity of our platform is validated by detecting known markers in a real sample and by a spiking experiment. We introduce an innovative two-dimensional (2-D) plot for displaying identification results combined with chromatographic data. This 2-D plot is very convenient for detecting differential proteins. We also adapt standard multivariate statistical techniques to show that peptide identification scores can be used for reliable and sensitive differential studies. The interest of the protein separation approach we generally apply is justified by numerous statistics, complemented by a comparison with a simple shotgun analysis performed on a small volume sample. By introducing an automatic integration step after mass spectrometry data identification, we are able to search numerous databases systematically, including the human genome and expressed sequence tags. Finally, we explain how rigorous data processing can be combined with the work of human experts to set high quality standards, and hence obtain reliable (false positive < 0.35%) and nonredundant protein identifications.

Body Fluids↗
PubMed1989

Incidence and prognostic significance of lymphatic and vascular invasion in radical prostatectomy specimens.

A review of 55 radical prostatectomy specimens from patients with clinically localized carcinoma of the prostate was performed. Blinded review of slides was performed by a single pathologist and urologist. Criteria for invasion were encroachment by tumor of the lymphatic or vascular lumen and evidence of reaction around or in the lymphatic or vascular channel. Notation was made of the degree and location of lymphatic and vascular invasion. All patients had a minimum of 5 years of follow-up. Twenty-one of 55 (38%) patients either had lymphatic or vascular invasion, and seven (13%) had both findings. In the majority of these patients the degree of invasion was rare (71%), while multifocal (19%) and diffuse (10%) involvement were seen less frequently. Nine patients experienced either progression of their tumors or death from disease. Those patients with evidence of lymphatic or vascular invasion had a fourfold greater incidence of progression and or death. However, the presence of lymphatic or vascular invasion was clearly related to both tumor grade and stage, and multivariate statistical analysis demonstrated that its prognostic significance was dependent upon tumor grade.

Carcinoma↗
PubMed2006

The detection of phenotypic differences in the metabolic plasma profile of three strains of Zucker rats at 20 weeks of age using ultra-performance liquid chromatography/orthogonal acceleration time-of-flight mass spectrometry.

Analysis of biological fluids using ultra-performance liquid chromatography/mass spectrometry (UPLC/MS) (metabonomics) can allow new insights to be gained into disease processes, with advances in chromatographic techniques enabling the detection of thousands of metabolites. In this work metabonomics has been used to investigate the metabolic processes involved in type II diabetes in the Zucker obese rat. Plasma was analyzed from three different strains, the Zucker (fa/fa) obese, Zucker lean and the lean/(fa) obese cross. Using UPLC/MS, ca. 10,000 ions were detected due to the narrow peak widths and excellent peak shapes achieved with this technology. Confidence in the chromatographic performance was demonstrated by the use of quality control standards. The positive and negative ion total ion chromatograms obtained from the three strains were readily distinguishable using multivariate statistical analysis. The greatest difference was observed between the Zucker lean and Zucker lean/(fa) rats compared to the Zucker (fa/fa) obese rats. Positive ions m/z 220 (4.36 min), 282(3.78 min), 359 (5.33 min) and 405 (7.77 min) were elevated in the plasma derived from Zucker lean rats whilst ions m/z 385 (6.80 min) and 646 (4.36 min) were at a lower concentration compared to the plasma from the Zucker (fa/fa) obese animals. Negative ions elevated in the Zucker lean rats included m/z 212 (2.30 min), 514 (2.85 min), 295 (4.39 min), 329 (3.11 min), 343 (2.86 min) and 512 (2.86 min) with ions m/z 538 (4.18 min), 568 (4.18 min), 568 (5.09 min) and 612 (4.30 min) being raised in the samples derived from Zucker (fa/fa) obese animals. The ion m/z 514 (3.85 min) was found to correspond to taurocholate, providing further support for an involvement of taurine metabolism in diabetes.

Animals↗
PubMed2007

High-throughput direct-infusion ion trap mass spectrometry: a new method for metabolomics.

