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Structure of the O-polysaccharide and serological studies of the lipopolysaccharide of Proteus penneri 60 classified into a new Proteus serogroup O70.

An alkali-treated lipopolysaccharide of Proteus penneri strain 60 was studied by chemical analyses and 1H, 13C and 31P NMR spectroscopy, and the following structure of the linear pentasaccharide-phosphate repeating unit of the O-polysaccharide was established: 6)-alpha-D-Galp-(1-->3)-alpha-L-FucpNAc-(1-->3)-alpha-D-GlcpNAc-(1-->3)-beta-D-Quip4NAc-(1-->6)-alpha-D-Glcp-1-P-(O--> Rabbit polyclonal O-antiserum against P. penneri 60 reacted with both core and O-polysaccharide moieties of the homologous LPS. Based on the unique O-polysaccharide structure and serological data, we propose to classify P. penneri 60 into a new, separate Proteus serogroup O70. A weak cross-reactivity of P. penneri 60 O-antiserum with the lipopolysaccharide of Proteus vulgaris O8, O15 and O19 was observed and discussed in view of the chemical structures of the O-polysaccharides.

Animals↗

Identification of 24 genes and two pseudogenes coding for olfactory receptors in Japanese loach, classified into four subfamilies: a putative evolutionary process for fish olfactory receptor genes by comprehensive phylogenetic analysis.

Twenty-four olfactory receptor (OR) genes and two pseudogenes have been identified in the genome of Japanese loach (Misgurnus anguillicaudatus). The genes were classified into four subfamilies according to the similarity of the amino acid sequences. In each subfamily, members showed high sequence similarity not only to each other but also to orthologues of other fish species. The number of members in each OR subfamily was roughly estimated to be from 3 to 10 by genomic Southern blot analysis. The genes of all four OR subfamilies were shown to express on olfactory neurons of the olfactory epithelium by in situ hybridization analysis. Two major features of fish OR genes were found by comprehensive and comparative analyses on OR genes of Japanese loach and other fish species including catfish, zebrafish and pufferfish. First, the phylogenetic tree comprising of representative subfamily members suggests the existence of several prototype genes common to the genomes of many fish species. Second, when all members of orthologous subfamilies identified in each clade of the tree are integrated, the members of a single species comprise a monophyletic group. This means that 'intraspecies' sequence homology, that is, homology among paralogous genes of the same subfamily in a species, is higher than 'interspecies' homology, that is, homology between orthologous genes of different species. This suggests that the subfamily members of a species have evolved recently. Taken together, fish OR genes have evolved from a limited number of prototype genes common to most fish species, and several genes in a subfamily have diversely evolved in each species from each prototype.

Amino Acid Sequence↗

Artificial neural networks and robust Bayesian classifiers for risk stratification following uncomplicated myocardial infarction.

OBJECTIVE: To compare artificial neural networks (ANN) and robust Bayesian classifiers (RBC) in predicting outcome following acute myocardial infarction (AMI). METHODS: Clinical, exercise ECG and stress echo variables by 496 patients with AMI were used to predict the cumulative end-point of cardiac death, nonfatal reinfarction and unstable angina. Revascularized patients were censored. Short (200 days)-, medium (400 days)- and long (1000 days)-term observation intervals, including 50%, 75% and 90% of the events, respectively, were considered. At each interval, any patient was binary assigned to the "event" or "no event" class. A multilayer feedforward ANN, trained by a back propagation algorithm, was used. RBC, using the leave-one-out technique, were derived. The accuracy of both techniques was compared to the default accuracy (DA) obtained by assigning all subjects to the largest class. RESULTS: 14 death, 27 reinfarction and 29 unstable angina were observed during a mean follow-up of 24 [95% confidence interval (CI) 19 to 22] months. The accuracy of ANN and RBC and DA were 70%, 81% and 74% at short, 67%, 73% and 56% at medium and 64%, 68% and 62% at long-term follow-up. CONCLUSIONS: (1) ANN do not improve the prognostic classification of patients with uncomplicated AMI as compared to RBC. (2) In particular, short-term prognostic accuracy seems insufficient.

Algorithms↗

Should we perform an echocardiogram in hypertensive patients classified as having low and medium risk?

