Biomedical subjects

Franck Le Duff

Publications and source records attributed to Franck Le Duff.

15 recordsLinked to original sources

PubMed2005

Problem-based learning in medical informatics for undergraduate medical students: an experiment in two medical schools.

PURPOSE: The objective of this work was to assess problem-based learning (PBL) as a method for teaching information and communication technology in medical informatics (MI) courses. A study was conducted in the Schools of Medicine of Rennes and Rouen (France) with third-year medical students. METHODS: The "PBL-in-MI" sessions included a first tutorial group meeting, then personal work, followed by a second tutorial group meeting. A problem that simulated practice and was focused on information technology was discussed. In Rouen, the students were familiar with PBL, and they enrolled on a voluntary basis, while in Rennes, the students were first-ever participants in PBL courses, and the program was mandatory. One hundred and seventy-seven students participated in the PBL-in-MI sessions and were given a questionnaire in order to evaluate qualitatively the sessions. RESULTS AND DISCUSSION: The response rate was 92.1%. The overall opinion of the students was good. 69.8% responded positively to the program. In Rouen, where the students participated in PBL-in-MI sessions on a voluntary basis, the students were significantly more enthusiastic about PBL-in-MI. Moreover, attitudes and opinions of students are plausibly related to differences in previous PBL skills. The fact that the naïve group had two tutors, one trained and one naïve as the students, has been investigated. Teacher naivety was an explanatory factor for the differences between Rennes and Rouen.

Consumer Behavior↗

PubMed2005

UMLF: a unified medical lexicon for French.

Medical Informatics has a constant need for basic medical language processing tasks, e.g. for coding into controlled vocabularies, free text indexing and information retrieval. Most of these tasks involve term matching and rely on lexical resources: lists of words with attached information, including inflected forms and derived words, etc. Such resources are publicly available for the English language with the UMLS Specialist Lexicon, but not in other languages. For the French language, several teams have worked on the subject and built local lexical resources. The goal of the present work is to pool and unify these resources and to add extensively to them by exploiting medical terminologies and corpora, resulting in a unified medical lexicon for French (UMLF). This paper exposes the issues raised by such an objective, describes the methods on which the project relies and illustrates them with experimental results.

Abstracting and Indexing↗

PubMed2004

Phenotypic and molecular variability of the holoprosencephalic spectrum.

Since 1996, a European network has been organized from Rennes, France and holoprosencephalic files were collected for clinical and molecular study. Familial instances of typical and atypical holoprosencephaly (HPE) were found in 30% of cases. All affected children had psychomotor delay with microcephaly, often associated with endocrine, digestive, and respiratory abnormalities, and thermal dysregulation. Among 173 subjects in the molecular study, 28 heterozygous mutations were identified (16%): 15 SHH mutations, 6 ZIC2 mutations, 5 SIX3 mutations, and 2 TGIF mutations.

Adult↗

PubMed2004

Molecular screening of SHH, ZIC2, SIX3, and TGIF genes in patients with features of holoprosencephaly spectrum: Mutation review and genotype-phenotype correlations.

Holoprosencephaly (HPE; 1 out of 16,000 live births; 1 out of 250 conceptuses) is a complex brain malformation resulting from incomplete cleavage of the prosencephalon, affecting both the forebrain and the face. Clinical expressivity is variable, ranging from a single cerebral ventricle and cyclopia to clinically unaffected carriers in familial dominant autosomic HPE. The disease is genetically heterogeneous, but additional environmental agents also contribute to the etiology of HPE. In our cohort of 200 patients, 34 heterozygous mutations were identified, 24 of them being novel ones: 13 out of 17 in the Sonic hedgehog gene (SHH); 4 out of 7 in ZIC2; and 7 out of 8 in SIX3. The two mutations identified in TGIF have already been reported. Novel phenotypes associated with a mutation have been described, such as abnormalities of the pituitary gland and corpus callosum, colobomatous microphthalmia, choanal aperture stenosis, and isolated cleft lip. This study confirms the great genetic heterogeneity of the disease, the important phenotypic variability in HPE families, and the difficulty to establish genotype-phenotype correlations.

Adult↗

PubMed2004

Predicting survival causes after out of hospital cardiac arrest using data mining method.

