PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction

There is an increasing interest in using literature mining techniques to complement information extracted from annotation databases or generated by bioinformatics applications. Here we present PLAN2L, a web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. Our system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. PLAN2L does not require registration and is freely accessible at http://zope.bioinfo.cnio.es/plan2l

A two-stage approach for the spatio-temporal analysis of high-throughput phenotyping data

High throughput phenotyping (HTP) platforms and devices are increasingly used for the characterization of growth and developmental processes for large sets of plant genotypes. Such HTP data require challenging statistical analyses in which longitudinal genetic signals need to be estimated against a background of spatio-temporal noise processes. We propose a two-stage approach for the analysis of such longitudinal HTP data. In a first stage, we correct for design features and spatial trends per time point. In a second stage, we focus on the longitudinal modelling of the spatially corrected data, thereby taking advantage of shared longitudinal features between genotypes and plants within genotypes. We propose a flexible hierarchical three-level P-spline growth curve model, with plants/plots nested in genotypes, and genotypes nested in populations. For selection of genotypes in a plant breeding context, we show how to extract new phenotypes, like growth rates, from the estimated genotypic growth curves and their first-order derivatives. We illustrate our approach on HTP data from the PhenoArch greenhouse platform at INRAE Montpellier and the outdoor Field Phenotyping platform at ETH Zürich.Ministerio de Ciencia, Innovación y Universidades | Ref. BCAM Severo Ochoa accreditation SEV-2017-0718Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung | Ref. project PhenoCOOL (project no. 169542)Horizon 2020 Framework Programme | Ref. grant agreement ID 731013 (EPPN2020)Ministerio de Ciencia, Innovación y Universidades | Ref. MTM2017-82379-

Slow oscillatory activity and levodopa-induced dyskinesias in Parkinson’s disease

The pathophysiology of levodopa-induced dyskinesias (LID) in Parkinson’s disease is not well understood. We have recorded local field potentials (LFP) from macroelectrodes implanted in the subthalamic nucleus (STN) of 14 patients with Parkinson’s disease following surgical treatment with deep brain stimulation. Patients were studied in the ‘Off’ medication state and in the ‘On’ motor state after administration of levodopa– carbidopa (po) or apomorphine (sc) that elicited dyskinesias in 11 patients. The logarithm of the power spectrum of the LFP in selected frequency bands (4–10, 11–30 and 60–80 Hz) was compared between the ‘Off’ and ‘On’ medication states. A peak in the 11–30 Hz band was recorded in the ‘Off’ medication state and reduced by 45.2% (P < 0.001) in the ‘On’ state. The ‘On’ was also associated with an increment of 77. 6% (P < 0.001) in the 4–10 Hz band in all patients who showed dyskinesias and of 17.8% (P < 0.001) in the 60–80 Hz band in the majority of patients. When dyskinesias were only present in one limb (n = 2), the 4–10 Hz peak was only recorded in the contralateralSTN. These findings suggest that the 4–10 Hz oscillation is associated with the expression of LID in Parkinson’s disease

Cost-effectiveness of introducing a rotavirus vaccine in developing countries: The case of Mexico

<p>Abstract</p> <p>Background</p> <p>In developing countries rotavirus is the leading cause of severe diarrhoea and diarrhoeal deaths in children under 5. Vaccination could greatly alleviate that burden, but in Mexico as in most low- and middle-income countries the decision to add rotavirus vaccine to the national immunisation program will depend heavily on its cost-effectiveness and affordability. The objective of this study was to assess the cost-effectiveness of including the pentavalent rotavirus vaccine in Mexico's national immunisation program.</p> <p>Methods</p> <p>A cost-effectiveness model was developed from the perspective of the health system, modelling the vaccination of a hypothetical birth cohort of 2 million children monitored from birth through 60 months of age. It compares the cost and disease burden of rotavirus in an unvaccinated cohort of children with one vaccinated as recommended at 2, 4, and 6 months.</p> <p>Results</p> <p>Including the pentavalent vaccine in the national immunisation program could prevent 71,464 medical visits (59%), 5,040 hospital admissions (66%), and 612 deaths from rotavirus gastroenteritis (70%). At US$10 per dose and a cost of administration of US$13.70 per 3-dose regimen, vaccination would cost US$122,058 per death prevented, US$4,383 per discounted life-year saved, at a total net cost of US$74.7 million dollars to the health care system. Key variables influencing the results were, in order of importance, case fatality, vaccine price, vaccine efficacy, serotype prevalence, and annual loss of efficacy. The results are also very sensitive to the discount rate assumed when calculated per life-year saved.</p> <p>Conclusion</p> <p>At prices below US$15 per dose, the cost per life-year saved is estimated to be lower than one GNP per capita and hence highly cost effective by the WHO Commission on Macroeconomics and Health criteria. The cost-effectiveness estimates are highly dependent upon the mortality in the absence of the vaccine, which suggests that the vaccine is likely to be significantly more cost-effective among poorer populations and among those with less access to prompt medical care – such that poverty reduction programs would be expected to reduce the future cost-effectiveness of the vaccine.</p

