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

Implementing rapid HIV testing with or without risk-reduction counseling in drug treatment centers: results of a randomized trial.

ObjectivesWe examined the effectiveness of risk reduction counseling and the role of on-site HIV testing in drug treatment.MethodsBetween January and May 2009, we randomized 1281 HIV-negative (or status unknown) adults who reported no past-year HIV testing to (1) referral for off-site HIV testing, (2) HIV risk-reduction counseling with on-site rapid HIV testing, or (3) verbal information about testing only with on-site rapid HIV testing.ResultsWe defined 2 primary self-reported outcomes a priori: receipt of HIV test results and unprotected anal or vaginal intercourse episodes at 6-month follow-up. The combined on-site rapid testing participants received more HIV test results than off-site testing referral participants (P<.001; Mantel-Haenszel risk ratio=4.52; 97.5% confidence interval [CI]=3.57, 5.72). At 6 months, there were no significant differences in unprotected intercourse episodes between the combined on-site testing arms and the referral arm (P=.39; incidence rate ratio [IRR]=1.04; 97.5% CI=0.95, 1.14) or the 2 on-site testing arms (P=.81; IRR=1.03; 97.5% CI=0.84, 1.26).ConclusionsThis study demonstrated on-site rapid HIV testing's value in drug treatment centers and found no additional benefit from HIV sexual risk-reduction counseling

Plasma biomarkers predict cognitive trajectories in an ethnoracially and clinically diverse cohort: Mediation with hippocampal volume

IntroductionWe examine whether the association between key plasma biomarkers (amyloid β [aβ] 42/40, total tau (t-tau), neurofilament light [NfL]) and cognitive trajectories (executive function [EF] and episodic memory [EM]) is mediated through neurodegeneration.MethodsAll participants were recruited from the University of California, Davis-Alzheimer's Disease Research Center (n = 473; baseline age range = 49-95 years, 60% women). We applied an accelerated longitudinal design to test latent growth models for EF and EM, and path and mediation analyses. Age was centered at 75 years, and all models were adjusted for sex, education, and ethnicity.ResultsHV differentially mediated the association aβ 42/40 and NfL on EF and EM level and change. Hippocampal volume (HV) did not mediate the association between t-tau and cognitive performance.DiscussionNeurodegeneration as represented with HV selectively mediates the association between key non-invasive plasma biomarkers and cognitive trajectories in an ethnoracially and clinically diverse community-based sample

MOVING THE NEEDLE ON TIME TO RESUSCITATION: AN EAST PROSPECTIVE MULTICENTER STUDY OF VASCULAR ACCESS IN HYPOTENSIVE INJURED PATIENTS USING TRAUMA VIDEO REVIEW.

INTRODUCTION: Vascular access in hypotensive trauma patients is challenging. Little evidence exists on the time required and success rates of vascular access types. We hypothesized that intraosseous (IO) access would be faster and more successful than peripheral IV (PIV) and central venous catheter (CVC) access in hypotensive patients. METHODS: An EAST prospective multicenter trial was performed; 19 centers provided data. Trauma video review (TVR) was used to evaluate the resuscitations of hypotensive (systolic blood pressure ≤ 90 mmHg) trauma patients. Highly granular data from video recordings were abstracted. Data collected included vascular access attempt type, location, success rate, and procedural time. Demographic and injury-specific variables were obtained from the medical record. Success rates, procedural durations, and time to resuscitation were compared among access strategies (IO vs PIV vs CVC). RESULTS: 1,410 access attempts occurred in 581 patients with a median age of 40[27-59] years and an ISS of 22[10-34]. 932 PIV, 204 IO and 249 CVC were attempted. 70% of access attempts were successful but were significantly less likely to be successful in females (64% vs. 71%, p = 0.01). Median time to any access was 5.0[3.2-8.0] minutes. IO had higher success rates than PIV or CVC (93% vs. 67% vs. 59%, p \u3c 0.001) and remained higher after subsequent failures (second attempt 85% vs. 59% vs. 69%, p = 0.08; third attempt 100% vs 33% vs. 67%, p = 0.002). Duration varied by access type (IO 36[23-60]sec; PIV 44[31-61]sec; CVC 171[105-298]sec) and was significantly different between IO vs. CVC (p \u3c 0.001) and PIV vs. CVC (p \u3c 0.001) but not PIV vs. IO. Time to resuscitation initiation was shorter in patients whose initial access attempt was IO, 5.8 minutes vs. 6.7 minutes (p = 0.015). This was more pronounced in patients arriving to the hospital with no established access (5.7 minutes vs. 7.5 minutes, p = 0.001). CONCLUSIONS: IO is as fast as PIV and more likely to be successful compared with other access strategies in hypotensive trauma patients. Patients whose initial access attempt was IO were resuscitated more expeditiously. IO access should be considered a first line therapy in hypotensive trauma patients. LEVEL OF EVIDENCE: Level II Therapeutic/Care Management