19 research outputs found

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

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    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

    Current accounts of antimicrobial resistance: stabilisation, individualisation and antibiotics as infrastructure.

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    Antimicrobial resistance (AMR) is one of the latest issues to galvanise political and financial investment as an emerging global health threat. This paper explores the construction of AMR as a problem, following three lines of analysis. First, an examination of some of the ways in which AMR has become an object for action-through defining, counting and projecting it. Following Lakoff's work on emerging infectious diseases, the paper illustrates that while an 'actuarial' approach to AMR may be challenging to stabilise due to definitional and logistical issues, it has been successfully stabilised through a 'sentinel' approach that emphasises the threat of AMR. Second, the paper draws out a contrast between the way AMR is formulated in terms of a problem of connectedness-a 'One Health' issue-and the frequent solutions to AMR being focused on individual behaviour. The paper suggests that AMR presents an opportunity to take seriously connections, scale and systems but that this effort is undermined by the prevailing tendency to reduce health issues to matters for individual responsibility. Third, the paper takes AMR as a moment of infrastructural inversion (Bowker and Star) when antimicrobials and the work they do are rendered more visible. This leads to the proposal of antibiotics as infrastructure-part of the woodwork that we take for granted, and entangled with our ways of doing life, in particular modern life. These explorations render visible the ways social, economic and political frames continue to define AMR and how it may be acted upon, which opens up possibilities for reconfiguring AMR research and action

    Implementation of the COP26 declaration to halt forest loss must safeguard and include Indigenous people

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    World and industry leaders at the 26th UN Climate Change Conference of the Parties (COP26) asserted in their declaration on Forest and Land Use a commitment to “halt and reverse forest loss and land degradation by 2030”1. Nothing less than decisive and coordi-nated global action is required as we near an apocalyptic future of environmental degrada-tion, species extinction, and catastrophic climate change. With the recent acceleration in newly created global commitments and successes such as the achievement of Aichi Target 11 in 20212, we should nonetheless pause and reflect about the implications of such top-down pledges to conserve forests for indigenous peoples worldwide. To successfully achieve our climate change mitigation goals through halting deforestation while safeguarding indigenous peoples’ and forest-dwelling communities’ dignity, rights, and livelihoods will require policy makers to be socially inclusive and ensuring that conser-vation initiatives learn from the long history and problematic history of forest conservation. It is important that the burden of addressing mitigating climate change should not fall on indigenous communities who are the least responsible for the current biodiversity and cli-mate crises

    Integrating Mobile Devices with Cohort Analysis into Personalised Weather-Based Healthcare

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    Mobile healthcare applications can empower users to self-monitor their health conditions without the need to visit any medical centre. However, the lack of attention on engagement aspects of mobile healthcare applications often result in users choosing to uninstall the application after the first usage experience. This results in failure of effective prolonged personalised healthcare, especially for users with chronic disease related to weather conditions such as asthma and eczema which require long-term monitoring and self-care. Therefore, this paper aims to identify the pattern of application user engagement with a weather-based mobile healthcare application through cohort retention analysis. Enhancement features for improving the engagement of personalised healthcare can provide meaningful insight. The proposed application allows the patient to conduct disease control tests to check the severity of their condition on a daily basis. To measure the application engagement, we distribute the mobile application designed for primary testing over a period of ten days. Based on the primary testing, data related to retention rate and the number of control test reported were collected via Firebase Analytic to determine the application engagement. Subsequently, we apply cohort analysis using a machine learning clustering technique implemented in Python to identify the pattern of the engagement by application users. Finally, useful insights were analysed and implemented as enhancement features within the application for improving the personalised weather-based mobile healthcare. The findings in this paper can assist machine learning facilitators design effective use policies for weather-based mobile healthcare with fundamental knowledge enhanced with personalisation and user engagement

    Effect of point-of-care C-reactive protein testing on antibiotic prescription in febrile patients attending primary care in Thailand and Myanmar: an open-label, randomised, controlled trial

