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PubMed1983

Verminous aneurysm caused by filaria.

Aneurysms caused by atherosclerosis are relatively frequent, as a consequence of the high incidence of this degenerative disease of the arteries. Other types of aneurysm, for example, those of infectious etiology, are more uncommon. Bacterias and fungi are able to cause aneurysms in several parts of the arterial tree. Stengel et al (1943), in a review of world literature described 217 cases of mycotic aneurysms. The Stedman's Medical Dictionary refers to a special type of aneurysm observed in horses, caused by intra-vascular migration of a worm, the Strongylus vulgaris. It has been named verminous aneurysm and generally involves the mesenteric arteries. We haven't found in medical literature any similar observations refering to human cases. The purpose of this paper is to describe a case of aneurysm the etiology of which we have imputed to the filaria (Wuchereria bancrofti). This case was observed in Marcilio Dias Naval Hospital, Rio de Janeiro, Brazil.

Adult↗
PubMedDate not supplied

The effects of an interactive instructional strategy for enhancing reading comprehension and content area learning for students with learning disabilities.

This study investigated the effectiveness of an interactive vocabulary instructional strategy, semantic-feature analysis (SFA), on the content area text comprehension of adolescents with learning disabilities. Prior to reading a social studies text, students in resource classes either completed a relationship chart as part of the SFA condition or used the dictionary to write definitions and sentences as part of the contrast condition. Passage comprehension was measured on a multiple-choice test consisting of two types of items, vocabulary and conceptual. Comprehension was measured immediately following teaching and again 6 months after teaching. Prior knowledge for the content of the passage served as a covariate. Results indicated that students in the SFA instructional condition had significantly greater measured comprehension immediately following and 6 months after initial teaching. These results are discussed in relation to concept-driven, interactive strategies for teaching content and facilitating text comprehension.

Adolescent↗
PubMedDate not supplied

The effect of five proofreading conditions on the spelling performance of college students with learning disabilities.

This study investigated the effect of five proofreading conditions on the spelling performance of 12 college students with learning disabilities on a composition activity. The proofreading conditions investigated were handwriting with no additional assistance, handwriting with a conventional print dictionary, handwriting with a handheld spelling checker, word processing with no additional assistance, and word processing with an integrated spelling checker. A repeated measures ANOVA was used to analyze the results, with proofreading condition used as a within-participants factor. Except for handwriting alone, all of the techniques resulted in significant reductions in the number of spelling errors in the students' written work; however, none of the techniques enabled the students to produce compositions with a mean level of spelling accuracy comparable to that of their nondisabled peers.

Achievement↗
PubMedDate not supplied

Emotion in language and speech: methodological issues in naturalistic approaches.

Researchers currently seek to improve validity in speech and language studies by adopting naturalistic procedures In emotion-display research, validity is threatened by standard experimental controls which diminish the naturalism of stimuli and response ranges. We report two experiments comparing the adequacy of naturalistic with standard procedures. Experiment 1 had 158 judges code 89 samples of naturally-occurring emotional speech with free-choice emotion labels, and later with labels from a standard set. When free-choice labels were similar across judges, they were consistent with standard labels, but showed a range of intensity and contextual relevance. We recommend that future studies include wider options for judges when coding emotions. Experiment 2 compared valency ratings of words when presented in, or out of, context. Standard procedures score lexical valencies using affective dictionaries, disregarding natural contexts. Experiment 2 compared 23 judges' valency ratings of words presented individually, and later in their original context. Between 30% and 44% of words were rated differently in context (depending on the statistical significance level adopted). We concluded from Experiment 2 that, where small corpora adequately model a domain, the improved accuracy of valency rating achieved by presenting words in their natural context justifies the extra procedures required.

Adult↗
PubMed1986

Computerized information resources in toxicology and industrial health--a review.

The explosion in scientific information presents problems for toxicologists and industrial health specialists who need to respond rapidly and comprehensively to the information needs of the public, government and industry. The application of information technology enables large volumes of toxicology and industrial health information to be stored and retrieved through a variety of data-base resources. Three different categories of databases are described: dictionary, bibliographic and informational types. Examples of specific toxicology and industrial health databases within each category are given; their origin, style and content are reviewed. Specialists in the industrial health field are encouraged to improve their knowledge and literacy in the new disciplines of information technology and information science.

