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PubMed2006

Automatic document classification of biological literature.

BACKGROUND: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. RESULTS: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. CONCLUSION: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept.

Abstracting and Indexing↗
PubMed2005

A comprehensive update of the sequence and structure classification of kinases.

BACKGROUND: A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. RESULTS: The new survey found the total number of kinase sequences in the protein database has increased more than three-fold (from 17,310 to 59,402), and the number of determined kinase structures increased two-fold (from 359 to 702) in the past three years. However, the framework of the original two-tier classification scheme (in families and fold groups) remains sufficient to describe all available kinases. Overall, the kinase sequences were classified into 25 families of homologous proteins, wherein 22 families (approximately 98.8% of all sequences) for which three-dimensional structures are known fall into 10 fold groups. These fold groups not only include some of the most widely spread proteins folds, such as the Rossmann-like fold, ferredoxin-like fold, TIM-barrel fold, and antiparallel beta-barrel fold, but also all major classes (all alpha, all beta, alpha+beta, alpha/beta) of protein structures. Fold predictions are made for remaining kinase families without a close homolog with solved structure. We also highlight two novel kinase structural folds, riboflavin kinase and dihydroxyacetone kinase, which have recently been characterized. Two protein families previously annotated as kinases are removed from the classification based on new experimental data. CONCLUSION: Structural annotations of all kinase families are now revealed, including fold descriptions for all globular kinases, making this the first large functional class of proteins with a comprehensive structural annotation. Potential uses for this classification include deduction of protein function, structural fold, or enzymatic mechanism of poorly studied or newly discovered kinases based on proteins in the same family.

Algorithms↗
PubMed2006

Intelligent Bayes Classifier (IBC) for ENT infection classification in hospital environment.

Electronic Nose based ENT bacteria identification in hospital environment is a classical and challenging problem of classification. In this paper an electronic nose (e-nose), comprising a hybrid array of 12 tin oxide sensors (SnO2) and 6 conducting polymer sensors has been used to identify three species of bacteria, Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Pseudomonas aeruginosa (P. aeruginosa) responsible for ear nose and throat (ENT) infections when collected as swab sample from infected patients and kept in ISO agar solution in the hospital environment. In the next stage a sub-classification technique has been developed for the classification of two different species of S. aureus, namely Methicillin-Resistant S. aureus (MRSA) and Methicillin Susceptible S. aureus (MSSA). An innovative Intelligent Bayes Classifier (IBC) based on "Baye's theorem" and "maximum probability rule" was developed and investigated for these three main groups of ENT bacteria. Along with the IBC three other supervised classifiers (namely, Multilayer Perceptron (MLP), Probabilistic neural network (PNN), and Radial Basis Function Network (RBFN)) were used to classify the three main bacteria classes. A comparative evaluation of the classifiers was conducted for this application. IBC outperformed MLP, PNN and RBFN. The best results suggest that we are able to identify and classify three bacteria main classes with up to 100% accuracy rate using IBC. We have also achieved 100% classification accuracy for the classification of MRSA and MSSA samples with IBC. We can conclude that this study proves that IBC based e-nose can provide very strong and rapid solution for the identification of ENT infections in hospital environment.

Algorithms↗
PubMed2006

Data processing and classification analysis of proteomic changes: a case study of oil pollution in the mussel, Mytilus edulis.

BACKGROUND: Proteomics may help to detect subtle pollution-related changes, such as responses to mixture pollution at low concentrations, where clear signs of toxicity are absent. The challenges associated with the analysis of large-scale multivariate proteomic datasets have been widely discussed in medical research and biomarker discovery. This concept has been introduced to ecotoxicology only recently, so data processing and classification analysis need to be refined before they can be readily applied in biomarker discovery and monitoring studies. RESULTS: Data sets obtained from a case study of oil pollution in the Blue mussel were investigated for differential protein expression by retentate chromatography-mass spectrometry and decision tree classification. Different tissues and different settings were used to evaluate classifiers towards their discriminatory power. It was found that, due the intrinsic variability of the data sets, reliable classification of unknown samples could only be achieved on a broad statistical basis (n > 60) with the observed expression changes comprising high statistical significance and sufficient amplitude. The application of stringent criteria to guard against overfitting of the models eventually allowed satisfactory classification for only one of the investigated data sets and settings. CONCLUSION: Machine learning techniques provide a promising approach to process and extract informative expression signatures from high-dimensional mass-spectrometry data. Even though characterisation of the proteins forming the expression signatures would be ideal, knowledge of the specific proteins is not mandatory for effective class discrimination. This may constitute a new biomarker approach in ecotoxicology, where working with organisms, which do not have sequenced genomes render protein identification by database searching problematic. However, data processing has to be critically evaluated and statistical constraints have to be considered before supervised classification algorithms are employed.

