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PubMedDate not supplied

[Some French doctors as writers in the first half of the XXth century].

The author recollects the memory of more than 50 French medical authors of this period. Some of tham are cited in the dictionary le Petit Robert. Many were novelists or literary critics. Among the cited authors numerous were known for their scientific work but Clemenceau is chiefly known for his political career and Schweitzer for his humanitarian action. The author underlines that the suffering and pains of soldiers during the First World War inspired real major works and some medical students became prominent writers.

France↗
PubMed2004

A knowledge based approach for automated signal generation in pharmacovigilance.

BACKGROUND: Pharmacovigilance experts detect new adverse drug reactions (ADR) by manually reviewing spontaneous reporting systems. Automated signal generation aims to focus the attention of experts on drug-adverse event associations which are disproportionally present in the database. Although adverse events are coded by means of controlled vocabularies such as the MedDRA dictionary, this semantic information is not taken into account for signal generation. OBJECTIVE: To improve the performance of current signal detection algorithms using knowledge based approach. METHOD: We developed a formal ontology of ADRs and built a data mining tool that uses description logic representations of MedDRA terms to group medically related case reports. RESULTS: This knowledge based approach increased the sensitivity of signal detection with no decrease in specificity. DISCUSSION: A knowledge based approach improved the performance of signal detection tools. However, the huge work-load involved in the knowledge engineering step limits the use of this approach for machine learning.

Adverse Drug Reaction Reporting Systems↗
PubMed2004

Development and representation of a fall-injury risk assessment instrument in a clinical information system.

The potential for informatics solutions to address inpatient safety issues is significant; however, several challenges are associated with the development of patient safety related informatics applications. These challenges include: 1) the identification and/or development of valid and reliable instruments; 2) adequate representation of key safety concepts, constructs, and associated concepts in the clinical information system; and 3) identification of data sources for instrument pre-population. As part of a larger project aimed at identifying and addressing the information needs of clinicians while using a clinical information system, an electronic fall and injury risk assessment instrument is in development to address a hospital-based fall and injury prevention initiative. The concepts contained in the instrument are well represented by Clinical LOINC and the UMLS. Associated concepts have been identified in the existing clinical information system data dictionary for pre-population of the instrument.

Accidental Falls↗
PubMed2004

A DNA Motif Lexicon: cataloguing and annotating sequences.

The rapid proliferation of genomic DNA sequences has created a significant need for software that can both focus on relatively small areas (such as within genes or promoters) and provide wide-zoom views of patterns across entire genomes. We present our DNA Motif Lexicon that enables users to perform genome-wide searches for motifs of interest and create customizable results pages, where results differ in the degree and extent of annotation. Searching for a particular motif is akin to a word search in a natural language; our motif lexicon speaks to this new time when we will increasingly rely upon DNA dictionaries that offer rich types of annotation. Indeed, the concept of "lexomics", introduced in this paper may be appropriate to the types of meta-analyses appropriate to the deciphering of regulatory information. Currently supporting five genomes, our web-based lexicon allows users to look up motifs of interest and build user-defined result pages to include the following: (1) all base pair locations where a motif is found with links to further search the "neighborhoods" near each of these locations; whether each location of the motif is genic (within) a gene, intergenic, or a bridging sequence (overlapping a gene boundary) (2) NCBI hot-links to nearest upstream and downstream genes for each location (3) statistical information about the query (4) whether the motif is a certain type of repeat (5) links for the reverse, complement and reverse-complement of the motif of interest and (6) hot-links to PubMed abstracts which mention the motif of interest. A software framework facilitates the continual development of new annotation modules. The tool is located at: http://genomics.wheatoncollege.edu/cgi-bin/lexicon.exe.

Animals↗
PubMed2004

Optimization of a vector quantization codebook for objective evaluation of surgical skill.