Computers↗
PubMed2005

On the fantastic apparitions of vision by Johannes Müller.

The history of the construction of the concept of hallucination remains biased in the favour of the French contribution. Important to this history are the first 30 years of the nineteenth century for it was then that it was decided that hallucinations were: (1) primary disorders of perception; (2) the same class of phenomena, regardless of the sense of modality in which they occurred; (3) generated by stimulation of brain regions related to perception and hence were mechanical responses with no semantic or informational import; and (4) medical problems. In 1826 Johannes Müller published a book on the fantastic phenomena of vision. Therein her proposed new rules for the description and explanation of hallucinations. Although published after Purkinje's books on an analogous theme, and after Esquirol's entry for the Panckoucke dictionary, Müller's book served as one of the foundations for the new nineteenth-century speculative physiology and physiopathology of hallucinations. This way of conceptualizing these phenomena was to culminate in the irritation model proposed by Tamburini in the 1880s. This paper justifies the choice of Müller's book as a classic text, provides biographical data about its author, and places the book in its historical context.

Germany↗
PubMed2002

PaSent--the patient's personal health adviser.

We have attempted to automate the search for medical information that is relevant to a patient s electronic record. We used anonymous medical reports sent from the University Hospital of Tromsø to general practitioners as input data. The medical reports were matched against the NEL, a Web-based medical dictionary and document collection service for general practitioners. We evaluated only the three top-scoring documents automatically selected by the system. A medical professional evaluated whether a selected document from the NEL was very relevant to the contents of the input report, relevant or irrelevant. Initial tests showed that 60% of the top three selected documents found by the PaSent system were very relevant or relevant to the contents of the medical report used as input data. Our preliminary conclusion is that automatic location of relevant information is possible using medical reports as input data.

Humans↗
PubMed2006

DEC-net: the development of the European register of clinical trials on medicines for children.

BACKGROUND: The need to register a clinical trial in a public database has been widely discussed in the last few years. Several general clinical trial registers have been developed, but none are dedicated to children. A web-based register of trials on drug therapy in children was therefore developed. PURPOSE: The general objective of the project, called DEC-NET (European register of clinical trials on medicines for children - drug evaluation in children) and supported by the European Community, is to provide the scientific community with a flexible tool for promoting communication and collaboration among researchers, disseminating clinical trial results and facilitating patient access and recruitment to trials. METHODS: We identified a set of trial data to be collected, including general trial information, recruitment information, eligibility criteria, clinical trial characteristics, location and contact information, study drugs, study sponsor and results. The system was set up to allow authorized users (working in Italy, Spain, France and UK) to enter, handle and monitor the trial information. Medical data dictionaries (ie, ICD-9 and ATC) were used in order to make the data-entry and the search and data analysis procedures easier. A multilingual approach in data handling and presentation made accessing trial information in English and in the language of the country where the study is located feasible. Search and browsing tools were set up to allow investigators, researchers, and citizens to freely search and browse the entire register and access the details of trials meeting the search criteria. RESULTS: The DEC-net register (http://www.dec-net.org) was opened for trial notification and consultation. LIMITATIONS: DEC-net currently involves four European countries and is a pilot project. CONCLUSIONS: It is hoped that what has been achieved so far represents only the beginning of a long-term project, and the next step will be to extend the register's use to other European countries.

Child↗
PubMedDate not supplied

Recent developments in information management for primary and community health services.

While health services provided outside the hospital environment are utilised by the majority of the community, until recently there has been little interest in developing a standard approach to information management in community health settings. With greater accountability for health services expected in the future, State and Federal governments have begun to set the necessary standards by the design of a common data model and data definitions for Primary and Community Health Services. This model will affect the manner in which the National Health Data Dictionary develops--from a primarily institution-based document to a broader approach which encompasses non-institutional care. Two new high level concepts have been introduced: "issue" and "activity". Four States have also formed a consortium to design and implement an information management system for Community Health Services. This necessitates adoption of standard classification systems which could be applied in this environment, especially to the two new high level concepts. This paper outlines recent developments in information management for Community Health and provides a brief summary of available classification systems.

Ambulatory Care Information Systems↗
PubMed2005

ProMiner: rule-based protein and gene entity recognition.

