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At least 1,045 records · Page 58Linked to original sources

PubMed2003

Sequence variation and evolution of Cryphonectria hypovirus 1 (CHV-1) in Europe.

Cryphonectria hypovirus 1 (CHV-1) acts as a naturally occurring biological control agent for chestnut blight, a destructive fungal disease of chestnut trees, which has been introduced into Europe in the 1930s. We have determined partial nucleotide and deduced amino acid sequences of the ORF A of 47 CHV-1 isolates collected in Europe over a period of 28 years. Phylogenetic analysis revealed the presence of four groups or single viruses, which showed sequence divergences ranging from 11 to 19%. These results confirm the previous subtype classification based on RFLP markers, with the exception of the two CHV-1 subtypes E and D, which appear to be related closer than anticipated previously. Dates of divergences between CHV-1 subtypes, calculated from nucleotide substitution rates, indicate that the CHV-1 subtypes diverged several hundreds years ago. Our results suggest that the genetic variation among CHV-1 subtypes did not evolve in Europe and support the hypothesis of multiple introductions of CHV-1 into Europe.

Ascomycota↗

PubMedDate not supplied

Analysis of probabilistic classification learning in patients with Parkinson's disease before and after pallidotomy surgery.

This study examined the characteristics of probabilistic classification learning, a form of implicit learning previously shown to be impaired in patients with basal ganglia dysfunction (e.g., Parkinson's disease). In this task, subjects learn to predict the weather using associations that are formed gradually across many trials, because of the probabilistic nature of the cue-outcome relationships. Patients with Parkinson's disease, both before and after pallidotomy, and age-matched control subjects, exhibited evidence of probabilistic classification learning across 100 training trials. However, pallidotomy appears to hinder the learning of associations most implicit in nature (i.e., weakly associated cues). Although subjects were most sensitive to single-cue associations when learning the task, there is evidence that cue combinations contribute significantly to probability learning. The utility of multiple dependent measures is discussed.

Aged↗

PubMed1995

Discriminant analysis in treatment evaluation of ectopic eruption of the maxillary first permanent molars.

The value of an analytical routine which could be used in the evaluation of clinical studies was assessed. Stepwise discriminant analysis with stepwise selection/elimination was used to reduce the amount of data without losing information before further analyses with canonical discriminant analysis. The purpose of canonical discriminant analysis was to reveal interactions between factors associated with the ectopic eruption of the first permanent molars. Two canonical discriminant functions were used to determine the accuracy of diagnosis and the effect of treatment. This information consisted of variables which were the most important (their ranks) and their single correlations (structure coefficients) to the function itself. This information was interpreted clinically. The coefficients of the canonical discriminant functions can be used for classification purposes. The use of a scatterplot instead of simple classification tables is suggested. The scatterplot was particularly informative on how well the procedure discriminated between groups. A table based on original data is included to allow the reader to test the validity of the findings on cases of his/her own. This multivariate strategy avoids spurious intercorrelations between two or more variables analysed as multiple single factors that has a high risk of erroneous conclusions.

Child↗

PubMed1997

Carotid plaque typing by multiple-parameter ultrasonic tissue characterization.

We evaluated the ability of ultrasonic tissue characterization (UTC), based on backscattered echo signals, to distinguish among the components of advanced carotid plaques. We performed spectral analysis of echo signals acquired from human carotid endarterectomy specimens in vitro to calculate three parameters of the calibrated power spectrum: slope, intercept and total power for fibrous, lipid pool and thrombus constituents of plaque. Plaque constituents were identified histologically. We evaluated classification efficacy by discriminant function analysis. Slope and intercept parameters alone provided correct classification in 92.5%, 57.6% and 72.4% of fibrous, lipid pool and thrombus plaque components, respectively. Slope, intercept and total power used in combination improved classification of the three tissue types to 93.0%, 69.7% and 81.0%. The overall proportion of correctly classified tissue regions increased from 84.5% to 88.0% by the combined use of the three parameters. The improvement in classification that occurred when we included total power as a third parameter suggests that ultrasound plaque components may not consist solely of small, randomly distributed isotropic scatterers. Our ability to identify plaque thrombi provides motivation for future studies of parameter-based imaging methods for identifying such plaque that presents an increased risk of embolic neurologic ischemic events.

