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

New filovirus disease classification and nomenclature.

The recent large outbreak of Ebola virus disease (EVD) in Western Africa resulted in greatly increased accumulation of human genotypic, phenotypic and clinical data, and improved our understanding of the spectrum of clinical manifestations. As a result, the WHO disease classification of EVD underwent major revision

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Adding 6 months of androgen deprivation therapy to postoperative radiotherapy for prostate cancer: a comparison of short-course versus no androgen deprivation therapy in the RADICALS-HD randomised controlled trial

Background Previous evidence indicates that adjuvant, short-course androgen deprivation therapy (ADT) improves metastasis-free survival when given with primary radiotherapy for intermediate-risk and high-risk localised prostate cancer. However, the value of ADT with postoperative radiotherapy after radical prostatectomy is unclear. Methods RADICALS-HD was an international randomised controlled trial to test the efficacy of ADT used in combination with postoperative radiotherapy for prostate cancer. Key eligibility criteria were indication for radiotherapy after radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to radiotherapy alone (no ADT) or radiotherapy with 6 months of ADT (short-course ADT), using monthly subcutaneous gonadotropin-releasing hormone analogue injections, daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as distant metastasis arising from prostate cancer or death from any cause. Standard survival analysis methods were used, accounting for randomisation stratification factors. The trial had 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 80% to 86% (hazard ratio [HR] 0·67). Analyses followed the intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov, NCT00541047. Findings Between Nov 22, 2007, and June 29, 2015, 1480 patients (median age 66 years [IQR 61–69]) were randomly assigned to receive no ADT (n=737) or short-course ADT (n=743) in addition to postoperative radiotherapy at 121 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 9·0 years (IQR 7·1–10·1), metastasis-free survival events were reported for 268 participants (142 in the no ADT group and 126 in the short-course ADT group; HR 0·886 [95% CI 0·688–1·140], p=0·35). 10-year metastasis-free survival was 79·2% (95% CI 75·4–82·5) in the no ADT group and 80·4% (76·6–83·6) in the short-course ADT group. Toxicity of grade 3 or higher was reported for 121 (17%) of 737 participants in the no ADT group and 100 (14%) of 743 in the short-course ADT group (p=0·15), with no treatment-related deaths. Interpretation Metastatic disease is uncommon following postoperative bed radiotherapy after radical prostatectomy. Adding 6 months of ADT to this radiotherapy did not improve metastasis-free survival compared with no ADT. These findings do not support the use of short-course ADT with postoperative radiotherapy in this patient population

Duration of androgen deprivation therapy with postoperative radiotherapy for prostate cancer: a comparison of long-course versus short-course androgen deprivation therapy in the RADICALS-HD randomised trial

Background Previous evidence supports androgen deprivation therapy (ADT) with primary radiotherapy as initial treatment for intermediate-risk and high-risk localised prostate cancer. However, the use and optimal duration of ADT with postoperative radiotherapy after radical prostatectomy remains uncertain. Methods RADICALS-HD was a randomised controlled trial of ADT duration within the RADICALS protocol. Here, we report on the comparison of short-course versus long-course ADT. Key eligibility criteria were indication for radiotherapy after previous radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to add 6 months of ADT (short-course ADT) or 24 months of ADT (long-course ADT) to radiotherapy, using subcutaneous gonadotrophin-releasing hormone analogue (monthly in the short-course ADT group and 3-monthly in the long-course ADT group), daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as metastasis arising from prostate cancer or death from any cause. The comparison had more than 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 75% to 81% (hazard ratio [HR] 0·72). Standard time-to-event analyses were used. Analyses followed intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov , NCT00541047 . Findings Between Jan 30, 2008, and July 7, 2015, 1523 patients (median age 65 years, IQR 60–69) were randomly assigned to receive short-course ADT (n=761) or long-course ADT (n=762) in addition to postoperative radiotherapy at 138 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 8·9 years (7·0–10·0), 313 metastasis-free survival events were reported overall (174 in the short-course ADT group and 139 in the long-course ADT group; HR 0·773 [95% CI 0·612–0·975]; p=0·029). 10-year metastasis-free survival was 71·9% (95% CI 67·6–75·7) in the short-course ADT group and 78·1% (74·2–81·5) in the long-course ADT group. Toxicity of grade 3 or higher was reported for 105 (14%) of 753 participants in the short-course ADT group and 142 (19%) of 757 participants in the long-course ADT group (p=0·025), with no treatment-related deaths. Interpretation Compared with adding 6 months of ADT, adding 24 months of ADT improved metastasis-free survival in people receiving postoperative radiotherapy. For individuals who can accept the additional duration of adverse effects, long-course ADT should be offered with postoperative radiotherapy. Funding Cancer Research UK, UK Research and Innovation (formerly Medical Research Council), and Canadian Cancer Society

Interpositional arthroplasty with Dx Reinforcement Matrix®: A possible solution in the surgical treatment of lateral TMT joints arthritis

