Do pelvic floor muscle function parameters differ in women according to continence status? A systematic review.

BACKGROUND: Current literature highlights the difficulty in identifying which pelvic floor muscle (PFM) functions are correlated with urinary incontinence (UI). AIM: In this study, we compared parameters of PFM function (strength, endurance, tone, control, reaction, and/or coordination) according to continence status in women (presence or absence, type and/or severity of urinary incontinence). EVIDENCE ACQUISITION: A systematic review was conducted following the 2020 PRISMA guidelines. Three databases (Pubmed, Web of Science, and LiSSa) were searched from inception to December 31, 2021. Assessment of risk of bias was performed using the Joanna Briggs Institute critical appraisal checklist. EVIDENCE SYNTHESIS: The initial research yielded 4733 studies. Forty-two studies met the inclusion criteria, including 4015 participants. No statistical association was found between PFM function and the presence or absence of UI, the different type of UI or the different levels of severity of UI. The heterogeneity in methodologies and analyzes of the results only with the P-value are important limitations of this review. CONCLUSION: It appears that muscle function is not always associated with presence or absence of UI. No association is found between PFM function and type or severity of UI. These results reinforce the need to carry out a bio-psycho-social evaluation of UI that does not only focus on PFM functions. As such, the results reported herein can be considered a resource for more specific research.

Designing Formulae for Ranking Search Results: Mixed Methods Evaluation Study.

BACKGROUND: A major factor in the success of any search engine is the relevance of the search results; a tool should sort the search results to present the most relevant documents first. Assessing the performance of the ranking formula is an important part of search engine evaluation. However, the methods currently used to evaluate ranking formulae mainly collect quantitative data and do not gather qualitative data, which help to understand what needs to be improved to tailor the formulae to their end users. OBJECTIVE: This study aims to evaluate 2 different parameter settings of the ranking formula of LiSSa (the French acronym for scientific literature in health care; Department of Medical Informatics and Information), a tool that provides access to health scientific literature in French, to adapt the formula to the needs of the end users. METHODS: To collect quantitative and qualitative data, user tests were carried out with representative end users of LiSSa: 10 general practitioners and 10 registrars. Participants first assessed the relevance of the search results and then rated the ranking criteria used in the 2 formulae. Verbalizations were analyzed to characterize each criterion. RESULTS: A formula that prioritized articles representing a consensus in the field was preferred. When users assess an article's relevance, they judge its topic, methods, and value in clinical practice. CONCLUSIONS: Following the evaluation, several improvements were implemented to give more weight to articles that match the search topic and to downgrade articles that have less informative or scientific value for the reader. Applying a qualitative methodology generates valuable user inputs to improve the ranking formula and move toward a highly usable search engine.

Performance evaluation of three semantic expansions to query PubMed.

BACKGROUND: PubMed is one of the most important basic tools to access medical literature. Semantic query expansion using synonyms can improve retrieval efficacy. OBJECTIVE: The objective was to evaluate the performance of three semantic query expansion strategies. METHODS: Queries were built for forty MeSH descriptors using three semantic expansion strategies (MeSH synonyms, UMLS mappings, and mappings created by the CISMeF team), then sent to PubMed. To evaluate expansion performances for each query, the first twenty citations were selected, and their relevance were judged by three independent evaluators based on the title and abstract. RESULTS: Queries built with the UMLS expansion provided new citations with a slightly higher mean precision (74.19%) than with the CISMeF expansion (70.28%), although the difference was not significant. Inter-rater agreement was 0.28. Results varied greatly depending on the descriptor selected. DISCUSSION: The number of citations retrieved by the three strategies and their precision varied greatly according to the descriptor. This heterogeneity could be explained by the quality of the synonyms. Optimal use of these different expansions would be through various combinations of UMLS and CISMeF intersections or unions. CONCLUSION: Information retrieval tools should propose different semantic expansions depending on the descriptor and the search objectives.

Identification of the Best Semantic Expansion to Query PubMed Through Automatic Performance Assessment of Four Search Strategies on All Medical Subject Heading Descriptors: Comparative Study.

