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

How Influenza A Virus Ecology is Evolving in Wild Birds

Book Description: Avian influenza, or “bird flu”, is a contagious disease of animals caused by viruses that normally infect only birds and, less commonly, pigs. Avian influenza viruses are highly species-specific, but have, on rare occasions, crossed the species barrier to infect humans. In domestic poultry, infection with avian influenza viruses causes two main forms of disease, distinguished by low and high extremes of virulence. The so-called “low pathogenic” form commonly causes only mild symptoms (ruffled feathers, a drop in egg production) and may easily go undetected. The highly pathogenic form is far more dramatic. It spreads very rapidly through poultry flocks, causes disease affecting multiple internal organs, and has a mortality that can approach 100%, often within 48 hours. Table of Contents: Preface Chapter I - Meeting the Challenge of Bird Flu; pp. 1-22 (U.S. Centers for Disease Control) Chapter II - SARS in China and Hong Kong; pp. 23-72 (S.H. Lee, Liming Lee, Qing-He Nie) Chapter III - Infection Control for Avian Influenza (H5N1) in Healthcare Settings; pp. 73-90 (Anucha Apisarnthanarak, Division of Infectious Diseases, Linda M. Mundy, Saint Louis Univ. School of Public Health, Saint Louis, Missouri) Chapter IV - How Influenza A Virus Ecology is Evolving in Wild Birds; pp. 91-107 (M Delogu, Facolta di Medicina Veterinaria, Dipartimento di Sanita Pubblica Veterinaria e Patologia Animale, Emilia, Italy, M.A. De Marco, Istituto Nazionale per la Fauna Selvatica, Veterinary Laboratory, Emilia, Italy, L. Campitelli, National Influenza Center, Rome, Italy) Chapter V - Comprehensive AI & Bio-statistical Analysis; pp.109-132 (E.Y.K. Ng, E.C. Kee, School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological Univ., Singapore) Chapter VI - Avian Influenza in Poultry and Wild Birds; pp. 133-148 (Jim Monke and M. Lynne Corn) Inde

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes

OBJECTIVE - Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired b-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS - We have conducted a meta-analysis of genome-wide association tests of ;2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS - Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10-8). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/ C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 3 10-4), improved b-cell function (P = 1.1 × 10-5), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10-6). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS - We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis

Constraints on the CKM angle γ\gamma from B±→Dh±B^\pm\rightarrow Dh^\pm decays using D→h±h′∓π0D\rightarrow h^\pm h^{\prime\mp}\pi^0 final states

A data sample collected with the LHCb detector, corresponding to an integrated luminosity of $9~{\rm fb}^{-1}$, is used to measure $CP$ observables in $B^\pm \to D h^\pm$ decays, where $h^{(\prime)}$ is either a kaon or a pion, and the neutral $D$ meson decay is reconstructed in the three-body final states $K^\pm \pi^\mp \pi^0$, $\pi^\pm \pi^\mp \pi^0$, and $K^\pm K^\mp \pi^0$. The most suppressed of these modes, $B^\pm \to [\pi^\pm K^\mp \pi^0]_D K^\pm$, is observed with a significance greater than seven standard deviations and constraints on the CKM angle $\gamma$ are calculated from the combination of the measurements