A fast method was developed to directly infuse raw plant extracts into a linear ion trap mass spectrometer, using the ion trap to isolate and fragment as many ions as possible from the extract. The full mass spectra can be analysed by multivariate statistics to determine discriminating ions, and the fragmentation data allows rapid classification or identification of these ions. The methodology was used to screen a wide range of strains of endophytic fungi in perennial ryegrass seeds for differences in metabolic profiles. The results show that this newly developed methodology is able to determine discriminating ions that can be present in very low concentrations. It also yielded sufficient fragmentation data to classify or identify the discriminating ions.

Ascomycota↗
PubMed2002

Classifying class I and class II compounds by hydrophobicity and hydrogen bonding descriptors.

The successful development of quantitative structure-activity relationships (QSARs) and the prediction of toxicity based on QSARs depend on the correct classification of the mechanism of toxic action of chemical compounds. The toxicity mechanism of a compound can be determined by a few existing methods, such as studying the chemical structure of the compound for certain substructures and assigning a mechanism accordingly. However, these methods are less reliable for compounds with complex structures and are usually complicated. A novel descriptor-based method employing a multivariate statistical technique--discriminant analysis--was developed in this study for the classification of class I and class II compounds. The discriminating variables used in discriminant analysis were the hydrophobicity descriptor log(K(ow)) and the hydrogen bonding descriptors E(LUMO), E(HOMO), Q(+), and Q(-). Because only numerical values of these descriptors are required for this method, which can be calculated, no additional experimental work was required for the toxicity mechanism classification of new compounds. A nonlinear discriminant function was generated that could not be expressed explicitly. Assessing the predicting ability of the discriminant function by the cross-validation method showed that a low total error rate, 4.2% was achieved.

Environmental Pollutants↗
PubMed1993

Synonymous codon usage in Kluyveromyces lactis.

The nature and variation of synonymous codon usage in 47 open reading frames from Kluyveromyces lactis have been investigated. Using multivariate statistical analysis, a single major trend among K. lactis genes was identified that differentiates among genes by expression level: highly expressed genes have high codon usage bias, while genes of low expression level have low bias. A relatively minor secondary trend differentiates among genes according to G+C content at silent sites. In these respects, K. lactis is similar to both Saccharomyces cerevisiae and Candida albicans, and the same 'optimal' codons appear to be selected in highly expressed genes in all three species. In addition, silent sites in K. lactis and S. cerevisiae have similar G+C contents, but in C. albicans genes they are more A+T-rich. Thus, in all essential features, codon usage in K. lactis is very similar to that in S. cerevisiae, even though silent sites in genes compared between these two species have undergone sufficient mutation to be saturated with changes. We conclude that the factors influencing overall codon usage, namely mutational biases and the abundances of particular tRNAs, have not diverged between the two species. Nevertheless, in a few cases, codon usage differs between homologous genes from K. lactis and S. cerevisiae. The strength of codon usage bias in cytochrome c genes differs considerably, presumably because of different expression patterns in the two species. Two other, linked, genes have very different G+C content at silent sites in the two species, which may be a reflection of their chromosomal locations. Correspondence analysis was used to identify two open reading frames with highly atypical codon usage that are probably not genes.

Base Sequence↗
PubMed1996

Absence of relationship between the level of electron transport chain activities and aging in human skeletal muscle.

We investigated the relationship between age and respiratory chain function of skeletal muscle mitochondria in 132 control individuals (15 to 95 years old). Muscle mitochondria were studied polarographically and spectrophotometrically. By regression analysis, we found a significant inverse correlation between age and oxygen uptake linked to substrate oxidation (succinate, glutamate-malate or ascorbate-TMPD). However, this significance disappeared after including physical activity and tobacco consumption as confounding variables in a multivariate statistical analysis. Similarly, the activity of respiratory chain complexes individually measured did not decline with age. It therefore appears that respiratory chain activity in human skeletal muscle mitochondria is substantially undamaged during the aging process.

Adolescent↗
PubMed1998

Evaluation of heavy metal sediment toxicity in littoral ecosystems using juveniles of the fish Sparus aurata.