Surgical robotic systems and virtual reality simulators have introduced an unprecedented precision of measurement for both tool-tissue and tool-surgeon interaction; thus holding promise for more objective analyses of surgical skill. Integrative or averaged metrics such as path length, time-to-task, success/failure percentages, etc., have often been employed towards this end but these fail to address the processes associated with a surgical task as a dynamic phenomena. Stochastic tools such as Markov modeling using a 'white-box' approach have proven amenable to this type of analysis. While such an approach reveals the internal structure of the of the surgical task as a process, it requires a task decomposition based on expert knowledge, which may result in a relatively large/complex model. In this work, a 'black box' approach is developed with generalized cross-procedural applications., the model is characterized by a compact topology, abstract state definitions, and optimized codebook size. Data sets of isolated tasks were extracted from the Blue DRAGON database consisting of 30 surgical subjects stratified into six training levels. Vector quantization (VQ) was employed on the entire database, thus synthesizing a lexicon of discrete, task-independent surgical tool/tissue interactions. VQ has successfully established a dictionary of 63 surgical code words and displayed non-temporal skill discrimination. VQ allows for a more cross-procedural analysis without relying on a thorough study of the procedure, links the results of the black-box approach to observable phenomena, and reduces the computational cost of the analysis by discretizing a complex, continuous data space.

Algorithms↗
PubMed2004

[Life and achievements of professor Irena Norska-Borówka the 75th birthday anniversary].

The purpose of the publication is to present the life, scientifical and social activity of the eminent pediatrician prof. Irena Norska-Borówka. The biography is based on personal data, biographical notes published in medical dictionaries, scientific publications and opinions of scientific authorities. Prof. Irena Norska-Borówka was the President of Scientific Committee of the eight previous Congresses ECOMED in Tarnów, the creator of Ecological Section of Polish Physicians Society, Polish and World precursor of Environmental Pediatrics and the UNICER expert. She has more than 300 publications, including 50 monographies. She has been awarded the I-st stage Award of the Minister of Health and Social Care for the studies on congenital toxoplasmosis. She also received SAM Rector's Awards for the publications of environmental pollution influence on the children's health and creation in 1980 the first in Poland Neonatal Pathology Clinic with an Intensive Care Department. She has become the ethical authority for her students and doctors. She has been appreciated by Upper Silesian inhabitants for her scientific work and social activity towards children and youth.

Awards and Prizes↗
PubMed2002

A multi-level text mining method to extract biological relationships.

Accurate and computationally efficient approaches in discovering relationships between biological objects from text documents are important for biologists to develop biological models. This paper presents a novel approach to extract relationships between multiple biological objects that are present in a text document. The approach involves object identification, reference resolution, ontology and synonym discovery, and extracting object-object relationships. Hidden Markov Models (HMMs), dictionaries, and N-Gram models are used to set the framework to tackle the complex task of extracting object-object relationships. Experiments were carried out using a corpus of one thousand Medline abstracts. Intermediate results were obtained for the object identification process, synonym discovery, and finally the relationship extraction. For a corpus of thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81%. The approach is both adaptable and scalable to new problems as opposed to rule-based methods.

Abstracting and Indexing↗
PubMed2002

DNA sequence compression using the burrows-wheeler transform.

We investigate off-line dictionary oriented approaches to DNA sequence compression, based on the Burrows-Wheeler Transform (BWT). The preponderance of short repeating patterns is an important phenomenon in biological sequences. Here, we propose off-line methods to compress DNA sequences that exploit the different repetition structures inherent in such sequences. Repetition analysis is performed based on the relationship between the BWT and important pattern matching data structures, such as the suffix tree and suffix array. We discuss how the proposed approach can be incorporated in the BWT compression pipeline.

Algorithms↗
PubMed2005

What is eHealth?: a systematic review of published definitions.