Arteriosclerosis↗

PubMed1994

Keratoconus and contact lens-induced corneal warpage analysis using the keratomorphic diagram.

PURPOSE: Videokeratography of early keratoconus may be difficult to distinguish from contact lens-induced corneal warpage, even by experienced examiners. Furthermore, topographic irregularity may be judged inconsistently if quantitative standards are not applied. Quantitative measures based on videokeratographic data were developed and evaluated to determine if improved corneal topographic classification can be achieved. METHODS: The Corneal Irregularity Coefficient (CIC) and Corneal Power Coefficient (CPC) were derived from multiple measures of mean corneal power and its variance for 207 videokeratographs of normal, warped, keratoconus, and keratoconus-suspect corneas. CIC was plotted against CPC, creating a distribution of points representing all maps that tended to be grouped according to surface conditions (the Keratomorphic Diagram). Normal, steep, abnormal, and warped zones were defined by CIC and CPC cutoff values chosen to distinguish normal from keratoconus corneas graphically. RESULTS: Seventy of 76 normal corneas were grouped in the normal zone and 6 in the steep zone; 84 of 84 keratoconus corneas were grouped in the abnormal zone; 35 of 35 contact lens-induced warpage cases were grouped in the warped zone; and 10 of 12 keratoconus-suspect corneas were grouped in the warped zone, with 2 in the abnormal zone. Serially plotted data of keratoconus progression and warpage regression demonstrated that the vector displacement of CIC and CPC values may provide a potentially useful means of distinguishing contact lens-induced warpage from keratoconus-suspect corneas. CONCLUSION: The Keratomorphic Diagram aids in classifying and comparing corneal shape by plotting indices along axes with easily recalled scales. The diagram may become a useful tool to assess presurgical corneal surface instability and postoperative progression of corneal shape change due to healing.

Contact Lenses↗

PubMedDate not supplied

Analysis of prognostic factors and proposal of a new classification for nasopharyngeal cancer.

A retrospective analysis was performed on 410 patients with nasopharyngeal carcinoma of squamous or undifferentiated histotype. All patients were classified according to the classification of the American Joint Committee for Cancer Staging and End-Results Reporting (AJC) and to that of the International Union Against Cancer (UICC, Geneva, 1978). The following prognostic factors were investigated by means of a Weibull multiple regression model: sex, age, histology, primary tumor extent, and nodal metastasis extent. With the exception of sex, all factors significantly influenced survival. With regards to nodal extent, only the level of the involved nodes was a significant variable. Both AJC and UICC classifications, when applied to the entire series of patients, appeared to be unsatisfactory. The authors propose an alternative classification based on a prognostic scoring system directly derived from the Weibull model.

Female↗

PubMed1996

Quantitative EEG correlates of panic disorder.

Quantitative analysis of electroencephalographic (EEG) signals recorded from multiple scalp sites was used to compare panic disorder patients (n = 34) with normal healthy controls. Patients exhibited greater overall absolute power in the delta, theta, and alpha frequency bands and less relative power in the beta band. Discriminant analysis of absolute power indices correctly classified 75% of the subjects, while relative power indices exhibited a 69% correct-classification rate. Absolute delta and theta power were positively correlated with observer ratings of anxiety, while relative beta power was related to self-ratings of anxiety.

Adult↗

PubMed1996

A predictive index of axillary nodal involvement in operable breast cancer.

We investigated the association between pathological characteristics of primary breast cancer and degree of axillary nodal involvement and obtained a predictive index of the latter from the former. In 2076 cases, 17 histological features, including primary tumour and local invasion variables, were recorded. The whole sample was randomly split in a training (75% of cases) and a test sample. Simple and multiple correspondence analysis were used to select the variables to enter in a multinomial logit model to build an index predictive of the degree of nodal involvement. The response variable was axillary nodal status coded in four classes (N0, N1-3, N4-9, N > or = 10). The predictive index was then evaluated by testing goodness-of-fit and classification accuracy. Covariates significantly associated with nodal status were tumour size (P < 0.0001), tumour type (P < 0.0001), type of border (P = 0.048), multicentricity (P = 0.003), invasion of lymphatic and blood vessels (P < 0.0001) and nipple invasion (P = 0.006). Goodness-of-fit was validated by high concordance between observed and expected number of cases in each decile of predicted probability in both training and test samples. Classification accuracy analysis showed that true node-positive cases were well recognised (84.5%), but there was no clear distinction among the classes of node-positive cases. However, 10 year survival analysis showed a superimposible prognostic behaviour between predicted and observed nodal classes. Moreover, misclassified node-negative patients (i.e. those who are predicted positive) showed an outcome closer to patients with 1-3 metastatic nodes than to node-negative ones. In conclusion, the index cannot completely substitute for axillary node information, but it is a predictor of prognosis as accurate as nodal involvement and identifies a subgroup of node-negative patients with unfavourable prognosis.