BACKGROUND: With the continuous expansion of available biomedical data, efficient and effective information retrieval has become of utmost importance. Semantic expansion of queries using synonyms may improve information retrieval. OBJECTIVE: The aim of this study was to automatically construct and evaluate expanded PubMed queries of the form "preferred term"[MH] OR "preferred term"[TIAB] OR "synonym 1"[TIAB] OR "synonym 2"[TIAB] OR …, for each of the 28,313 Medical Subject Heading (MeSH) descriptors, by using different semantic expansion strategies. We sought to propose an innovative method that could automatically evaluate these strategies, based on the three main metrics used in information science (precision, recall, and F-measure). METHODS: Three semantic expansion strategies were assessed. They differed by the synonyms used to build the queries as follows: MeSH synonyms, Unified Medical Language System (UMLS) mappings, and custom mappings (Catalogue et Index des Sites Médicaux de langue Française [CISMeF]). The precision, recall, and F-measure metrics were automatically computed for the three strategies and for the standard automatic term mapping (ATM) of PubMed. The method to automatically compute the metrics involved computing the number of all relevant citations (A), using National Library of Medicine indexing as the gold standard ("preferred term"[MH]), the number of citations retrieved by the added terms ("synonym 1"[TIAB] OR "synonym 2"[TIAB] OR …) (B), and the number of relevant citations retrieved by the added terms (combining the previous two queries with an "AND" operator) (C). It was possible to programmatically compute the metrics for each strategy using each of the 28,313 MeSH descriptors as a "preferred term," corresponding to 239,724 different queries built and sent to the PubMed application program interface. The four search strategies were ranked and compared for each metric. RESULTS: ATM had the worst performance for all three metrics among the four strategies. The MeSH strategy had the best mean precision (51%, SD 23%). The UMLS strategy had the best recall and F-measure (41%, SD 31% and 36%, SD 24%, respectively). CISMeF had the second best recall and F-measure (40%, SD 31% and 35%, SD 24%, respectively). However, considering a cutoff of 5%, CISMeF had better precision than UMLS for 1180 descriptors, better recall for 793 descriptors, and better F-measure for 678 descriptors. CONCLUSIONS: This study highlights the importance of using semantic expansion strategies to improve information retrieval. However, the performances of a given strategy, relatively to another, varied greatly depending on the MeSH descriptor. These results confirm there is no ideal search strategy for all descriptors. Different semantic expansions should be used depending on the descriptor and the user's objectives. Thus, we developed an interface that allows users to input a descriptor and then proposes the best semantic expansion to maximize the three main metrics (precision, recall, and F-measure).

Word Embedding for French Natural Language in Healthcare: A Comparative Study.

Structuring raw medical documents with ontology mapping is now the next step for medical intelligence. Deep learning models take as input mathematically embedded information, such as encoded texts. To do so, word embedding methods can represent every word from a text as a fixed-length vector. A formal evaluation of three word embedding methods has been performed on raw medical documents. The data corresponds to more than 12M diverse documents produced in the Rouen hospital (drug prescriptions, discharge and surgery summaries, inter-services letters, etc.). Automatic and manual validation demonstrates that Word2Vec based on the skip-gram architecture had the best rate on three out of four accuracy tests. This model will now be used as the first layer of an AI-based semantic annotator.

Word Embedding for the French Natural Language in Health Care: Comparative Study.

BACKGROUND: Word embedding technologies, a set of language modeling and feature learning techniques in natural language processing (NLP), are now used in a wide range of applications. However, no formal evaluation and comparison have been made on the ability of each of the 3 current most famous unsupervised implementations (Word2Vec, GloVe, and FastText) to keep track of the semantic similarities existing between words, when trained on the same dataset. OBJECTIVE: The aim of this study was to compare embedding methods trained on a corpus of French health-related documents produced in a professional context. The best method will then help us develop a new semantic annotator. METHODS: Unsupervised embedding models have been trained on 641,279 documents originating from the Rouen University Hospital. These data are not structured and cover a wide range of documents produced in a clinical setting (discharge summary, procedure reports, and prescriptions). In total, 4 rated evaluation tasks were defined (cosine similarity, odd one, analogy-based operations, and human formal evaluation) and applied on each model, as well as embedding visualization. RESULTS: Word2Vec had the highest score on 3 out of 4 rated tasks (analogy-based operations, odd one similarity, and human validation), particularly regarding the skip-gram architecture. CONCLUSIONS: Although this implementation had the best rate for semantic properties conservation, each model has its own qualities and defects, such as the training time, which is very short for GloVe, or morphological similarity conservation observed with FastText. Models and test sets produced by this study will be the first to be publicly available through a graphical interface to help advance the French biomedical research.

