Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Disrupting research in orthopedics: Reasons for facing the challenge of change

International audienc

Bibliometric evaluation of orthopaedics and traumatology publications from France: 20-year trends (1998–2017) and international positioning

International audienceBackgroundLittle is known about the scientific publication output for individual countries and medical specialties. The contribution of French authors to the currently expanding volume of publications on orthopaedics and traumatology (OT) is unclear. Orthopaedics & Traumatology: Surgery & Research (OTSR) is an English-language version of a preexisting French journal that was launched in 2009 to increase the dissemination of research done in France. The objective of this study was to use Web of Science (WoS) data from 1998 to 2017 to determine (i) the contribution of OT publications to the total worldwide volume of scientific publications, (ii) the contribution of OT publications from France to the total worldwide volume of OT publications, and (iii) changes over time in the proportion of OT publications from France with special attention to potential effects of the creation of OTSR.HypothesisThe proportion of OT publications from France increased after 2010–2012, indicating a positive effect of OTSR.Material and methodsWoS data were used to identify original studies and review articles written by at least one French author, published between 1998 and 2017, and dealing with OT (defined as orthopaedics and/or traumatology in adult and/or paediatric patients). The worldwide volumes of publications in OT and other specialties were compared. Within worldwide OT publications, the proportion from France was determined. Indicators of impact were evaluated during successive 5-year periods. Finally, the position of OT in worldwide research was assessed and OT journals were analysed.ResultsAmong worldwide scientific medical publications, the proportion dealing with OT increased year on year from 1.93% in 1998 to 2.65% in 2017. Among annual publications from France, the proportion dealing with OT rose similarly, from 1.32% to 2.40%. Over the 20-year study period, France moved from the sixth to the ninth position, chiefly due to a large increase in publications from Asia. However, France remained in third position among European countries and increased its OT production 3-fold between 1998 and 2017. The proportion of OT articles from France that ranked among the top 1% most cited articles increased by 65% from 2008–2012 (20 articles) to 2013–2017 (33 articles), and the proportion in the top 10% increased by 31.8% (211 in 2008–2012 and 278 in 2013–2017). This rate of progression was faster than in any of the other western countries. Between 1998–2011 and 2012–2017, the contribution of French OT to publication output showed a 1.56-fold greater increase than did the contribution of OT to the worldwide volume of scientific medical publications.DiscussionOT publications from France have kept pace with the steady increase seen worldwide over the last 20 years. Although the US and UK remain in the lead, and despite the considerable growth in the output of Asian countries, France occupies a prominent position on the international OT scene. The creation of OTSR has elevated the international profile of French OT centres.Level of evidenceIV, retrospective study with no control group

Publication output of French orthopedic and trauma surgeons: Quantitative and qualitative bibliometric analysis of their scientific production in orthopedics and other medical fields

International audienceIntroductionBibliometric analysis is being used more and more in orthopedics and traumatology. However, the quantity and quality of publications authored by French orthopedic and trauma surgeons outside their discipline have never been analyzed, nor has the change in the quality of orthopedics publications. This led us to carry out a bibliometric analysis to answer the following questions: 1) How has the quantity of scientific production by French orthopedists changed over the past 10 years? 2) How has the quality of the overall scientific production by French orthopedists changed over the past 10 years?HypothesisFrom 2008 to 2017, the production of French orthopedists has increased in quantity and quality in orthopedics and other medical fields.Material and methodsThe analysis was performed by cross-referencing the list of SOFCOT (French Society for Orthopaedic Surgery and Traumatology) members with the French SIGAPS database and the InCites platform. Out of 3979 SOFCOT members, 972 (24%) had authored publications during this period and were included in the analysis. Several indicators were analyzed: number of publications; SIGAPS score (production quality) for the various Web of Science (WoS) categories; number and percentage of publications in the top 1% and top 10% (most highly cited articles worldwide).ResultsThe “Orthopedics” discipline was still the most prevalent with 68% of all publications identified. The “Surgery” discipline was stable, and the share of publications had increased in five other disciplines: Sports Sciences, Clinical Neurology, Emergency Medicine, Engineering–Biomedical and Material Science–Biomaterials. Of the 727 journals indexed in PubMed in which at least one author is a French orthopedic or trauma surgeon, 79 journals (11%) had at least 10 articles authored by a French orthopedists, making up 4680/6056 published articles (77%) during the study period. The highest SIGAPS score was in the “Orthopedics” discipline followed by “Surgery”, and then by “Sport Sciences” with a large number of publications in the SIGAPS B category. Publications in “Orthopedics” category A and B journals increased 14% during this period. When all disciplines are pooled, the share of publications in SIGAPS A, B and C categories increased by 10% from 2008 to 2017. The largest increase in publications for categories A and B and the top 1% and 10% was in “Sports Sciences”.DiscussionOver the past 10 years, French orthopedists have continued to increase their scientific production in the orthopedics field and in related fields such as Sport Sciences, Clinical Neurology and Biomedical Engineering. The quality of the scientific production of French orthopedists in their discipline and outside of it has greatly improved, as evidenced by the shift toward SIGAPS A and B journals.Level of evidenceIV, retrospective study without control group