CONTEXT: The term eHealth is widely used by many individuals, academic institutions, professional bodies and funding organisations. It has become an accepted neologism despite the lack of an agreed-upon clear or precise definition. We believe that communication among the many individuals and organisations that use the term could be improved by comprehensive data about the range of meanings encompassed by the term. OBJECTIVE: To report the results of a systematic review of published, suggested or proposed definitions of eHealth. DATA SOURCES: Using hte search query string 'eHealth' OR 'e-Health' OR 'electronic health', we searched the following databases: Medline and Premedline (1996-June 2004), EMBASE (1980-May 2004), International Pharmaceutical Abstracts (1970-May 2004), Web of Science (all years), Information Sciences Abstracts (1996-May 2004), Library Information Sciences Abstracts (1969-May 2004), and Wilson Business Abstracts (1982-March 2004), In addition, we searched dictionaries and an Internet search engine. STUDY SELECTION: We included any source published in either print format or on the Internet, available in English, and containing text that defines or attempts to define eHealth in explicit terms. Two of us independently reviewed titles and abstracts of citations identified in the bibliographic databases and Internet search, reaching consensus on relevance by discussion. DATA EXTRACTION: We retrieved relevant reports, articles, references, letters and websites containing definitions of eHealth. Two of us qualitatively analysed the definitions and coded them for content, emerging themes, patterns and novel ideas. DATA SYNTHESIS: The 51 unique definitions that we retrieved showed a wide range of themes, but no clear consensus about the meaning of the term eHealth. We identified two universal themes (health and technology) and six less general (commerce, activities, stakeholders, outcomes, place, and perspectives). CONCLUSIONS: The widespread use of the term eHealth suggests that it is an important concept, and that there is a tacit understanding of its meaning. This compendium of proposed definitions may improve communication among the many individuals and organisations that use the term.

Journal Article↗
PubMedDate not supplied

[Life and work of Dr. Bozo Pericić (1865-1947), genius of our medicine].

The paper describes the life and work of on of our most distinguished physicians--Dr Bozo Pericić. Togheter with another young physician Dr Nikola Lalić the Sibenik hospital became a sort of Meca for medical people. Dr Pericić succeded to clarify an unknown disease--so called "Skrljevo disease", paved the path of to the knowledge about achinococcus etc. He published also number of valuable medical articles and books and avarded a number af aknowledgements. One of the biggest was his nomination for membership of the Supreme Haelth Council in Wienna. He contributed e lot to the medical journals, especially to the "Physician's Journal". As person of wide culture, famous linguist and polyglot Dr Pericić published the "Medical dictionary of Croatian and German Language". He lay foundation of the craniology, quite a new branch of arheology at the time. His accounts of travels, reviews on famous writers, translation of Hamlet, etc--are valuable literary works.

Croatia↗
PubMed2005

PRIME: automatically extracted PRotein Interactions and Molecular Information databasE.

With the exponentially increasing amount of information in the biomedical field, the significance of advanced information retrieval and information extraction, as well as the role of databases, has been increasing. PRIME is an integrated gene/protein informatics database based on natural language processing. It provides automatically extracted protein/family/gene/compound interaction information including both physical and genetic interactions, gene ontology based functions, and graphic pathway viewers. Gene/protein/family names and functional terms are recognized based on dictionaries developed in our laboratory. The interaction and functional information are extracted by syntactic dependencies and various phrase patterns. We have included about 920,000 (non-redundant) protein interactions and 360,000 annotated gene-function relationships for major eukaryotes. By combining the sequence and text information, the pathway comparison between two organisms and simple pathway deduction based on other organism interaction data, and pathway filtering using tissue expression data, are also available. This database is accessible at http://prime.ontology.ims.u-tokyo.ac.jp:8081.

Abstracting and Indexing↗
PubMed1992

[Cognitive style of schizophrenic patients: ambiguity avoidance and decreased abstract thinking].

