Mapping the Space of Genomic Signatures

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to $k$ (herein $k=9$) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence homology and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information.Comment: 14 pages, 7 figures. arXiv admin note: substantial text overlap with arXiv:1307.375

Trends in and predictors of carbapenem consumption across North American hospitals: Results from a multicenter survey by the MAD-ID research network

This Special Issue is dedicated to the late Dr. Charles (Charlie) D. Hufford, former Professor of Pharmacognosy and Associate Dean for Research and Graduate Studies at University of Mississippi [...]

Energy transfer in pendant perylene diimide copolymers

We report the synthesis, characterisation and polymerisation of two novel asymmetric perylene diimide acrylate monomers. The novel monomers form a sensitiser–acceptor pair capable of undergoing Förster resonance energy transfer, and were incorporated as copolymers with tert-butyl acrylate. The tert-butyl acrylate units act as spacers along the polymer chain allowing high concentrations of dye while mitigating aggregate quenching, leading to persistent fluorescence in the solid state at high concentrations of up to 0.3 M. Analysis of fluorescence kinetics showed efficient energy transfer between the optically dense sensitiser and the lower concentration acceptor luminophores within the polymer. This reduced reabsorption within the material demonstrates that the copolymer-scaffold energy transfer system has potential for use in luminescent solar concentrators

CHERI Concentrate: Practical Compressed Capabilities

We present CHERI Concentrate, a new fat-pointer compression scheme applied to CHERI, the most developed capability-pointer system at present. Capability fat-pointers are a primary candidate for enforcing fine-grained and non-bypassable security properties in future computer systems, although increased pointer size can severely affect performance. Thus, several proposals for capability compression have been suggested but these did not support legacy instruction sets, ignored features critical to the existing software base, and also introduced design inefficiencies to RISC-style processor pipelines. CHERI Concentrate improves on the state-of-the-art region-encoding efficiency, solves important pipeline problems, and eases semantic restrictions of compressed encoding, allowing it to protect a full legacy software stack. We analyze and extend logic from the open-source CHERI prototype processor design on FPGA to demonstrate encoding efficiency, minimize delay of pointer arithmetic, and eliminate additional load-to-use delay. To verify correctness of our proposed high-performance logic, we present a HOL4 machine-checked proof of the decode and pointer-modify operations. Finally, we measure a 50%-75% reduction in L2 misses for many compiled C-language benchmarks running under a commodity operating system using compressed 128-bit and 64-bit formats, demonstrating both compatibility with and increased performance over the uncompressed, 256-bit format