Journal Article↗
PubMed2006

Validation of the reshaped shared epitope HLA-DRB1 classification in rheumatoid arthritis.

Recently, we proposed a classification of HLA-DRB1 alleles that reshapes the shared epitope hypothesis in rheumatoid arthritis (RA); according to this model, RA is associated with the RAA shared epitope sequence (72-74 positions) and the association is modulated by the amino acids at positions 70 and 71, resulting in six genotypes with different RA risks. This was the first model to take into account the association between the HLA-DRB1 gene and RA, and linkage data for that gene. In the present study we tested this classification for validity in an independent sample. A new sample of the same size and population (100 RA French Caucasian families) was genotyped for the HLA-DRB1 gene. The alleles were grouped as proposed in the new classification: S1 alleles for the sequences A-RAA or E-RAA; S2 for Q or D-K-RAA; S3D for D-R-RAA; S3P for Q or R-R-RAA; and X alleles for no RAA sequence. Transmission of the alleles was investigated. Genotype odds ratio (OR) calculations were performed through conditional logistic regression, and we tested the homogeneity of these ORs with those of the 100 first trio families (one case and both parents) previously reported. As previously observed, the S2 and S3P alleles were significantly over-transmitted and the S1, S3D and X alleles were under-transmitted. The latter were grouped as L alleles, resulting in the same three-allele classification. The risk hierarchy of the six derived genotypes was the same: (by decreasing OR and with L/L being the reference genotype) S2/S3P, S2/S2, S3P/S3P, S2/L and S3P/L. The homogeneity test between the ORs of the initial and the replication samples revealed no significant differences. The new classification was therefore considered validated, and both samples were pooled to provide improved estimates of RA risk genotypes from the highest (S2/S3P [OR 22.2, 95% confidence interval 9.9-49.7]) to the lowest (S3P/L [OR 4.4, 95% confidence interval 2.3-8.4]).

Arthritis, Rheumatoid↗
PubMed1984

Classification of anxiety.

Current psychiatric classifications of anxiety are examined critically. In the European literature a specific cluster of symptoms is diagnostic of anxiety neurosis and their subsidiary classification is based on precipitating factors and duration of symptoms. In the American literature, exemplified by DSM-III, greater emphasis is placed on symptomatic classification and panic is given separate diagnostic status, both alone and in conjunction with agoraphobia. In both classifications generalized anxiety is at the bottom of a diagnostic hierarchy so that all other symptoms take precedence. It is argued that neither classification properly identifies a discrete syndrome of pathological anxiety that is recognizable in clinical practice.

Anxiety Disorders↗
PubMed1987

Modification of Kiel and working formulation classifications for improved survival prediction in non-Hodgkin's lymphoma.

The total survival of 203 patients with non-Hodgkin's lymphoma (NHL) was analyzed according to the working formulation (WF) and "expanded" Kiel classifications. The original Kiel classification consisting of low grade (LG) and high grade (HG) forms corresponded well to the LG and HG forms of the WF. When an expanded Kiel containing an intermediate grade (IG) composed of the original LG diffuse group was devised, this gave a much better separation of survival of the three grades as compared with the WF where the survival of IG and HG forms were nonsignificantly different. The main reason for this difference was the inclusion of the so-called centroblastic diffuse form in the HG Kiel, but in the IG according to the WF. In a "modified" WF analysis where this histologic entity was placed in the HG subgroup, the three survival curves then gave excellent separation like the expanded Kiel classification. Since the centroblastic diffuse form (and its analogous forms according to other classifications) has a poor prognosis, it is important that it be so recognized and treated accordingly with aggressive therapy. We propose either our expanded Kiel or modified WF classification of the three grade forms as an excellent predictor of survival.