Adult↗

PubMed1998

Constructing multigenome views of whole microbial genomes.

We have designed and implemented a system to carry out cross-genome comparisons of open reading frames (ORFs) from multiple genomes. This implementation includes a genome profiling system that allows us to explore pairwise comparisons at different levels of match similarity and ask biologically motivated queries involving number and identity of ORFs, their function, functional category, distribution in genomes or in biological domains, and statistics on their matches and match families. This analysis required precise definition of new classification terms and concepts. We define the terms genomic signature, summary signature, biologic domain signature, domain class, match level, match family, and extended match family, then use these terms to define concepts, including genomically universal proteins and proteins characteristics of sets of genomes. We initiate an analysis based on automated FASTA (Pearson, 1996) comparison of 22,419 conceptually translated protein sequences from nine microbial genomes.

Amino Acid Sequence↗

PubMed2004

Convolutional face finder: a neural architecture for fast and robust face detection.

In this paper, we present a novel face detection approach based on a convolutional neural architecture, designed to robustly detect highly variable face patterns, rotated up to +/-20 degrees in image plane and turned up to +/-60 degrees, in complex real world images. The proposed system automatically synthesizes simple problem-specific feature extractors from a training set of face and nonface patterns, without making any assumptions or using any hand-made design concerning the features to extract or the areas of the face pattern to analyze. The face detection procedure acts like a pipeline of simple convolution and subsampling modules that treat the raw input image as a whole. We therefore show that an efficient face detection system does not require any costly local preprocessing before classification of image areas. The proposed scheme provides very high detection rate with a particularly low level of false positives, demonstrated on difficult test sets, without requiring the use of multiple networks for handling difficult cases. We present extensive experimental results illustrating the efficiency of the proposed approach on difficult test sets and including an in-depth sensitivity analysis with respect to the degrees of variability of the face patterns.

Algorithms↗

PubMed2006

Association of serum lipids with diabetic retinopathy in urban South Indians--the Chennai Urban Rural Epidemiology Study (CURES) Eye Study--2.

AIMS: To study the association of serum lipids with diabetic retinopathy (DR) in Type 2 diabetic subjects. METHODS: Type 2 diabetic subjects (n = 1736) were randomly selected from the Chennai Urban Rural Epidemiology Study (CURES), which was carried out on a representative population of Chennai in South India. DR was diagnosed by retinal colour photography and classified according to the Early Treatment Diabetic Retinopathy Study (ETDRS) grading system. Classification of lipid abnormalities was done according to the National Cholesterol Education Programme-Adult Treatment Panel III (NCEP-ATP III) Guidelines. RESULTS: The mean serum cholesterol (P = 0.024), serum triglycerides (P = 0.017) and non-high-density lipoprotein (HDL)-cholesterol (P = 0.025) concentrations were higher in subjects with DR compared with those without DR. Multiple logistic regression analysis revealed that after adjusting for age, gender, duration of diabetes, total cholesterol Standardised regression estimate (SRE) = 1.178, 95% confidence interval (CI) 1.042, 1.331, P = 0.014), non-HDL-cholesterol (SRE = 1.169, 95% CI 1.040, 1.313, P = 0.012) and serum triglycerides (SRE = 1.292, 95% CI 1.136, 1.467, P = 0.001) were associated with DR and non-HDL-cholesterol (SRE = 1.264, 95% CI 1.000, 1.592, P = 0.045) and low-density lipoprotein (LDL)-cholesterol (SRE = 1.453, 95% CI 1.107, 1.896, P = 0.005) with diabetic macular oedema (DME). After adjusting for HbA(1c) and body mass index, only triglycerides maintained a significant association with DR (SRE = 1.137, 95% CI 1.000, 1.291, P = 0.007) and LDL-cholesterol with macular oedema (SRE = 1.358, 95% CI 1.034, 1.774, P = 0.026). CONCLUSIONS: There is a significant association of serum triglycerides with DR and LDL-cholesterol with DME.

