WormBase 2012: more genomes, more data, new website

Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community

Crecimiento y productividad de 12 hibridos de maíz de precocidad intermedia en la VII Región de Chile

Resumen (Spanish, English)72 p.Se analizó el crecimiento, producción de biomasa al estado de ensilaje y el rendimiento de grano de 12 híbridos de maíz en la VII Región, para determinar la capacidad productiva de este cultivo en la zona Centro-sur de Chile. La investigación se realizó en la Estación Experimental de la Universidad de Talca (35 25’LS; 71 41’LW; 90 m.s.n.m.) durante la temporada 1992-93. La producción de biomasa resultó muy estable, debido a la similitud de precocidades del material genético. Se evaluó el número de granos por planta a través del tiempo en 4 de los 12 genotipos, formulándose un modelo de regresión de la forma Y=aXb, que describe la evolución de este componente entre floración y cosecha. Se validó este modelo simple con resultados obtenidos en otros experimentos, resultando un adecuado predictor, cuando el cultivo crece bajo apropiadas condiciones de manejo. Al compararlo con un cultivo sometido a grados crecientes de competencia por luz o déficit de nitrógeno, las predicciones son menos ajustadas a medida que se intensifica la competencia. Se formuló un modelo térmico siguiendo la metodología descrita por Fuenzalida (1988), para predecir la producción de maíz en la VII Región, comparándose los resultados de producción de MS con los valores estimados a partir del modelo simple formulado por Correa (1990) en la IX Región de Chile, resultando muy similares, pese a las diferencias climáticas que presentan ambas localidades; además se validó con valores de experimentos efectuados entre los años 1992 y 1994 en la misma estación experimental. Finalmente, se evaluó el contenido de humedad del grano en 4 de los 12 híbridos entre grano lechoso y cosecha; éste disminuyó rápidamente a partir de un 55% de humedad, lo cual es muy dependiente de la acumulación térmica y se describe como una función de tipo lineal

Towards an International Consensus on the Prevention, Treatment, and Management of High-Risk Substance Use and Overdose among Youth

Background and Objectives: Now more than ever, there is an obvious need to reduce the overall burden of disease and risk of premature mortality that are associated with mental health and substance use disorders among young people. However, the current state of research and evidence-based clinical care for high-risk substance use among youth is fragmented and scarce. The objective of the study is to establish consensus for the prevention, treatment, and management of high-risk substance use and overdose among youth (10 to 24 years old). Materials and Methods: A modified Delphi technique was used based on the combination of scientific evidence and clinical experience of a group of 31 experts representing 10 countries. A semi-structured questionnaire with five domains (clinical risks, target populations, intervention goals, intervention strategies, and settings/expertise) was shared with the panelists. Based on their responses, statements were developed, which were subsequently revised and finalized through three iterations of feedback. Results: Among the five major domains, 60 statements reached consensus. Importantly, experts agreed that screening in primary care and other clinical settings is recommended for all youth, and that the objectives of treating youth with high-risk substance use are to reduce harm and mortality while promoting resilience and healthy development. For all substance use disorders, evidence-based interventions should be available and should be used according to the needs and preferences of the patient. Involuntary admission was the only topic that did not reach consensus, mainly due to its ethical implications and resulting lack of comparable evidence. Conclusions: High-risk substance use and overdoses among youth have become a major challenge. The system’s response has been insufficient and needs substantial change. Internationally devised consensus statements provide a first step in system improvement and reform

WormBase 2016: expanding to enable helminth genomic research

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Measurement of the cosmic ray spectrum above 4×10184{\times}10^{18} eV using inclined events detected with the Pierre Auger Observatory

A measurement of the cosmic-ray spectrum for energies exceeding $4{\times}10^{18}$ eV is presented, which is based on the analysis of showers with zenith angles greater than $60^{\circ}$ detected with the Pierre Auger Observatory between 1 January 2004 and 31 December 2013. The measured spectrum confirms a flux suppression at the highest energies. Above $5.3{\times}10^{18}$ eV, the "ankle", the flux can be described by a power law $E^{-\gamma}$ with index $\gamma=2.70 \pm 0.02 \,\text{(stat)} \pm 0.1\,\text{(sys)}$ followed by a smooth suppression region. For the energy ($E_\text{s}$) at which the spectral flux has fallen to one-half of its extrapolated value in the absence of suppression, we find $E_\text{s}=(5.12\pm0.25\,\text{(stat)}^{+1.0}_{-1.2}\,\text{(sys)}){\times}10^{19}$ eV.Comment: Replaced with published version. Added journal reference and DO

