Deforestation, agriculture and farm jobs: a good recipe for Plasmodium vivax in French Guiana.

BACKGROUND: In a malaria-endemic area the distribution of patients is neither constant in time nor homogeneous in space. The WHO recommends the stratification of malaria risk on a fine geographical scale. In the village of Cacao in French Guiana, the study of the spatial and temporal distribution of malaria cases, during an epidemic, allowed a better understanding of the environmental factors promoting malaria transmission. METHODS: A dynamic cohort of 839 persons living in 176 households (only people residing permanently in the village) was constituted between January 1st, 2002 and December 31st, 2007.The information about the number of inhabitants per household, the number of confirmed cases of Plasmodium vivax and house GPS coordinates were collected to search for spatial or temporal clustering using Kurlldorff's statistical method. RESULTS: Of the 839 persons living permanently in the village of Cacao, 359 persons presented at least one vivax malaria episode between 2002 and 2007. Five temporal clusters and four spatial clusters were identified during the study period. In all temporal clusters, April was included. Two spatial clusters were localized at the north of the village near the Comté River and two others localized close to orchards. CONCLUSION: The spatial heterogeneity of malaria in the village may have been influenced by environmental disturbances due to local agricultural policies: deforestation, cultures of fresh produce, or drainage of water for agriculture. This study allowed generating behavioural, entomological, or environmental hypotheses that could be useful to improve prevention campaigns.

Influence of climate and river level on the incidence of malaria in Cacao, French Guiana.

BACKGROUND: The epidemiological profiles of vector-borne diseases, such as malaria, are strongly associated with environmental conditions. An understanding of the effect of the climate on the occurrence of malaria may provide indirect insight into the anopheles mosquito vectors endemic to a particular region. The association between meteorological and hydrographical factors and the occurrence of malaria was studied in a village in French Guiana during an epidemic caused essentially by Plasmodium vivax. METHODS: A cohort of confirmed cases of P. vivax malaria occurring between 2002 and 2007 was studied to search for an association between the number of new infection episodes occurring each month, mean, maximum and minimum monthly temperatures, cumulative rainfall for the month and the mean monthly height of the river bordering the village, with the aid of time series. Cross-correlation analysis revealed that these meteorological factors had large effects on the number of episodes, over a study period of 12 months. RESULTS: Climatic factors supporting the continuance of the epidemic were identified in the short-term (low minimum temperatures during the month), medium-term (low maximum temperatures two months before) and long-term (low maximum temperatures nine months before and high lowest level of the river 12 months before). Cross-correlation analysis showed that the effects of these factors were greatest at the beginning of the short rainy season. CONCLUSION: The association between the river level and the number of malaria attacks provides clues to better understand the environment of malaria transmission and the ecological characteristics of the vectors in the region.

Assisting the translation of the CORE subset of SNOMED CT into French.

BACKGROUND: the Core Subset of SNOMED CT is part of the UMLS-Core Project dedicated to study problem list vocabularies. SNOMED CT is not yet translated into French. OBJECTIVE: to propose an automated method to assist the translation of the CORE Subset of SNOMED CT into French. MATERIAL: the 2009 AA versions of the CORE Subset of SNOMED CT and UMLS; use of four French-language terminologies integrated into the UMLS Metathesaurus: SNOMED International, ICD10, MedDRA, and MeSH. METHOD: an exact mapping completed by a close mapping between preferred terms of the CORE Subset of SNOMED CT and those of the four terminologies. RESULTS: 89% of the preferred terms of the CORE Subset of SNOMED CT are mapped with at least one preferred term in one of the four terminologies. DISCUSSION: if needed, synonymous terms could be added by the means of synonyms in the terminologies; the proposed method is independent from French and could be applied to other natural languages.

Mapping the ATC classification to the UMLS metathesaurus: some pragmatic applications.