The toxicity of sediments from two littoral ecosystems of the Gulf of Cadiz was tested using juveniles of the fish Sparus aurata (seabream). Concentrations of total carbon and nitrogen, organic carbon, 14 heavy metals (Fe, Mn, Cu, Zn, Pb, Cd, Ag, Hg, As, Sn, V, Ni, Co, Cr), and the surfactant linear alkyl benzenesulfonate (LAS) in the sediments were measured. Chemical analysis was performed in the stations to determine the degree and nature of contamination. Four different endpoints were selected in the toxicity test: survival, superficial alteration, hematocrit analysis, and histological damage. After 14 days, survival, superficial alteration, and hematocrit analysis did not reveal effects of the different sediments tested. The histological and cellular damage revealed a more sensitive response to measured chemicals in sediments and they were found to be a powerful tool to evaluate sediment toxicity effects. Semiquantitative evaluation of the histological damage demonstrated correlation with sediment concentrations of some of the heavy metals (Cr, Cd, Pb, Ag, Cu) and the surfactant (LAS). Data derived from chemical concentrations and toxicity tests were assembled by multivariate statistical techniques (principal components analysis) to identify the ranges of chemical concentrations associated with an adverse effect. The results obtained, as suggested by site-specific sediment quality values, were the following: Cr>/=90.2; Cd>/=1.24; Pb>/=52.5; Ag>/=0.68; Cu>/=71.2; LAS>/=8.7 mg kg-1 of dry sediment. These results are mainly in concordance with studies performed in other areas of the world and therefore support wide application of the method.

Animals↗
PubMedDate not supplied

Fungal volatiles as indicators of food and feeds spoilage.

Fungal growth leads to spoilage of food and animal feeds and to formation of mycotoxins and potentially allergenic spores. Fungi produce volatile compounds, during both primary and secondary metabolism, which can be used for detection and identification. Fungal volatiles from mainly Aspergillus, Fusarium, and Penicillium have been characterized with gas chromatography, mass spectrometry, and sensory analysis. Common volatiles are 2-methyl-1-propanol, 3-methyl-1-butanol, 1-octen-3-ol, 3-octanone, 3-methylfuran, ethyl acetate, and the malodorous 2-methyl-isoborneol and geosmin. Volatile sesquiterpenes can be used for taxonomic classification and species identification in Penicillium, as well as to indicate mycotoxin formation in Fusarium and Aspergillus. Developments in sensor technology have led to the construction of "electronic noses" (volatile compound mappers). Exposure of different nonspecific sensors to volatile compounds produces characteristic electrical signals. These are collected by a computer and processed by multivariate statistical methods or in an artificial neural network (ANN). Such systems can grade cereal grain with regard to presence of molds as efficiently as sensory panels evaluating grain odor. Volatile compound mapping can also be used to predict levels of ergosterol and fungal colony-forming units in grain. Further developments should make it possible to detect individual fungal species as well as the degree of mycotoxin contamination of food and animal feeds.

Animal Feed↗
PubMed2001

The Composition of the Milk Fat Globule Surface Alters the Structural Characteristics of the Coagulum.

The effects of the composition of a fat globule surface in reconstituted milks on the properties of rennet-induced coagulums were studied by rheological measurements and by front-face fluorescence spectroscopy in combination with a multivariate statistical method to investigate, at a molecular level, the evolution of the structure during the milk coagulation process. Reconstituted milks used in this study were prepared from different fat-in-water emulsions stabilized by whole skim-milk proteins, beta-casein, or beta-lactoglobulin. Coagulation of milk reconstituted with natural fat globules was also investigated. The study showed that the fat droplet/water interface influences the rheological properties (G' modulus) of the reconstituted milks during the coagulation process. The tryptophan fluorescence emission spectra of proteins were recorded during the kinetics of coagulation. The results of the principal component analysis performed on the spectral data showed a discrimination in the different systems investigated. It was shown that the fluorescence properties of protein tryptophans and, consequently, the structures of the protein networks were different for the investigated systems. The development of fluorescence transfer between protein tryptophans and fat-globule vitamin A during the coagulation kinetics agreed with the interactions between the protein network and fat globules. Copyright 2001 Academic Press.

