ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

Aspiration therapy for the treatment of obesity: 4-year results of a multicenter randomized controlled trial.

BackgroundThe AspireAssist is the first Food and Drug Administration-approved endoluminal device indicated for treatment of class II and III obesity.ObjectivesWe earlier reported 1-year results of the PATHWAY study. Here, we report 4-year outcomes.SettingUnited States-based, 10-center, randomized controlled trial involving 171 participants with the treatment arm receiving Aspiration Therapy (AT) plus Lifestyle Therapy and the control arm receiving Lifestyle Therapy (2:1 randomization).MethodsAT participants were permitted to continue in the study for an additional year up to a maximum of 5 years providing they maintained at least 10% total weight loss (TWL) from baseline at each year end. For AT participants who continued the study, 5 medical monitoring visits were provided at weeks 60, 68, 76, 90, and 104 and thereafter once every 13 weeks up to week 260. Exclusion criteria were a history of eating disorder or evidence of eating disorder on a validated questionnaire. Follow-up weight, quality of life, and co-morbidities were compared with the baseline levels. In addition, rates of serious adverse event, persistent fistula, withdrawal, and A-tube replacement were reported. All analyses were performed using a per-protocol analysis.ResultsOf the 82 AT participants who completed 1 year, 58 continued to this phase of the trial. Mean baseline body mass index of these 58 patients was 41.6 ± 4.5 kg/m2. At the end of first year (at the beginning of the follow-up study), these 58 patients had a body mass index of 34.1 ± 5.4 kg/m2 and had achieved an 18.3 ± 8.0% TWL. On a per protocol basis, patients experienced 14.2%, 15.3%, 16.6%, and 18.7% TWL at 1, 2, 3, and 4 years, respectively (P < .01 for all). Forty of 58 patients (69%) achieved at least 10% TWL at 4 years or at time of study withdrawal. Improvements in quality of life scores and select cardiometabolic parameters were also maintained through 4 years. There were 2 serious adverse events reported in the second through fourth years, both of which resolved with removal or replacement of the A tube. Two persistent fistulas required surgical repair, representing approximately 2% of all tube removals. There were no clinically significant metabolic or electrolytes disorders observed, nor any evidence for development of any eating disorders.ConclusionsThe results of this midterm study have shown that AT is a safe, effective, and durable weight loss alternative for people with class II and III obesity and who are willing to commit to using the therapy and adhere to adjustments in eating behavior

On the tropospheric response to anomalous stratospheric wave drag and radiative heating

Observational and numerical evidence suggest that variability in the extratropical stratospheric circulation has a demonstrable impact on tropospheric variability on intraseasonal time scales. In this study, it is demonstrated that the amplitude of the observed tropospheric response to vacillations in the stratospheric flow is quantitatively similar to the zonal-mean balanced response to the anomalous wave forcing at stratospheric levels. It is further demonstrated that the persistence of the tropospheric response is consistent with the impact of anomalous diabatic heating in the polar stratosphere as stratospheric temperatures relax to climatology. The results contradict previous studies that suggest that variations in stratospheric wave drag are too weak to account for the attendant changes in the tropospheric flow. However, the results also reveal that stratospheric processes alone cannot account for the observed meridional redistribution of momentum within the troposphere

Sequential design of computer experiments for the estimation of a probability of failure

This paper deals with the problem of estimating the volume of the excursion set of a function $f:\mathbb{R}^d \to \mathbb{R}$ above a given threshold, under a probability measure on $\mathbb{R}^d$ that is assumed to be known. In the industrial world, this corresponds to the problem of estimating a probability of failure of a system. When only an expensive-to-simulate model of the system is available, the budget for simulations is usually severely limited and therefore classical Monte Carlo methods ought to be avoided. One of the main contributions of this article is to derive SUR (stepwise uncertainty reduction) strategies from a Bayesian-theoretic formulation of the problem of estimating a probability of failure. These sequential strategies use a Gaussian process model of $f$ and aim at performing evaluations of $f$ as efficiently as possible to infer the value of the probability of failure. We compare these strategies to other strategies also based on a Gaussian process model for estimating a probability of failure.Comment: This is an author-generated postprint version. The published version is available at http://www.springerlink.co

Notch regulates BMP responsiveness and lateral branching in vessel networks via SMAD6

Functional blood vessel growth depends on generation of distinct but coordinated responses from endothelial cells. Bone morphogenetic proteins (BMP), part of the TGFβ superfamily, bind receptors to induce phosphorylation and nuclear translocation of SMAD transcription factors (R-SMAD1/5/8) and regulate vessel growth. However, SMAD1/5/8 signalling results in both pro- and anti-angiogenic outputs, highlighting a poor understanding of the complexities of BMP signalling in the vasculature. Here we show that BMP6 and BMP2 ligands are pro-angiogenic in vitro and in vivo, and that lateral vessel branching requires threshold levels of R-SMAD phosphorylation. Endothelial cell responsiveness to these pro-angiogenic BMP ligands is regulated by Notch status and Notch sets responsiveness by regulating a cell-intrinsic BMP inhibitor, SMAD6, which affects BMP responses upstream of target gene expression. Thus, we reveal a paradigm for Notch-dependent regulation of angiogenesis: Notch regulates SMAD6 expression to affect BMP responsiveness of endothelial cells and new vessel branch formation