Full-text publication rate of studies reported as 2013 SoFCOT meeting abstracts

International audienceBackgroundPublication of scientific work, although mandatory to ensure dissemination of novel research findings and obtain further funding, can require considerably more time and effort compared to conference presentations. Several national or scientific societies have determined the publication rate of studies reported at their meetings. The French Society for Orthopaedic and Trauma Surgery (Société française de chirurgie orthopédique et traumatologique, SoFCOT) has not yet measured this parameter. The objective of this study was to (i) evaluate the full-text publication rate of studies accepted in abstract form for podium presentations or posters at the 2013 SoFCOT meeting and (ii) identify characteristics of abstracts associated with subsequent full-text publication.HypothesisThe full-text publication rate of abstracts accepted for the 2013 SoFCOT meeting was equal to or greater than the mean reported by national societies, i.e., 44.5%.Material and methodsPublication rates of the 503 studies reported as abstracts at the 2013 SoFCOT meeting were studied. The time horizon was thus at least 5 years. The topic was orthopaedic surgery for 315 (62.6%) abstracts, trauma surgery for 153 (30.4%) abstracts, and fractures in elderly patients – the cross-field theme for that year – for 35 (7.0%) abstracts. Reporting was as a podium presentation for 275 (54.7%) abstracts, an e-poster for 205 (40.8%) abstracts, an instructional course lecture for 20 (4.0%) abstracts, a symposium for 2 (0.4%) abstracts, and a round table for 1 (0.2%) abstract.ResultsThe full-text publication rate was 35.6% overall and 47.1% (139 publications) for podium presentations. Mean time from podium or poster presentation at the SoFCOT meeting to full-text publication was 1.2 ± 1.5 years (range: −2.5 to 6.1 years). The full-text publications had 0.8 ± 2.3 (range: −6 to 11) more authors compared to the abstract. They appeared in 54 journals with a mean impact factor of 1.9 ± 1.3 (range: 0.25 to 13.77; median: 1.41; interquartile range: 1.26 to 2.47). Subgroup comparisons showed that full-text publication was more common for prospective than retrospective studies (50.0% versus 30.5%, p < 0.0001) and for studies showing a significant difference (48.6% versus 33.0%, p < 0.0001). Systematic reviews were more often published in full than were anecdotal case-reports. The full-text publication rate was also higher for studies reported as podium presentations than as e-posters (47.1% versus 17.6%, p < 0.0001). Finally, studies of orthopaedic surgery were more often published in full than were studies of trauma surgery (39.7% versus 28.2%, p = 0.033).DiscussionThe 5-year full-text publication rate of studies reported as abstracts at the 2013 SoFCOT meeting was consistent with previously reported data. The impact factors of the journals in which the studies were published are evidence of the high quality of the information shared at SoFCOT meetings.Level of evidenceIV, systematic retrospective analysis

Usefulness of Sepsis-3 in diagnosing and predicting mortality of ventilator-associated lower respiratory tract infections.

BackgroundEarly distinguishing ventilator-associated tracheobronchitis (VAT) and ventilator-associated pneumonia (VAP) remains difficult in the daily practice. However, this question appears clinically relevant, as treatments of VAT and VAP currently differ. In this study, we assessed the accuracy of sepsis criteria according to the Sepsis-3 definition in the early distinction between VAT and VAP.MethodsRetrospective single-center cohort, including all consecutive patients with a diagnosis of VAT (n = 70) or VAP (n = 136), during a 2-year period. Accuracy of sepsis criteria according to Sepsis-3, total SOFA and respiratory SOFA, calculated at time of microbiological sampling were assessed in differentiating VAT from VAP, and in predicting mortality on ICU discharge.ResultsSensitivity and specificity of sepsis criteria were found respectively at 0.4 and 0.91 to distinguish VAT from VAP, and at 0.38 and 0.75 for the prediction of mortality in VA-LRTI. A total SOFA ≥ 6 and a respiratory SOFA ≥ 3 were identified as the best cut-offs for these criteria in differentiating VAT from VAP, with sensitivity and specificity respectively found at 0.63 and 0.69 for total SOFA, and at 0.49 and 0.7 for respiratory SOFA. Additionally, for prediction of mortality, a total SOFA ≥ 7 and a respiratory SOFA = 4 were identified as the best-cut-offs, respectively yielding sensitivity and specificity at 0.56 and 0.61 for total SOFA, and at 0.22 and 0.95 for respiratory SOFA.ConclusionsSepsis criteria according to the Sepsis-3 definition show a high specificity but a low sensitivity for the diagnosis of VAP. Our results do not support the use of these criteria for the early diagnosis of VAP in patients with VA-LRTI

