Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

<p>Abstract</p> <p>Background</p> <p>For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.</p> <p>Results</p> <p>We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.</p> <p>Conclusions</p> <p>By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.</p

The Effects of Winter Pulsed Warming and Snowmelt on Nitrogen Cycling in Agricultural Soils: A Lysimeter Study

In cold regions, climate change is expected to result in warmer winter temperatures and increased temperature variability. Coupled with changing precipitation regimes, these changes can decrease soil insulation by reducing snow cover, exposing soils to colder temperatures and more frequent and extensive soil freezing and thawing. Freeze-thaw events can exert an important control over winter soil processes and the cycling of nitrogen (N), with consequences for soil health, nitrous oxide (N2O) emissions, and nearby water quality. These impacts are especially important for agricultural soils and practices in cold regions. We conducted a lysimeter experiment to assess the effects of winter pulsed warming, soil texture, and snow cover on N cycling in agricultural soils. We monitored the subsurface soil temperature, moisture, and porewater geochemistry together with air temperature, precipitation, and N2O fluxes in four agricultural field-controlled lysimeter systems (surface area of 1 m2 and depth of 1.5 m) at the University of Guelph’s Elora Research Station over one winter (December 2020 to April 2021). The lysimeters featured two soil types (loamy sand and silt loam) which were managed under a corn-soybean-wheat rotation with cover crops. Additionally, ceramic infrared heaters located above two of the lysimeters were turned on after each snowfall event to melt the snow and then turned off to mimic snow-free winter conditions with increased soil freezing. Porewater samples collected from five depths in the lysimeters were analyzed for total dissolved nitrogen (TDN), nitrate (NO3-), nitrite (NO2-), and ammonium (NH4+). N2O fluxes were measured using automated soil gas chambers installed on each lysimeter. The results from the snow removed lysimeters were compared to those of lysimeters without heaters (with snow). As expected, the removal of the insulating snow cover resulted in more intense soil freeze-thaw events, causing increased dissolved N loss from the lysimeter systems as N2O (from the silt loam system) and via NO3- leaching (from the loamy sand system). In the silt loam lysimeter, we attribute the freeze thaw-enhanced N2O fluxes to de novo processes rather than gas build up and release. In the loamy sand lysimeter, we attribute the increased NO3- leaching to the larger pore size and therefore lower water retention capacity of this soil type. Overall, our study illustrates the important role of winter snow cover dynamics and soil freezing in modulating the coupled responses of soil moisture, temperature, and N cycling

LASSO: Large Adaptive optics Survey for Substellar Objects using the new SAPHIRA detector on Robo-AO

We report on initial results from the largest infrared AO direct imaging survey searching for wide orbit (>100 AU) massive exoplanets and brown dwarfs as companions around young nearby stars using Robo-AO at the 2.1-m telescope on Kitt Peak, Arizona. The occurrence rates of these rare substellar companions are critical to furthering our understanding of the origin of planetary-mass companions on wide orbits. The observing efficiency of Robo-AO allows us to conduct a survey an order of magnitude larger than previously possible. We commissioned a low-noise high-speed SAPHIRA near-infrared camera to conduct this survey and report on its sensitivity, performance, and data reduction process.Comment: 10 pages, 7 figures, SPIE conference proceeding

Protocol: Barriers and facilitators to stakeholder engagement in health guideline development: a qualitative evidence synthesis

Background There is a need for the development of comprehensive, global, evidence-based guidance for stakeholder engagement in guideline development. Stakeholders are any individual or group who is responsible for or affected by health- and healthcare-related decisions. This includes patients, the public, providers of health care and policymakers for example. As part of the guidance development process, Multi-Stakeholder Engagement (MuSE) Consortium set out to conduct four concurrent systematic reviews to summarise the evidence on: (1) existing guidance for stakeholder engagement in guideline development, (2) barriers and facilitators to stakeholder engagement in guideline development, (3) managing conflicts of interest in stakeholder engagement in guideline development and (4) measuring the impact of stakeholder engagement in guideline development. This protocol addresses the second systematic review in the series. Objectives The objective of this review is to identify and synthesise the existing evidence on barriers and facilitators to stakeholder engagement in health guideline development. We will address this objective through two research questions: (1) What are the barriers to multi-stakeholder engagement in health guideline development across any of the 18 steps of the GIN-McMaster checklist? (2) What are the facilitators to multi-stakeholder engagement in health guideline development across any of the 18 steps of the GIN-McMaster checklist? Search Methods A comprehensive search strategy will be developed and peer-reviewed in consultation with a medical librarian. We will search the following databases: MEDLINE, Cumulative Index to Nursing & Allied Health Literature (CINAHL), EMBASE, PsycInfo, Scopus, and Sociological Abstracts. To identify grey literature, we will search the websites of agencies who actively engage stakeholder groups such as the AHRQ, Canadian Institutes of Health Research (CIHR) Strategy for Patient-Oriented Research (SPOR), INVOLVE, the National Institute for Health and Care Excellence (NICE) and the PCORI. We will also search the websites of guideline-producing agencies, such as the American Academy of Pediatrics, Australia's National Health Medical Research Council (NHMRC) and the WHO. We will invite members of the team to suggest grey literature sources and we plan to broaden the search by soliciting suggestions via social media, such as Twitter. Selection Criteria We will include empirical qualitative and mixed-method primary research studies which qualitatively report on the barriers or facilitators to stakeholder engagement in health guideline development. The population of interest is stakeholders in health guideline development. Building on previous work, we have identified 13 types of stakeholders whose input can enhance the relevance and uptake of guidelines: Patients, caregivers and patient advocates; Public; Providers of health care; Payers of health services; Payers of research; Policy makers; Program managers; Product makers; Purchasers; Principal investigators and their research teams; and Peer-review editors/publishers. Eligible studies must describe stakeholder engagement at any of the following steps of the GIN-McMaster Checklist for Guideline Development. Data Collection and Analysis All identified citations from electronic databases will be imported into Covidence software for screening and selection. Documents identified through our grey literature search will be managed and screened using an Excel spreadsheet. A two-part study selection process will be used for all identified citations: (1) a title and abstract review and (2) full-text review. At each stage, teams of two review authors will independently assess all potential studies in duplicate using a priori inclusion and exclusion criteria. Data will be extracted by two review authors independently and in duplicate according to a standardised data extraction form. Main Results The results of this review will be used to inform the development of guidance for multi-stakeholder engagement in guideline development and implementation. This guidance will be official GRADE (Grading of Recommendations Assessment, Development and Evaluation) Working Group guidance. The GRADE system is internationally recognised as a standard for guideline development. The findings of this review will assist organisations who develop healthcare, public health and health policy guidelines, such as the World Health Organization, to involve multiple stakeholders in the guideline development process to ensure the development of relevant, high quality and transparent guidelines