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations]

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

Reliability of Bioelectrical Impedance Analysis for Estimating Whole‐Fish Energy Density and Percent Lipids

We evaluated bioelectrical impedance analysis (BIA) as a nonlethal means of predicting energy density and percent lipids for three fish species: Yellow perch Perca flavescens, walleye Sander vitreus, and lake whitefish Coregonus clupeaformis. Although models that combined BIA measures with fish wet mass provided strong predictions of total energy, total lipids, and total dry mass for whole fish, including BIA provided only slightly better predictions than using fish mass alone. Regression models that used BIA measures to directly predict the energy density or percent lipids of whole fish were generally better than those using body mass alone (based on Akaike’s information criterion). However, the goodness of fit of models that used BIA measures varied widely across species and at best explained only slightly more than one‐half the variation observed in fish energy density or percent lipids. Models that combined BIA measures with body mass for prediction had the strongest correlations between predicted and observed energy density or percent lipids for a validation group of fish, but there were significant biases in these predictions. For example, the models underestimated energy density and percent lipids for lipid‐rich fish and overestimated energy density and percent lipids for lipid‐poor fish. A comparison of observed versus predicted whole‐fish energy densities and percent lipids demonstrated that models that incorporated BIA measures had lower maximum percent error than models without BIA measures in them, although the errors for the BIA models were still generally high (energy density: 15‐18%; percent lipids: 82‐89%). Considerable work is still required before BIA can provide reliable predictions of whole‐fish energy density and percent lipids, including understanding how temperature, electrode placement, and the variation in lipid distribution within a fish affect BIA measures.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141722/1/tafs1519.pd

ACC/AHA Guidelines for the Management of Patients With ST-Elevation Myocardial Infarction—Executive Summary A Report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Writing Committee to Revise the 1999 Guidelines for the Management of Patients With Acute Myocardial Infarction)

Although considerable improvement has occurred in the process of care for patients with ST-elevation myocardial infarction (STEMI), room for improvement exists (1–3). The purpose of the present guideline is to focus on the numerous advances in the diagnosis and management of patients with STEMI since 1999. This is reflected in the changed name of the guideline: “ACC/AHA Guidelines for the Management of Patients With ST-Elevation Myocardial Infarction.” The final recommendations for indications for a diagnostic procedure, a particular therapy, or an intervention in patients with STEMI summarize both clinical evidence and expert opinion (Table 1).To provide clinicians with a set of recommendations that can easily be translated into the practice of caring for patients with STEMI, this guideline is organized around the chronology of the interface between the patient and the clinician. The full guideline is available at http://www.acc.org/clinical/guidelines/stemi/index.htm

EON-ROSE and the Canadian Cordillera Array – Building Bridges to Span Earth System Science in Canada

EON-ROSE (Earth-System Observing Network - Réseau d’Observation du Système terrestrE) is a new initiative for a pan-Canadian research collaboration to holistically examine Earth systems from the ionosphere into the core. The Canadian Cordillera Array (CC Array) is the pilot phase, and will extend across the Cordillera from the Beaufort Sea to the U.S. border. The vision for EON-ROSE is to install a network of telemetered observatories to monitor solid Earth, environmental and atmospheric processes. EON-ROSE is an inclusive, combined effort of Canadian universities, federal, provincial and territorial government agencies, industry, and international collaborators. Brainstorming sessions and several workshops have been held since May 2016. The first station will be installed at Kluane Lake Research Station in southwestern Yukon during the summer of 2018. The purpose of this report is to provide a framework for continued discussion and development.RÉSUMÉEON-ROSE (Earth-System Observing Network - Réseau d’Observation du Système terrestrE) est une nouvelle initiative de collaboration de recherche pancanadienne visant à étudier de manière holistique les systèmes terrestres, depuis l’ionosphère jusqu’au noyau. Le Réseau canadien de la cordillère (CC Array) en est la phase pilote, laquelle couvrira toute la Cordillère, de la mer de Beaufort jusqu’à la frontière étasunienne. L’objectif d’EON-ROSE est d’installer un réseau d’observatoires télémétriques pour suivre en continu les processusterrestres, environnementaux et atmosphériques. EON-ROSE est un effort combiné et inclusif des universités canadiennes, des organismes gouvernementaux fédéraux, provinciaux et territoriaux, de l’industrie et de collaborateurs internationaux. Des séances de remue-méninges et plusieurs ateliers ont été tenus depuis mai 2016. La première station sera installée à la station de recherche du lac Kluane, dans le sud-ouest du Yukon, au cours de l’été 2018. Le but du présent rapport est de fournir un cadre de discussion et de développement continu