Adult↗

PubMedDate not supplied

Development of the Nursing Outcome (NOC) label: hyperactivity level.

TOPIC: Hyperactivity, a persistent, severe pattern of inattention or impulsivity, places children at risk for impaired functioning in many developmental areas. This behavior is characterized by short attention span, low frustration tolerance, impulsivity, distractibility, and increased physical activity. Responses from multiple sources in the child's environment must be monitored to manage childhood hyperactivity. PURPOSE: Success at school, in peer relationships, and parent-child interactions is frequently affected by hyperactivity. Using a focus group approach, a Nursing Outcomes Classification (NOC) label, definition, and indicators were developed for Hyperactivity Level. SOURCES: Review of the literature allowed for a content analysis approach and conceptualization of hyperactivity at several levels. CONCLUSION: Twenty three (23) measurable indicators were formulated and refined into conceptually and clinically coherent outcomes. Clinical relevance and utility were presented through a case study approach.

Adaptation, Psychological↗

PubMed1986

Diagnostic value of immunological leukemia phenotyping.

The diagnostic value of immunological leukemia phenotyping using a panel of reagents in immunofluorescence assays was assessed in 309 consecutive patients. The cells from 307 patients could be clearly phenotyped and assigned to one of the subgroups with a definite immunophenotype. Each phenotype was characterized by a distinct marker profile. A simplified classification scheme based on surface antigen expression is presented. A combination of complementary reagents ('first panel') was used for the first-line screening. The application of selected reagents from the 'second panel' allowed for further subtyping and confirmation of the primary diagnosis. The contribution of different key reagents to the identification of distinct immunophenotypes is discussed. Multiple marker analysis, i.e. the combination of information from several disciplines, is a necessary and very useful tool in the routine investigation of patients with hematopoietic malignancies.

Antigens, Neoplasm↗

PubMed2006

bioNMF: a versatile tool for non-negative matrix factorization in biology.

BACKGROUND: In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment. RESULTS: In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process. CONCLUSION: bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at http://www.dacya.ucm.es/apascual/bioNMF.

Algorithms↗

PubMed2002

Integrated acquisition of analytical and biopharmaceutical screening data for beta-adrenergic-drugs employing diversified macrocycle supported potentiometric detection in HPLC systems.

Potentiometric detection with poly(vinyl chloride) (PVC) based liquid membrane electrode coatings is presented for a series of eighteen beta-adrenoceptor binding drugs (five agonists and thirteen antagonists) in cation exchange-HPLC and RP-HPLC systems. Incorporation of lipophilic cation-exchanger tetrakis(p-chlorophenyl)borate (TCPB) alone or in combination with trioctylated alpha-cyclodextrin into the polymeric liquid membrane gives very sensitive responses for racemic forms of bufuralol, propranolol, carazolol, clenbuterol, mabuterol, cimaterol, bisoprolol, oxprenolol, alprenolol, tertatolol, and bevantolol, especially in the cation-exchange HPLC system applying acetonitrile -- 40 mM phosphoric acid (15: 85, v/v, pH* = 2.35) as the mobile phase. In both applied orthogonal HPLC modes we observed that use of TCPB containing electrodes (no addition of neutral macrocyclic ionophores) gives more than five fold improvement in limit of detection down to 10(-7) M for mabuterol, bufuralol, alprenolol and tertatolol in comparison with UV detection. These results suggest that potentiometric detection, especially in RP-HPLC employing hybrid polymer-silica packings, can be considered as the promising alternative in the high-throughput drug abuse or doping control procedures of investigated beta-adrenergic agonists and beta-adrenolytics in humans and animals. The quantitative structure - potentiometric response relationships were developed for a set of eighteen beta-adrenenergic drugs and a set of PVC based electrodes using TCPB alone or in admixture with trioctylated alpha-cyclodextrin, dibenzo-18-crown-6 or calix[6]arene hexaethylacetate ester. A multiple linear regression model based on computationally derived set of molecular descriptors was used to predict detection limits of beta-blocking agents and beta-adrenergic agonists from their molecular structure in the developed potentiometric detectors. Principal components analysis (PCA) of data considering determined potentiometric detection limits revealed that it can be used to establish a reliable pharmacological classification of compounds with beta-adrenoceptor activity, especially for the differentiation of cardioselective and non-cardioselective beta1-antagonists.