Lost in translation? A multilingual Query Builder improves the quality of PubMed queries: a randomised controlled trial.

BACKGROUND: MEDLINE is the most widely used medical bibliographic database in the world. Most of its citations are in English and this can be an obstacle for some researchers to access the information the database contains. We created a multilingual query builder to facilitate access to the PubMed subset using a language other than English. The aim of our study was to assess the impact of this multilingual query builder on the quality of PubMed queries for non-native English speaking physicians and medical researchers. METHODS: A randomised controlled study was conducted among French speaking general practice residents. We designed a multi-lingual query builder to facilitate information retrieval, based on available MeSH translations and providing users with both an interface and a controlled vocabulary in their own language. Participating residents were randomly allocated either the French or the English version of the query builder. They were asked to translate 12 short medical questions into MeSH queries. The main outcome was the quality of the query. Two librarians blind to the arm independently evaluated each query, using a modified published classification that differentiated eight types of errors. RESULTS: Twenty residents used the French version of the query builder and 22 used the English version. 492 queries were analysed. There were significantly more perfect queries in the French group vs. the English group (respectively 37.9% vs. 17.9%; p < 0.01). It took significantly more time for the members of the English group than the members of the French group to build each query, respectively 194 sec vs. 128 sec; p < 0.01. CONCLUSIONS: This multi-lingual query builder is an effective tool to improve the quality of PubMed queries in particular for researchers whose first language is not English.

Behavior and attitudes of residents and general practitioners in searching for health information: From intention to practice.

BACKGROUND: Physicians are increasingly encouraged to practice evidence-based medicine (EBM), and their decisions require evidence based on valid research. Existing literature shows a mismatch between general practitioners' (GPs) information needs and evidence available online. The aim of this study was to explore the attitudes and behavior of residents in general medicine and GPs when seeking medical information online. METHODS: Five focus groups (FGs) involving residents in general medicine and GPs were conducted between October 2013 and January 2014. The overall number of participants recruited was 35. The focus group discussion guide focused on participants' experiences in searching for health information on the Internet, perceived barriers and possible solutions for improving the quality of their own search processes. Descriptive analysis was performed by three researchers. RESULTS: Participants described a wide range of research topics, covering all general medicine core competencies, and especially patient-oriented topics. They used a limited list of websites. Participants were not confident about their ability to assess the quality of the information they found. Their assessment of data quality was based on intuition, and they mainly sought concordance with their existing knowledge. The way the data were exposed was considered very important. Participants were looking for information that was directly linked to their clinical practice. Information seeking processes varied among participants. They felt they had not mastered query building for conducting searches, and were aware of the impact this shortcoming had on the quality of their search for information. CONCLUSIONS: Residents in general medicine and GPs understood the importance of EBM and the need for objective and reliable information. The present study highlights the difficulties in identifying this kind of information, and suggests ideas for improvement. Available search tools should change in order to fill the gap with real-world clinical practice, for example by integrating a patient-centred approach.

Evaluation of Internet Social Networks using Net scoring Tool: A Case Study in Adverse Drug Reaction Mining.