The hypothesis of specific cognitive dynamics in schizophrenics is derived and tested in this study. This cognitive style should be characterized by a reduction of cognitive ambiguity and could be demonstrated in borderline patients in a previous study. This hypothesis is tested by applying Ertel's (1972) DOTA-dictionary to responses of 25 acute and 25 chronic schizophrenics in the Holtzman Inkblot Technique. Furthermore the level of abstractness of the responses is investigated with the method of Günther and Groeben (1978). According to the results both groups of schizophrenics had a significantly higher "Dogmatismus-Quotient" (Ertel, 1972) than a sample of neurotics, but did not differ from borderline patients. Both acute and chronic schizophrenics used significantly less abstract nouns than borderline patients and neurotics. In contrast to borderline patients the reduction of cognitive ambiguity in schizophrenics is not connected with strong affects of anxiety and hostility.

Adult↗
PubMed2005

[Czech terms for rod-shaped bacteria].

With increasing frequency, the rod-shaped bacteria have been recently referred to in Czech as tyce (the singular is tyc) instead of the diminutive tycinky (the singular is tycinka) as used in classical Czech textbooks and handbooks of medical microbiology. This discordance might result from inadequate translation of the English term rods. Although the English-Czech dictionary gives three equivalents for the analyzed meaning of this word, i.e. tyc, tycka, tycinka, the first option, a mono-syllable as the English rod is, is often selected without further consideration. Nevertheless, such simplification is not justified; to avoid confusion it is preferable to use conventional terminology.

Bacteria↗
PubMed2005

The Community Physicians' Network (CPN): an academic-community partnership to eliminate healthcare disparities.

INTRODUCTION: Disparities in health care are maintained by three primary factors: 1) patient factors which include multiple risk factors and comorbidities; 2) healthcare practitioner factors comprising inconsistent application of practice guidelines due to a limited database of clinical trials of effective therapies in African Americans and other underrepresented minorities; and 3) barriers in the healthcare delivery system resulting in poor access to care. The Morehouse School of Medicine Community Physicians' Network (CPN) was established to address disparities in health care by focusing on provider-specific strategies. OBJECTIVES: To: 1) use disease-specific registries to identify treatment gaps and facilitate quality improvement processes among CPN practices; 2) develop practice-specific and guideline-based educational messages to promote quality care; 3) engage and train CPN-physicians for participation in approved NIH, other government, and industry-supported clinical protocols; and 4) develop a data repository of all CPN-sponsored clinical trials that include significant numbers of African Americans and other underrepresented minorities. METHODS: The disease-specific outpatient registries will have the following features: 1) data structures and data elements will use standard database codes and a data dictionary; 2) HIPPA-compliant data abstraction and data transfer tool; 3) baseline chart review to establish practice patterns and provide practice-specific feedback; 4) annual update of registry; 5) data registry and repository maintained on Morehouse School of Medicine's secure servers; 6) registry publications will include only aggregate data, without identification of contributing practices; 7) an electronic medical records platform will be encouraged as the ultimate data management tool for CPN practices. In addition, up to three continuing medical education (CME) programs each year will feature national speakers and promote evidence-based practice guidelines. RESULTS: Eighty-five primary care and subspecialty practices are actively enrolled in CPN with a total of 385,000 annual outpatient visits. The makeup of insurance status is: HMO/PPO (45%); Medicare only (19%); Medicare HMO (11%); Medicare plus (8%); Medicaid (6%); Uninsured (11%). CONCLUSIONS: The Community Physicians' Network will address specific gaps in the health care of African-American and other minority patients by promoting quality care among its members and by facilitating participation in approved clinical trial protocols. The unique academic community partnership is consistent with the NIH roadmap goal of eliminating healthcare disparities.

Black or African American↗
PubMed2006

Descriptions of clinical semiology of seizures in literature.