BACKGROUND: The prognosis of life for patients with heart failure remains poor. By using data mining methods, the purpose of this study was to evaluate the most important criteria for predicting patient survival and to profile patients to estimate their survival chances together with the most appropriate technique for health care. METHODS: Five hundred and thirty three patients who had suffered from cardiac arrest were included in the analysis. We performed classical statistical analysis and data mining analysis using mainly Bayesian networks. RESULTS: The mean age of the 533 patients was 63 (+/- 17) and the sample was composed of 390 (73 %) men and 143 (27 %) women. Cardiac arrest was observed at home for 411 (77 %) patients, in a public place for 62 (12 %) patients and on a public highway for 60 (11 %) patients. The belief network of the variables showed that the probability of remaining alive after heart failure is directly associated to five variables: age, sex, the initial cardiac rhythm, the origin of the heart failure and specialized resuscitation techniques employed. CONCLUSIONS: Data mining methods could help clinicians to predict the survival of patients and then adapt their practices accordingly. This work could be carried out for each medical procedure or medical problem and it would become possible to build a decision tree rapidly with the data of a service or a physician. The comparison between classic analysis and data mining analysis showed us the contribution of the data mining method for sorting variables and quickly conclude on the importance or the impact of the data and variables on the criterion of the study. The main limit of the method is knowledge acquisition and the necessity to gather sufficient data to produce a relevant model.

Bayes Theorem↗

PubMed2003

Collaborative environment for clinical reasoning and distance learning sessions.

BACKGROUND: The medical curriculum has changed with the adoption of the student-centered learning paradigm. Clinical reasoning learning (CRL) is used in order to develop and improve students' clinical reasoning and problem-solving skills. PURPOSE: We have observed that, in complement to traditional CRL sessions, students commonly consult resources available on the internet. Based on this observation, our objective is to create computer tools to coordinate CRL sessions at distance, integrating these electronic resources at every step of the reasoning process. MATERIAL AND METHODS: In order to create the system, we elaborated an object-oriented model of a computer-supported collaborative learning environment. The proposed system includes a local web-server to store electronic resources and a relational database to store their electronic addresses (urls). JAVA was used as the programming language. RESULTS: We developed a set of cooperative platform-independent tools. This environment includes a communication tool. Multimedia data exchange is possible. Information is shared thanks to an electronic notepad and whiteboard tools. PERSPECTIVES: This learning environment will be integrated in the French Virtual Medical University project, and is intended to be used for undergraduate, internships, residency or continuing medical education.

Computers, Handheld↗

PubMed2003

BioMeKe: an ontology-based biomedical knowledge extraction system devoted to transcriptome analysis.

Semantic interoperability between knowledge bases in medicine, and knowledge base in genomics and molecular biology will lead to advances in fundamental research as well as to improved patient care. DNA chips strategy is used for transcriptome analysis in order to identify deregulated genes in physio-pathological conditions. The objective of the BioMedical Knowledge Extraction project (BioMeKe) is to develop a knowledge warehouse in the context of transcriptome analysis during liver diseases. Knowledge sources include ontologies, related terminologies and annotations linked towards public databases (e.g., SWISSPROT). BioMeKe has been developed to have access to information using systematic investigation upon a concept, gene, gene products, pathology, or any target keyword, and is based on the combination of several relevant resources: UMLS, GeneOntology, MeSH supplementary terms, GOA, and HUGO. Current efforts are focusing on exploiting this ontology-based Knowledge Extractor, to enrich the expression data on genes delivered by a liver specific DNA microarray for better assistance of analysis.

Databases, Genetic↗

PubMed2003

Towards a unified medical lexicon for French.

Medical Informatics has a constant need for basic Medical Language Processing tasks, e.g., for coding into controlled vocabularies, free text indexing and information retrieval. Most of these tasks involve term matching and rely on lexical resources: lists of words with attached information, including inflected forms and derived words, etc. Such resources are publicly available for the English language with the UMLS Specialist Lexicon, but not in other languages. For the French language, several teams have worked on the subject and built local lexical resources. The goal of the present work is to pool and unify these resources and to add extensively to them by exploiting medical terminologies and corpora, resulting in a unified medical lexicon for French (UMLF). This paper exposes the issues raised by such an objective, describes the methods on which the project relies and illustrates them with experimental results.

Algorithms↗

PubMed2003

Method for automatic management of the semantic network ambiguity in the UMLS: possible application for information retrieval on the Web.

