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PubMed2002

[Characteristics of selected features of hereditary ovarian cancer in carriers of constitutional BRCA1 gene mutation].

BACKGROUND: Hereditary ovarian cancer in BRCA1 constitutional mutation carriers shows a characteristic clinical pattern. AIM OF THE STUDY: Evaluation of the type of mutation, age of onset, clinical stage (FIGO) and morphological grade (G) of ovarian cancers in BRCA1 mutation carriers. MATERIAL AND METHOD: We analyzed 16 cases of hereditary ovarian cancers from 14 families. The cases were included into studied group as a result of evaluation of pedigree criteria and molecular-genetic analyses detecting constitutional mutation--5382insC, C61G, 4153delA--founder mutations dominating the Polish population. The following features were compared between studied and control group: C1--age of onset of ovarian cancer in 5-year intervals (below 35, 40, 45, 50 and 55 years of age); C2--clinical staging (FIGO) I/II or III/IV: C3--grading (G1-G3). The data were analyzed statistically. RESULTS: Age of onset < 50, OR--2.52 is highly characteristic for BRCA1 mutation carries. Similarly the staging III/IV is more often observed in studied group--OR 2.71. The most characteristic of studied group is high morphological grading--OR 12.38. CONCLUSIONS: 1. Features of HOC in studied material and in other populations are similar 2. High morphological grading is the most characteristic for HOC in BRCA1 carriers.

Adult↗
PubMed2003

[Selected features determine pathogenicity of Staphylococcus haemolyticus].

The study have been done on S. haemolyticus strains isolated from patients hospitalized an Surgical Unit. Aim of the study was to determine pathogenic traits of S. haemolyticus: slime producing, adhesion to biomaterials, antibiotics susceptibility and the profiles of surface proteins. Among 44 S. haemolyticus strains, in the test-tube method, there have been 38% labeled as slime producing and 62% as non-producing. In the plate method at 48% slime production was noticed, while 52% strains did not produce slime. It is quite significant that all CNS strains which have an ability to produce mucus, that was proved by means of two methods (test-tube and plate), show a high level of TTC's reduction to formazan. The analysis of resistance to antibiotics in relation to slime production demonstrated more frequent antibiotic resistance of the slime-producing strains.

Animals↗
PubMed2004

A log likelihood predictor for genomic classification of oral cancer using principle component analysis for feature selection.

DNA microarrays are powerful tools for exploring gene expression and predicting disease state. However, since the number of variables (genes) typically exceeds the number of samples (tissue specimens), many potentially spurious genes may be selected for a predictor function. Principle component analysis (PCA) can greatly reduce the high-dimensional microarray data space while retaining most of the inherent variability. We propose a methodology that uses PCA to identify a predictor vector between two mutually exclusive and collectively exhaustive classes. By projecting the training set upon this vector a distribution of projections can be computed for each class. A log-likelihood ratio is then calculated for class membership. We used this methodology to classify 48 biopsy specimens as either oral squamous cell carcinoma or normal oral mucosa using oligonucleotide microarrays. The system was trained using a set of half the samples, and correctly predicted the membership of the other half. The three most highly positively and three most highly negative predictive genes were all keratins that are known markers of squamous cell carcinoma.

Biopsy↗
PubMed1989

Effects of polymyxin B on selected features of equine carbohydrate overload.

Gram negative endotoxins play a contributory role in the syndrome which results from over consumption of carbohydrates by horses and ponies. Since the antibiotic polymyxin B exerts a direct anti-endotoxin effect by chemically modifying the active lipid A moiety of endotoxin, it might be expected to protect horses after carbohydrate overload and provide a new therapeutic and experimental tool for this condition. The present study was undertaken to evaluate the effect of polymyxin B on hemostatic, hemodynamic, acid-base, and clinical aspects of the syndrome resulting from carbohydrate overload. Experimentally-induced carbohydrate overload resulted in lactic acidosis, hypercoagulability, hypovolemic shock and lameness. Although there was a slight delay in the onset of clinical signs resulting from experimental carbohydrate overload in treated animals, polymyxin B administered iv at 2.5 mg/kg every 6 hr failed to significantly ameliorate the coagulopathy, acidosis, lameness and shock induced by alimentary carbohydrate overload.