There are two main categories of surgical management for lateral TMT joints arthritis: fusion and motion preserving surgeries, which include resection arthroplasty, tendon interpositional arthroplasty and ceramic interpositional arthroplasty. This article reports the first case of interposition arthroplasty of the 5th TMT joint with Dx Reinforcement Matrix®, a porcine dermal extracellular matrix.We present the case of a 22-year-old male who suffered a motorcycle accident which caused closed fractures of the 2nd, 3rd and 4th metatarsal diaphysis, an articular fracture of the 5th metatarsal base and an impaction fracture of the cuboid distal articular surface. Two years later, he presented pain in the lateral aspect of the midfoot and the radiographs and CT scan showed impaction of the fifth metatarsal base in the cuboid, with post-traumatic arthritis of the 5th TMT joint. An interposition arthroplasty of the 5th TMT joint with a porcine acellular dermal extracellular matrix (Dx Reinforcement Matrix® – Arthrex), was performed. At 3 years follow-up, the patient was asymptomatic, had a symmetric mobility comparatively to the contralateral foot and an AOFAS Midfoot scale of 100/100.From a biomechanical point of view, fusion of the lateral TMT joints seems less desirable due to the motion of the lateral column. Motion preserving surgeries have been described, with small case series and equivalent satisfactory results. We presented the case of a young patient with isolated lateral TMT joint arthritis and reported the first case of interposition arthroplasty with Dx Reinforcement Matrix® with a good clinical result at 3 years follow-up

Self-assembled titanosilicate TS-1 nanocrystals in hierarchical structures

International audienceHierarchical structures consisting of microporous titanosilicate TS-1 nanocrystals (MFI-type structure) are obtained by controlled evaporation of colloidal suspensions. The TS-1 nanocrystals with diameter of 60-80 nm are prepared by hydrothermal treatment of clear precursor suspension. The purified TS-1 colloidal suspensions are dried under controlled conditions in order to form hierarchical structures with uniform micropores originated from the TS-1 nanocrystals, mesopores coming from the interparticles spacing and macropores emerging from the controlled evaporation of the solvent. The as-prepared micro/meso/macroporous TS-1 materials are treated by non-thermal plasma to remove the organic template and subsequently characterized by spectroscopy (DLS, IR, UV-vis), microscopy (TEM, SEM), X-ray diffraction, nitrogen sorption and mercury intrusion porosimetry. Besides, the sorption and confinement of 2,4,6-trimethylpyridine (collidine) probe molecule in the micro/meso/macroporous TS-1 structure is followed by FTIR. (C) 2011 Elsevier B.V. All rights reserved

Self-assembled titanosilicate TS-1 nanocrystals in hierarchical structures

International audienceHierarchical structures consisting of microporous titanosilicate TS-1 nanocrystals (MFI-type structure) are obtained by controlled evaporation of colloidal suspensions. The TS-1 nanocrystals with diameter of 60-80 nm are prepared by hydrothermal treatment of clear precursor suspension. The purified TS-1 colloidal suspensions are dried under controlled conditions in order to form hierarchical structures with uniform micropores originated from the TS-1 nanocrystals, mesopores coming from the interparticles spacing and macropores emerging from the controlled evaporation of the solvent. The as-prepared micro/meso/macroporous TS-1 materials are treated by non-thermal plasma to remove the organic template and subsequently characterized by spectroscopy (DLS, IR, UV-vis), microscopy (TEM, SEM), X-ray diffraction, nitrogen sorption and mercury intrusion porosimetry. Besides, the sorption and confinement of 2,4,6-trimethylpyridine (collidine) probe molecule in the micro/meso/macroporous TS-1 structure is followed by FTIR. (C) 2011 Elsevier B.V. All rights reserved

Learning from situated experiences for a contextual planning guidance

International audienceThis paper presents AgLOTOS as an algebraic language dedicated to the specification of agent plans in ambient systems. AgLOTOS offers two levels of plans: elementary plans which are composed to produce an intention plan; The intention plans which are, in turn, composed to build an agent plan. The composition relies on several operators such as alternative and concurrency. Consequently, the plans can be built automatically as a system of concurrent processes. At the execution level, our approach helps the agent to select an optimal plan preserving the consistency of its intentions. The selection is based on an original and formal construction called contextual planning system (CPS), which presents the potential paths with the associated contexts while removing the inconsistent options. Finally, our CPS is improved by using past-experiences for a better guidance of the agent

A Dynamical Plan Revising for Ambient Systems

pp. 37-44International audienceThe proposed AgLOTOS formal specification language is dedicated to express BDI agent plans, according to the features and requirements of Ambient Intelligence (AmI). It offers a rich modular approach to express and compose elementary plans in order to execute them concurrently. We show how a plan is built automatically as a system of concurrent processes from the mental attitudes of the agent. In contrast to existing approaches, the plan is viewed as the realization of a whole set of partially ordered intentions. The AgLOTOS semantics accords with the possibility of updating some sub-plans on the fly, as the intention set of the BDI agent is revised