Patients' point of view on the long-term results of total ankle arthroplasty, tibiotalar and tibiotalocalcaneal arthrodeses

Introduction: Total ankle arthroplasty (TAA), tibiotalar (TT) arthrodesis and tibiotalocalcaneal (TTC) arthrodesis are common surgical procedures that are sometimes concurrent. The functional results of TTC are deemed to be inferior because of the double joint sacrifice. Patient-Reported Outcome Measures (PROMs), as well as satisfaction scores, are commonly used to assess the outcome of these surgeries, but lack at capturing patients' ability to cope with potential functional limitations. The objective of our study was to compare the results of TAA, TT and TTC arthrodeses according to patients' point of view. We proposed two hypotheses: 1) TAA confer better results than TT arthrodeses, 2) and TT arthrodeses confer better results than TTC arthrodeses, on this specific criterion. Material and methods: We carried out a retrospective study integrating all TAA, TT and TTC arthrodeses performed in our center from 2010 to 2017. These surgeries were compared using PROMs (Foot Function Index (FFI), Foot and Ankle Outcome Scale (FAOS) and 12-Item Short Form Survey (SF-12)), a satisfaction rating and self-reported perceived recovery state. Results: Fifty-one patients were included in the TAA group, 50 in the TT group and 51 in the TTC group. The mean duration of follow-up was 46±20.8 months. The TAA group had better results than the TT group regarding the FFI score and satisfaction, thus confirming our primary hypothesis. On the other hand, no significant difference was found between the TT group and the TTC group, which invalidated our secondary hypothesis. No significant difference between the groups was found regarding the distribution of patients' perceived recovery state. Conclusion: Our hypothesis was not confirmed. In fact, TAAs, TT and TTC arthrodeses presented substantially similar results. Although it is difficult to compare surgeries with different indications, it is surprising to find that the patients' perceived recovery state, deviating from the usual clinical and radiological results, are relatively similar. Level of evidence: IV; Retrospective study

Virtual evaluation of stent graft deployment: a validated modeling and simulation study

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Overview on wearable sensors for the management of Parkinson’s disease

Abstract Parkinson’s disease (PD) is affecting about 1.2 million patients in Europe with a prevalence that is expected to have an exponential increment, in the next decades. This epidemiological evolution will be challenged by the low number of neurologists able to deliver expert care for PD. As PD is better recognized, there is an increasing demand from patients for rigorous control of their symptoms and for therapeutic education. In addition, the highly variable nature of symtoms between patients and the fluctuations within the same patient requires innovative tools to help doctors and patients monitor the disease in their usual living environment and adapt treatment in a more relevant way. Nowadays, there are various body-worn sensors (BWS) proposed to monitor parkinsonian clinical features, such as motor fluctuations, dyskinesia, tremor, bradykinesia, freezing of gait (FoG) or gait disturbances. BWS have been used as add-on tool for patients’ management or research purpose. Here, we propose a practical anthology, summarizing the characteristics of the most used BWS for PD patients in Europe, focusing on their role as tools to improve treatment management. Consideration regarding the use of technology to monitor non-motor features is also included. BWS obviously offer new opportunities for improving management strategy in PD but their precise scope of use in daily routine care should be clarified

Symptoms assessment and decision to treat patients with advanced Parkinson’s disease based on wearables data

International audienceBody-worn sensors (BWS) could provide valuable information in the management of Parkinson’s disease and support therapeutic decisions based on objective monitoring. To study this pivotal step and better understand how relevant information is extracted from BWS results and translated into treatment adaptation, eight neurologists examined eight virtual cases composed of basic patient profiles and their BWS monitoring results. Sixty-four interpretations of monitoring results and the subsequent therapeutic decisions were collected. Relationship between interrater agreements in the BWS reading and the severity of symptoms were analyzed via correlation studies. Logistic regression was used to identify associations between the BWS parameters and suggested treatment modifications. Interrater agreements were high and significantly associated with the BWS scores. Summarized BWS scores reflecting bradykinesia, dyskinesia, and tremor predicted the direction of treatment modifications. Our results suggest that monitoring information is robustly linked to treatment adaptation and pave the way to loop systems able to automatically propose treatment modifications from BWS recordings information