BACKGROUND: Left ventricular hypertrophy is an important predictor of cardiovascular risk and its detection contributes to risk stratification. However, echocardiography is not a routine procedure and electrocardiography (ECG) underestimates its prevalence. OBJECTIVE: To evaluate the prevalence of echocardiographic left ventricular hypertrophy in low and medium risk non-treated hypertensive subjects, in order to find out the percentage of them who would be reclassified as high risk patients. METHODS: Cross-sectional, multicenter study was performed in hospital located hypertension units. An echocardiogram was performed in 197 previously untreated hypertensive patients, > 18 years, classified as having low (61%) or medium (39%) risk, according to the OMS/ISH classification. The presence of left ventricular hypertrophy was considered if left ventricular mass index was > or = 134 or 110 g/m(2) in men and women, respectively (Devereux criteria). A logistic regression analysis was performed to identify factors associated to left ventricular hypertrophy. RESULTS: The prevalence of left ventricular hypertrophy was 23.9% (95% CI:17.9-29.9), 25.6% in men and 22.6% in women. In the low risk group its prevalence was 20.7% and in medium risk group 29.5%. Factors associated to left ventricular hypertrophy were: years since the diagnosis of hypertension, OR:1.1 (95% CI:1.003-1.227); systolic blood pressure, OR:1.08 (95% CI:1.029-1.138); diastolic blood pressure, OR:0.9 (95% CI:0.882-0.991); and family history of cardiovascular disease, OR:4.3 (95% CI:1.52-12.18). CONCLUSIONS: These findings underline the importance of performing an echocardiogram in low and high risk untreated hypertensive patients in which treatment would otherwise be delayed for even one year.

Adult↗

Expert opinion elicitation for assisting deep learning based Lyme disease classifier with patient data.

BACKGROUND: Diagnosing erythema migrans (EM) skin lesion, the most common early symptom of Lyme disease, using deep learning techniques can be effective to prevent long-term complications. Existing works on deep learning based EM recognition only utilizes lesion image due to the lack of a dataset of Lyme disease related images with associated patient data. Doctors rely on patient information about the background of the skin lesion to confirm their diagnosis. To assist deep learning model with a probability score calculated from patient data, this study elicited opinions from fifteen expert doctors. To the best of our knowledge, this is the first expert elicitation work to calculate Lyme disease probability from patient data. METHODS: For the elicitation process, a questionnaire with questions and possible answers related to EM was prepared. Doctors provided relative weights to different answers to the questions. We converted doctors' evaluations to probability scores using Gaussian mixture based density estimation. We exploited formal concept analysis and decision tree for elicited model validation and explanation. We also proposed an algorithm for combining independent probability estimates from multiple modalities, such as merging the EM probability score from a deep learning image classifier with the elicited score from patient data. RESULTS: We successfully elicited opinions from fifteen expert doctors to create a model for obtaining EM probability scores from patient data. CONCLUSIONS: The elicited probability score and the proposed algorithm can be utilized to make image based deep learning Lyme disease pre-scanners robust. The proposed elicitation and validation process is easy for doctors to follow and can help address related medical diagnosis problems where it is challenging to collect patient data.

Humans↗

Is "shy bladder syndrome" (paruresis) correctly classified as social phobia?

Paruresis manifests in an inability to urinate in public restrooms followed by a considerable avoidance behavior. According to DSM-IV TR this disorder is classified as social phobia. A sample of N = 226 subjects completed different questionnaires concerning paruresis, social phobic symptoms, lower urinary tract symptoms and depressive symptoms. These individuals were divided into four groups: no symptoms, suffering primarily from paruresis, non-generalized social phobia and generalized social phobia. The paruretic group differs significantly in all symptom variables from both the non-generalized and the generalized social phobia groups. Regression analysis separated by groups shows that the interference with everyday life can be mainly explained by paruretic symptoms (in the paruretic group) or by social anxiety and depressive symptoms, respectively (in the social phobic groups). These results question the classification of paruresis as simply being a form of social phobia.

Adolescent↗

Using name-internal and contextual features to classify biological terms.

