Conceptual design study for Infrared Limb Experiment (IRLE)

The phase A engineering design study for the Infrared Limb Experiment (IRLE) instrument, the infrared portion of the Mesosphere-Lower Thermosphere Explorer (MELTER) satellite payload is given. The IRLE instrument is a satellite instrument, based on the heritage of the Limb Infrared Monitor of the Stratosphere (LIMS) program, that will make global measurements of O3, CO2, NO, NO2, H2O, and OH from earth limb emissions. These measurements will be used to provide improved understanding of the photochemistry, radiation, dynamics, energetics, and transport phenomena in the lower thermosphere, mesosphere, and stratosphere. The IRLE instrument is the infrared portion of the MELTER satellite payload. MELTER is being proposed to NASA Goddard by a consortium consisting of the University of Michigan, University of Colorado and NASA Langley. It is proposed that the Space Dynamics Laboratory at Utah State University (SDL/USU) build the IRLE instrument for NASA Langley. MELTER is scheduled for launch in November 1994 into a sun-synchronous, 650-km circular orbit with an inclination angle of 97.8 deg and an ascending node at 3:00 p.m. local time

Mapping canopy nitrogen-scapes to assess foraging habitat for a vulnerable arboreal folivore in mixed-species Eucalyptus forests

Herbivore foraging decisions are closely related to plant nutritional quality. For arboreal folivores with specialized diets, such as the vulnerable greater glider (Petauroides volans), the abundance of suitable forage trees can influence habitat suitability and species occurrence. The ability to model and map foliar nitrogen would therefore enhance our understanding of folivore habitat use at finer scales. We tested whether high-resolution multispectral imagery, collected by a lightweight and low-cost commercial unoccupied aerial vehicle (UAV), could be used to predict total and digestible foliar nitrogen (N and digN) at the tree canopy level and forest stand-scale from leaf-scale chemistry measurements across a gradient of mixed-species Eucalyptus forests in southeastern Australia. We surveyed temperate Eucalyptus forests across an elevational and topographic gradient from sea level to high elevation (50–1200 m a.s.l.) for forest structure, leaf chemistry, and greater glider occurrence. Using measures of multispectral leaf reflectance and spectral indices, we estimated N and digN and mapped N and favorable feeding habitat using machine learning algorithms. Our surveys covered 17 Eucalyptus species ranging in foliar N from 0.63% to 1.92% dry matter (DM) and digN from 0.45% to 1.73% DM. Both multispectral leaf reflectance and spectral indices were strong predictors for N and digN in model cross-validation. At the tree level, 79% of variability between observed and predicted measures of nitrogen was explained. A spatial supervised classification model correctly identified 80% of canopy pixels associated with high N concentrations (≥1% DM). We developed a successful method for estimating foliar nitrogen of a range of temperate Eucalyptus species using UAV multispectral imagery at the tree canopy level and stand scale. The ability to spatially quantify feeding habitat using UAV imagery allows remote assessments of greater glider habitat at a scale relevant to support ground surveys, management, and conservation for the vulnerable greater glider across southeastern Australia

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

BACKGROUND: Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. RESULTS: Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. CONCLUSIONS: We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.This research was funded by GlaxoSmithKline, the Centre for Environment, Fisheries and Aquaculture Science and the Biotechnology and Biological Sciences Research Council under an industrial CASE studentship. The funder Centre for Environment, Fisheries and Aquaculture Science provided support in the form of salaries, research materials and facilities for authors DVJ and CBA, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funder GlaxoSmithKline provided support in the form of salaries for author JR, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final version. It was first published by PLOS at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133492

Feather development genes and associated regulatory innovation predate the origin of Dinosauria

The evolution of avian feathers have recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near IGFBP2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.Organismic and Evolutionary Biolog