ATC classification is a WHO international classification used to classify drugs. The aim of this paper is to evaluate two lexical methods in English and in French to map ATC to UMLS. Several applications have been impemented to illustrate the use of the ATC mapping in English and French: (a) MeSH translation in Norwegian, (b) Drug Information Portal, and (c) ATC to PubMed tool. Two lexical methods were used to map ATC to UMLS. The first approach used a French natural language processing tool to map French terms of ATC to the French terminologies of UMLS. The second approach used the MetaMap tool to map English terms of ATC to UMLS. The English MetaMap provides slightly more mappings than the French NLP tool (3,170 vs. 2,992). On the other hand, the French NLP tool provides a slightly better precision than MetaMap (88% vs. 86%). Using a manual mapping between ATC and MeSH, the union of the validated mappings between ATC and MeSH provides 2,824 mappings (68.7% of ATC codes of the fifth level). Lexical methods are powerful methods to map health terminologies to the UMLS Metathesaurus. Manual mapping is still necessary to complete the mapping.

An automated approach to map a French terminology to UMLS.

BACKGROUND: CCAM is a French terminology for coding clinical procedures. CCAM is a multi-hierarchical structured classification for procedures used in France for reimbursement in health care, which is external to UMLS. OBJECTIVE: The objective of this work is to describe a French lexical approach allowing mapping CCAM procedures to the UMLS Metathesaurus to achieve interoperability to multiple international terminologies. This approach used a preliminary step intended to take only the significant characters used to code CCAM corresponding to anatomical and actions axes. RESULTS: According to the 7,926 CCAM codes used in this study, 5,212 possible matches (exact matching, single to multiple matching, partial matching) are found using the French CCAM to UMLS based mapping, 65% of the corresponding anatomical terms in the CCAM code are mapped to at least one UMLS Concept and 37% of the corresponding action terms in the CCAM code are mapped to at least one UMLS Concept. For all the exact matches found (n=200), 91% were rated by a human expert as narrower than the mapped UMLS Concepts, while only 3% were irrelevant.

Design and evaluation of a semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European EU-ADR project.

The overall objective of the EU-ADR project is the design, development, and validation of a computerised system that exploits data from electronic health records and biomedical databases for the early detection of adverse drug reactions. Eight different databases, containing health records of more than 30 million European citizens, are involved in the project. Unique queries cannot be performed across different databases because of their heterogeneity: Medical record and Claims databases, four different terminologies for coding diagnoses, and two languages for the information described in free text. The aim of our study was to provide database owners with a common basis for the construction of their queries. Using the UMLS, we provided a list of medical concepts, with their corresponding terms and codes in the four terminologies, which should be considered to retrieve the relevant information for the events of interest from the databases.

Automatic indexing in a drug information portal.

OBJECTIVE: The objective of this work is to create a bilingual (French/English) Drug Information Portal (DIP), in a multi-terminological context and to emphasize its exploitation by an ATC automatic indexing allowing having more pertinent information about substances, organs or systems on which drugs act and their therapeutic and chemical characteristics. METHODS: The development of the DIP was based on the CISMeF portal, which catalogues and indexes the most important and quality-controlled sources of institutional health information in French. DIP has created specific functionalities and uses specific drugs terminologies such as the ATC classification which used to automatic index the DIP resources. RESULTS: DIP is the result of collaboration between the CISMeF team and the VIDAL Company, specialized in drug information. DIP is conceived to facilitate the user information retrieval. The ATC automatic indexing provided relevant results in 76% of cases. CONCLUSION: Using multi-terminological context and in the framework of the drug field, indexing drugs with the appropriate codes or/and terms revealed to be very important to have the appropriate information storage and retrieval. The main challenge in the coming year is to increase the accuracy of the approach.

Projection and inheritance of SNOMED CT relations between MeSH terms.

This paper proposes a methodology to achieve the automatic inheritance of SNOMED CT relations applied to MeSH preferred terms using UMLS as knowledge source server. We propose an interoperability wildcard to achieve this objective. A quantitative and a qualitative analysis were performed on top four SNOMED CT relations inherited between MeSH preferred terms. A total of 12,030 couples of MeSH preferred terms are in relation via at least one SNOMED CT relationship. For the top-four relations inherited between MeSH preferred terms, overall 79.25% of them are relevant, 16.25% as intermediate and 4.5% as irrelevant, as judged by a medical librarian. This work should lead to an optimization of multi-terminology indexing tools, multi-terminology information retrieval and navigation among a multi-terminology server.

