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

Intercomparison and analyses of the climatology of the West African Monsoon in the West African Monsoon Modeling and Evaluation project (WAMME) first model intercomparison experiment

International audienceThis paper briefly presents the West African Monsoon (WAM) Modeling and Evaluation Project (WAMME) and evaluates WAMME general circulation models' (GCM) performances in simulating variability of WAM precipitation, surface temperature, and major circulation features at seasonal and intraseasonal scales in the first WAMME experiment. The analyses indicate that models with specified sea surface temperature generally have reasonable simulations of the pattern of spatial distribution of WAM seasonal mean precipitation and surface temperature as well as the averaged zonal wind in latitude-height cross-section and low level circulation. But there are large differences among models in simulating spatial correlation, intensity, and variance of precipitation compared with observations. Furthermore, the majority of models fail to produce proper intensities of the African Easterly Jet (AEJ) and the tropical easterly jet. AMMA Land Surface Model Intercomparison Project (ALMIP) data are used to analyze the association between simulated surface processes and the WAM and to investigate the WAM mechanism. It has been identified that the spatial distributions of surface sensible heat flux, surface temperature, and moisture convergence are closely associated with the simulated spatial distribution of precipitation; while surface latent heat flux is closely associated with the AEJ and contributes to divergence in AEJ simulation. Common empirical orthogonal functions (CEOF) analysis is applied to characterize the WAM precipitation evolution and has identi- fied a major WAM precipitation mode and two temperature modes (Sahara mode and Sahel mode). Results indicate that the WAMME models produce reasonable temporal evolutions of major CEOF modes but have deficiencies/ uncertainties in producing variances explained by major modes. Furthermore, the CEOF analysis shows that WAM precipitation evolution is closely related to the enhanced Sahara mode and the weakened Sahel mode, supporting the evidence revealed in the analysis using ALMIP data. An analysis of variability of CEOF modes suggests that the Sahara mode leads the WAM evolution, and divergence in simulating this mode contributes to discrepancies in the precipitation simulation

The role of tumour biological factors in technical anatomical resectability assessment of colorectal liver metastases following induction systemic treatment: An analysis of the Dutch CAIRO5 trial.

BACKGROUND: Large inter-surgeon variability exists in technical anatomical resectability assessment of colorectal cancer liver-only metastases (CRLM) following induction systemic therapy. We evaluated the role of tumour biological factors in predicting resectability and (early) recurrence after surgery for initially unresectable CRLM. METHODS: 482 patients with initially unresectable CRLM from the phase 3 CAIRO5 trial were selected, with two-monthly resectability assessments by a liver expert panel. If no consensus existed among panel surgeons (i.e. same vote for (un)resectability of CRLM), conclusion was based on majority. The association of tumour biological (sidedness, synchronous CRLM, carcinoembryonic antigen and RAS/BRAF(V600E) mutation status) and technical anatomical factors with consensus among panel surgeons, secondary resectability and early recurrence (<6 months) without curative-intent repeat local treatment was analysed by uni- and pre-specified multivariable logistic regression. RESULTS: After systemic treatment, 240 (50%) patients received complete local treatment of CRLM of which 75 (31%) patients experienced early recurrence without repeat local treatment. Higher number of CRLM (odds ratio 1.09 [95% confidence interval 1.03-1.15]) and age (odds ratio 1.03 [95% confidence interval 1.00-1.07]) were independently associated with early recurrence without repeat local treatment. In 138 (52%) patients, no consensus among panel surgeons was present prior to local treatment. Postoperative outcomes in patients with and without consensus were comparable. CONCLUSIONS: Almost a third of patients selected by an expert panel for secondary CRLM surgery following induction systemic treatment experience an early recurrence only amenable to palliative treatment. Number of CRLM and age, but no tumour biological factors are predictive, suggesting that until there are better biomarkers; resectability assessment remains primarily a technical anatomical decision

Electronic Health Program to Empower Patients in Returning to Normal Activities After General Surgical and Gynecological Procedures: Intervention Mapping as a Useful Method for Further Development

Contains fulltext : 215610.pdf (publisher's version ) (Open Access)BACKGROUND: Support for guiding and monitoring postoperative recovery and resumption of activities is usually not provided to patients after discharge from the hospital. Therefore, a perioperative electronic health (eHealth) intervention ("ikherstel" intervention or "I recover" intervention) was developed to empower gynecological patients during the perioperative period. This eHealth intervention requires a need for further development for patients who will undergo various types of general surgical and gynecological procedures. OBJECTIVE: This study aimed to further develop the "ikherstel" eHealth intervention using Intervention Mapping (IM) to fit a broader patient population. METHODS: The IM protocol was used to guide further development of the "ikherstel" intervention. First, patients' needs were identified using (1) the information of a process evaluation of the earlier performed "ikherstel" study, (2) a review of the literature, (3) a survey study, and (4) focus group discussions (FGDs) among stakeholders. Next, program outcomes and change objectives were defined. Third, behavior change theories and practical tools were selected for the intervention program. Finally, an implementation and evaluation plan was developed. RESULTS: The outcome for an eHealth intervention tool for patients recovering from abdominal general surgical and gynecological procedures was redefined as "achieving earlier recovery including return to normal activities and work." The Attitude-Social Influence-Self-Efficacy model was used as a theoretical framework to transform personal and external determinants into change objectives of personal behavior. The knowledge gathered by needs assessment and using the theoretical framework in the preparatory steps of the IM protocol resulted in additional tools. A mobile app, an activity tracker, and an electronic consultation (eConsult) will be incorporated in the further developed eHealth intervention. This intervention will be evaluated in a multicenter, single-blinded randomized controlled trial with 18 departments in 11 participating hospitals in the Netherlands. CONCLUSIONS: The intervention is extended to patients undergoing general surgical procedures and for malignant indications. New intervention tools such as a mobile app, an activity tracker, and an eConsult were developed. TRIAL REGISTRATION: Netherlands Trial Registry NTR5686; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=5686

Circulating microRNAs in sera correlate with soluble biomarkers of immune activation but do not predict mortality in ART treated individuals with HIV-1 infection: A case control study

10.1371/journal.pone.0139981PLoS ONE1010e013998