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

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

The large-scale structure of the halo of the Andromeda galaxy II. Hierarchical structure in the Pan-Andromeda Archaeological Survey

The Pan-Andromeda Archaeological Survey is a survey of $>400$ square degrees centered on the Andromeda (M31) and Triangulum (M33) galaxies that has provided the most extensive panorama of a $L_\star$ galaxy group to large projected galactocentric radii. Here, we collate and summarise the current status of our knowledge of the substructures in the stellar halo of M31, and discuss connections between these features. We estimate that the 13 most distinctive substructures were produced by at least 5 different accretion events, all in the last 3 or 4 Gyrs. We suggest that a few of the substructures furthest from M31 may be shells from a single accretion event. We calculate the luminosities of some prominent substructures for which previous estimates were not available, and we estimate the stellar mass budget of the outer halo of M31. We revisit the problem of quantifying the properties of a highly structured dataset; specifically, we use the OPTICS clustering algorithm to quantify the hierarchical structure of M31's stellar halo, and identify three new faint structures. M31's halo, in projection, appears to be dominated by two `mega-structures', that can be considered as the two most significant branches of a merger tree produced by breaking M31's stellar halo into smaller and smaller structures based on the stellar spatial clustering. We conclude that OPTICS is a powerful algorithm that could be used in any astronomical application involving the hierarchical clustering of points. The publication of this article coincides with the public release of all PAndAS data products.Comment: Accepted for publication in the Astrophysical Journal. 51 pages, 24 figures, 5 tables. Some figures have degraded resolution. All PAndAS data products are available via the CADC at http://www.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/en/community/pandas/query.html where you can also find a version of the paper with full resolution figure

Assessment of Damage on a Dual Mobility Acetabular System

Background: Dual mobility designs were introduced to increase stability and reduce the risk of dislocation, both being common reasons for surgical revision after total hip arthroplasty. The in vivo behavior of dual mobility constructs remains unclear, and to our knowledge, no data have been published describing in vivo surface damage to the polyethylene bearing surfaces. Methods: We used surface damage assessed on the inner and outer polyethylene bearing surfaces in 33 short-term retrieved dual mobility liners as evidence of relative motion at the 2 bearings. A lever out test was performed to determine the force required for dislocation of the cobalt-chromium femoral head from the polyethylene liner. Results: Both bearings showed damage; however, the inner polyethylene bearings had higher damage scores, lower prevalence of remaining machining marks, and higher incidence of concentric wear, all consistent with more motion at the inner polyethylene bearing. The inner polyethylene bearings also had a higher occurrence of embedded titanium debris. The damage sustained in vivo was insufficient to lead to intraprosthetic dislocation in any of the retrieved components. Lever out tests of 12 retrievals had a mean dislocation load of 261 +/- 52 N, which was unrelated to the length of implantation. Conclusion: Our short-term retrieval data of 33 highly cross-linked polyethylene dual mobility components suggest that although motion occurs at both bearing articulations, the motion of the femoral head against the inner polyethylene bearing dominates. Although damage was not severe enough to lead to intraprosthetic dislocation, failure may occur long term and should be assessed in future studies. (C) 2016 Elsevier Inc. All rights reserved

Risk Factors Associated With Mortality and Neurologic Disability After Intracerebral Hemorrhage in a Racially and Ethnically Diverse Cohort

Intracerebral hemorrhage (ICH) is the most severe subtype of stroke. Its mortality rate is high, and most survivors experience significant disability. To assess primary patient risk factors associated with mortality and neurologic disability 3 months after ICH in a large, racially and ethnically balanced cohort. This cohort study included participants from the Ethnic/Racial Variations of Intracerebral Hemorrhage (ERICH) study, which prospectively recruited 1000 non-Hispanic White, 1000 non-Hispanic Black, and 1000 Hispanic patients with spontaneous ICH to study the epidemiological characteristics and genomics associated with ICH. Participants included those with uniform data collection and phenotype definitions, centralized neuroimaging review, and telephone follow-up at 3 months. Analyses were completed in November 2021. Patient demographic and clinical characteristics as well as hospital event and imaging variables were examined, with characteristics meeting P < .20 considered candidates for a multivariate model. Elements included in the ICH score were specifically analyzed. Individual characteristics were screened for association with 3-month outcome of neurologic disability or mortality, as assessed by a modified Rankin Scale (mRS) score of 4 or greater vs 3 or less under a logistic regression model. A total of 25 characteristics were tested in the final model, which minimized the Akaike information criterion. Analyses were repeated removing individuals who had withdrawal of care. A total of 2568 patients (mean [SD] age, 62.4 [14.7] years; 1069 [41.6%] women and 1499 [58.4%] men) had a 3-month outcome determination available, including death. The final logistic model had a significantly higher area under the receiver operating characteristics curve (C = 0.88) compared with ICH score alone (C = 0.76; P < .001). Among characteristics associated with neurologic disability and mortality were larger log ICH volume (OR, 2.74; 95% CI, 2.36-3.19; P < .001), older age (OR per 1-year increase, 1.04; 95% CI, 1.02-1.05; P < .001), pre-ICH mRS score (OR, 1.62; 95% CI, 1.41-1.87; P < .001), lobar location (OR, 0.22; 95% CI, 0.16-0.30; P < .001), and presence of infection (OR, 1.85; 95% CI, 1.42-2.41; P < .001). The findings of this cohort study validate ICH score elements and suggest additional baseline and interim patient characteristics were associated with variation in 3-month outcome

Hypertension and intracerebral hemorrhage recurrence among white, black, and Hispanic individuals

To clarify whether recurrence risk for intracerebral hemorrhage (ICH) is higher among black and Hispanic individuals and whether this disparity is attributable to differences in blood pressure (BP) measurements and their variability.We analyzed data from survivors of primary ICH enrolled in 2 separate studies: (1) the longitudinal study conducted at Massachusetts General Hospital (n = 759), and (2) the ERICH (Ethnic/Racial Variations of Intracerebral Hemorrhage) study (n = 1,532). Participants underwent structured interview at enrollment (including self-report of race/ethnicity) and were followed longitudinally via phone calls and review of medical records. We captured systolic BP (SBP) and diastolic BP measurements, and quantified variability as SBP and diastolic BP variation coefficients. We used multivariable (Cox regression) survival analysis to identify risk factors for ICH recurrence.We followed 2,291 ICH survivors (1,121 white, 529 black, 605 Hispanic, and 36 of other race/ethnicity). Both black and Hispanic patients displayed higher SBP during follow-up (< 0.05). Black participants also displayed greater SBP variability during follow-up (= 0.032). In univariable analyses, black and Hispanic patients were at higher ICH recurrence risk (< 0.05). After adjusting for BP measurements and their variability, both Hispanic (hazard ratio = 1.51, 95% confidence interval 1.14-2.00,0.004) and black (hazard ratio = 1.98, 95% confidence interval 1.36-2.86,< 0.001) patients remained at higher risk of ICH recurrence.Black and Hispanic patients are at higher risk of ICH recurrence; hypertension severity (average BP and its variability) does not fully account for this finding. Additional studies will be required to further elucidate determinants for this health disparity