Journal Article↗
PubMed1999

The reaction center complex from the green sulfur bacterium Chlorobium tepidum: a structural analysis by scanning transmission electron microscopy.

The three-dimensional (3D) structure of the reaction center (RC) complex isolated from the green sulfur bacterium Chlorobium tepidum was determined from projections of negatively stained preparations by angular reconstitution. The purified complex contained the PscA, PscC, PscB, PscD subunits and the Fenna-Matthews-Olson (FMO) protein. Its mass was found to be 454 kDa by scanning transmission electron microscopy (STEM), indicating the presence of two copies of the PscA subunit, one copy of the PscB and PscD subunits, three FMO proteins and at least one copy of the PscC subunit. An additional mass peak at 183 kDa suggested that FMO trimers copurify with the RC complexes. Images of negatively stained RC complexes were recorded by STEM and aligned and classified by multivariate statistical analysis. Averages of the major classes indicated that different morphologies of the elongated particles (length=19 nm, width=8 nm) resulted from a rotation around the long axis. The 3D map reconstructed from these projections allowed visualization of the RC complex associated with one FMO trimer. A second FMO trimer could be correspondingly accommodated to yield a symmetric complex, a structure observed in a small number of side views and proposed to be the intact form of the RC complex.

Bacterial Proteins↗
PubMedDate not supplied

4-A projection map of bacteriophage T4 DNA helix-destabilizing protein (gp32*I) crystal by 400-kV electron cryomicroscopy.

Ice-embedded crystals of bacteriophage T4 DNA helix-destabilizing protein gp32*I were imaged by computer-controlled spot-scanning on a 400-kV electron cryomicroscope. gp32*I crystals generally have different steps of thickness within a crystal; each step can have different symmetry. Multivariate statistical analysis enabled us to unambiguously select spot-scan images that consist entirely of one motif which were processed subsequently by crystallographic Fourier-averaging techniques. The computed phases of the resulting reflections were evaluated for symmetry in projection, and some of those images were correlated with independent thickness measurements of freeze-dried samples of the same crystals. The structure factors with pgg symmetry from nine spot-scan images were merged, and the mean figure of merit of merged phases was better than 0.9 for data at resolution up to 4 A. A projection map was generated and showed multiple density peaks that corresponded to the high-resolution features of gp32*I.

Bacteriophage T4↗
PubMedDate not supplied

Structure of Lumbricus terrestris hemoglobin at 30 A resolution determined using angular reconstitution.

The three-dimensional (3D) structure of the giant hemoglobin of the common earthworm Lumbricus terrestris was determined from cryomicroscopical images of a vitrified molecular solution. From about 5000 molecular images, the best-fit 3D structure was calculated using recently developed analysis techniques. Multivariate statistical analysis data compression and automatic classification were used to find the characteristic projection images of the oligomer. The angular reconstitution approach was then applied to find the Euler angle orientations of these characteristic views. The Lumbricus hemoglobin molecule has an overall D6 (622) point-group symmetry and is found to have a local threefold symmetry axis within the 1/12th subunit. This additional symmetry appears to predict the presence of 36 abcd globin tetramers in the Lumbricus hemoglobin or a total of 144 heme chains for the whole oligomer. A distinct doughnut-shaped structure is elucidated in the center of the molecule. This central subunit, representing around 10% of the protein volume, may consist of non-heme-containing linker chains found generally in giant annelid hemoglobins.

Animals↗
PubMed1997

Electron Tomography of Single Ice-Embedded Macromolecules: Three-Dimensional Alignment and Classification

From 3-D reconstructions of automatically recorded tilt series of ice-embedded macromolecules, several hundred 3-D images of single particles can be extracted. Here we describe correlation-based techniques to align the particles with respect to translation and orientation in 3-D and the calculation of an averaged reconstruction after application of the correct weighting function to the particle projections. Multivariate statistical analysis and classification are applied to the set of three-dimensionally reconstructed particles to investigate interimage variations on the 3-D level. Copyright 1997 Academic Press. Copyright 1997 Academic Press

Journal Article↗