There has been considerable work done recently in recognizing named entities in biomedical text. In this paper, we investigate the named entity classification task, an integral part of the named entity extraction task. We focus on the different sources of information that can be utilized for classification, and note the extent to which they are effective in classification. To classify a name, we consider features that appear within the name as well as nearby phrases. We also develop a new strategy based on the context of occurrence and show that they improve the performance of the classification system. We show how our work relates to previous works on named entity classification in the biological domain as well as to those in generic domains. The experiments were conducted on the GENIA corpus Ver. 3.0 developed at University of Tokyo. We achieve f value of 86 in 10-fold cross validation evaluation on this corpus.

Abstracting and Indexing↗

Complaint-severity and cervical spine problems successfully classified patients with shoulder complaints.

OBJECTIVE: To construct a classification of patients with shoulder complaints based on their physical examination. To investigate (1) the interobserver reliability, (2) to what extent the setting in which the patients were recruited, and demographic and clinical characteristics are related to the classification. STUDY DESIGN AND SETTING: Data from 132 patients with shoulder complaints recruited in various health care settings in The Netherlands were examined. Two observers independently performed a physical examination of the cervical spine and shoulder joint. A nonmetric multidimensional scaling procedure was performed for each observer separately. The interobserver reliability of both observers was computed. Differences between setting, demographic and clinical characteristics, and the resulting dimensions were investigated. RESULTS: For both observers two dimensions (severity of complaints of the shoulder joint, and severity of problems of the cervical spine) were sufficient to classify all patients. Agreement between the two observers was good (r=0.84) to moderate (r=0.69). Patients with neck pain in history taking showed higher scores on both dimensions. CONCLUSION: Despite moderate interobserver agreement for each variable from physical examination found in previous studies, observers agree on the scores of the patients on the relevant dimensions. Given the limited number of effective treatments available to the general practitioner, a more sophisticated classification system seems unnecessary.

Adolescent↗

A comparison of two consensus methods for classifying morbidities in a single professional group showed the same outcomes.

OBJECTIVE: To investigate whether consensus differs when reached by the Nominal or the Delphi method. STUDY DESIGN AND SETTING: Seventeen general practices from North Staffordshire, England were randomly allocated to Delphi (postal feedback only) or Nominal group (also had group discussion). General practitioners classified 56 morbidities according to four scales of severity (chronicity, time course, health care use, patient impact) in two consensus rounds. Consensus outcomes were assessed by between-group comparison of severity scores at baseline and follow-up rounds, and consensus process by within-group change in the variance of severity scores between the two rounds. RESULTS: Consensus rounds were completed by 21 out of 35 Nominal GPs and 23 out of 43 Delphi GPs. Baseline scores for three of the four severity scales were significantly higher for Nominal compared to Delphi GPs, but there were no differences at follow-up. Between the two rounds, variance reduced within the Nominal and Delphi group, respectively, by 61% and 35% (chronicity), 40% and 62% (time course), 42% and 36% (health care use), and 19% and 38% (patient impact). CONCLUSION: The Nominal and Delphi methods did not result in different outcomes and we conclude that either method can be used in health services research.

Consensus↗

A review of approaches for classifying benthic habitats and evaluating habitat quality.

We have assessed the current state of knowledge relative to methods used in assessing sub-tidal benthic habitat quality and the classification of benthic habitats. While our main focus is on marine habitat, we extensively draw on knowledge gained in freshwater systems where benthic assessment procedures are at an advanced stage of maturity. We found a broad range of sophistication/complication in terms of the methods applied in assessing and mapping benthic habitats. The simplest index or metric involved some assessment of species richness, while the most complicated required utilizing multi-variate analysis. The simplest mapping attempts equated physical substrate with benthic habitat while the most sophisticated relied on extensive environmental preference and groundtruth data for species of concern. The leading edge of methods for benthic habitat mapping involves combining the advances in optical and acoustic methods that allow for routine classifying and mapping of the seafloor with biological and habitat data for species of concern. The objective of this melding of dispirit methods is to produce benthic habitat maps with broad system wide coverage and sound biological underpinning. It is clear that the disparity in information density between the physical and biological sides of the equation currently hinder applicability and acceptability of benthic habitat mapping efforts. In addition to the lack of basic information on the biological and environmental tolerances of targeted species, the proliferation of metrics for characterizing and assessing biological conditions further clouds the usefulness of any broad scale mapping attempt. The problem of data density mismatch between physical and biological methods will likely not be solved until acoustic methods can routinely resolve the elusive biological components that make a physical substrate a habitat.

