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

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

Multi-trait genome-wide association study identifies new loci associated with optic disc parameters

A new avenue of mining published genome-wide association studies includes the joint analysis of related traits. The power of this approach depends on the genetic correlation of traits, which reflects the number of pleiotropic loci, i.e. genetic loci influencing multiple traits. Here, we applied new meta-analyses of optic nerve head (ONH) related traits implicated in primary open-angle glaucoma (POAG); intraocular pressure and central corneal thickness using Haplotype reference consortium imputations. We performed a multi-trait analysis of ONH parameters cup area, disc area and vertical cup-disc ratio. We uncover new variants; rs11158547 in PPP1R36-PLEKHG3 and rs1028727 near SERPINE3 at genome-wide significance that replicate in independent Asian cohorts imputed to 1000 Genomes. At this point, validation of these variants in POAG cohorts is hampered by the high degree of heterogeneity. Our results show that multi-trait analysis is a valid approach to identify novel pleiotropic variants for ONH

On the improvements of the particle swarm optimization algorithm

Since a particle swarm optimization (PSO) algorithm uses a coordinated search to find the optimum solution, it has a better chance of finding the global solution. Despite this advantage, it is also observed that some parameters used in PSO may affect the solution significantly. Following this observation, this research tries to tune some of the parameters and to add mechanisms to the PSO algorithm in order to improve its robustness in finding the global solution. The main approaches include using uniform design to ensure uniform distribution of the initial particles in the design space, adding a mutation operation to increase the diversity of particles, decreasing the maximum velocity limitation and the velocity inertia automatically to balance the local and the global search efforts, reducing velocity when constraints are violated, and using Gaussian distribution based local searches to escape local minima. Besides these efforts, an algorithm is also developed to find multiple solutions in a single run. The results show that the overall effect of these approaches can yield better results for most test problems. (C) 2009 Elsevier Ltd. All rights reserved

Amplitude modulation as a source of low frequency facilitating the propagation of marmot (Mammalia, Rodentia) vocal signals in burrows

[No abstract available

Amplitude modulation as a source of low frequency facilitating the propagation of marmot (Mammalia, Rodentia) vocal signals in burrows

[No abstract available

Two Lily SEPALLATA-Like Genes Cause Different Effects on Floral Formation and Floral Transition in Arabidopsis

Two AGL2-like MADS-box genes, Lily MADS Box Gene (LMADS) 3 and LMADS4, with extensive homology of LMADS3 to the Arabidopsis SEPALLATA3 were characterized from the lily (Lilium longiflorum). Both LMADS3 and LMADS4 mRNA were detected in the inflorescence meristem, in floral buds of different developmental stages, and in all four whorls of the flower organ. LMADS4 mRNA is also expressed in vegetative leaf and in the inflorescence stem where LMADS3 expression is absent. Transgenic Arabidopsis, which ectopically expresses LMADS3, showed novel phenotypes by significantly reducing plant size, flowering extremely early, and loss of floral determinacy. By contrast, 35S::LMADS4 transgenic plants were morphologically indistinguishable from wild-type plants. The early-flowering phenotype in 35S::LMADS3 transgenic Arabidopsis plants was correlated with the up-regulation of flowering time genes FT, SUPPRESSOR OF OVEREXPRESSION OF CO 1, LUMINIDEPENDENS, and flower meristem identity genes LEAFY and APETALA1. This result was further supported by the ability of 35S::LMADS3 to rescue the late-flowering phenotype in gigantea-1 (gi-1), constans-3 (co-3), and luminidependens-1 but not for ft-1 or fwa-1 mutants. The activation of these flowering time genes is, however, indirect because their expression was unaffected in plants transformed with LMADS3 fused with rat glucocorticoid receptor in the presence of both dexamethasone and cycloheximide

Skeletal modification in response to flow during growth in colonies of the sea whip, Junceella fragilis

Sessile marine organisms depend on water motion for important physiological functions yet face dislodgement or breakage caused by hydrodynamic forces. During growth, these organisms are subjected to increasing bending moments as height increases and they may modify their mechanical supports accordingly. Here we used the sea whip Junceellafragilis as a model species to examine how sessile organisms modify their skeletal supports to cope with hydrodynamic forces during growth. Eighty-one colonies of J fragilis (height 5-156 cm) were collected from two populations in southern Taiwan. Within-colony variations in skeletal elements, namely the axial skeleton and sclerites, as well as the coenenchyme and water content were investigated by measurements taken from the base, middle, and top of colonies. The typological distribution of sclerites within colonies was examined in another 31 colonies. The results showed that the relative weight of axial skeleton increases while that of sclerites decreases with colony height, which suggests that the colony switches from using sclerites to axial skeleton as the main support system during growth. The axial skeleton at the colony base thickens in such a way as to maintain or slightly decrease its bending stress. A greater density of sclerites, mostly double-heads, found at the colony base also adds to the resistance to bending. Moreover, colonies living in environments with greater flows seem to incorporate more skeletal materials. This study demonstrates how sessile marine or2anisnis cope with increasing hydrodynamic forces during their life history by modifying the constitution and construction of their skeleton elements. (c) 2007 Elsevier B.V All rights reserved

Silicon-based solar cell fabricated by metal-induced lateral crystallization of amorphous silicon film

Silicon-based polycrystalline solar cells are first fabricated by metal-induced lateral crystallization in which n-type polycrystalline-silicon (poly-Si) films, processed using nickel-induced amorphous silicon, are grown on p-silicon substrate at 550 degrees C by furnace annealing. The fabricated n-type poly-Si/p-substrate solar cell exhibits a conversion efficiency of 10.4% and an open-circuit voltage of 0.54V without any passivation or antireflection coating layers