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    Background In southeast Asia, antibiotic prescription in febrile patients attending primary care is common, and a probable contributor to the high burden of antimicrobial resistance. The objective of this trial was to explore whether C-reactive protein (CRP) testing at point of care could rationalise antibiotic prescription in primary care, comparing two proposed thresholds to classify CRP concentrations as low or high to guide antibiotic treatment. Methods We did a multicentre, open-label, randomised, controlled trial in participants aged at least 1 year with a documented fever or a chief complaint of fever (regardless of previous antibiotic intake and comorbidities other than malignancies) recruited from six public primary care units in Thailand and three primary care clinics and one outpatient department in Myanmar. Individuals were randomly assigned using a computer-based randomisation system at a ratio of 1:1:1 to either the control group or one of two CRP testing groups, which used thresholds of 20 mg/L (group A) or 40 mg/L CRP (group B) to guide antibiotic prescription. Health-care providers were masked to allocation between the two intervention groups but not to the control group. The primary outcome was the prescription of any antibiotic from day 0 to day 5 and the proportion of patients who were prescribed an antibiotic when CRP concentrations were above and below the 20 mg/L or 40 mg/L thresholds. The primary outcome was analysed in the intention-to-treat and per-protocol populations. The trial is registered with ClinicalTrials.gov, number NCT02758821, and is now completed. Findings Between June 8, 2016, and Aug 25, 2017, we recruited 2410 patients, of whom 803 patients were randomly assigned to CRP group A, 800 to CRP group B, and 807 to the control group. 598 patients in CRP group A, 593 in CRP group B, and 767 in the control group had follow-up data for both day 5 and day 14 and had been prescribed antibiotics (or not) in accordance with test results (per-protocol population). During the trial, 318 (39%) of 807 patients in the control group were prescribed an antibiotic by day 5, compared with 290 (36%) of 803 patients in CRP group A and 275 (34%) of 800 in CRP group B. The adjusted odds ratio (aOR) of 0·80 (95% CI 0·65–0·98) and risk difference of −5·0 percentage points (95% CI −9·7 to −0·3) between group B and the control group were significant, although lower than anticipated, whereas the reduction in prescribing in group A compared with the control group was not significant (aOR 0·86 [0·70–1·06]; risk difference −3·3 percentage points [–8·0 to 1·4]). Patients with high CRP concentrations in both intervention groups were more likely to be prescribed an antibiotic than in the control group (CRP ≥20 mg/L: group A vs control group, p<0·0001; CRP ≥40 mg/L: group B vs control group, p<0·0001), and those with low CRP concentrations were more likely to have an antibiotic withheld (CRP <20 mg/L: group A vs control group, p<0·0001; CRP <40 mg/L: group B vs control group, p<0·0001). 24 serious adverse events were recorded, consisting of 23 hospital admissions and one death, which occurred in CRP group A. Only one serious adverse event was thought to be possibly related to the study (a hospital admission in CRP group A). Interpretation In febrile patients attending primary care, testing for CRP at point of care with a threshold of 40 mg/L resulted in a modest but significant reduction in antibiotic prescribing, with patients with high CRP being more likely to be prescribed an antibiotic, and no evidence of a difference in clinical outcomes. This study extends the evidence base from lower-income settings supporting the use of CRP tests to rationalise antibiotic use in primary care patients with an acute febrile illness. A key limitation of this study is the individual rather than cluster randomised study design which might have resulted in contamination between the study groups, reducing the effect size of the intervention

    Effect of point-of-care C-reactive protein testing on antibiotic prescription in febrile patients attending primary care in Thailand and Myanmar: an open-label, randomised, controlled trial

