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

Analyzing the vulnerability of wireless sensor networks to a malicious matched protocol attack

Safety critical, Internet of Things (IoT) and space-based applications have recently begun to adopt wireless networks based on commercial off the shelf (COTS) devices and standardized protocols, which inherently establishes the security challenge of malicious intrusions. Malicious intrusions can cause severe consequences if undetected, including, complete denial of services. Particularly, any safety critical application requires all services to operate correctly, as any loss can be detrimental to safety and/or privacy. Therefore, in order for these safety critical services to remain operational and available, any and all intrusions need to be detected and mitigated. Whilst intrusion detection is not a new research area, new vulnerabilities in wireless networks, especially wireless sensor networks (WSNs), can be identified. In this paper, a specific vulnerability of WSNs is explored, termed here the matched protocol attack. This malicious attack uses protocol-specific structures to compromise a network using that protocol. Through attack exploration, this paper provides evidence that traditional spectral techniques are not sufficient to detect an intrusion using this style of attack. Furthermore, a ZigBee cluster head network, which co-exists with ISM band services, consisting of XBee COTS devices is utilized, along with a real time spectrum analyzer, to experimentally evaluate the effect of matched protocol interference on a realistic network model. Results of this evaluation are provided in terms of device errors and spectrum use. This malicious challenge is also examined through Monte-Carlo simulations. A potential detection technique, based on coarse inter-node distance measurements, which can theoretically be used to detect matched protocol interference and localize the origin of the source, is also suggested as a future progression of this work. Insights into how this attack style preys on some of the main security risks of any WSN (interoperability, device limitations and operation in hostile environments) are also provided

Explanations for social inequalities in preterm delivery in the prospective lifeways cohort in the republic of ireland

Background: Social inequalities in pregnancy outcomes have been extensively described but studies that explain these inequalities comprehensively are lacking. This analysis evaluated the contribution of material, psychosocial, behavioural, nutritional and obstetrical factors in explaining social inequalities in preterm delivery. Methods: The data were based on a prospective cohort of 1109 Irish pregnant women. Preterm delivery was obtained from clinical hospital records. Socio-economic status was measured using educational level. The contribution of the above factors in explaining the association between educational level and preterm delivery was examined using Cox models. Results: Educational level was found to be a significant predictive factor of preterm delivery; women with low educational level were more likely to have a preterm delivery [hazard ratio (HR) = 2.14, 95% confidence interval (95% CI): 1.04-4.38)] after adjustment for age and parity. Rented and crowded home, smoking, alcohol consumption and intake of saturated fatty acids displayed educational differences and were predictive of preterm delivery. Material factors (rented and crowded home) reduced the HR of preterm delivery for low compared with highest educated women by 33%. The additional independent contribution of behavioural factors (smoking and alcohol consumption) was 5% and of saturated fatty acids intake was 4%. All these factors combined reduced the HR of preterm delivery for low educated women by 42% (HR = 1.66, 95% CI: 0.76-3.63). Conclusion: This study underlines the importance of material, behavioural and nutritional factors in explaining social inequalities in preterm delivery. These findings have cross-sectoral public policy implications

Non-pharmacological Interventions to Prevent or Treat Delirium in Older Patients: Clinical Practice Recommendations The SENATOR-ONTOP Series