Relevance of Google-customized search engine vs. CISMeF quality-controlled health gateway.

CISMeF (acronym for Catalog and Index of French Language Health Resources on the Internet) is a quality-controlled health gateway conceived to catalog and index the most important and quality-controlled sources of institutional health information in French. The goal of this study is to compare the relevance of results provided by this gateway from a small set of documents selected and described by human experts to those provided by a search engine from a large set of automatically indexed and ranked resources. The Google-Customized search engine (CSE) was used. The evaluation was made using the 10th first results of 15 queries and two blinded physician evaluators. There was no significant difference between the relevance of information retrieval in CISMeF and Google CSE. In conclusion, automatic indexing does not lead to lower relevance than a manual MeSH indexing and may help to cope with the increasing number of references to be indexed in a controlled health quality gateway.

Drug information portal in Europe: information retrieval with multiple health terminologies.

The objective of this work is the creation of a bilingual (French/English) drug information portal (DIP), in a multi-terminological context. The development of the DIP was based on the CISMeF portal, which catalogues and indexes the most important and quality-controlled sources of institutional health information in French. DIP has created specific functionalities related to drug and used specific drugs terminologies and classifications: the ATC classification, the CAS numbers, the French codes CIS, and CIP, as well as trade names and the International Nonproprietary Names of the drugs. DIP is the result of collaboration between the CISMeF team and the VIDAL private Company, specialized in drug information. DIP is conceived to facilitate the user information retrieval using several health terminologies. In the framework of the drug field, using multi-terminological context, indexing drugs with the appropriate codes or/and terms revealed to be very important to have the appropriate information storage and retrieval.

Automatic construction of dictionaries, application to product characteristics indexing.

Summary of Product Characteristics (SPC) indexing enables to extract all the information needed to analyze a prescription and find some inappropriate medications. We evaluate a French Multi-Terminology Indexer tool (F-MTI) for SPC automatic indexing. This tool uses a dictionary containing the textual forms that are likely to appear in natural language text for the drug clinical particular terms contained in the Vidal thesaurus (TUV). We developed a method to automatically generate this dictionary. The evaluation showed a precision of 52.9% and a recall of 46.2%. F-MTI will be integrated in a semi-automatic indexing tool.

A semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European eu-ADR project.

The overall objective of the eu-ADR project is the design, development, and validation of a computerised system that exploits data from electronic health records and biomedical databases for the early detection of adverse drug reactions. Eight different databases, containing health records of more than 30 million European citizens, are involved in the project. Unique queries cannot be performed across different databases because of their heterogeneity: Medical record and Claims databases, four different terminologies for coding diagnoses, and two languages for the information described in free text. The aim of our study was to provide database owners with a common basis for the construction of their queries. Using the UMLS, we provided a list of medical concepts, with their corresponding terms and codes in the four terminologies, which should be considered to retrieve the relevant information for the events of interest from the databases.

Using knowledge for indexing health web resources in a quality-controlled gateway.

OBJECTIVES: The aim of this study is to provide to indexers MeSH terms to be considered as major ones in a list of terms automatically extracted from a document. MATERIAL AND METHODS: We propose a method combining symbolic knowledge - the UMLS Metathesaurus and Semantic Network - and statistical knowledge drawn from co-occurrences of terms in the CISMeF database (a French-language quality-controlled health gateway) using data mining measures. The method was tested on CISMeF corpus of 293 resources. RESULTS: There was a proportion of 0.37+/-0.26 major terms in the processed records. The method produced lists of terms with a proportion of terms initially pointed out as major of 0.54+/-0.31. DISCUSSION: The method we propose reduces the number of terms, which seem not useful for content description of resources, such as "check tags", but retains the most descriptive ones. Discarding these terms is accounted for by: 1) the removal by using semantic knowledge of associations of concepts bearing no real medical significance, 2) the removal by using statistical knowledge of nonstatistically significant associations of terms. CONCLUSION: This method can assist effectively indexers in their daily work and will be soon applied in the CISMeF system.

