Metabonomics: evaluation of nuclear magnetic resonance (NMR) and pattern recognition technology for rapid in vivo screening of liver and kidney toxicants.
(17/3779)
The purpose of this study was to evaluate the feasibility of metabonomics technology for developing a rapid-throughput toxicity screen using 2 known hepatotoxicants: carbon tetrachloride (CCl(4)) and alpha-naphthylisothiocyanate (ANIT) and 2 known nephrotoxicants: 2-bromoethylamine (BEA) and 4-aminophenol (PAP). In addition, the diuretic furosemide (FURO) was also studied. Single doses of CCl(4) (0.1 and 0.5 ml/kg), ANIT (10 and 100 mg/kg), BEA (15 and 150 mg/kg), PAP (15 and 150 mg/kg) and FURO (1 and 5 mg) were administered as single IP or oral doses to groups of 4 male Wistar rats/dose. Twenty-four-h urine samples were collected pretest, daily through Day 4, and on Day 10 (high dose CCl(4) and BEA only). Blood samples were taken on Days 1, 2, and 4 or 1, 4, and 10 for clinical chemistry assessment, and the appropriate target organ was examined microscopically. NMR spectra of urine were acquired and the data processed and subjected to principal component analyses (PCA). The results demonstrated that the metabonomic approach could readily distinguish the onset and reversal of toxicity with good agreement between clinical chemistry and PCA data. In at least 2 instances (ANIT and BEA), PCA analysis suggested effects at low doses, which were not as evident by clinical chemistry or microscopic analysis. Furosemide, which had no effect at the doses employed, did not produce any changes in PCA patterns. These data support the contention that the metabonomic approach represents a promising new technology for the development of a rapid throughput in vivo toxicity screen. (+info)
Ultrasonographic tissue characterization in monitoring tumor response to neoadjuvant chemotherapy in locally advanced breast cancer (work in progress).
(18/3779)
A program of computer-assisted texture analysis was applied to evaluate its usefulness for objective description of changes in tumor architecture due to primary medical treatment in patients with locally advanced breast cancer. Changes in values of parameters of the statistical pattern recognition technique were compared to ultrasonographically depictable, subjectively recorded changes in echogenicity and echotexture (brightness, homogeneity) and reviewed with regard to histopathologic evaluation of tumor regression. Characteristic trends of defined quantitative texture parameters (mean gradient, mean gray value, contrast from the co-occurrence matrix) corresponded to visually depictable changes of the B-mode image and underlying histopathologic changes. The results indicate that quantitative texture analysis may aid in noninvasive monitoring of tumor response to neoadjuvant chemotherapy. (+info)
Multidimensional rhythm disturbances as a precursor of sustained ventricular tachyarrhythmias.
(19/3779)
Cardiac cycle dynamics reflect underlying physiological changes that could predict imminent arrhythmias but are obscured by high complexity, nonstationarity, and large interindividual differences. To overcome these problems, we developed an adaptive technique, referred to as the modified Karhunen-Loeve transform (MKLT), that identifies an individual characteristic ("core") pattern of cardiac cycles and then tracks the changes in the pattern by projecting the signal onto characteristic eigenvectors. We hypothesized that disturbances in the core pattern, indicating progressive destabilization of cardiac rhythm, would predict the onset of spontaneous sustained ventricular tachyarrhythmias (VTAs) better than previously reported methods. We analyzed serial ambulatory ECGs recorded in 57 patients at the time of VTA and non-VTA 24-hour periods. The disturbances in the pattern were found in 82% of the recordings before the onset of impending VTA, and their dimensionality, defined as the number of unstable orthogonal projections, increased gradually several hours before the onset. MKLT provided greater sensitivity and specificity (70% and 93%) compared with the best traditional method (68% and 67%, respectively). We present a theoretical analysis of MKLT and describe the effects of ectopy and slow changes in cardiac cycles on the disturbances in the pattern. We conclude that MKLT provides greater predictive accuracy than previously reported methods. The improvement is due to the use of individual patterns as a reference for tracking the changes. Because this approach is independent of the group reference values or the underlying clinical context, it should have substantial potential for predicting other forms of arrhythmic events in other populations. (+info)
APAP, a sequence-pattern recognition approach identifies substance P as a potential apoptotic peptide.
