Viral pathogen discovery.

Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples. Although numerous challenges remain to be addressed, including the bioinformatics analysis and interpretation of large datasets, these technologies have been successful in rapidly identifying emerging outbreak threats, screening vaccines and other biological products for microbial contamination, and discovering novel viruses associated with both acute and chronic illnesses. Downstream studies such as genome assembly, epidemiologic screening, and a culture system or animal model of infection are necessary to establish an association of a candidate pathogen with disease

Clinical metagenomics.

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health

Away-side azimuthal distribution in a Markovian parton scattering model

An event generator is constructed on the basis of a model of multiple scattering of partons so that the trajectory of a parton traversing a dense and expanding medium can be tracked. The parameters in the code are adjusted to fit the \Delta\phi azimuthal distribution on the far side when the trigger momentum is in the non-perturbative region, p_T(trigger)<4 GeV/c. The dip-bump structure for 1<p_T(assoc)<2.5 GeV/c is reproduced by averaging over the exit tracks of deflected jets. An essential characteristic of the model, called Markovian Parton Scattering (MPS) model, is that the scattering angle is randomly selected in the forward cone at every step of a trajectory that is divided into many discrete steps in a semi-classical approximation of the non-perturbative scattering process. Energy loss to the medium is converted to thermal partons which hadronize by recombination to give rise to the pedestal under the bumps. When extended to high trigger momentum with \pt(trigger) >8 GeV/c, the model reproduces the single-peak structure observed by STAR without invoking any new dynamical mechanism.Comment: 20 pages + 3 figure

Autocorrelation of Hadrons in Jets Produced in Heavy-Ion Collisions

Autocorrelation of two pions produced in heavy-ion collisions at intermediate $p_T$ is calculated in the framework of the recombination model. The differences of the pseudo-rapidities and azimuthal angles of the two pions are related to the angle between two shower partons in a jet. It is shown how the autocorrelation distribution reveals the properties of jet cone of the shower partons created by high-$p_T$ partons in hard collisions.Comment: 24 pages in latex and 3 figures. This is an expanded version with more discussion and references without any change in the physical conten

First Complete Genome Sequence of Corynebacterium riegelii.

Here, we report the first complete genome sequence of Corynebacterium riegelii strain PUDD_83A45, isolated from the urine of a patient with urinary tract infection. The genome measured 2.56 Mb and contained no plasmid