Animals↗

Testing strategy for classifying self-heating substances for transport of dangerous goods.

A testing strategy for the classification of self-heating substances for transport of dangerous goods is proposed. The strategy was developed based on the tests described and correlations used in the UN Recommendations. It was demonstrated that the value of activation energy of the exothermic reaction has a significant impact on the extrapolation of test results with regard to different container sizes and temperatures. Based on a combination of the Grewer Oven test screening, the 25 mm cube test at 140 degrees C, and the determination of the activation energy of a specific material, a flowchart is presented for classifying chemicals as self-heating. The presented approach allows predicting chemical stability in large containers more accurately and eliminates the need to perform hazardous large-scale tests of energetic chemicals in a laboratory.

Hazardous Substances↗

Use of fecal elastase-1 to classify pancreatic status in patients with cystic fibrosis.

OBJECTIVE: To test the hypothesis that some patients with cystic fibrosis (CF) are misclassified as pancreatic insufficient, using fecal elastase-1 (FE-1) to define pancreatic status. STUDY DESIGN: Subjects with CF at 33 CF centers filled out questionnaires and submitted a stool specimen that was analyzed for FE-1. Subjects taking pancreatic enzyme supplements (PES) were asked to discontinue them and perform a 3-day fecal fat balance study if their FE-1 was >200 microg/g stool and they had never had pancreatitis. RESULTS: The median value for FE-1 in 1215 subjects was 0 microg/g stool (range, 0-867). There was a significant difference between patients who had been prescribed PES (n=1131) and those who had FE-1 <200 microg/g stool (n=1074; P<.0001). Sixty-seven subjects met criteria for discontinuation of PES. The mean coefficient of fat absorption for these subjects was 96.1%. CONCLUSIONS: FE-1 is an accurate, easily obtained screening test to classify pancreatic status in patients with CF. This information is important for prognostication, treatment, and to avoid misclassification in clinical research. Measurement of FE-1 should become a standard of care for patients with CF.

Adolescent↗

Using LogitBoost classifier to predict protein structural classes.

Prediction of protein classification is an important topic in molecular biology. This is because it is able to not only provide useful information from the viewpoint of structure itself, but also greatly stimulate the characterization of many other features of proteins that may be closely correlated with their biological functions. In this paper, the LogitBoost, one of the boosting algorithms developed recently, is introduced for predicting protein structural classes. It performs classification using a regression scheme as the base learner, which can handle multi-class problems and is particularly superior in coping with noisy data. It was demonstrated that the LogitBoost outperformed the support vector machines in predicting the structural classes for a given dataset, indicating that the new classifier is very promising. It is anticipated that the power in predicting protein structural classes as well as many other bio-macromolecular attributes will be further strengthened if the LogitBoost and some other existing algorithms can be effectively complemented with each other.

Animals↗

Benthic biotope index for classifying habitats in the Sado Estuary: Portugal.

An integration of sediment physical, chemical, biological, and toxicity data is necessary for a meaningful interpretation of the complex sediment conditions in the marine environment. Assessment of benthic community is a vital component for that interpretation, yet their evaluation is complex and requires a large expenditure of time and funds. Thus, there is a need for new tools that are less expensive and more understandable for managers. This paper presents a benthic biotope index to predict from physical and chemical variables the occurrence of macrobenthic habitats. Parameters such as sediment type, organic matter, depth, and hydrodynamic parameters were selected, through a discriminant analysis, to compute the index. Other authors have used multivariate methods to determine the benthic biotopes for Sado Estuary. The index proved to be a valid tool to classify and assess the spatial patterns of benthic habitat and to synthesize stress biotope gradients.

Animals↗

A new classifier based on information theoretic learning with unlabeled data.

Supervised learning is conventionally performed with pairwise input-output labeled data. After the training procedure, the adaptive system's weights are fixed while the testing procedure with unlabeled data is performed. Recently, in an attempt to improve classification performance unlabeled data has been exploited in the machine learning community. In this paper, we present an information theoretic learning (ITL) approach based on density divergence minimization to obtain an extended training algorithm using unlabeled data during the testing. The method uses a boosting-like algorithm with an ITL based cost function. Preliminary simulations suggest that the method has the potential to improve the performance of classifiers in the application phase.