DESCRIPTION: The ONTOP project aims to undertake a literature search of systematic reviews concerning evidence-based non-pharmacological interventions of prevalent medical conditions affecting older people, including delirium. OBJECTIVES: To develop explicit and transparent recommendations for non-pharmacological interventions in older subjects at risk of developing delirium, as well as in older subjects with delirium, based on the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach to rating the quality of evidence and the strength of recommendations. METHODS: A multidisciplinary panel was constituted comprising geriatricians, research nurse and a clinical epidemiologist. The panel developed a systematic overview of non-pharmacological interventions to prevent or treat delirium. The GRADE approach was used to rate the evidence and to formulate recommendations. RESULTS: The critical outcomes were delirium incidence, for delirium prevention, and delirium improvement and functional status, for delirium treatment. The non-pharmacological interventions were identified and categorized as multicomponent and single component. Strong recommendations in favor of multicomponent interventions to prevent delirium, in surgical or medicals wards, were formulated. In the latter case the evidence applied to older patients at intermediate - high risk of developing delirium. Weak recommendations, to prevent delirium, were formulated for multicomponent interventions provided by family members (medical ward), staff education (medical ward), ear plugs (intensive care unit), reorientation protocol (intensive care unit), and the use of a software to perform drug review. Weak recommendations were provided for the use of multicomponent interventions to prevent delirium in medical wards in patients not selected according to the risk of delirium. Strong recommendations not to use bright light therapy to prevent delirium in intensive care unit settings were articulated. Weak recommendations not to use music therapy to prevent delirium for patients undergoing surgical interventions were specified. The ability to make strong recommendations was limited by the low quality of evidence and the presence of uncertainty. Moreover, weak recommendations were provided for the use of multicomponent interventions to treat delirium of older patients (medical wards). CONCLUSIONS: Overall, the panel developed 12 recommendations for the delivery of non-pharmacological interventions to older patients at risk of developing or, with delirium

Covid-19 in Critically Ill Patients in the Seattle Region — Case Series

BACKGROUND Community transmission of coronavirus 2019 (Covid-19) was detected in the state of Washington in February 2020. METHODS We identified patients from nine Seattle-area hospitals who were admitted to the intensive care unit (ICU) with confirmed infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Clinical data were obtained through review of medical records. The data reported here are those available through March 23, 2020. Each patient had at least 14 days of follow-up. RESULTS We identified 24 patients with confirmed Covid-19. The mean (±SD) age of the patients was 64±18 years, 63% were men, and symptoms began 7±4 days before admission. The most common symptoms were cough and shortness of breath; 50% of patients had fever on admission, and 58% had diabetes mellitus. All the patients were admitted for hypoxemic respiratory failure; 75% (18 patients) needed mechanical ventilation. Most of the patients (17) also had hypotension and needed vasopressors. No patient tested positive for influenza A, influenza B, or other respiratory viruses. Half the patients (12) died between ICU day 1 and day 18, including 4 patients who had a do-not-resuscitate order on admission. Of the 12 surviving patients, 5 were discharged home, 4 were discharged from the ICU but remained in the hospital, and 3 continued to receive mechanical ventilation in the ICU. CONCLUSIONS During the first 3 weeks of the Covid-19 outbreak in the Seattle area, the most common reasons for admission to the ICU were hypoxemic respiratory failure leading to mechanical ventilation, hypotension requiring vasopressor treatment, or both. Mortality among these critically ill patients was high. (Funded by the National Institutes of Health.

Intravenous aviptadil and remdesivir for treatment of COVID-19-associated hypoxaemic respiratory failure in the USA (TESICO): a randomised, placebo-controlled trial.