Protocol for the development of guidance for stakeholder engagement in health and healthcare guideline development and implementation

Stakeholder engagement has become widely accepted as a necessary component of guideline development and implementation. While frameworks for developing guidelines express the need for those potentially affected by guideline recommendations to be involved in their development, there is a lack of consensus on how this should be done in practice. Further, there is a lack of guidance on how to equitably and meaningfully engage multiple stakeholders. We aim to develop guidance for the meaningful and equitable engagement of multiple stakeholders in guideline development and implementation. METHODS: This will be a multi-stage project. The first stage is to conduct a series of four systematic reviews. These will (1) describe existing guidance and methods for stakeholder engagement in guideline development and implementation, (2) characterize barriers and facilitators to stakeholder engagement in guideline development and implementation, (3) explore the impact of stakeholder engagement on guideline development and implementation, and (4) identify issues related to conflicts of interest when engaging multiple stakeholders in guideline development and implementation. DISCUSSION: We will collaborate with our multiple and diverse stakeholders to develop guidance for multi-stakeholder engagement in guideline development and implementation. We will use the results of the systematic reviews to develop a candidate list of draft guidance recommendations and will seek broad feedback on the draft guidance via an online survey of guideline developers and external stakeholders. An invited group of representatives from all stakeholder groups will discuss the results of the survey at a consensus meeting which will inform the development of the final guidance papers. Our overall goal is to improve the development of guidelines through meaningful and equitable multi-stakeholder engagement, and subsequently to improve health outcomes and reduce inequities in health

Planet Hunters. VIII. Characterization of 41 Long-Period Exoplanet Candidates from Kepler Archival Data

The census of exoplanets is incomplete for orbital distances larger than 1 AU. Here, we present 41 long-period planet candidates in 38 systems identified by Planet Hunters based on Kepler archival data (Q0-Q17). Among them, 17 exhibit only one transit, 14 have two visible transits and 10 have more than three visible transits. For planet candidates with only one visible transit, we estimate their orbital periods based on transit duration and host star properties. The majority of the planet candidates in this work (75%) have orbital periods that correspond to distances of 1-3 AU from their host stars. We conduct follow-up imaging and spectroscopic observations to validate and characterize planet host stars. In total, we obtain adaptive optics images for 33 stars to search for possible blending sources. Six stars have stellar companions within 4". We obtain high-resolution spectra for 6 stars to determine their physical properties. Stellar properties for other stars are obtained from the NASA Exoplanet Archive and the Kepler Stellar Catalog by Huber et al. (2014). We validate 7 planet candidates that have planet confidence over 0.997 (3-{\sigma} level). These validated planets include 3 single-transit planets (KIC-3558849b, KIC-5951458b, and KIC-8540376c), 3 planets with double transits (KIC-8540376b, KIC-9663113b, and KIC-10525077b), and 1 planet with 4 transits (KIC-5437945b). This work provides assessment regarding the existence of planets at wide separations and the associated false positive rate for transiting observation (17%-33%). More than half of the long-period planets with at least three transits in this paper exhibit transit timing variations up to 41 hours, which suggest additional components that dynamically interact with the transiting planet candidates. The nature of these components can be determined by follow-up radial velocity and transit observations.Comment: Published on ApJ, 815, 127 Notations of validated planets are changed in accordance with naming convention of NASA Exoplanet Archiv

LASSO: Large Adaptive optics Survey for Substellar Objects using the new SAPHIRA detector on Robo-AO

We report on initial results from the largest infrared AO direct imaging survey searching for wide orbit (≳ 100 AU) massive exoplanets and brown dwarfs as companions around young nearby stars using Robo-AO at the 2.1-m telescope on Kitt Peak, Arizona. The occurrence rates of these rare substellar companions are critical to furthering our understanding of the origin of planetary-mass companions on wide orbits. The observing efficiency of Robo-AO allows us to conduct a survey an order of magnitude larger than previously possible. We commissioned a low-noise high-speed SAPHIRA near-infrared camera to conduct this survey and report on its sensitivity, performance, and data reduction process