Algorithms↗

Bayesian approach to feature selection and parameter tuning for support vector machine classifiers.

A Bayesian point of view of SVM classifiers allows the definition of a quantity analogous to the evidence in probabilistic models. By maximizing this one can systematically tune hyperparameters and, via automatic relevance determination (ARD), select relevant input features. Evidence gradients are expressed as averages over the associated posterior and can be approximated using Hybrid Monte Carlo (HMC) sampling. We describe how a Nyström approximation of the Gram matrix can be used to speed up sampling times significantly while maintaining almost unchanged classification accuracy. In experiments on classification problems with a significant number of irrelevant features this approach to ARD can give a significant improvement in classification performance over more traditional, non-ARD, SVM systems. The final tuned hyperparameter values provide a useful criterion for pruning irrelevant features, and we define a measure of relevance with which to determine systematically how many features should be removed. This use of ARD for hard feature selection can improve classification accuracy in non-ARD SVMs. In the majority of cases, however, we find that in data sets constructed by human domain experts the performance of non-ARD SVMs is largely insensitive to the presence of some less relevant features. Eliminating such features via ARD then does not improve classification accuracy, but leads to impressive reductions in the number of features required, by up to 75%.

Algorithms↗

Efficient information theoretic strategies for classifier combination, feature extraction and performance evaluation in improving false positives and false negatives for spam e-mail filtering.

Spam emails are considered as a serious privacy-related violation, besides being a costly, unsolicited communication. Various spam filtering techniques have been so far proposed, mainly based on Naïve Bayesian algorithms. Other Machine Learning algorithms like Boosting trees, or Support Vector Machines (SVM) have already been used with success. However, the number of False Positives (FP) and False Negatives (FN) resulting through applying various spam e-mail filters still remains too high and the problem of spam e-mail categorization cannot be solved completely from a practical viewpoint. In this paper, we propose a novel approach for spam e-mail filtering based on efficient information theoretic techniques for integrating classifiers, for extracting improved features and for properly evaluating categorization accuracy in terms of FP and FN. The goal of the presented methodology is to empirically but explicitly minimize these FP and FN numbers by combining high-performance FP filters with high-performance FN filters emerging from a previous work of the authors [Zorkadis, V., Panayotou, M., & Karras, D. A. (2005). Improved spam e-mail filtering based on committee machines and information theoretic feature extraction. Proceedings of the International Joint Conference on Neural Networks, July 31-August 4, 2005, Montreal, Canada]. To this end, Random Committee-based filters along with ADTree-based ones are efficiently combined through information theory, respectively. The experiments conducted are of the most extensive ones so far in the literature, exploiting widely accepted benchmarking e-mail data sets and comparing the proposed methodology with the Naive Bayes spam filter as well as with the Boosting tree methodology, the classification via regression and other machine learning models. It is illustrated by means of novel information theoretic measures of FP & FN filtering performance that the proposed approach is very favorably compared to the other rival methods. Finally, it is found that the proposed information theoretic Boolean features present a remarkably high spam categorization performance.

Algorithms↗

Classifying episodes in schizophrenia and bipolar disorder: criteria for relapse and remission applied to recent-onset samples.

Research on predicting and preventing episodes of schizophrenia and mood disorder lacks consistent, specific definitions of episodes. We present an operational system for identifying relapse, exacerbation, and remission of schizophrenia and bipolar disorder within longitudinal studies that involve repeated symptom assessments. Three major classes of episodic outcome are defined: relapse or significant exacerbation, nonrelapse, and stable, severe persisting symptoms. These major classes are further subdivided to distinguish nine categories of episodic outcome. To examine ease of use, interrater reliability, and validity, the classification system was applied to recent-onset samples of schizophrenia patients (N=77) and bipolar mood disorder patients (N=23) followed on medication for 9- to 12-month periods. A range of episodic outcomes were distinguished with high interrater reliability. Despite being prescribed continuous medication, 21% of the recent-onset schizophrenia patients and 61% of bipolar patients met criteria for relapse or significant exacerbation during this follow-up period. Predictive relationships support the validity of this system for classifying episodes. A computer program is available to facilitate its use. Use of these explicit definitions of episodes may help to clarify the relationship between episodic outcome and other fundamental domains of illness outcome, particularly other symptom dimensions, work functioning, and social functioning.

Adult↗