BACKGROUND: There is a clinical need for therapeutics for COVID-19 patients with acute hypoxemic respiratory failure whose 60-day mortality remains at 30-50%. Aviptadil, a lung-protective neuropeptide, and remdesivir, a nucleotide prodrug of an adenosine analog, were compared with placebo among patients with COVID-19 acute hypoxaemic respiratory failure. METHODS: TESICO was a randomised trial of aviptadil and remdesivir versus placebo at 28 sites in the USA. Hospitalised adult patients were eligible for the study if they had acute hypoxaemic respiratory failure due to confirmed SARS-CoV-2 infection and were within 4 days of the onset of respiratory failure. Participants could be randomly assigned to both study treatments in a 2 × 2 factorial design or to just one of the agents. Participants were randomly assigned with a web-based application. For each site, randomisation was stratified by disease severity (high-flow nasal oxygen or non-invasive ventilation vs invasive mechanical ventilation or extracorporeal membrane oxygenation [ECMO]), and four strata were defined by remdesivir and aviptadil eligibility, as follows: (1) eligible for randomisation to aviptadil and remdesivir in the 2 × 2 factorial design; participants were equally randomly assigned (1:1:1:1) to intravenous aviptadil plus remdesivir, aviptadil plus remdesivir matched placebo, aviptadil matched placebo plus remdesvir, or aviptadil placebo plus remdesivir placebo; (2) eligible for randomisation to aviptadil only because remdesivir was started before randomisation; (3) eligible for randomisation to aviptadil only because remdesivir was contraindicated; and (4) eligible for randomisation to remdesivir only because aviptadil was contraindicated. For participants in strata 2-4, randomisation was 1:1 to the active agent or matched placebo. Aviptadil was administered as a daily 12-h infusion for 3 days, targeting 600 pmol/kg on infusion day 1, 1200 pmol/kg on day 2, and 1800 pmol/kg on day 3. Remdesivir was administered as a 200 mg loading dose, followed by 100 mg daily maintenance doses for up to a 10-day total course. For participants assigned to placebo for either agent, matched saline placebo was administered in identical volumes. For both treatment comparisons, the primary outcome, assessed at day 90, was a six-category ordinal outcome: (1) at home (defined as the type of residence before hospitalisation) and off oxygen (recovered) for at least 77 days, (2) at home and off oxygen for 49-76 days, (3) at home and off oxygen for 1-48 days, (4) not hospitalised but either on supplemental oxygen or not at home, (5) hospitalised or in hospice care, or (6) dead. Mortality up to day 90 was a key secondary outcome. The independent data and safety monitoring board recommended stopping the aviptadil trial on May 25, 2022, for futility. On June 9, 2022, the sponsor stopped the trial of remdesivir due to slow enrolment. The trial is registered with ClinicalTrials.gov, NCT04843761. FINDINGS: Between April 21, 2021, and May 24, 2022, we enrolled 473 participants in the study. For the aviptadil comparison, 471 participants were randomly assigned to aviptadil or matched placebo. The modified intention-to-treat population comprised 461 participants who received at least a partial infusion of aviptadil (231 participants) or aviptadil matched placebo (230 participants). For the remdesivir comparison, 87 participants were randomly assigned to remdesivir or matched placebo and all received some infusion of remdesivir (44 participants) or remdesivir matched placebo (43 participants). 85 participants were included in the modified intention-to-treat analyses for both agents (ie, those enrolled in the 2 x 2 factorial). For the aviptadil versus placebo comparison, the median age was 57 years (IQR 46-66), 178 (39%) of 461 participants were female, and 246 (53%) were Black, Hispanic, Asian or other (vs 215 [47%] White participants). 431 (94%) of 461 participants were in an intensive care unit at baseline, with 271 (59%) receiving high-flow nasal oxygen or non-invasive ventiliation, 185 (40%) receiving invasive mechanical ventilation, and five (1%) receiving ECMO. The odds ratio (OR) for being in a better category of the primary efficacy endpoint for aviptadil versus placebo at day 90, from a model stratified by baseline disease severity, was 1·11 (95% CI 0·80-1·55; p=0·54). Up to day 90, 86 participants in the aviptadil group and 83 in the placebo group died. The cumulative percentage who died up to day 90 was 38% in the aviptadil group and 36% in the placebo group (hazard ratio 1·04, 95% CI 0·77-1·41; p=0·78). The primary safety outcome of death, serious adverse events, organ failure, serious infection, or grade 3 or 4 adverse events up to day 5 occurred in 146 (63%) of 231 patients in the aviptadil group compared with 129 (56%) of 230 participants in the placebo group (OR 1·40, 95% CI 0·94-2·08; p=0·10). INTERPRETATION: Among patients with COVID-19-associated acute hypoxaemic respiratory failure, aviptadil did not significantly improve clinical outcomes up to day 90 when compared with placebo. The smaller than planned sample size for the remdesivir trial did not permit definitive conclusions regarding safety or efficacy. FUNDING: National Institutes of Health