Actuarial Analysis↗
PubMed1999

Attachment-based classifications of children's family drawings: psychometric properties and relations with children's adjustment in kindergarten.

Investigated an attachment-based theoretical framework and classification system, introduced by Kaplan and Main (1986), for interpreting children's family drawings. This study concentrated on the psychometric properties of the system and the relation between drawings classified using this system and teacher ratings of classroom social-emotional and behavioral functioning, controlling for child age, ethnic status, intelligence, and fine motor skills. This nonclinical sample consisted of 200 kindergarten children of diverse racial and socioeconomic status (SES). Limited support for reliability of this classification system was obtained. Kappas for overall classifications of drawings (e.g., secure) exceeded .80 and mean kappa for discrete drawing features (e.g., figures with smiles) was .82. Coders' endorsement of the presence of certain discrete drawing features predicted their overall classification at 82.5% accuracy. Drawing classification was related to teacher ratings of classroom functioning independent of child age, sex, race, SES, intelligence, and fine motor skills (with p values for the multivariate effects ranging from .043-.001). Results are discussed in terms of the psychometric properties of this system for classifying children's representations of family and the limitations of family drawing techniques for young children.

Art↗
PubMed2005

Prediction of outcome in traumatic brain injury with computed tomographic characteristics: a comparison between the computed tomographic classification and combinations of computed tomographic predictors.

BACKGROUND AND OBJECTIVE: The Marshall computed tomographic (CT) classification identifies six groups of patients with traumatic brain injury (TBI), based on morphological abnormalities on the CT scan. This classification is increasingly used as a predictor of outcome. We aimed to examine the predictive value of the Marshall CT classification in comparison with alternative CT models. METHODS: The predictive value was investigated in the Tirilazad trials (n = 2269). Alternative models were developed with logistic regression analysis and recursive partitioning. Six month mortality was used as outcome measure. Internal validity was assessed with bootstrapping techniques and expressed as the area under the receiver operating curve (AUC). RESULTS: The Marshall CT classification indicated reasonable discrimination (AUC = 0.67), which could be improved by rearranging the underlying individual CT characteristics (AUC = 0.71). Performance could be further increased by adding intraventricular and traumatic subarachnoid hemorrhage and by a more detailed differentiation of mass lesions and basal cisterns (AUC = 0.77). Models developed with logistic regression analysis and recursive partitioning showed similar performance. For clinical application we propose a simple CT score, which permits a more clear differentiation of prognostic risk, particularly in patients with mass lesions. CONCLUSION: It is preferable to use combinations of individual CT predictors rather than the Marshall CT classification for prognostic purposes in TBI. Such models should include at least the following parameters: status of basal cisterns, shift, traumatic subarachnoid or intraventricular hemorrhage, and presence of different types of mass lesions.

Adolescent↗
PubMed2002

Pressure ulcer classification: defining early skin damage.

This article is the second of a two-part series. The first part (Russell, 2002) looked at various systems and pitfalls of pressure ulcer classification systems. This article focuses on the difficulties of defining early skin damage. Patients' quality of life suffers significantly with a pressure ulcer. The smell of the exudate may be an embarrassment to the patient. The pain and the distress the patient will experience will not easily be forgotten, i.e. the number of dressings required for a deep pressure ulcer, even after the pressure ulcer has healed, will be a memorable intrusion to the patient's daily routine. Early detection of pressure ulcers and timely intervention are essential in the management of patients with pressure ulcers. Controversy exists over the definition of the first three stages of pressure ulcers, but there is consensus on the definition of deep tissue damage. If the pressure ulcer is covered with black necrotic tissue it is difficult to establish depth of the tissue damage. Intact skin can cause problems, as a sacrum may be purple but intact. There is still considerable debate with regard to reactive hyperaemia, as the exact time parameters for persistent erythema to occur are unknown. Little is understood with regard to the exact pathophysiology of reactive hyperaemia and this area requires further investigation. Blistered skin and skin tone also cause confusion in grading of pressure ulcers. The problems associated with classification of pressure ulcers, using colour classification systems, are discussed and the implications for practice are considered. The confusion surrounding early classification of pressure ulcers is discussed and it is hoped that such confusion can be addressed by standardizing training using one national classification system.