Literary texts are an important part of the cultural history of many fields of medicine. Accounts of epilepsy are frequent, and descriptions of seizure semiology are often included with varying detail. This review looks at these, and considers the authors' background knowledge of epilepsy. The first group of writers suffered seizures themselves. Some of them provide remarkable and novel insights into the subjective symptoms and experiences in and around seizures.A second group draws from their own observations of seizures in others who may have been close relatives or fortuitous strangers. Here, the outside view prevails, and seizures may be described with clinical objectiveness. Commonly, the reactions of onlookers become part of the narrative beyond the seizure description. The third group writes from second-hand knowledge, which may be other observer reports, interviews with people with epilepsy or with experts, information being available in dictionaries, medical textbooks and the like. The professional standard of most writers means that the resulting descriptions are quite accurate, but there are also examples of poor use of such information. Many authors' sources are not known, but can be assumed to belong to one of the above categories, and we can sometimes guess. It appears that even authors with no first-hand knowledge are often aware of seizure types other than the most widely known, generalised tonic-clonic, and there is a widespread interest in warnings and how the afflicted respond to them. The quality of an author's fictional account of epilepsy should not be judged from a translation, because specific aspects and the language involved in the description may have been misunderstood by the translator.

Epilepsy↗
PubMed2006

[caCORE: core architecture of bioinformation on cancer research in America].

A critical factor in the advancement of biomedical research is the ease with which data can be integrated, redistributed and analyzed both within and across domains. This paper summarizes the Biomedical Information Core Infrastructure built by National Cancer Institute Center for Bioinformatics in America (NCICB). The main product from the Core Infrastructure is caCORE--cancer Common Ontologic Reference Environment, which is the infrastructure backbone supporting data management and application development at NCICB. The paper explains the structure and function of caCORE: (1) Enterprise Vocabulary Services (EVS). They provide controlled vocabulary, dictionary and thesaurus services, and EVS produces the NCI Thesaurus and the NCI Metathesaurus; (2) The Cancer Data Standards Repository (caDSR). It provides a metadata registry for common data elements. (3) Cancer Bioinformatics Infrastructure Objects (caBIO). They provide Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. The vision for caCORE is to provide a common data management framework that will support the consistency, clarity, and comparability of biomedical research data and information. In addition to providing facilities for data management and redistribution, caCORE helps solve problems of data integration. All NCICB-developed caCORE components are distributed under open-source licenses that support unrestricted usage by both non-profit and commercial entities, and caCORE has laid the foundation for a number of scientific and clinical applications. Based on it, the paper expounds caCORE-base applications simply in several NCI projects, of which one is CMAP (Cancer Molecular Analysis Project), and the other is caBIG (Cancer Biomedical Informatics Grid). In the end, the paper also gives good prospects of caCORE, and while caCORE was born out of the needs of the cancer research community, it is intended to serve as a general resource. Cancer research has historically contributed to many areas beyond tumor biology. At the same time, the paper makes some suggestions about the study at the present time on biomedical informatics in China.

Computational Biology↗
PubMed2005

Extracting diagnoses from discharge summaries.

We have developed a program for extracting the diagnoses and procedures from the past medical history and discharge diagnoses in the discharge summary of a case and coding these using SNOMED-CT in the UMLS. The program uses a limited amount of natural language processing. Rather, it makes use of the relatively standard structure of the discharge summary, a small dictionary to divide the text into phrases, and the extensive collection of phrases for concepts in the UMLS to do the coding. With this approach the program finds 240 of 250 desired concepts with 19 false positives in 23 discharge summaries.

Diagnosis↗
PubMed2005

Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference.

OBJECTIVE: To investigate the indirect alignment of two anatomical ontologies through a reference ontology and to compare it to direct alignment between these two ontologies. The ontologies under investigation are the Adult Mouse Anatomical Dictionary (MA) and the NCI Thesaurus (NCI). The Foundational Model of Anatomy serves as reference ontology. METHODS: The direct alignment employs a combination of lexical and structural similarity. The indirect alignment simply derives mappings from direct alignments to the reference ontology. RESULTS: The indirect MA-NCI alignment yielded 703 mappings and the direct alignment 715, 654 of which are common to both. The mappings specific to one approach were analyzed. CONCLUSIONS: When a reference ontology exists, indirect alignment of multiple ontologies through a reference represents a valid, cost-effective alternative to pairwise alignment.

Anatomy↗