Amphibianâ killing chytrid in Brazil comprises both locally endemic and globally expanding populations

Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is the emerging infectious disease implicated in recent population declines and extinctions of amphibian species worldwide. Bd strains from regions of diseaseâ associated amphibian decline to date have all belonged to a single, hypervirulent clonal genotype (Bdâ GPL). However, earlier studies in the Atlantic Forest of southeastern Brazil detected a novel, putatively enzootic lineage (Bdâ Brazil), and indicated hybridization between Bdâ GPL and Bdâ Brazil. Here, we characterize the spatial distribution and population history of these sympatric lineages in the Brazilian Atlantic Forest. To investigate the genetic structure of Bd in this region, we collected and genotyped Bd strains along a 2400â km transect of the Atlantic Forest. Bdâ Brazil genotypes were restricted to a narrow geographic range in the southern Atlantic Forest, while Bdâ GPL strains were widespread and largely geographically unstructured. Bd population genetics in this region support the hypothesis that the recently discovered Brazilian lineage is enzootic in the Atlantic Forest of Brazil and that Bdâ GPL is a more recently expanded invasive. We collected additional hybrid isolates that demonstrate the recurrence of hybridization between panzootic and enzootic lineages, thereby confirming the existence of a hybrid zone in the Serra da Graciosa mountain range of Paraná State. Our field observations suggest that Bdâ GPL may be more infective towards native Brazilian amphibians, and potentially more effective at dispersing across a fragmented landscape. We also provide further evidence of pathogen translocations mediated by the Brazilian ranaculture industry with implications for regulations and policies on global amphibian trade.See also the Perspective by Ghosh and FisherPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/122445/1/mec13599.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/122445/2/mec13599_am.pd

Measurement of total and differential cross sections of neutrino and antineutrino coherent pi(+/-) production on carbon

Neutrino induced coherent charged pion production on nuclei, (nu) over bar (mu)A -\u3e mu(+/-)pi(-/+) A, is a rare inelastic interaction in which the four-momentum squared transferred to the nucleus is nearly zero, leaving it intact. We identify such events in the scintillator of MINERvA by reconstructing vertical bar t vertical bar from the final state pion and muon momenta and by removing events with evidence of energetic nuclear recoil or production of other final state particles. We measure the total neutrino and antineutrino cross sections as a function of neutrino energy between 2 and 20 GeV and measure flux integrated differential cross sections as a function of Q(2), E-pi, and theta(pi). The Q(2) dependence and equality of the neutrino and antineutrino cross sections at finite Q(2) provide a confirmation of Adler\u27s partial conservation of axial current hypothesis

Measurements of the inclusive neutrino and antineutrino charged current cross sections in MINERvA using the low-nu flux method

The total cross sections are important ingredients for the current and future neutrino oscillation experiments. We present measurements of the total charged-current neutrino and antineutrino cross sections on scintillator (CH) in the NuMI low-energy beamline using an in situ prediction of the shape of the flux as a function of neutrino energy from 2-50 GeV. This flux prediction takes advantage of the fact that neutrino and antineutrino interactions with low nuclear recoil energy (nu) have a nearly constant cross section as a function of incident neutrino energy. This measurement is the lowest energy application of the low-nu flux technique, the first time it has been used in the NuMI antineutrino beam configuration, and demonstrates that the technique is applicable to future neutrino beams operating at multi-GeVenergies. The cross section measurements presented are the most precise measurements to date below 5 GeV