BACKGROUND: Identification of gene and protein names in biomedical text is a challenging task as the corresponding nomenclature has evolved over time. This has led to multiple synonyms for individual genes and proteins, as well as names that may be ambiguous with other gene names or with general English words. The Gene List Task of the BioCreAtIvE challenge evaluation enables comparison of systems addressing the problem of protein and gene name identification on common benchmark data. METHODS: The ProMiner system uses a pre-processed synonym dictionary to identify potential name occurrences in the biomedical text and associate protein and gene database identifiers with the detected matches. It follows a rule-based approach and its search algorithm is geared towards recognition of multi-word names. To account for the large number of ambiguous synonyms in the considered organisms, the system has been extended to use specific variants of the detection procedure for highly ambiguous and case-sensitive synonyms. Based on all detected synonyms for one abstract, the most plausible database identifiers are associated with the text. Organism specificity is addressed by a simple procedure based on additionally detected organism names in an abstract. RESULTS: The extended ProMiner system has been applied to the test cases of the BioCreAtIvE competition with highly encouraging results. In blind predictions, the system achieved an F-measure of approximately 0.8 for the organisms mouse and fly and about 0.9 for the organism yeast.

Computational Biology↗
PubMed2005

BioCreAtIvE task1A: entity identification with a stochastic tagger.

BACKGROUND: Our approach to Task 1A was inspired by Tanabe and Wilbur's ABGene system. Like Tanabe and Wilbur, we approached the problem as one of part-of-speech tagging, adding a GENE tag to the standard tag set. Where their system uses the Brill tagger, we used TnT, the Trigrams 'n' Tags HMM-based part-of-speech tagger. Based on careful error analysis, we implemented a set of post-processing rules to correct both false positives and false negatives. We participated in both the open and the closed divisions; for the open division, we made use of data from NCBI. RESULTS: Our base system without post-processing achieved a precision and recall of 68.0% and 77.2%, respectively, giving an F-measure of 72.3%. The full system with post-processing achieved a precision and recall of 80.3% and 80.5% giving an F-measure of 80.4%. We achieved a slight improvement (F-measure = 80.9%) by employing a dictionary-based post-processing step for the open division. We placed third in both the open and the closed division. CONCLUSION: Our results show that a part-of-speech tagger can be augmented with post-processing rules resulting in an entity identification system that competes well with other approaches.

Databases, Genetic↗
PubMed2005

Recognition of protein/gene names from text using an ensemble of classifiers.

This paper proposes an ensemble of classifiers for biomedical name recognition in which three classifiers, one Support Vector Machine and two discriminative Hidden Markov Models, are combined effectively using a simple majority voting strategy. In addition, we incorporate three post-processing modules, including an abbreviation resolution module, a protein/gene name refinement module and a simple dictionary matching module, into the system to further improve the performance. Evaluation shows that our system achieves the best performance from among 10 systems with a balanced F-measure of 82.58 on the closed evaluation of the BioCreative protein/gene name recognition task (Task 1A).

Biomedical Research↗
PubMed2006

Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm.

BACKGROUND: Metabolomic studies are targeted at identifying and quantifying all metabolites in a given biological context. Among the tools used for metabolomic research, mass spectrometry is one of the most powerful tools. However, metabolomics by mass spectrometry always reveals a high number of unknown compounds which complicate in depth mechanistic or biochemical understanding. In principle, mass spectrometry can be utilized within strategies of de novo structure elucidation of small molecules, starting with the computation of the elemental composition of an unknown metabolite using accurate masses with errors <5 ppm (parts per million). However even with very high mass accuracy (<1 ppm) many chemically possible formulae are obtained in higher mass regions. In automatic routines an additional orthogonal filter therefore needs to be applied in order to reduce the number of potential elemental compositions. This report demonstrates the necessity of isotope abundance information by mathematical confirmation of the concept. RESULTS: High mass accuracy (<1 ppm) alone is not enough to exclude enough candidates with complex elemental compositions (C, H, N, S, O, P, and potentially F, Cl, Br and Si). Use of isotopic abundance patterns as a single further constraint removes >95% of false candidates. This orthogonal filter can condense several thousand candidates down to only a small number of molecular formulas. Example calculations for 10, 5, 3, 1 and 0.1 ppm mass accuracy are given. Corresponding software scripts can be downloaded from http://fiehnlab.ucdavis.edu. A comparison of eight chemical databases revealed that PubChem and the Dictionary of Natural Products can be recommended for automatic queries using molecular formulae. CONCLUSION: More than 1.6 million molecular formulae in the range 0-500 Da were generated in an exhaustive manner under strict observation of mathematical and chemical rules. Assuming that ion species are fully resolved (either by chromatography or by high resolution mass spectrometry), we conclude that a mass spectrometer capable of 3 ppm mass accuracy and 2% error for isotopic abundance patterns outperforms mass spectrometers with less than 1 ppm mass accuracy or even hypothetical mass spectrometers with 0.1 ppm mass accuracy that do not include isotope information in the calculation of molecular formulae.