Erythema↗
PubMed2005

Sanders classification of fractures of the os calcis. An analysis of inter- and intra-observer variability.

Our study was undertaken to assess the inter- and intra-observer variability of the classification system of Sanders for calcaneal fractures. Five consultant orthopaedic surgeons with different subspecialty interests classified CT scans of 28 calcaneal fractures using this classification system. After six months, they reclassified the scans. Kappa statistics were used to analyse the two groups. The interobserver variability of the classification system was 0.32 (95% confidence interval (CI) 0.26 to 0.38). The subclasses were then combined and assessment of agreement between the general classes as a whole gave a kappa value of 0.33 (95% CI 0.25 to 0.41). The mean kappa value for intra-observer variability of the classification system was 0.42 (95% CI 0.22 to 0.62). When the subclasses were combined, it was 0.45 (95% CI 0.21 to 0.65). Our results show that, despite its popularity, the classification system of Sanders has only fair agreement among users.

Calcaneus↗
PubMed2001

Realistic pathologic classification of acute myeloid leukemias.

Most classification systems of acute myeloid leukemia (AML) rely largely on the criteria proposed by the French-American-British (FAB) Cooperative Group. The recently proposed World Health Organization (WHO) classification of neoplastic diseases of the hematopoietic and lymphoid tissues includes a classification of AMLs. The proposed WHO classification of AMLs includes traditional FAB-type categories of disease, as well as additional disease types that correlate with specific cytogenetic findings and AML associated with myelodysplasia. This system includes a large number of disease categories, many of which are of unknown clinical significance, and there seems to be substantial overlap between disease groups in the WHO proposal. Some disease types in the WHO proposal cannot be diagnosed without detailed clinical information, or they are diagnosed only by the cytogenetic findings. In this report, a realistic pathologic classification for AML is proposed that includes disease types that correlate with specific cytogenetic translocations and can be recognized reliably by morphologic evaluation and immunophenotyping and that incorporates the importance of associated myelodysplastic changes. This system would be supported by cytogenetic or molecular genetic studies and could be expanded as new recognizable clinicopathologic entities are described.

Acute Disease↗
PubMed2006

Evaluating support for the current classification of eukaryotic diversity.

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification--plants, animals, fungi, and protists--have been transformed through numerous permutations into the current system of six "supergroups." The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

Animals↗
PubMed2005

Classification and pathology of pituitary tumors.

Pituitary adenomas originating in adenohypophysial cells represent the most common neoplasms of the sella turcica. The pathologist's goal is the optimal diagnosis and classification of pituitary adenomas. Lack of clinicopathological correlations in the past classification of pituitary adenomas, which was based on the tinctorial properties of adenoma cells, limited the importance of histological diagnosis. Morphologic separation of pituitary cells by electron microscopy provided fundamental knowledge to classify pituitary adenomas. Immunohistochemistry represents the gold standard of the current classification. Combined morphologic and immunohistochemical diagnostic approaches resulted in the clinicopathologic classification of pituitary adenomas. The WHO classification of 2004 is based on morphologic features and takes into consideration findings from imaging procedures and clinical symptoms. Morphologic characterization of pituitary tumors and correlation of the hormone product with hormone secretion provides the clinician with useful information. In addition, the utility of tumor markers offers objective information in managing the patient and predicting responses to specific treatment. The Ki-67 labeling index (LI) is widely used for it correlates with invasiveness and probably prognosis. Adenomas showing increased ( >3%) LI and extensive p53 immunoreactivity should be termed "atypical adenomas" suggesting aggressive potential or malignant transformation. Morphologic separation of adenoma from carcinoma is not feasible. The term pituitary carcinoma should be exclusively applied when cerebrospinal and/or systemic metastases are definite.

Adenoma↗
PubMed2001

Moving towards rational pharmacological management of pain with an improved classification system of pain.

Recognition that untreated pain can have serious deleterious effects has lead to significant resources being devoted towards understanding physiology, controlling nociception and implementing standards that promise to improve treatment of pain. Recently, improved knowledge and the appreciation of the need for a polypharmaceutical approach has lead to an appreciation that the classification of pain syndromes is the best approach towards rationalising treatment approaches. Older classification approaches such as acute and chronic, neuropathic, or nociceptive have not been universally useful for the clinician [1]. These classification schemes do not recognise that patients with pain often have mixed pain syndromes and do not fall neatly into these schemes. In addition, these classification schemes cannot represent newer advances in the understanding of pain and its physiology. Due to the growing variety of treatment approaches, classification of pain syndromes is often the best first step towards understanding a patient's pathophysiological process, initiating appropriate treatment and improving patient outcomes.