Searching related resources in a quality controlled health gateway: a feasibility study.

OBJECTIVE: The neighbors of a document are those documents in a corpus that are most similar to it. The objective of this paper is to develop and evaluate the related resources algorithm (CISMeF-RRA) in the context of a quality-controlled health gateway on the Internet CISMeF. METHOD: CISMeF-RRA is inspired by the PubMed Related Citations Articles. CISMeF-RRA combines statistical distances with a semantic distance using MeSH terms/qualifiers. MATERIAL: In this feasibility study an evaluation was performed using 50 CISMeF resources randomly chosen. RESULTS: Overall, 49% of the related documents were ranked as relevant. CONCLUSION: if this feasibility study is confirmed by another evaluation of more resources, CISMeF-RRA will be implemented in the CISMeF catalog.

Collaborative and workflow-oriented digital portfolio: Creating a web-based tool to support a nationwide program of practices evaluation in the blood transfusion area.

PURPOSE: The French National Blood Transfusion Institute received approval from the French National Health Authority to organize a nationwide program for the evaluation of professional practices in the area of blood transfusion. Major issues of the project were: (1) managing numerous physicians spread nationwide; (2) tracking and storing the physician's entire process (from his/her enrollment to his/her lifelong follow-up); (3) creating a collaborative technique for processing an evaluation program; (4) enhancing exchanges between participants; (5) proposing effective implementation of the assessment. METHODS: As faculty members with experience in distance learning, we considered the digital/electronic portfolio to be one of the most suitable techniques to support such a project. Due to the lack of methods and tools to meet users' expectations, the decision was made to prototype a new and innovative assessment environment. A team was formed to complete the design phase within 6 months (information content, roles and functions). Implementation of the prototype, which includes tests, was also planned over a 6-month period. The methodology involves two approaches: one concerns business process modelling; the other is related to object-oriented methods for design and implementation. RESULTS: This primary work was aimed at describing a specific object, the evaluation program, which can be shared between players within a web-based collaborative platform. Four types of players were identified: (1) physicians enrolled into the assessment program; (2) tutors assigned to follow physicians' assessment process; (3) program directors who manage the content of the assessment program and the application of follow-up rules; (4) supervisors who administrate the global system. The evaluation program is composed of a set of actions, which has to be performed by the physicians. These actions are directly related to the activities of the business processes to which the candidate belongs. For each action, elements of proof have to be uploaded by the physician, according to a predefined schedule. The status of this object and its changes are followed and managed by a workflow engine. Implementation of the system required an object-oriented content management system (Zope/Plone). CONCLUSION: The object-oriented approach helped us to focus on the topic of interest, the assessment program, without being concerned by the whole environment. The assessment model we designed attempts to make a link with the business process performed in daily routine. This article explores the way business process modelling can contribute to the modelling of a professional practices assessment system. Apart from the modelling and technical aspects, this nationwide project contains major challenges: to enroll all physicians on an individualized basis and to create appropriate conditions for the extension of the evaluation program and device to other specialties.

WRAPIN: a tool for patient empowerment within EHR.

Legal and technologic trends are making medical records progressively more patient-accessible. In the near future, information technology may make it even easier to provide patients a chance to review their records. One may wonder, however, about the practical use of this technology by patients. Understanding his/her own health record will certainly be one of the main concerns of patients. WRAPIN has been designed to provide patients and citizens with trusted health information. It will help to determine the reliability of documents by checking the ideas contained against established benchmarks, and enable users to determine the relevance of a given document from a page of search results. First, we present what is, in our opinion, the most original and important patient-centred WRAPIN characteristics and functionalities. Then, we compare these characteristics with those of representatives of two main trends in information retrieval: systems based on the popularity of web sites, and on the clustering of web sites. This comparison shows that, even though patients are tempted to use popular search engines, these are not sufficiently specialized in the medical domain to help them understand their own HER.. Finally, we discuss the complexity of medical readings over the Internet and the efforts that are still required in this domain.

From the description of activities to the identification of risks for clinical management: a proposal of building, merging and sharing knowledge representations of care processes.