Cinnamon Use in Type 2 Diabetes: An Updated Systematic Review and Meta-Analysis

PURPOSE Cinnamon has been studied in randomized controlled trials (RCTs) for its glycemic-lowering effects, but studies have been small and show conflicting results. A prior meta-analysis did not show significant results, but several RCTs have been published since then. We conducted an updated systematic review and meta-analysis of RCTs evaluating cinnamon’s effect on glycemia and lipid levels. METHODS MEDLINE, Embase, and Cochrane Central Register of Controlled Trials (CENTRAL) were searched through February 2012. Included RCTs evaluated cinnamon compared with control in patients with type 2 diabetes and reported at least one of the following: glycated hemoglobin (A1c), fasting plasma glucose, total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), or triglycerides. Weighted mean differences (with 95% confidence intervals) for endpoints were calculated using random-effects models. RESULTS In a meta-analysis of 10 RCTs (n = 543 patients), cinnamon doses of 120 mg/d to 6 g/d for 4 to 18 weeks reduced levels of fasting plasma glucose (−24.59 mg/dL; 95% CI, −40.52 to −8.67 mg/dL), total cholesterol (−15.60 mg/dL; 95% CI, −29.76 to −1.44 mg/dL), LDL-C (−9.42 mg/dL; 95% CI, −17.21 to −1.63 mg/dL), and triglycerides (−29.59 mg/dL; 95% CI, −48.27 to −10.91 mg/dL). Cinnamon also increased levels of HDL-C (1.66 mg/dL; 95% CI, 1.09 to 2.24 mg/dL). No significant effect on hemoglobin A1c levels (−0.16%; 95%, CI −0.39% to 0.02%) was seen. High degrees of heterogeneity were present for all analyses except HDL-C (I2 ranging from 66.5% to 94.72%). CONCLUSIONS The consumption of cinnamon is associated with a statistically significant decrease in levels of fasting plasma glucose, total cholesterol, LDL-C, and triglyceride levels, and an increase in HDL-C levels; however, no significant effect on hemoglobin A1c was found. The high degree of heterogeneity may limit the ability to apply these results to patient care, because the preferred dose and duration of therapy are unclear

Twittering about research : a case study of the world's first Twitter poster competition

The Royal Society of Chemistry held, to our knowledge, the world’s first Twitter conference at 9am on February 5th, 2015. This paper reports the details of the event and discusses the outcomes, such as the potential for the use of social media to enhance scientific communication at conferences. In particular, the present work argues that social media outlets such as Twitter broaden audiences, speed up communication, and force clearer and more concise descriptions of a researcher’s work. The benefits of poster presentations are also discussed in terms of potential knowledge exchange and networking. This paper serves as a proof-of-concept approach for improving both the public opinion of the poster, and the enhancement of the poster through an innovative online format that some may feel more comfortable with, compared to face-to-face communication

Pectus excavatum and chest pain: a case report

© 2008 Kim and Baker; licensee BioMed Central Ltd

Optical Spectropolarimetry of Quasi-Stellar Objects Discovered by the Two-Micron All Sky Survey

Highly polarized QSOs discovered in the Two-Micron All Sky Survey (2MASS) have been observed to determine the source(s) of optical polarization in this near-infrared color-selected sample. Broad emission lines are observed in the polarized flux spectra of most objects, and the polarization of the lines is at about the same level and position angle as the continuum. Generally, the continuum is bluer and the broad-line Balmer decrement is smaller in polarized light than for the spectrum of total flux. Narrow emission lines are much less polarized than the broad lines and continuum for all polarized objects. These properties favor scattering by material close to a partially obscured and reddened active nucleus, but exterior to the regions producing the broad-line emission, as the source of polarized flux in 2MASS QSOs. The largely unpolarized narrow-line features require that the electrons or dust polarizing the light be located at distances from the nucleus not much greater than the extent of the narrow emission-line region. In addition to known high-polarization objects, four 2MASS QSOs with AGN spectral types of 1.9 and 2 were observed to search for hidden broad emission-line regions. Broad lines were detected in polarized light for two of these objects, and the polarizing mechanism appears to be the same for these objects as for the highly polarized QSOs in the sample that readily show broad emission lines in their spectra. The observations also show that starlight from the host galaxy contributes a significant amount of optical flux, especially for the narrow-line objects, and support the suggestion that many 2MASS QSOs are measured to have low polarization simply because of dilution of the polarized AGN light by the host galaxy.Comment: 27 pages; 3 tables; 8 figures; Accepted for publication in The Astrophysical Journal (Part 1