Acid-Base Imbalance↗
PubMed1987

Mammography equipment: principles, features, selection.

1. Three-phase and constant potential generators may offer advantages over single-phase generators. These include shorter exposure times with less chance for motion unsharpenss, more adequate exposure and possible lower dose, and longer tube life. 2. Control of tube voltage in increments of 1 kVp are desirable for screen-film mammography and 2 kVp for xeromammography. 3. Tube loading limitations should be capable of allowing an adequate mA and mAs output. A mammography unit with a lower mA output may require longer exposure times with consequent motion unsharpness and/or higher dose. The maximum mA output is limited by the power rating of the tube and not by the power rating of the generator, which is usually much higher. Thus, tube rating charts rather than generator power rating should be used to compare the mA output of different mammography units. 4. Phototimer capability can reduce exam time, facilitate proper exposure, and reduce radiation dose. Units with a greater number of density steps and three or more photocell locations, one of which is near the edge of the film holder, provide better phototimer results. 5. A molybdenum target, beryllium window tube with 0.03 mm molybdenum added filtration is presently preferred for screen-film mammography. A tungsten target tube with 1 to 2 mm added aluminum filtration is advised for xeromammography. 6. Effective local spot size for contact mammography should be in the range of 0.2 to 0.5 mm. However, high resolution also requires sufficiently long source-to-image-receptor distances. Using measured focal spot size and source-to-image-receptor distance, it has been shown that some mammography units do not fully utilize the resolution capabilities of some available screen-film systems. On the other hand, a focal spot that is too small may limit the field size and lead to uneven energy distribution in the x-ray field. 7. In order to perform standard and supplementary mammographic projections, the C arm assembly must be capable of being located at multiple positions within a 180 degrees rotation. Greater degrees of rotation are not required. 8. The heat dissipation capability should be adequate to accommodate the anticipated work-load in terms of number of patients and patient scheduling. A mammographic unit with an anode heat capacity of 90,000 heat units or more should be adequate for most practices. A mammography unit with a heat capacity of 20,000 heat units or less may require waiting time between exposures or studies in a high-volume mammography practice. 9. The compression plate should be made of plastic, usually 1 to 4 mm thick.(ABSTRACT TRUNCATED AT 400 WORDS)

Female↗
PubMed1997

Ticks and tick-borne diseases as a constraint to sheep and goat production in Italy. Selected features.

The paper reviews basic information on small ruminant production in Italy and on the tick species commonly found on them. A total of 13 Ixodidae species have been reported to parasitise sheep in the country. The tick species were belonging to five genera: Ixodes (two species), Haemaphysalis (four species), Dermacentor (one species), Rhipicephalus (three species) and Hyalomma (three species). The same species, with the exception of Haemaphysalis inermis and Hyalomma detritum have been reported also on goats. Scarse data are available on the impact of tick borne diseases on small ruminants productivity. The zoonotic role which may be played by ticks in transmitting occupationally acquired diseases to people involved in animal husbandry and to common public which may accidentally invade grazing areas is also discussed.

Animal Husbandry↗
PubMed2001

Physicochemical and graph theoretical descriptors in developmental toxicity SAR: a comparative study.

Chemical insults to the developing fetus can lead to growth retardation, malformation, death, and functional deficits. The present study seeks to determine if physicochemical and/or graph theoretical parameters can be used to determine a structure-activity relationship (SAR) for developmental toxicity, and if consistency is observed among the selected features. The biological data utilized consists of a diverse series of compounds evaluated within the Chernoff-Kavlock in vivo mouse assay. Physicochemical parameters calculated correspond to electronic, steric, and transport properties. Graph theoretical parameters calculated include the simple, valence, and kappa indices. Both sets of parameters were independently applied to derive SARs in order to compare the quality of the respective models. Multiple random sampling, without replacement, was utilized to obtain ten training/test partitions. Models were built by linear discriminant analysis, decision trees, and neural networks respectively. Comparisons on identical sets of data were carried out to determine if any of the model building procedures had a significant advantage in terms of predictive performance. Furthermore, comparison of the features selected within and across the model building processes led to the determination of model consistency. Our results indicate that consistent features related to developmental toxicity are observed and that both physicochemical and graph theoretical parameters have equal utility.