BACKGROUND AND OBJECTIVES: Suspected adverse drug reactions (ADR) reported by patients through social media can be a complementary tool to already existing ADRs signal detection processes. However, several studies have shown that the quality of medical information published online varies drastically whatever the health topic addressed. The aim of this study is to use an existing rating tool on a set of social network web sites in order to assess the capabilities of these tools to guide experts for selecting the most adapted social network web site to mine ADRs. METHODS: First, we reviewed and rated 132 Internet forums and social networks according to three major criteria: the number of visits, the notoriety of the forum and the number of messages posted in relation with health and drug therapy. Second, the pharmacist reviewed the topic-oriented message boards with a small number of drug names to ensure that they were not off topic. Six experts have been chosen to assess the selected internet forums using a French scoring tool: Net scoring. Three different scores and the agreement between experts according to each set of scores using weighted kappa pooled using mean have been computed. RESULTS: Three internet forums were chosen at the end of the selection step. Some criteria get high score (scores 3-4) no matter the website evaluated like accessibility (45-46) or design (34-36), at the opposite some criteria always have bad scores like quantitative (40-42) and ethical aspect (43-44), hyperlinks actualization (30-33). Kappa were positives but very small which corresponds to a weak agreement between experts. CONCLUSION: The personal opinion of the expert seems to have a major impact, undermining the relevance of the criterion. Our future work is to collect results given by this evaluation grid and proposes a new scoring tool for Internet social networks assessment.

A search engine to access PubMed monolingual subsets: proof of concept and evaluation in French.

BACKGROUND: PubMed contains numerous articles in languages other than English. However, existing solutions to access these articles in the language in which they were written remain unconvincing. OBJECTIVE: The aim of this study was to propose a practical search engine, called Multilingual PubMed, which will permit access to a PubMed subset in 1 language and to evaluate the precision and coverage for the French version (Multilingual PubMed-French). METHODS: To create this tool, translations of MeSH were enriched (eg, adding synonyms and translations in French) and integrated into a terminology portal. PubMed subsets in several European languages were also added to our database using a dedicated parser. The response time for the generic semantic search engine was evaluated for simple queries. BabelMeSH, Multilingual PubMed-French, and 3 different PubMed strategies were compared by searching for literature in French. Precision and coverage were measured for 20 randomly selected queries. The results were evaluated as relevant to title and abstract, the evaluator being blind to search strategy. RESULTS: More than 650,000 PubMed citations in French were integrated into the Multilingual PubMed-French information system. The response times were all below the threshold defined for usability (2 seconds). Two search strategies (Multilingual PubMed-French and 1 PubMed strategy) showed high precision (0.93 and 0.97, respectively), but coverage was 4 times higher for Multilingual PubMed-French. CONCLUSIONS: It is now possible to freely access biomedical literature using a practical search tool in French. This tool will be of particular interest for health professionals and other end users who do not read or query sufficiently in English. The information system is theoretically well suited to expand the approach to other European languages, such as German, Spanish, Norwegian, and Portuguese.

Evaluating alignment quality between iconic language and reference terminologies using similarity metrics.

BACKGROUND: Visualization of Concepts in Medicine (VCM) is a compositional iconic language that aims to ease information retrieval in Electronic Health Records (EHR), clinical guidelines or other medical documents. Using VCM language in medical applications requires alignment with medical reference terminologies. Alignment from Medical Subject Headings (MeSH) thesaurus and International Classification of Diseases - tenth revision (ICD10) to VCM are presented here. This study aim was to evaluate alignment quality between VCM and other terminologies using different measures of inter-alignment agreement before integration in EHR. METHODS: For medical literature retrieval purposes and EHR browsing, the MeSH thesaurus and the ICD10, both organized hierarchically, were aligned to VCM language. Some MeSH to VCM alignments were performed automatically but others were performed manually and validated. ICD10 to VCM alignment was entirely manually performed. Inter-alignment agreement was assessed on ICD10 codes and MeSH descriptors, sharing the same Concept Unique Identifiers in the Unified Medical Language System (UMLS). Three metrics were used to compare two VCM icons: binary comparison, crude Dice Similarity Coefficient (DSCcrude), and semantic Dice Similarity Coefficient (DSCsemantic), based on Lin similarity. An analysis of discrepancies was performed. RESULTS: MeSH to VCM alignment resulted in 10,783 relations: 1,830 of which were manually performed and 8,953 were automatically inherited. ICD10 to VCM alignment led to 19,852 relations. UMLS gathered 1,887 alignments between ICD10 and MeSH. Only 1,606 of them were used for this study. Inter-alignment agreement using only validated MeSH to VCM alignment was 74.2% [70.5-78.0]CI95%, DSCcrude was 0.93 [0.91-0.94]CI95%, and DSCsemantic was 0.96 [0.95-0.96]CI95%. Discrepancy analysis revealed that even if two thirds of errors came from the reviewers, UMLS was nevertheless responsible for one third. CONCLUSIONS: This study has shown strong overall inter-alignment agreement between MeSH to VCM and ICD10 to VCM manual alignments. VCM icons have now been integrated into a guideline search engine (http://www.cismef.org) and a health terminologies portal (http://www.hetop.eu).

