Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation.

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Implementation and Evaluation of a Wiki Involving Multiple Stakeholders Including Patients in the Promotion of Best Practices in Trauma Care: The WikiTrauma Interrupted Time Series Protocol

Contains fulltext : 152344.pdf (publisher's version ) (Open Access)BACKGROUND: Trauma is the most common cause of mortality among people between the ages of 1 and 45 years, costing Canadians 19.8 billion dollars a year (2004 data), yet half of all patients with major traumatic injuries do not receive evidence-based care, and significant regional variation in the quality of care across Canada exists. Accordingly, our goal is to lead a research project in which stakeholders themselves will adapt evidence-based trauma care knowledge tools to their own varied institutional contexts and cultures. We will do this by developing and assessing the combined impact of WikiTrauma, a free collaborative database of clinical decision support tools, and Wiki101, a training course teaching participants how to use WikiTrauma. WikiTrauma has the potential to ensure that all stakeholders (eg, patients, clinicians, and decision makers) can all contribute to, and benefit from, evidence-based clinical knowledge about trauma care that is tailored to their own needs and clinical setting. OBJECTIVE: Our main objective will be to study the combined effect of WikiTrauma and Wiki101 on the quality of care in four trauma centers in Quebec. METHODS: First, we will pilot-test the wiki with potential users to create a version ready to test in practice. A rapid, iterative prototyping process with 15 health professionals from nonparticipating centers will allow us to identify and resolve usability issues prior to finalizing the definitive version for the interrupted time series. Second, we will conduct an interrupted time series to measure the impact of our combined intervention on the quality of care in four trauma centers that will be selected-one level I, one level II, and two level III centers. Participants will be health care professionals working in the selected trauma centers. Also, five patient representatives will be recruited to participate in the creation of knowledge tools destined for their use (eg, handouts). All participants will be invited to complete the Wiki101 training and then use, and contribute to, WikiTrauma for 12 months. The primary outcome will be the change over time of a validated, composite, performance indicator score based on 15 process performance indicators found in the Quebec Trauma Registry. RESULTS: This project was funded in November 2014 by the Canadian Medical Protective Association. We expect to start this trial in early 2015 and preliminary results should be available in June 2016. Two trauma centers have already agreed to participate and two more will be recruited in the next months. CONCLUSIONS: We expect that this study will add important and unique evidence about the effectiveness, safety, and cost savings of using collaborative platforms to adapt knowledge implementation tools across jurisdictions

Ground-based near-UV observations of 15 transiting exoplanets: constraints on their atmospheres and no evidence for asymmetrical transits

Transits of exoplanets observed in the near-UV have been used to study the scattering properties of their atmospheres and possible star-planet interactions. We observed the primary transits of 15 exoplanets (CoRoT-1b, GJ436b, HAT-P-1b, HAT-P-13b, HAT-P-16b, HAT-P-22b, TrES-2b, TrES-4b, WASP-1b, WASP-12b, WASP-33b, WASP-36b, WASP-44b, WASP-48b, and WASP-77Ab) in the near-UV and several optical photometric bands to update their planetary parameters, ephemerides, search for a wavelength dependence in their transit depths to constrain their atmospheres, and determine if asymmetries are visible in their light curves. Here, we present the first ground-based near-UV light curves for 12 of the targets (CoRoT-1b, GJ436b, HAT-P-1b, HAT-P-13b, HAT-P-22b, TrES-2b, TrES-4b, WASP-1b, WASP-33b, WASP-36b, WASP-48b, and WASP-77Ab). We find that none of the near-UV transits exhibit any non-spherical asymmetries, this result is consistent with recent theoretical predictions by Ben-Jaffel et al. and Turner et al. The multiwavelength photometry indicates a constant transit depth from near-UV to optical wavelengths in 10 targets (suggestive of clouds), and a varying transit depth with wavelength in 5 targets (hinting at Rayleigh or aerosol scattering in their atmospheres). We also present the first detection of a smaller near-UV transit depth than that measured in the optical in WASP-1b and a possible opacity source that can cause such radius variations is currently unknown. WASP-36b also exhibits a smaller near-UV transit depth at 2.6 sigma. Further observations are encouraged to confirm the transit depth variations seen in this study.NASA's Planetary Atmospheres programme; Virginia Space Grant Consortium Graduate Research Fellowship Program; National Science Foundation [DGE-1315231]; University of Arizona Astronomy Club; Steward Observatory TAC; Lunar and Planetary LaboratoryThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Preserving accuracy in GenBank

GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors, common annotation errors also reduce the value of this database. In fact, for organisms such as fungi, which are notoriously difficult to identify, up to 20% of DNA sequence records may have erroneous lineage designations in GenBank. Gene function annotation in protein sequence databases is similarly error-prone. Because identity and function of new sequences are often determined by bioinformatic analyses, both types of errors are propagated into new accessions, leading to long-term degradation of the quality of the database. Currently, primary sequence data are annotated by the authors of those data, and can only be reannotated by the same authors. This is inefficient and unsustainable over the long term as authors eventually leave the field. Although it is possible to link third-party databases to GenBank records, this is a short-term solution that has little guarantee of permanence. Similarly, the current third-party annotation option in GenBank (TPA) complicates rather than solves the problem by creating an identical record with a new annotation, while leaving the original record unflagged and unlinked to the new record. Since the origin of public zoological and botanical specimen collections, an open system of cumulative annotation has evolved, whereby the original name is retained, but additional opinion is directly appended and used for filing and retrieval. This was needed as new specimens and analyses allowed for reevaluation of older specimens and the original depositors became unavailable. The time has come for the public sequence database to incorporate a community-curated, cumulative annotation process that allows third parties to improve the annotations of sequences when warranted by published peer-reviewed analyses.Fil: Bidartondo, Martin I.. Imperial College London; Reino Unido. Royal Botanic Gardens; Reino UnidoFil: Bruns, Thomas D.. University of California at Berkeley; Estados UnidosFil: Blackwell, Meredith. Louisiana State University; Estados UnidosFil: Edwards, Ivan. University of Michigan; Estados UnidosFil: Taylor, Andy F. S.. Swedish University of Agricultural Sciences; SueciaFil: Bianchinotti, Maria Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur; ArgentinaFil: Padamsee, Mahajabeen. University of Minnesota; Estados UnidosFil: Callac, Philippe. Institut National de la Recherche Agronomique; FranciaFil: Lima, Nelson. Universidade do Minho; PortugalFil: White, Merlin M.. Boise State University; Estados UnidosFil: Barreau Daly, Camila. Centre National de la Recherche Scientifique; Francia. Institut National de la Recherche Agronomique; FranciaFil: Juncai, M. A.. Chinese Academy of Sciences; República de ChinaFil: Buyck, Bart. Museum National d'Histoire Naturelle; FranciaFil: Rabeler, Richard K.. University of Michigan; Estados UnidosFil: Liles, Mark R.. Auburn University; Estados UnidosFil: Estes, Dwayne. Austin Peay State University; Estados UnidosFil: Carter, Richard. Valdosta State University; Estados UnidosFil: Herr Jr., J. M.. University of South Carolina; Estados UnidosFil: Chandler, Gregory. University of North Carolina; Estados UnidosFil: Kerekes, Jennifer. University of California at Berkeley; Estados UnidosFil: Cruse Sanders, Jennifer. Salem College Herbarium; Estados UnidosFil: Galán Marquez, R.. Universidad de Alcalá; EspañaFil: Horak, Egon. Zurich Herbarium; SuizaFil: Fitzsimons, Michael. University of Chicago; Estados UnidosFil: Döering, Heidi. Royal Botanic Gardens; Reino UnidoFil: Yao, Su. China Center of Industrial Culture Collection; ChinaFil: Hynson, Nicole. University of California at Berkeley; Estados UnidosFil: Ryberg, Martin. University Goteborg; SueciaFil: Arnold, A. E.. University of Arizona; Estados UnidosFil: Hughes, Karen. University of Tennessee; Estados Unido