    No full text
    Background In southeast Asia, antibiotic prescription in febrile patients attending primary care is common, and a probable contributor to the high burden of antimicrobial resistance. The objective of this trial was to explore whether C-reactive protein (CRP) testing at point of care could rationalise antibiotic prescription in primary care, comparing two proposed thresholds to classify CRP concentrations as low or high to guide antibiotic treatment. Methods We did a multicentre, open-label, randomised, controlled trial in participants aged at least 1 year with a documented fever or a chief complaint of fever (regardless of previous antibiotic intake and comorbidities other than malignancies) recruited from six public primary care units in Thailand and three primary care clinics and one outpatient department in Myanmar. Individuals were randomly assigned using a computer-based randomisation system at a ratio of 1:1:1 to either the control group or one of two CRP testing groups, which used thresholds of 20 mg/L (group A) or 40 mg/L CRP (group B) to guide antibiotic prescription. Health-care providers were masked to allocation between the two intervention groups but not to the control group. The primary outcome was the prescription of any antibiotic from day 0 to day 5 and the proportion of patients who were prescribed an antibiotic when CRP concentrations were above and below the 20 mg/L or 40 mg/L thresholds. The primary outcome was analysed in the intention-to-treat and per-protocol populations. The trial is registered with ClinicalTrials.gov, number NCT02758821, and is now completed. Findings Between June 8, 2016, and Aug 25, 2017, we recruited 2410 patients, of whom 803 patients were randomly assigned to CRP group A, 800 to CRP group B, and 807 to the control group. 598 patients in CRP group A, 593 in CRP group B, and 767 in the control group had follow-up data for both day 5 and day 14 and had been prescribed antibiotics (or not) in accordance with test results (per-protocol population). During the trial, 318 (39%) of 807 patients in the control group were prescribed an antibiotic by day 5, compared with 290 (36%) of 803 patients in CRP group A and 275 (34%) of 800 in CRP group B. The adjusted odds ratio (aOR) of 0·80 (95% CI 0·65–0·98) and risk difference of −5·0 percentage points (95% CI −9·7 to −0·3) between group B and the control group were significant, although lower than anticipated, whereas the reduction in prescribing in group A compared with the control group was not significant (aOR 0·86 [0·70–1·06]; risk difference −3·3 percentage points [–8·0 to 1·4]). Patients with high CRP concentrations in both intervention groups were more likely to be prescribed an antibiotic than in the control group (CRP ≥20 mg/L: group A vs control group, p<0·0001; CRP ≥40 mg/L: group B vs control group, p<0·0001), and those with low CRP concentrations were more likely to have an antibiotic withheld (CRP <20 mg/L: group A vs control group, p<0·0001; CRP <40 mg/L: group B vs control group, p<0·0001). 24 serious adverse events were recorded, consisting of 23 hospital admissions and one death, which occurred in CRP group A. Only one serious adverse event was thought to be possibly related to the study (a hospital admission in CRP group A). Interpretation In febrile patients attending primary care, testing for CRP at point of care with a threshold of 40 mg/L resulted in a modest but significant reduction in antibiotic prescribing, with patients with high CRP being more likely to be prescribed an antibiotic, and no evidence of a difference in clinical outcomes. This study extends the evidence base from lower-income settings supporting the use of CRP tests to rationalise antibiotic use in primary care patients with an acute febrile illness. A key limitation of this study is the individual rather than cluster randomised study design which might have resulted in contamination between the study groups, reducing the effect size of the intervention

    Antibiotic knowledge, attitudes and practices: new insights from cross-sectional rural health behaviour surveys in low-income and middle-income South-East Asia

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    Introduction: Low-income and middle-income countries (LMICs) are crucial in the global response to antimicrobial resistance (AMR), but diverse health systems, healthcare practices and cultural conceptions of medicine can complicate global education and awareness-raising campaigns. Social research can help understand LMIC contexts but remains under-represented in AMR research. Objective: To (1) Describe antibiotic-related knowledge, attitudes and practices of the general population in two LMICs. (2) Assess the role of antibiotic-related knowledge and attitudes on antibiotic access from different types of healthcare providers. Design: Observational study: cross-sectional rural health behaviour survey, representative of the population level. Setting: General rural population in Chiang Rai (Thailand) and Salavan (Lao PDR), surveyed between November 2017 and May 2018. Participants: 2141 adult members (≥18 years) of the general rural population, representing 712,000 villagers. Outcome measures: Antibiotic-related knowledge, attitudes and practices across sites and healthcare access channels. Findings: Villagers were aware of antibiotics (Chiang Rai: 95.7%; Salavan: 86.4%; p&lt;0.001) and drug resistance (Chiang Rai: 74.8%; Salavan: 62.5%; p&lt;0.001), but the usage of technical concepts for antibiotics was dwarfed by local expressions like ‘anti-inflammatory medicine’ in Chiang Rai (87.6%; 95% CI 84.9% to 90.0%) and ‘ampi’ in Salavan (75.6%; 95% CI 71.4% to 79.4%). Multivariate linear regression suggested that attitudes against over-the-counter antibiotics were linked to 0.12 additional antibiotic use episodes from public healthcare providers in Chiang Rai (95% CI 0.01 to 0.23) and 0.53 in Salavan (95% CI 0.16 to 0.90). Conclusions: Locally specific conceptions and counterintuitive practices around antimicrobials can complicate AMR communication efforts and entail unforeseen consequences. Overcoming ‘knowledge deficits’ alone will therefore be insufficient for global AMR behaviour change. We call for an expansion of behavioural AMR strategies towards ‘AMR-sensitive interventions’ that address context-specific upstream drivers of antimicrobial use (eg, unemployment insurance) and complement education and awareness campaigns. Trial Registration Number: clinicaltrials.gov identifier NCT03241316.</p
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