Design and usability study of an iconic user interface to ease information retrieval of medical guidelines.

BACKGROUND AND OBJECTIVE: Doc'CISMeF (DC) is a semantic search engine used to find resources in CISMeF-BP, a quality controlled health gateway, which gathers guidelines available on the internet in French. Visualization of Concepts in Medicine (VCM) is an iconic language that may ease information retrieval tasks. This study aimed to describe the creation and evaluation of an interface integrating VCM in DC in order to make this search engine much easier to use. METHODS: Focus groups were organized to suggest ways to enhance information retrieval tasks using VCM in DC. A VCM interface was created and improved using the ergonomic evaluation approach. 20 physicians were recruited to compare the VCM interface with the non-VCM one. Each evaluator answered two different clinical scenarios in each interface. The ability and time taken to select a relevant resource were recorded and compared. A usability analysis was performed using the System Usability Scale (SUS). RESULTS: The VCM interface contains a filter based on icons, and icons describing each resource according to focus group recommendations. Some ergonomic issues were resolved before evaluation. Use of VCM significantly increased the success of information retrieval tasks (OR=11; 95% CI 1.4 to 507). Nonetheless, it took significantly more time to find a relevant resource with VCM interface (101 vs 65 s; p=0.02). SUS revealed 'good' usability with an average score of 74/100. CONCLUSIONS: VCM was successfully implemented in DC as an option. It increased the success rate of information retrieval tasks, despite requiring slightly more time, and was well accepted by end-users.

Multi-lingual search engine to access PubMed monolingual subsets: a feasibility study.

PubMed contains many articles in languages other than English but it is difficult to find them using the English version of the Medical Subject Headings (MeSH) Thesaurus. The aim of this work is to propose a tool allowing access to a PubMed subset in one language, and to evaluate its performance. Translations of MeSH were enriched and gathered in the information system. PubMed subsets in main European languages were also added in our database, using a dedicated parser. The CISMeF generic semantic search engine was evaluated on the response time for simple queries. MeSH descriptors are currently available in 11 languages in the information system. All the 654,000 PubMed citations in French were integrated into CISMeF database. None of the response times exceed the threshold defined for usability (2 seconds). It is now possible to freely access biomedical literature in French using a tool in French; health professionals and lay people with a low English language may find it useful. It will be expended to several European languages: German, Spanish, Norwegian and Portuguese.

Validating the semantics of a medical iconic language using ontological reasoning.

To help clinicians read medical texts such as clinical practice guidelines or drug monographs, we proposed an iconic language called VCM. This language can use icons to represent the main medical concepts, including diseases, symptoms, treatments and follow-up procedures, by combining various pictograms, shapes and colors. However, the semantics of this language have not been formalized, and users may create inconsistent icons, e.g. by combining the "tumor" shape and the "sleeping" pictograms into a "tumor of sleeping" icon. This work aims to represent the VCM language using DLs and OWL for evaluating its semantics by reasoners, and in particular for determining inconsistent icons. We designed an ontology for formalized the semantics of VCM icons using the Protégé editor and scripts for translating the VCM lexicon in OWL. We evaluated the ability of the ontology to determine icon consistency for a set of 100 random icons. The evaluation showed good results for determining icon consistency, with a high sensitivity. The ontology may also be useful for the design of mapping between VCM and other medical terminologies, for generating textual labels for icons, and for developing user interfaces for creating VCM icons.

