A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete

Regenerated Cellulose Fiber Solar Cell

Wearable electronics and smart textiles are growing fields in the cause to integrate modern communication and computing tools into clothing instead of carrying around smart phones and tablets. Naturally, this also requires power sources to be integrated in textiles. In this paper, a proof-of-concept is presented in form of a photovoltaic cell based on a commercially available viscose fiber. This has been realized using a silver nanowire network around the viscose fiber to establish electrical contact and a photoactive coating using the standard workhorse among organic thin film solar cells, a blend of poly(3-hexylthiophene) (P3HT) and phenyl-C61-butyric acid methyl ester (PCBM). Structure and performance of single fiber devices demonstrate their feasibility and functionality. The applied materials and methods are compatible to solution processing therewith qualifying for potential roll-to-roll large-scale production

Untwisting of a Strained Cholesteric Elastomer by Disclination Loop Nucleation

The application of a sufficiently strong strain perpendicular to the pitch axis of a monodomain cholesteric elastomer unwinds the cholesteric helix. Previous theoretical analyses of this transition ignored the effects of Frank elasticity which we include here. We find that the strain needed to unwind the helix is reduced because of the Frank penalty and the cholesteric state becomes metastable above the transition. We consider in detail a previously proposed mechanism by which the topologically stable helical texture is removed in the metastable state, namely by the nucleation of twist disclination loops in the plane perpendicular to the pitch axis. We present an approximate calculation of the barrier energy for this nucleation process which neglects possible spatial variation of the strain fields in the elastomer, as well as a more accurate calculation based on a finite element modeling of the elastomer.Comment: 12 pages, 9 figure

A mathematical transformation of multi-angular remote sensing data for the study of vegetation change

Vegetation change is an important factor affecting the global carbon cycle, land-atmosphere interaction, and terrestrial ecology. The study of vegetation change on a global scale can be used to evaluate the impact of global climate change on terrestrial ecosystems. Satellite remote sensing can monitor vegetation change at the global scale, providing continuous samples of radiation reflected by vegetated surfaces with a temporal resolution of days. The MISR instrument offers the potential to sample the specular anisotropy of the Earth from up to 9 angles. Characterization of the specular anisotropy of vegetated surfaces on a global scale will provide information on the physical characteristics of vegetation affecting anisotropy not available from nadir-view only remote sensing. The objective of this study is to develop a Principal Components Analysis (PCA) transformation of multi-angular measurements of the Earth’s surface acquired by the MISR instrument, to examine the feasibility of quantifying the structural characteristics of different vegetation communities at a global scale. This transformation will be applied to a time-series analysis of the Kalmioposis Wilderness in the Siskiyou National Forest in Southwestern Oregon to better understand the changes in spectral and angular reflectance of a forest stand during re-growth after a stand-replacing disturbance. A sample encompassing a full phenologic cycle, of the red bands only from MISR cameras Ca – Cf, at scaled surface reflectance, provided the template on which PCA was performed. The sample of MISR data was created using imagery collected from 2001 – 2005 to provide a wide variety of vegetation and soils reflectance over a phenologic cycle. Sample data was rotated to the principal components as the new axes using the coefficients of rotation from an un-standardized PCA. Samples were evaluated at various latitudes, differing topography, and varying vegetation density and land cover to determine the properties of the scene controlling the range and magnitude of the principal components. Principal component 1 was found to have high negative correlation to NDVI. Principal component 2 was found to have high positive correlation to both the solar zenith angle and the relative azimuth angle between the MISR sensor and the path of incident radiation. Principal component 3 could not be correlated to any available metric, although evidence suggests that component 3 may carry useful information. The PCA transformation proved useful at relating the changes in vegetation after a fire at the Biscuit Complex. The changes in the BRDF as sampled by MISR were expressed through the principal components, but these changes could not be directly related to changing structural characteristics of the vegetation. The goal of assessing structural characteristics of vegetation through the PCA transformation to a single metric of vegetation structure was unsuccessful. The PCA transformation of the MISR sample successfully yielded a transformation where different classes of vegetation occupied distinct and unique regions of PCA space. The first two principal components were successfully correlated to measurable and definable metrics of vegetation and solar illumination. The third principal component, for which a correlation could not be found, was suggestive of carrying unique information and merits further investigation. The transformation of multi-angular red band reflectance as presented in this study may prove to be a valuable method of estimating biomass at a global scale. With principal components correlated to measures of biomass in NDVI and to the shadowing of the ground through the angle of solar illumination, the PCA relates characteristics of vegetated scenes in a minimum of bands

Ground Improvement by Dynamic Compaction at a Tailings Disposal Facility

This paper presents two case histories of ground improvement by dynamic compaction (DC) at the Myra Falls mine in Vancouver Island, British Columbia, Canada. Dynamic compaction was employed to densify soils at two sites within the operating mine: a waste rock dump beneath a new processing plant to reduce settlements beneath the structure foundations (Site A); and coarse fluvial and colluvial soils at the toe of an existing tailings embankment to improve seismic resistance against liquefaction (Site B). At Site A, the variable plant loadings required variable compaction energy to achieve uniform foundation performance. At Site B, the foundation soils contained some fine grained soils that dictated a time-controlled sequential DC approach to allow excess pore pressures to dissipate between passes. Because of large uncertainties in the expected performance of DC at both sites, a fair and cost effective DC contract based on unit price per energy was adopted, instead of the traditional performance-based lump sum price contract. This paper describes the ground conditions at the two sites, DC methodologies employed, and ground improvement performance based on measurements of crater volumes and pre- and post-densification in-situ testing by Becker Penetration Tests

How much would it cost to monitor farmland biodiversity in Europe?

International audienceTo evaluate progress on political biodiversity objectives, biodiversity monitoring provides information on whether intended results are being achieved. Despite scientific proof that monitoring and evaluation increase the (cost) efficiency of policy measures, cost estimates for monitoring schemes are seldom available, hampering their inclusion in policy programme budgets. Empirical data collected from 12 case studies across Europe were used in a power analysis to estimate the number of farms that would need to be sampled per major farm type to detect changes in species richness over time for four taxa (vascular plants, earthworms, spiders and bees). A sampling design was developed to allocate spatially, across Europe, the farms that should be sampled. Cost estimates are provided for nine monitoring scenarios with differing robustness for detecting temporal changes in species numbers. These cost estimates are compared with the Common Agricultural Policy (CAP) budget (2014-2020) to determine the budgetallocation required for the proposed farmland biodiversity monitoring. Results show that the bee indicator requires the highest number of farms to be sampled and the vascular plant indicator the lowest. The costs for the nine farmland biodiversity monitoring scenarios corresponded to 001%-074% of the total CAP budget and to 004%-248% of the CAP budget specifically allocated to environmental targets.Synthesis and applications. The results of the cost scenarios demonstrate that, based on the taxa and methods used in this study, a Europe-wide farmland biodiversity monitoring scheme would require a modest share of the Common Agricultural Policy budget. The monitoring scenarios are flexible and can be adapted or complemented with alternate data collection options (e.g. at national scale or voluntary efforts), data mobilization, data integration or modelling efforts. Editor's Choic

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance

Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance.This work was supported by grants BIO2012-34937, CSD2009-00088, and BIO2015-66426-R (J.M.S.-R.) from MINECO/FEFER and grant P09-CVI-5073 (B.I.-M.) from the “Junta de Andalucía” and Feder Funds