Algorithms↗
PubMed2007

A generalized analysis of hydrophobic and loop clusters within globular protein sequences.

BACKGROUND: Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. RESULTS: The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for alpha-helices or beta-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that beta-strands and especially alpha-helices are generally over-predicted within the limits of typical beta and alpha hydrophobic clusters. CONCLUSION: The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction.

Cluster Analysis↗
PubMed2004

Resources for comparing the speed and performance of medical autocoders.

BACKGROUND: Concept indexing is a popular method for characterizing medical text, and is one of the most important early steps in many data mining efforts. Concept indexing differs from simple word or phrase indexing because concepts are typically represented by a nomenclature code that binds a medical concept to all equivalent representations. A concept search on the term renal cell carcinoma would be expected to find occurrences of hypernephroma, and renal carcinoma (concept equivalents). The purpose of this study is to provide freely available resources to compare speed and performance among different autocoders. These tools consist of: 1) a public domain autocoder written in Perl (a free and open source programming language that installs on any operating system); 2) a nomenclature database derived from the unencumbered subset of the publicly available Unified Medical Language System; 3) a large corpus of autocoded output derived from a publicly available medical text. METHODS: A simple lexical autocoder was written that parses plain-text into a listing of all 1,2,3, and 4-word strings contained in text, assigning a nomenclature code for text strings that match terms in the nomenclature. The nomenclature used is the unencumbered subset of the 2003 Unified Medical Language System (UMLS). The unencumbered subset of UMLS was reduced to exclude homonymous one-word terms and proper names, resulting in a term/code data dictionary containing about a half million medical terms. The Online Mendelian Inheritance in Man (OMIM), a 92+ Megabyte publicly available medical opus, was used as sample medical text for the autocoder. RESULTS: The autocoding Perl script is remarkably short, consisting of just 38 command lines. The 92+ Megabyte OMIM file was completely autocoded in 869 seconds on a 2.4 GHz processor (less than 10 seconds per Megabyte of text). The autocoded output file (9,540,442 bytes) contains 367,963 coded terms from OMIM and is distributed with this manuscript. CONCLUSIONS: A public domain Perl script is provided that can parse through plain-text files of any length, matching concepts against an external nomenclature. The script and associated files can be used freely to compare the speed and performance of autocoding software.

Abstracting and Indexing↗
PubMed2006

Some Lithuanian ethnobotanical taxa: a linguistic view on thorn apple and related plants.

BACKGROUND: The perception and use of plants correspond with common plant names. The study of plant names may give insight into historical and recent use of plants. METHODS: Plant names in dictionaries and folklore have been evaluated. A etymological analysis of the names is provided. Onomasiological and semasiological aspects have been considered. Therefore, species named with names related to each other have been selected. RESULTS: Plant names containing the stem dag- or deg- may belong to either of two categories: incenses or thorny plants. Plants named in durn- have been in use as psychopharmaca. The name rymo points not to Rome but to the use of plants as anodyne or psychopharmaca.

Atropa belladonna↗
PubMed2006

Secular humanism and "scientific psychiatry".

The Council for Secular Humanism identifies Secular Humanism as a "way of thinking and living" committed to rejecting authoritarian beliefs and embracing "individual freedom and responsibility ... and cooperation." The paradigmatic practices of psychiatry are civil commitment and insanity defense, that is, depriving innocent persons of liberty and excusing guilty persons of their crimes: the consequences of both are confinement in institutions ostensibly devoted to the treatment of mental diseases. Black's Law Dictionary states: "Every confinement of the person is an 'imprisonment,' whether it be in a common prison, or in private house, or in the stocks, or even by forcibly detaining one in the public streets." Accordingly, I maintain that Secular Humanism is incompatible with the principles and practices of psychiatry.

Behavior Control↗