Informatics for RNA sequencing: A web resource for analysis on the cloud

Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki

Wind field and sex constrain the flight speeds of central-place foraging albatrosses

By extracting energy from the highly dynamic wind and wave fields that typify pelagic habitats, albatrosses are able to proceed almost exclusively by gliding flight. Although energetic costs of gliding are low, enabling breeding albatrosses to forage hundreds to thousands of kilometers from their colonies, these and time costs vary with relative wind direction. This causes albatrosses in some areas to route provisioning trips to avoid headwind flight, potentially limiting habitat accessibility during the breeding season. In addition, because female albatrosses have lower wing loadings than males, it has been argued that they are better adapted to flight in light winds, leading to sexual segregation of foraging areas. We used satellite telemetry and immersion logger data to quantify the effects of relative wind speed, sex, breeding stage, and trip stage on the ground speeds (Vg) of four species of Southern Ocean albatrosses breeding at South Georgia. Vg was linearly related to the wind speed component in the direction of flight (Vwf), its effect being greatest on Wandering Albatrosses Diomedea exulans, followed by Black-browed Albatrosses Thalassarche melanophrys, Light-mantled Sooty Albatrosses Phoebatria palpebrata, and Gray-headed Albatrosses T. chrysostoma. Ground speeds at Vwf = 0 were similar to airspeeds predicted by aerodynamic theory and were higher in males than in females. However, we found no evidence that this led to sexual segregation, as males and females experienced comparable wind speeds during foraging trips. Black-browed, Gray-headed, and Light-mantled Sooty Albatrosses did not engage in direct, uninterrupted bouts of flight on moonless nights, but Wandering Albatrosses attained comparable Vg night and day, regardless of lunar phase. Relative flight direction was more important in determining Vg than absolute wind speed. When birds were less constrained in the middle stage of foraging trips, all species flew predominantly across the wind. However, in some instances, commuting birds encountered headwinds during outward trips and tail winds on their return, with the result that Vg was 1.0–3.4 m/s faster during return trips. This, we hypothesize, could result from constraints imposed by the location of prey resources relative to the colony at South Georgia or could represent an energy optimization strategy

The Nature of the Density Clump in the Fornax Dwarf Spheroidal Galaxy

We have imaged the recently discovered stellar overdensity located approximately one core radius from the center of the Fornax dwarf spheroidal galaxy using the Magellan Clay 6.5m telescope with the Magellan Instant Camera (MagIC). Superb seeing conditions allowed us to probe the stellar populations of this overdensity and of a control field within Fornax to a limiting magnitude of R=26. The color-magnitude diagram of the overdensity field is virtually identical to that of the control field with the exception of the presence of a population arising from a very short (less than 300 Myr in duration) burst of star formation 1.4 Gyr ago. Coleman et al. have argued that this overdensity might be related to a shell structure in Fornax that was created when Fornax captured a smaller galaxy. Our results are consistent with this model, but we argue that the metallicity of this young component favors a scenario in which the gas was part of Fornax itself.Comment: 24 pages including 8 figures and 3 tables. Accepted by Astronomical Journa

Video Monitoring a Simulation-Based Quality Improvement Program in Bihar, India.

BACKGROUND: Simulation-based training has become an accepted clinical training andragogy in high-resource settings with its use increasing in low-resource settings. Video recordings of simulated scenarios are commonly used by facilitators. Beyond using the videos during debrief sessions, researchers can also analyze the simulation videos to quantify technical and nontechnical skills during simulated scenarios over time. Little is known about the feasibility and use of large-scale systems to video record and analyze simulation and debriefing data for monitoring and evaluation in low-resource settings. METHODS: This manuscript describes the process of designing and implementing a large-scale video monitoring system. Mentees and Mentors were consented and all simulations and debriefs conducted at 320 Primary Health Centers (PHCs) were video recorded. The system design, number of video recordings, and inter-rater reliability of the coded videos were assessed. RESULTS: The final dataset included a total of 11,278 videos. Overall, a total of 2,124 simulation videos were coded and 183 (12%) were blindly double-coded. For the double-coded sample, the average inter-rater reliability (IRR) scores were 80% for nontechnical skills, and 94% for clinical technical skills. Among 4,450 long debrief videos received, 216 were selected for coding and all were double-coded. Data quality of simulation videos was found to be very good in terms of recorded instances of "unable to see" and "unable to hear" in Phases 1 and 2. CONCLUSION: This study demonstrates that video monitoring systems can be effectively implemented at scale in resource limited settings. Further, video monitoring systems can play several vital roles within program implementation, including monitoring and evaluation, provision of actionable feedback to program implementers, and assurance of program fidelity

Character building in childrens’ online information behaviours: applying a virtue epistemology perspective to information literacy.

This paper advances our understanding of the theoretical and practical challenges of developing intellectual character in children’s online information behaviours. We argue that widely reported issues such as misinformation and disinformation extend IL education beyond considerations of ability to considerations of disposition, and highlight this as an understudied topic within IL education. We introduce the classical concept of intellectual character and discuss virtues traits in the IL context. Applying Baehr’s nine intellectual virtues to two commonly cited IL models, we evidence limited presence of virtues in IL models, and propose an important agenda for future research