A deep seismic investigation of the Flemish Cap margin: implications for the origin of deep reflectivity and evidence for asymmetric break-up between Newfoundland and Iberia

Author Posting. © Blacwell, 2006. This article is posted here by permission of Blackwell for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 164 (2006): 501–515, doi:10.1111/j.1365-246X.2006.02800.x.Seismic reflection and refraction data were acquired along the southeast margin of Flemish Cap at a position conjugate to drilling and geophysical surveys across the Galicia Bank margin. The data document first-order asymmetry during final break-up between Newfoundland and Iberia. An abrupt necking profile of continental crust observed off Flemish Cap contrasts strongly with gradual tapering on the conjugate margin. There is no evidence beneath Flemish Cap for a final phase of continental extension that resulted in thin continental crust underlain by a strong 'S'-like reflection, which indicates that this mode of extension occurred only on the Galicia Bank margin. Compelling evidence for a broad zone of exhumed mantle or for peridotite ridges is also lacking along the Flemish Cap margin. Instead, anomalously thin, 3–4-km-thick oceanic crust is observed. This crust is highly tectonized and broken up by high-angle normal faulting. The thin crust and rift structures that resemble the abandoned spreading centre in the Labrador sea suggest that initial seafloor spreading was affected by processes observed in present-day ultra-slow spreading environments. Landwards, Flemish Cap is underlain by a highly reflective lower crust. The reflectivity most likely originates from older Palaeozoic orogenic structures that are unrelated to extension and break-up tectonics.This work was supported by the Danish National Research Foundation, U.S. National Science Foundation grants OCE-9819053 and OCE-0326714, and the Natural Science and Engineering Research Council of Canada. Additional support for Hopper was provided by the German Research Foundation grant MO-961/4-1. Tucholke also acknowledges support from Henry Bryant Bigelow Chair in Oceanography at Woods Hole Oceanographic Institution

Energy Estimation of Cosmic Rays with the Engineering Radio Array of the Pierre Auger Observatory

The Auger Engineering Radio Array (AERA) is part of the Pierre Auger Observatory and is used to detect the radio emission of cosmic-ray air showers. These observations are compared to the data of the surface detector stations of the Observatory, which provide well-calibrated information on the cosmic-ray energies and arrival directions. The response of the radio stations in the 30 to 80 MHz regime has been thoroughly calibrated to enable the reconstruction of the incoming electric field. For the latter, the energy deposit per area is determined from the radio pulses at each observer position and is interpolated using a two-dimensional function that takes into account signal asymmetries due to interference between the geomagnetic and charge-excess emission components. The spatial integral over the signal distribution gives a direct measurement of the energy transferred from the primary cosmic ray into radio emission in the AERA frequency range. We measure 15.8 MeV of radiation energy for a 1 EeV air shower arriving perpendicularly to the geomagnetic field. This radiation energy -- corrected for geometrical effects -- is used as a cosmic-ray energy estimator. Performing an absolute energy calibration against the surface-detector information, we observe that this radio-energy estimator scales quadratically with the cosmic-ray energy as expected for coherent emission. We find an energy resolution of the radio reconstruction of 22% for the data set and 17% for a high-quality subset containing only events with at least five radio stations with signal.Comment: Replaced with published version. Added journal reference and DO

Measurement of the Radiation Energy in the Radio Signal of Extensive Air Showers as a Universal Estimator of Cosmic-Ray Energy

We measure the energy emitted by extensive air showers in the form of radio emission in the frequency range from 30 to 80 MHz. Exploiting the accurate energy scale of the Pierre Auger Observatory, we obtain a radiation energy of 15.8 \pm 0.7 (stat) \pm 6.7 (sys) MeV for cosmic rays with an energy of 1 EeV arriving perpendicularly to a geomagnetic field of 0.24 G, scaling quadratically with the cosmic-ray energy. A comparison with predictions from state-of-the-art first-principle calculations shows agreement with our measurement. The radiation energy provides direct access to the calorimetric energy in the electromagnetic cascade of extensive air showers. Comparison with our result thus allows the direct calibration of any cosmic-ray radio detector against the well-established energy scale of the Pierre Auger Observatory.Comment: Replaced with published version. Added journal reference and DOI. Supplemental material in the ancillary file