(20/3779)
We have previously described a novel cancer chemotherapeutic approach based on the induction of apoptosis in targeted cells by homing pro-apoptotic peptides. In order to improve this approach we developed a computational method (approach for detecting potential apoptotic peptides, APAP) to detect short PAPs, based on the prediction of the helical content of peptides, the hydrophobic moment, and the isoelectric point. PAPs are toxic against bacteria and mitochondria, but not against mammalian cells when applied extracellularly. Among other peptides, substance P was identified as a PAP and subsequently demonstrated to be a pro-apoptotic peptide experimentally. APAP thus provides a method to detect and ultimately improve pro-apoptotic peptides for chemotherapy. (+info)
Unsupervised classification of noisy chromosomes.
(21/3779)
MOTIVATION: Almost all methods of chromosome recognition assume supervised training; i.e. we are given correctly classified chromosomes to start the training phase. Noise, if any, is confined only in the representation of the chromosomes and not in the classification of the chromosomes. During the recognition phase, the problem is simply to calculate the string edit distance of the unknowns to the representatives chosen from the training phase and classify the unknowns accordingly. RESULTS: In this paper, a general method to tackle the difficult unsupervised induction problem is described. The success of the method is demonstrated by showing how the inductive agent learns weights in a dynamic manner that allows it to distinguish between noisy median and telocentric chromosomes without knowing their proper labels. The process of learning is characterized as the process of finding the right distance function, i.e. the distance function that can nicely separate the classes. (+info)
A prospective optical surface scanning and cephalometric assessment of the effect of functional appliances on the soft tissues.
(22/3779)
The aim of this study was to evaluate the effect of different functional appliances on the soft tissues as assessed by cephalometry and optical surface scanning. Forty-two patients were randomly allocated to Bass, Twin Block (TB), and Twin Block + Headgear (TB + Hg) groups. Lateral cephalograms and optical surface scans were recorded before and after the 10-month study period. ANOVA was used to test the cephalometric variables for differences at the 5 per cent level. The optical surface scanning and cephalometric results were consistent in the sagittal dimension. In the vertical dimension, however, the optical surface scans consistently recorded a greater increase compared with cephalometric values. No differences were detected with regard to cephalometric values at the 5 per cent level. However, the Bass appliance produced greater forward positioning of soft tissue pogonion as assessed by optical surface scanning. (+info)
New aspects of using the structural graph-grammar based techniques for recognition of selected medical images.
(23/3779)
This report will describe the application of syntactic pattern recognition methods for analysis of morphology and recognition of pathologic symptoms of chronic diseases such as upper urinary tract disorders. Detection of these lesions will be assisted by the special graph-grammar developed in our institute for efficient analysis and recognition of such lesions. We present key points of methodology and practical results of its application. (+info)
The role of pattern databases in sequence analysis.
(24/3779)
In the wake of the numerous now-fruitful genome projects, we are entering an era rich in biological data. The field of bioinformatics is poised to exploit this information in increasingly powerful ways, but the abundance and growing complexity both of the data and of the tools and resources required to analyse them are threatening to overwhelm us. Databases and their search tools are now an essential part of the research environment. However, the rate of sequence generation and the haphazard proliferation of databases have made it difficult to keep pace with developments. In an age of information overload, researchers want rapid, easy-to-use, reliable tools for functional characterisation of newly determined sequences. But what are those tools? How do we access them? Which should we use? This review focuses on a particular type of database that is increasingly used in the task of routine sequence analysis--the so-called pattern database. The paper aims to provide an overview of the current status of pattern databases in common use, outlining the methods behind them and giving pointers on their diagnostic strengths and weaknesses. (+info)