Performance evaluation of Unified Medical Language System®'s synonyms expansion to query PubMed.

BACKGROUND: PubMed is the main access to medical literature on the Internet. In order to enhance the performance of its information retrieval tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System' (UMLS) synonyms i.e. all the terms gathered under one unique Concept Unique Identifier. METHODS: This method was evaluated using queries constructed to emphasize the differences between this new method and the current PubMed automatic term mapping. Four experts assessed citation relevance. RESULTS: Using UMLS, we were able to retrieve new citations in 45.5% of queries, which implies a small increase in recall. The new strategy led to a heterogeneous 23.7% mean increase in non-indexed citation retrieved. Of these, 82% have been published less than 4 months earlier. The overall mean precision was 48.4% but differed according to the evaluators, ranging from 36.7% to 88.1% (Inter rater agreement was poor: kappa = 0.34). CONCLUSIONS: This study highlights the need for specific search tools for each type of user and use-cases. The proposed strategy may be useful to retrieve recent scientific advancement.

Towards iconic language for patient records, drug monographs, guidelines and medical search engines.

Practicing physicians have limited time for consulting medical knowledge and records. We have previously shown that using icons instead of text to present drug monographs may allow contraindications and adverse effects to be identified more rapidly and more accurately. These findings were based on the use of an iconic language designed for drug knowledge, providing icons for many medical concepts, including diseases, antecedents, drug classes and tests. In this paper, we describe a new project aimed at extending this iconic language, and exploring the possible applications of these icons in medicine. Based on evaluators' comments, focus groups of physicians and opinions of academic, industrial and associative partners, we propose iconic applications related to patient records, for example summarizing patient conditions, searching for specific clinical documents and helping to code structured data. Other applications involve the presentation of clinical practice guidelines and improving the interface of medical search engines. These new applications could use the same iconic language that was designed for drug knowledge, with a few additional items that respect the logic of the language.

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.

Multi-terminology indexing for the assignment of MeSH descriptors to medical abstracts in French.

BACKGROUND: To facilitate information retrieval in the biomedical domain, a system for the automatic assignment of Medical Subject Headings to documents curated by an online quality-controlled health gateway was implemented. The French Multi-Terminology Indexer (F-MTI) implements a multiterminology approach using nine main medical terminologies in French and the mappings between them. OBJECTIVE: This paper presents recent efforts to assess the added value of (a) integrating four new terminologies (Orphanet, ATC, drug names, MeSH supplementary concepts) into F-MTI's knowledge sources and (b) performing the automatic indexing on the titles and abstracts (vs. title only) of the online health resources. METHODS: F-MTI was evaluated on a CISMeF corpus comprising 18,161 manually indexed resources. RESULTS: The performance of F-MTI including nine health terminologies on CISMeF resources with Title only was 27.9% precision and 19.7% recall, while the performance on CISMeF resources with Title and Abstract is 14.9 % precision (-13.0%) and 25.9% recall (+6.2%). CONCLUSION: In a few weeks, CISMeF will launch the indexing of resources based on title and abstract, using nine terminologies.

Using multi-terminology indexing for the assignment of MeSH descriptors to health resources in a French online catalogue.

BACKGROUND: To assist with the development of a French online quality-controlled health gateway(CISMeF), an automatic indexing tool assigning MeSH descriptors to medical text in French was created. The French Multi-Terminology Indexer (FMTI) relies on a multi-terminology approach involving four prominent medical terminologies and the mappings between them. OBJECTIVE: In this paper,we compare lemmatization and stemming as methods to process French medical text for indexing. We also evaluate the multi-terminology approach implemented in F-MTI. METHODS: The indexing strategies were assessed on a corpus of 18,814 resources indexed manually. RESULTS: There is little difference in the indexing performance when lemmatization or stemming is used. However, the multi-terminology approach outperforms indexing relying on a single terminology in terms of recall. CONCLUSION: F-MTI will soon be used in the CISMeF production environment and in a Health MultiTerminology Server in French.