Management of clinical processes and hospital activities takes advantage of business process reengineering methodology. It is now recognized that care process modeling must integrate the definition of goals and the assessment of risk. Two kinds of issues have been outlined: 1) the lack of an integrated model to identify and describe processes and their components according to a functional point of view; and 2) an increasing amount of documents that hospital staff members have to create, collect, index and maintain. As initial models focused only on a structural view of activities, we reviewed different sources of standards and norms to extract and classify a set of metadata aimed at describing any activity and its outcomes. The model includes links to structured terminologies to name attributes or value them. An object-oriented information model has been created and implemented to test the relevance and the feasibility of the modeling approach. Conceptually speaking, this model gives opportunity to bridge tacit and explicit knowledge. Practically speaking, limits to generalization remain partly due to the lack of a template processes database.

Evaluation of a simple method for the automatic assignment of MeSH descriptors to health resources in a French online catalogue.

BACKGROUND: The growing number of resources to be indexed in the catalogue of online health resources in French (CISMeF) calls for curating strategies involving automatic indexing tools while maintaining the catalogue's high indexing quality standards. OBJECTIVE: To develop a simple automatic tool that retrieves MeSH descriptors from documents titles. METHODS: In parallel to research on advanced indexing methods, a bag-of-words tool was developed for timely inclusion in CISMeF's maintenance system. An evaluation was carried out on a corpus of 99 documents. The indexing sets retrieved by the automatic tool were compared to manual indexing based on the title and on the full text of resources. RESULTS: 58% of the major main headings were retrieved by the bag-of-words algorithm and the precision on main heading retrieval was 69%. CONCLUSION: Bag-of-words indexing has effectively been used on selected resources to be included in CISMeF since August 2006. Meanwhile, on going work aims at improving the current version of the tool.

Awareness of mother-to-child transmission of human T-cell lymphotropic virus (HTLV) type I through breastfeeding in a small group of HTLV-positive women in Maripasoula and Papaïchton, French Guiana.

The aim of this study was to assess the awareness of human T-cell lymphotropic virus (HTLV) transmission, especially through breastfeeding, in a small group of 40 HTLV-seropositive women in French Guiana and to examine the public health policies in place to reduce transmission. The results show that the majority of HTLV-positive women were aware of having a blood virus, diagnosed antenatally, and were advised to avoid breastfeeding. This advice was followed in the majority of cases despite financial difficulty. Participants were largely unaware of other modes of transmission. Public awareness was low, leading to increased stigmatising of people with HTLV, more so than HIV. Health policies in place to reduce transmission of HTLV are focused on vertical transmission, with women being routinely tested antenatally and advised to avoid breastfeeding. There was no further advice routinely given on other modes of transmission. There was no routine follow-up of HTLV-positive women. Suggestions include public education programmes such as those that are in place for HIV, education of healthcare workers, and setting up a network for systematic follow-up and support of HTLV patients.

Health search engine with e-document analysis for reliable search results.

OBJECTIVE: After a review of the existing practical solution available to the citizen to retrieve eHealth document, the paper describes an original specialized search engine WRAPIN. METHOD: WRAPIN uses advanced cross lingual information retrieval technologies to check information quality by synthesizing medical concepts, conclusions and references contained in the health literature, to identify accurate, relevant sources. Thanks to MeSH terminology [1] (Medical Subject Headings from the U.S. National Library of Medicine) and advanced approaches such as conclusion extraction from structured document, reformulation of the query, WRAPIN offers to the user a privileged access to navigate through multilingual documents without language or medical prerequisites. RESULTS: The results of an evaluation conducted on the WRAPIN prototype show that results of the WRAPIN search engine are perceived as informative 65% (59% for a general-purpose search engine), reliable and trustworthy 72% (41% for the other engine) by users. But it leaves room for improvement such as the increase of database coverage, the explanation of the original functionalities and an audience adaptability. CONCLUSION: Thanks to evaluation outcomes, WRAPIN is now in exploitation on the HON web site (http://www.healthonnet.org), free of charge. Intended to the citizen it is a good alternative to general-purpose search engines when the user looks up trustworthy health and medical information or wants to check automatically a doubtful content of a Web page.