Adrenergic beta-Agonists↗

PubMed2000

A neural network ActiveX based integrated image processing environment.

The paper outlines an integrated image processing environment that uses neural networks ActiveX technology for object recognition and classification. The image processing environment which is Windows based, encapsulates a Multiple-Document Interface (MDI) and is menu driven. Object (shape) parameter extraction is focused on features that are invariant in terms of translation, rotation and scale transformations. The neural network models that can be incorporated as ActiveX components into the environment allow both clustering and classification of objects from the analysed image. Mapping neural networks perform an input sensitivity analysis on the extracted feature measurements and thus facilitate the removal of irrelevant features and improvements in the degree of generalisation. The program has been used to evaluate the dimensions of the hydrocephalus in a study for calculating the Evans index and the angle of the frontal horns of the ventricular system modifications.

Humans↗

PubMed2005

Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins.

Plasma protein profiling using separations coupled to matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) has great potential in translational research; it can be used for biomarker discovery and contribute to disease diagnosis and therapy. Previously reported biomarker searches have been done solely by MS protein profiling followed by bioinformatics analysis of the data. To add to current methods, we tested an alternative strategy for plasma protein profiling using pancreatic cancer as the model. First, offline solid-phase extraction is done with 96-well plates to fractionate and partially purify the proteins. Then, multiple profiling and identification experiments can be conducted on the same protein fractions because only 5% of the fractions are used for MALDI MS profiling. After MALDI MS analysis, the mass spectra are normalized and subjected to a peak detection algorithm. Over three sets of mass spectra acquired using different instrument variables, approximately 400 unique ion signals were detected. Classification schemes employing as many as eight individual peaks were developed using a training set with 123 members (82 cancer patients) and a blinded validation set with 125 members (57 cancer patients). The sensitivity of the study was 88%, but the specificity was significantly lower, 75%. The reason for the low specificity becomes apparent upon protein identification of the ion signals used for the classification. The identifications reveal only common serum proteins and components of the acute phase response, including serum amyloid A, alpha-1-antitrypsin, alpha-1-antichymotrypsin, and inter-alpha-trypsin inhibitor.

Acute-Phase Proteins↗

PubMed1995

[Risk factors of wound infection following cardiac surgery and antimicrobial prophylaxis].

To make investigation about risk of wound infection following cardiac surgery, we analyzed cases of primary aorto-coronary bypass surgery and/or primary valvular surgery. Cases required respirator for longer than 2 days, and those with drainage tube for longer than 5 days were excluded from this study, because these cases had antimicrobial agent postoperatively as therapeutic use rather than prophylactic use. Those received preoperative antimicrobial agent for infectious endocarditis and so on were also excluded for the same reason. 523 cases were entered this study. These cases received cefazolin (CEZ) postoperatively as prophylaxis. Sternal wound and leg/groin wound were separately analyzed. Risk factors (age, sex, diabetes mellitus, unstable angina, use of intraaortic balloon, internal thoracic artery harvest, re-exploration, previous myocardial infarction, NYHA classification, emergent operation, operation time, extracorporeal circulation time, blood product use, preoperative blood hemoglobin concentration, preoperative serum albumin, preoperative creatinine clearance (Ccr), duration of drainage tube insertion, body surface area, daily dose of CEZ, duration of prophylaxis) were examined using univariate (Chi square test was used for contingency table analysis, unpaired t test was used to compare averages) and multiple regression analysis. For sternal wound infection, only Ccr showed significant (P = 0.027) correlation. For leg/groin wound infection, 2 factors (smaller daily dose of CEZ: P = 0.009, more severe NYHA class: P = 0.03) showed significant correlation. To investigate appropriate duration of CEZ prophylaxis, cases were divided into 2 groups, those had CEZ within 48 hours postoperatively (group S) and those had CEZ for longer than 48 hours (group L).(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