Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine 14 pathogen or host-pathogen differential gene expression data sets to assess whether using longer reads is warranted. A variety of data sets was used to assess what genomic attributes might affect the outcome of differential gene expression analysis including: gene density, operons, gene length, number of introns/exons and intron length. No genome attribute was found to influence the data in principal components analysis, hierarchical clustering with bootstrap support, or regression analyses of pairwise comparisons that were undertaken on the same reads, looking at all combinations of paired and unpaired reads trimmed to 36, 54, 72 and 101 bp. Read pairing had the greatest effect when there was little variation in the samples from different conditions or in their replicates (e.g. little differential gene expression). But overall, 54 and 72 bp reads were typically most similar. Given differences in costs and mapping percentages, we recommend 54 bp reads for organisms with no or few introns and 72 bp reads for all others. In a third of the data sets, read pairing had absolutely no effect, despite paired reads having twice as much data. Therefore, single-end reads seem robust for differential-expression analyses, but in eukaryotes paired-end reads are likely desired to analyse splice variants and should be preferred for data sets that are acquired with the intent to be community resources that might be used in secondary data analyses

Assessing the continuity of the blue ice climate record at Patriot Hills, Horseshoe Valley, West Antarctica

We use high resolution Ground Penetrating Radar (GPR) to assess the continuity of the Blue Ice Area (BIA) horizontal climate record at Patriot Hills, Horseshoe Valley, West Antarctica. The sequence contains three pronounced changes in deuterium isotopic values at ~18 cal ka, ~12 cal ka and ~8 cal ka. GPR surveys along the climate sequence reveal continuous, conformable dipping isochrones, separated by two unconformities in the isochrone layers, which correlate with the two older deuterium shifts. We interpret these incursions as discontinuities in the sequence, rather than direct measures of climate change. Ice-sheet models and Internal Layer Continuity Index plots suggest that the unconformities represent periods of erosion occurring as the former ice surface was scoured by katabatic winds in front of mountains at the head of Horseshoe Valley. This study demonstrates the importance of high resolution GPR surveys for investigating both paleo-flow dynamics and interpreting BIA climate records

Interannual surface evolution of an Antarctic blue-ice moraine using multi-temporal DEMs

Multi-temporal and fine resolution topographic data products are increasingly used to quantify surface elevation change in glacial environments. In this study, we employ 3D digital elevation model (DEM) differencing to quantify the topographic evolution of a blue-ice moraine complex in front of Patriot Hills, Heritage Range, Antarctica. Terrestrial laser scanning (TLS) was used to acquire multiple topographic datasets of the moraine surface at the beginning and end of the austral summer season in 2012/2013 and during a resurvey field campaign in 2014. A complementary topographic dataset was acquired at the end of season 1 through the application of Structure-from-Motion with multi-view stereo (SfM-MVS) photogrammetry to a set of aerial photographs acquired from an unmanned aerial vehicle (UAV).Three-dimensional cloud-to-cloud differencing was undertaken using the Multiscale Model to Model Cloud Comparison (M3C2) algorithm. DEM differencing revealed net uplift and lateral movement of the moraine crests within season 1 (mean uplift ~0.10 m), and surface lowering of a similar magnitude in some inter-moraine depressions and close to the current ice margin, although we are unable to validate the latter. Our results indicate net uplift across the site between seasons 1 and 2 (mean 0.07 m). This research demonstrates that it is possible to detect dynamic surface topographical change across glacial moraines over short (annual to intra-annual) timescales through the acquisition and differencing of fine-resolution topographic datasets. Such data offer new opportunities to understand the process linkages between surface ablation, ice flow, and debris supply within moraine ice

Sedimentological characterization of Antarctic moraines using UAVs and Structure-from-Motion photogrammetry

In glacial environments particle-size analysis of moraines provides insights into clast origin, transport history, depositional mechanism and processes of reworking. Traditional methods for grain-size classification are labour-intensive, physically intrusive and are limited to patch-scale (1m2) observation. We develop emerging, high-resolution ground- and unmanned aerial vehicle-based ‘Structure-from-Motion’ (UAV-SfM) photogrammetry to recover grain-size information across an moraine surface in the Heritage Range, Antarctica. SfM data products were benchmarked against equivalent datasets acquired using terrestrial laser scanning, and were found to be accurate to within 1.7 and 50mm for patch- and site-scale modelling, respectively. Grain-size distributions were obtained through digital grain classification, or ‘photo-sieving’, of patch-scale SfM orthoimagery. Photo-sieved distributions were accurate to <2mm compared to control distributions derived from dry sieving. A relationship between patch-scale median grain size and the standard deviation of local surface elevations was applied to a site-scale UAV-SfM model to facilitate upscaling and the production of a spatially continuous map of the median grain size across a 0.3 km2 area of moraine. This highly automated workflow for site scale sedimentological characterization eliminates much of the subjectivity associated with traditional methods and forms a sound basis for subsequent glaciological process interpretation and analysis