The Unified Medical Language System (UMLS) is an extensive collection of terms and concepts. The UMLS includes biomedical terms from standard classifications. The semantic network (SN) links the concepts, sometimes ambiguously. In this paper we try, on one hand to describe the relationship between concepts more efficiently and on the other hand to find new relationships. Assuming that re-usability and automatic extraction of knowledge from existing thesaurus enables an improvement of the metatheasaurus, we cross the SN with linked concepts from the ADM (Assisted Medical Diagnosis). Results are presented and our discussion concerns firstly the use of the SN only; secondly the improvement that allows pre-selection of linked concepts, and thirdly the possibility to coincide with other developments that improve the metathesaurus.

Electronic Data Processing↗

PubMed2003

Medical pedagogical resources management.

The main objective of this work is to help the management of training resources for students using a pedagogical network available at the Medical School of Rennes. With the increase of the number of connections and the number of medical documents available on this network, the management of new contents requires a lot of efforts for the webmaster. In order to improve the management of the resources, we implemented an automatic web engine for teachers, able to manage the links for the most interesting resources for their practice.

Computer-Assisted Instruction↗

PubMed2003

UMLF: a Unified Medical Lexicon for French.

Lexical resources for medical language, such as lists of words with inflectional and derivational information, are publicly available for the English lantuate with the UMLS Specialist Lexicon. The goal of the UMLF project is to pool and unify existing resources and to add extensively to them by exploiting medical terminologies and corpora, resulting in a Unified Medical Lexicon for French. We present here the current status of the project.

France↗

PubMed2002

Representation of roles in biomedical ontologies: a case study in functional genomics.

OBJECTIVE: Representing roles, i.e. functions of proteins, sequences and structures, is the cornerstone of knowledge representation in functional genomics. The objective of this study is to investigate representation of roles as functional categories or associative relations. We focus on GeneOntology (GO) and the UMLS and take examples from iron metabolism. METHODS: The terms corresponding to the main proteins involved in iron metabolism were mapped to GO (including the annotations) and the UMLS. The representation of their biological roles was then analyzed. RESULTS: Functional aspects are represented in both GO and the UMLS. However, the granularity may not be appropriate. DISCUSSION: Advantages and limits of functional categories and associative relations are discussed.

Genes↗

PubMed2002

Integration of electronic resources and communication technologies during Clinical Reasoning Learning sessions.

In the last few years, Clinical Reasoning Learning has been used during clinical training courses in many universities. The goal of this educational activity is to develop problem solving and diagnosis skills in medicine, using previously acquired medical knowledge. We propose the integration of educational resources and computer systems to help students during the reasoning process, and in order to prepare students to look for medical information. We also describe a Computer-Supported Collaborative Learning Environment that integrates Information and Communication Technologies in order to improve the Clinical Reasoning Learning Sessions.

Clinical Competence↗

PubMed2002

Web impact factor: a bibliometric criterion applied to medical informatics societies' web sites.

Several methods are available to evaluate and compare medical journals. The most popular is the journal Impact Factor, derived from averaging counts of citations to articles. Ingwersen adapted this method to assess the attractiveness of Web sites, defining the external Web Impact Factor (WIF) to be the number of external pages containing a link to a given Web site. This paper applies the WIF to 43 medical informatics societies' Web sites using advanced search engine queries to obtain the necessary link counts. The WIF was compared to the number of publications available in the Medline bibliographic database in medical informatics in these 43 countries. Between these two metrics, the observed Pearson correlation was 0.952 (p < 0.01) and the Spearman rank correlation was 0.548 (p < 0.01) showing in both cases a positive and strong significant correlation. The WIF of medicalm informatics society's Web site is statistically related to national productivity and discrepancies can be used to indicate countries where there are either weak medical informatics associations, or ones that do not make optimal use of the Web.

Bibliometrics↗

PubMed2002

Automatic conceptual indexing of French pharmaceutical theses.

French pharmaceutical theses are rarely quoted. If the main obstacles originate from language or access barriers, proper indexation could also be blamed. Manually extracted key-words don't necessary come from a structured thesaurus. In the following work, this manual indexing method is compared to an automated one, "Nomindex", based on UMLS. The automated method is improved by the addition of a relevance scoring system. The first indexing step consists of downloading, adapting and indexing theses in electronic format. Results will then be analyzed and sorted by relevance, through the comparison of classic statistical indices (noise, silence and relevance). It was assumed that the manually obtained key-words were always relevant. The silence of manual indexing is nevertheless high: seven new key-words are proposed by Nomindex, which results are mixed (10% of silence, but 50% of noise). These results are promising on the first experiment on pharmaceutical document without lexicon improvement. The indexing, if it is currently insufficient for a real life use, could easily be improved by specific updates of the lexicon.

Abstracting and Indexing↗