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

A new species of Calamaria (Squamata: Colubridae) from Guangdong Province, southern China

A new species of the genus Calamaria Boie, 1827, Calamaria arcana sp. nov., is described based on a single male specimen collected from Mt. Dadongshan, Guangdong, southern China. The new species can be distinguished from all known congeners by the significant genetic divergence in the mitochondrial cytochrome-b gene fragment (p-distance ≥ 13.9%), and morphologically by the combination of the following characters: (1) ten modified maxillary teeth; (2) four supralabials, second and third supralabials entering orbit; (3) preocular present; (4) mental not touching anterior chin shields; (5) six scales and shields surrounding the paraparietal; (6) 170 ventral scales; (7) 22 paired subcaudals; (8) tail not gradually tapering, abruptly tapering at the tip; (9) dorsal scales reduced to five rows above last subcaudal at tail; (10) dorsum of body and tail brownish; (11) dark collar on nuchal region absent; (12) two outermost dorsal scale rows light yellow with upper margins partly dark pigmented; (13) ventral scales immaculate, without dark outermost corners and pigmentation anteriorly; and (14) absence of distinct dark longitudinal line or scattered spots on the underside of tail. Calamaria arcana sp. nov., represents the fifth species of the genus recorded in China. Following the IUCN Red List Categories and Criteria, we propose the new species to be listed as Data Deficient

Growth Rate and an Evaluation of Age Estimation for the Endangered Big-Headed Turtle ( Platysternon megacephalum

Understanding growth patterns is critical for determining age and size at sexual maturity and longevity in species that are severely threatened by over-collection and habitat loss, particularly in poorly understood species in tropical East Asia. Using data collected during a 9-year mark-recapture study, we fit the von Bertalanffy and logistic growth models to examine growth patterns of the endangered Big-headed Turtle (Platysternon megacephalum). Growth rate of P. megacephalum was best described by the von Bertalanffy model. Mean age at maturation for female and male P. megacephalum was 8 and 13 years. At maturity for female and male P. megacephalum, mean carapace length was 100 mm and 130 mm, respectively. We determined that counting growth rings on the carapace and plastron was not a reliable method for estimating ages. The long time to maturation in P. megacephalum may be costly in harvested populations, with individuals potentially being removed from populations prior to first reproduction. The growth patterns we have documented, and associated information on body size and age at sexual maturity, yield metrics that may be used to assess the effects of harvesting in populations and may contribute to conservation efforts for this endangered species

Growth rate and an evaluation of age estimation for the endangered big-headed turtle (platysternon megacephalum) in China

Understanding growth patterns is critical for determining age and size at sexual maturity and longevity in species that are severely threatened by over-collection and habitat loss, particularly in poorly understood species in tropical East Asia. Using data collected during a 9-year mark-recapture study, we fit the von Bertalanffy and logistic growth models to examine growth patterns of the endangered Big-headed Turtle (Platysternon megacephalum). Growth rate of P. megacephalum was best described by the von Bertalanffy model. Mean age at maturation for female and male P. megacephalum was 8 and 13 years. At maturity for female and male P. megacephalum, mean carapace length was 100 mm and 130 mm, respectively. We determined that counting growth rings on the carapace and plastron was not a reliable method for estimating ages. The long time to maturation in P. megacephalum may be costly in harvested populations, with individuals potentially being removed from populations prior to first reproduction. The growth patterns we have documented, and associated information on body size and age at sexual maturity, yield metrics that may be used to assess the effects of harvesting in populations and may contribute to conservation efforts for this endangered species

Branching fraction and CP asymmetries of B0→KS0KS0KS0

We present measurements of the branching fraction and time-dependent CP-violating asymmetries in B0→K0SK0SK0S decays based on 227×106 Υ(4S)→BB decays collected with the BABAR detector at the PEP-II asymmetric-energy B factory at SLAC. We obtain a branching fraction of (6.9+0.9−0.8±0.6)×10−6, and CP asymmetries C=−0.34+0.28−0.25±0.05 and S=−0.71+0.38−0.32±0.04, where the first uncertainties are statistical and the second systematic

Improved Measurement of the Cabibbo-Kobayashi-Maskawa Angle α Using B0(B¯)→ρ+ρ- Decays

We present results from an analysis of B0(B̅ 0)→ρ+ρ- using 232×106 Υ(4S)→BB̅ decays collected with the BABAR detector at the PEP-II asymmetric-energy B factory at SLAC. We measure the longitudinal polarization fraction fL=0.978±0.014(stat)+0.021/-0.029(syst) and the CP-violating parameters SL=-0.33±0.24(stat)+0.08/-0.14(syst) and CL=-0.03±0.18(stat)±0.09(syst). Using an isospin analysis of B→ρρ decays, we determine the unitarity triangle parameter α. The solution compatible with the standard model is α=(100±13)°

Improved measurement of the Cabibbo-Kobayashi-Maskawa angle α using B0(B)→p+p- decays

We present results from an analysis of B0(B¯¯¯0)→ρ+ρ− using 232×106 Υ(4S)→BB¯¯¯ decays collected with the BABAR detector at the PEP-II asymmetric-energy B factory at SLAC. We measure the longitudinal polarization fraction fL=0.978±0.014(stat)+0.021−0.029(syst) and the CP-violating parameters SL=−0.33±0.24(stat)+0.08−0.14(syst) and CL=−0.03±0.18(stat)±0.09(syst). Using an isospin analysis of B→ρρ decays, we determine the unitarity triangle parameter α. The solution compatible with the standard model is α=(100±13)°

Search for strange-pentaquark production in e+e− annihilation at √s=10.58 GeV

We search for strange pentaquark states that have been previously reported by other experiments -- the Θ(1540)+, Ξ5(1860)−−, and Ξ5(1860)0 -- in 123 fb−1 of data recorded with the BaBar detector at the PEP-II e+e− storage ring. We find no evidence for these states and set 95% confidence level upper limits on the number of Θ(1540)+ and Ξ5(1860)−− pentaquarks produced per e+e− annihilation event that are about eight and four times lower than the rates measured for ordinary baryons of similar mass

Measurements of branching fractions and time-dependent CP-violating asymmetries in B→η'K decays

We present measurements of the B -> eta' K branching fractions:for B+ -> eta' K+ we measure also the time-integrated charge asymmetry Ach, and for B0 -> eta' K0S the time dependent CP-violation parameters S and C. The data sample corresponds to 232 million B Bbar pairs produced by e+ e- annihilation at the Upsilon(4S). The results are BF(B+ -> eta' K+) = (68.9 +- 2.0 +- 3.2) * 10^-6, BF(B0 -> eta' K0) = (67.4 +- 3.3 +- 3.2) * 10^-6, Ach = 0.033 +- 0.028 +- 0.005, S=0.30 +- 0.14 +- 0.02, C=-0.21 +- 0.10 +- 0.02, where the first error is statistical and the second systematic