Class-based probability estimation using a semantic hierarchy

This article concerns the estimation of a particular kind of probability, namely, the probability of a noun sense appearing as a particular argument of a predicate. In order to overcome the accompanying sparse-data problem, the proposal here is to define the probabilities in terms of senses from a semantic hierarchy and exploit the fact that the senses can be grouped into classes consisting of semantically similar senses. There is a particular focus on the problem of how to determine a suitable class for a given sense, or, alternatively, how to determine a suitable level of generalization in the hierarchy. A procedure is developed that uses a chi-square test to determine a suitable level of generalization. In order to test the performance of the estimation method, a pseudo-disambiguation task is used, together with two alternative estimation methods. Each method uses a different generalization procedure; the first alternative uses the minimum description length principle, and the second uses Resnik's measure of selectional preference. In addition, the performance of our method is investigated using both the standard Pearson chi-square statistic and the log-likelihood chi-square statistic

Statins and Exercise Training Response in Heart Failure Patients: Insights From HF-ACTION.

OBJECTIVES: The aim of this study was to assess for a treatment interaction between statin use and exercise training (ET) response. BACKGROUND: Recent data suggest that statins may attenuate ET response, but limited data exist in patients with heart failure (HF). METHODS: HF-ACTION (Heart Failure: A Controlled Trial Investigating Outcomes of Exercise Training) was a randomized trial of 2,331 patients with chronic HF with ejection fraction ≤35% who were randomized to usual care with or without ET. We evaluated whether there was a treatment interaction between statins and ET response for the change in quality of life and aerobic capacity (peak oxygen consumption and 6-min walk distance) from baseline to 3 months. We also assessed for a treatment interaction among atorvastatin, simvastatin, and pravastatin and change in these endpoints with ET. Multiple linear regression analyses were performed for each endpoint, adjusting for baseline covariates. RESULTS: Of 2,331 patients in the HF-ACTION trial, 1,353 (58%) were prescribed statins at baseline. Patients treated with statins were more likely to be older men with ischemic HF etiology but had similar use of renin angiotensin system blockers and beta-blockers. There was no evidence of a treatment interaction between statin use and ET on changes in quality of life or exercise capacity, nor was there evidence of differential association between statin type and ET response for these endpoints (all p values \u3e0.05). CONCLUSIONS: In a large chronic HF cohort, there was no evidence of a treatment interaction between statin use and short-term change in aerobic capacity and quality of life with ET. These findings contrast with recent reports of an attenuation in ET response with statins in a different population, highlighting the need for future prospective studies. (Exercise Training Program to Improve Clinical Outcomes in Individuals With Congestive Heart Failure; NCT00047437)

Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity.

Descriptions of resources, like the genome assemblies reported in Microbiology Resource Announcements, are often frozen at their time of publication, yet they will need to be interpreted in the midst of continually evolving technologies. It is therefore important to ensure that researchers accessing published resources have access to all of the information required to repeat, interpret, and extend these original analyses. Here, we provide a set of suggestions to help make certain that published resources remain useful and repeatable for the foreseeable future

Embodied cognitive ecosophy: the relationship of mind, body, meaning and ecology

The concept of embodied cognition has had a major impact in a number of disciplines. The extent of its consequences on general knowledge and epistemology are still being explored. Embodied cognition in human geography has its own traditions and discourses but these have become somewhat isolated in the discipline itself. This paper argues that findings in other disciplines are of value in reconceptualising embodied cognition in human geography and this is explored by reconsidering the concept of ecosophy. Criticisms of ecosophy as a theory are considered and recent work in embodied cognition is applied to consider how such criticisms might be addressed. An updated conceptualisation is proposed, the embodied cognitive ecosophy, and three characteristics arising from this criticism and synthesis are presented with a view to inform future discussions of ecosophy and emotional geography