Animals↗
PubMedDate not supplied

Prediction of protein retention times in anion-exchange chromatography systems using support vector regression.

Quantitative Structure-Retention Relationship (QSRR) models are developed for the prediction of protein retention times in anion-exchange chromatography systems. Topological, subdivided surface area, and TAE (Transferable Atom Equivalent) electron-density-based descriptors are computed directly for a set of proteins using molecular connectivity patterns and crystal structure geometries. A novel algorithm based on Support Vector Machine (SVM) regression has been employed to obtain predictive QSRR models using a two-step computational strategy. In the first step, a sparse linear SVM was utilized as a feature selection procedure to remove irrelevant or redundant information. Subsequently, the selected features were used to produce an ensemble of nonlinear SVM regression models that were combined using bootstrap aggregation (bagging) techniques, where various combinations of training and validation data sets were selected from the pool of available data. A visualization scheme (star plots) was used to display the relative importance of each selected descriptor in the final set of "bagged" models. Once these predictive models have been validated, they can be used as an automated prediction tool for virtual high-throughput screening (VHTS).

Anion Exchange Resins↗
PubMed1994

Practical aspects of fixatives in high resolution nuclear image analysis.

Three different methods of fixation (ethanol/Carbowax, formaldehyde, and Carnoy) and four different protocols (without Böhm post-fixation on an uncoated slide, and with Böhm post-fixation on Poly-L-Lysine coated slide, an uncoated slide and a previously Papanicolaou stained slide) were evaluated for their application in high resolution image analysis of Feulgen stained nuclei. The aim of the study was to find a combination with the best reproducibility and the least variance under normal laboratory conditions. Care was taken not to exclude any "normal" laboratory variability. The combinations were evaluated for densitometric, geometric, as well as texture features. Selected features were determined on a CAS-100 using the Cell Measurement Program (Cell Analysis Systems, Inc. Lombard, IL). Diploid and tetraploid rat liver nuclei were used. Ethanol/Carbowax fixation-with Böhm post-fixation proved most stable. This fixation method also gave feature values for previously Papanicolaou stained slides that were comparable to direct Feulgen stained nuclei. Acceptable results were achieved with all three fixatives and the various combinations if one adhered strictly to protocol. In routine practice this usually does not happen. Therefore Ethanol/Carbowax fixation with Böhm post-fixation was considered most suited for routine determination of feature values on the CAS-100.

Acetates↗
PubMed1990

Spatial patterns underlying population differences in the background EEG.

A method is described which can be used to extract common spatial patterns underlying the EEGs from two human populations. These spatial patterns account, in the least-squares sense, maximally for the variance in the EEGs from one population and minimally for the variance in the other population and therefore would seem to be optimal for quantitatively discriminating between the individual EEGs in the two populations. By using this method, it is suggested that the problems associated with the more common approach to discriminating EEGs, significance probability mapping, can be avoided. The method is tested using EEGs from a population of normal subjects and using the EEGs from a population of patients with neurologic disorders. The results in most cases are excellent and the misclassification which occurs in some cases is attributed to the nonhomogeneity of the patient population particularly. The advantages of the method for feature selection, for automatically classifying the clinical EEG, and with respect to the reference-free nature of the selected features are discussed.

Adolescent↗
PubMed2004

Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D).

A novel method (MOLPRINT 3D) for virtual screening and the elucidation of ligand-receptor binding patterns is introduced that is based on environments of molecular surface points. The descriptor uses points relative to the molecular coordinates, thus it is translationally and rotationally invariant. Due to its local nature, conformational variations cause only minor changes in the descriptor. If surface point environments are combined with the Tanimoto coefficient and applied to virtual screening, they achieve retrieval rates comparable to that of two-dimensional (2D) fingerprints. The identification of active structures with minimal 2D similarity ("scaffold hopping") is facilitated. In combination with information-gain-based feature selection and a naive Bayesian classifier, information from multiple molecules can be combined and classification performance can be improved. Selected features are consistent with experimentally determined binding patterns. Examples are given for angiotensin-converting enzyme inhibitors, 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors, and thromboxane A2 antagonists.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2000

[A probe for evaluating the role of HLA class II antigens coded with the DRB gene in etiopathogenesis of familial sarcoidosis in Poland using the K-nearest neighbor experimental statistical method].