Analgesics↗
PubMed2006

Clinical classification of tetanus patients.

The authors propose a clinical classification to monitor the evolution of tetanus patients, ranging from grade I to IV according to severity. It was applied on admission and repeated on alternate days up to the 10th day to patients aged > or = 12 years admitted to the State University Hospital, Recife, Brazil. Patients were also classified upon admission according to three prognostic indicators to determine if the proposed classification is in agreement with the traditionally used indicators. Upon admission, the distribution of the 64 patients among the different levels of the proposed classification was similar for the groups of better and worse prognosis according to the three indicators (P > 0.05), most of the patients belonging to grades I and II of the proposed classification. In the later reclassifications, severe forms of tetanus (grades III and IV) were more frequent in the categories of worse prognosis and these differences were statistically significant. There was a reduction in the proportion of mild forms (grades I and II) of tetanus with time for the categories of worse prognostic indicators (chi-square for trend: P = 0.00006, 0.03, and 0.00000) whereas no such trend was observed for the categories of better prognosis (grades I and II). This serially used classification reflected the prognosis of the traditional indicators and permitted the comparison of the dynamics of the disease in different groups. Thus, it becomes a useful tool for monitoring patients by determining clinical category changes with time, and for assessing responses to different therapeutic measures.

Adolescent↗
PubMedDate not supplied

[Correlation between TNM classification, histological grading and anatomical location in oral squamous cell carcinoma].

The aim of this study was to investigate the existence of correlation between the TNM clinical classification, histologic malignancy grading and anatomical location of oral squamous cell carcinoma. A total of 120 oral squamous cell carcinomas were selected from the files of the Dr. Luiz Antonio Hospital (Natal, Rio Grande do Norte, Brazil). Data concerning TNM clinical classification and anatomical location of lesions were obtained. Histologic malignancy grading was carried out following the criteria defined by Wahi22 (1971). Pearson's correlation test was applied for the statistical analysis of data. It revealed a statistically significant correlation (r = 0.2993, p = 0.01) between TNM clinical classification and histologic malignancy grading. It also revealed correlation between TNM classification and the anatomical location of oral squamous cell carcinomas (r = 0.4463, p = 0.01). We concluded that TNM classification presented correlation with histological grading and with the different anatomical locations of oral squamous cell carcinomas.

Adult↗
PubMed1993

The Neer classification system for proximal humeral fractures. An assessment of interobserver reliability and intraobserver reproducibility.

The radiographs of fifty fractures of the proximal part of the humerus were used to assess the interobserver reliability and intraobserver reproducibility of the Neer classification system. A trauma series consisting of scapular anteroposterior, scapular lateral, and axillary radiographs was available for each fracture. The radiographs were reviewed by an orthopaedic shoulder specialist, an orthopaedic traumatologist, a skeletal radiologist, and two orthopaedic residents, in their fifth and second years of postgraduate training. The radiographs were reviewed on two different occasions, six months apart. Interobserver reliability was assessed by comparison of the fracture classifications determined by the five observers. Intraobserver reproducibility was evaluated by comparison of the classifications determined by each observer on the first and second viewings. Kappa (kappa) reliability coefficients were used. All five observers agreed on the final classification for 32 and 30 per cent of the fractures on the first and second viewings, respectively. Paired comparisons between the five observers showed a mean reliability coefficient of 0.48 (range, 0.43 to 0.58) for the first viewing and 0.52 (range, 0.37 to 0.62) for the second viewing. The attending physicians obtained a slightly higher kappa value than the orthopaedic residents (0.52 compared with 0.48). Reproducibility ranged from 0.83 (the shoulder specialist) to 0.50 (the skeletal radiologist), with a mean of 0.66. Simplification of the Neer classification system, from sixteen categories to six more general categories based on fracture type, did not significantly improve either interobserver reliability or intraobserver reproducibility.

Evaluation Studies as Topic↗