The aim of this study was evaluation of the significance of HLA-DRB1,-DRB3,-DRB4,-DRB5 associated alleles in the genetic susceptibility to sarcoidosis. We investigated 17 Polish 'families with' familial occurrence of the disease. Thirty three affected family members and 78 healthy relatives and 101 healthy individuals (control group) have been typed for HLA class II DR antigens. Assuming that relatives from families with two or more affected members are more susceptible to develop sarcoidosis we considered two classes: affected and healthy family members taken together (class 1, N = 111) and healthy control group (class 2, N = 101). HLA antigens from both classes were compared using a statistical pattern recognition method. This method, called k-NN method, assumes that objects (individuals) are described by a certain number of variables called features. Selected features that played an important role in the decision to which class an individual person would be classified were: HLA-DR7, HLA-DR2(16), HLA-DR1, HLA-DR5(12), HLA-DR6(14), HLA-DR6(13), HLA-DR9, HLA-DR5(11) and HLA-DRw52. K-NN method allowed to classify properly 76% of studied subjects to healthy or disease susceptible group. However, 24 out of 100 individuals would be misclassified which gives the total error rate of 0.24. We concluded that using HLA-DR antigens as features characterising every individual we can predict with high probability to which class ("high risk" or "healthy") individual would belong.

Case-Control Studies↗
PubMed2006

In silico prediction of yeast deletion phenotypes.

Analysis of gene deletions is a fundamental approach for investigating gene function. We evaluated an algorithm that uses classification techniques to predict the phenotypic effects of gene deletions in yeast. We used a modified simulated annealing algorithm for feature selection and weighting. The selected features with high weights were phylogenetic conservation scores for bacteria, fungi (excluding Ascomycota), Ascomycota (excluding Saccharomyces cerevisiae), plants, and mammals, degree of paralogy, and number of protein-protein interactions. Classification was performed by weighted k-nearest neighbor and with support vector machine algorithms. To demonstrate how this approach might complement existing experimental procedures, we applied our algorithm to predict essential genes and genes causing morphological alterations in yeast.

Algorithms↗
PubMed1998

Design of a high-sensitivity classifier based on a genetic algorithm: application to computer-aided diagnosis.

A genetic algorithm (GA) based feature selection method was developed for the design of high-sensitivity classifiers, which were tailored to yield high sensitivity with high specificity. The fitness function of the GA was based on the receiver operating characteristic (ROC) partial area index, which is defined as the average specificity above a given sensitivity threshold. The designed GA evolved towards the selection of feature combinations which yielded high specificity in the high-sensitivity region of the ROC curve, regardless of the performance at low sensitivity. This is a desirable quality of a classifier used for breast lesion characterization, since the focus in breast lesion characterization is to diagnose correctly as many benign lesions as possible without missing malignancies. The high-sensitivity classifier, formulated as the Fisher's linear discriminant using GA-selected feature variables, was employed to classify 255 biopsy-proven mammographic masses as malignant or benign. The mammograms were digitized at a pixel size of 0.1 mm x 0.1 mm, and regions of interest (ROIs) containing the biopsied masses were extracted by an experienced radiologist. A recently developed image transformation technique, referred to as the rubber-band straightening transform, was applied to the ROIs. Texture features extracted from the spatial grey-level dependence and run-length statistics matrices of the transformed ROIs were used to distinguish malignant and benign masses. The classification accuracy of the high-sensitivity classifier was compared with that of linear discriminant analysis with stepwise feature selection (LDAsfs). With proper GA training, the ROC partial area of the high-sensitivity classifier above a true-positive fraction of 0.95 was significantly larger than that of LDAsfs, although the latter provided a higher total area (Az) under the ROC curve. By setting an appropriate decision threshold, the high-sensitivity classifier and LDAsfs correctly identified 61% and 34% of the benign masses respectively without missing any malignant masses. Our results show that the choice of the feature selection technique is important in computer-aided diagnosis, and that the GA may be a useful tool for designing classifiers for lesion characterization.

Algorithms↗