Whole-genome sequencing of Klebsiella pneumoniae isolates to track strain progression in a single patient with recurrent urinary tract infection

Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Evidence suggests that some same-strain recurrences in women with frequent urinary tract infections (UTIs) may emanate from a persistent intravesicular reservoir. Our objective was to analyze K. pneumoniae isolates collected over weeks from multiple body sites of a single patient with recurrent UTI in order to track ordered strain progression across body sites, as has been employed across patients in outbreak settings. Whole-genome sequencing of 26 K. pneumoniae isolates was performed utilizing the Illumina platform. PacBio sequencing was used to create a refined reference genome of the original urinary isolate (TOP52). Sequence variation was evaluated by comparing the 26 isolate sequences to the reference genome sequence. Whole-genome sequencing of the K. pneumoniae isolates from six different body sites of this patient with recurrent UTI demonstrated 100% chromosomal sequence identity of the isolates, with only a small P2 plasmid deletion in a minority of isolates. No single nucleotide variants were detected. The complete absence of single-nucleotide variants from 26 K. pneumoniae isolates from multiple body sites collected over weeks from a patient with recurrent UTI suggests that, unlike in an outbreak situation with strains collected from numerous patients, other methods are necessary to discern strain progression within a single host over a relatively short time frame.</p

Enhanced virome sequencing using targeted sequence capture

Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications

The Korean War and the Post-war Prisoner of War Regime, 1945–1956

This paper examines the framework for the treatment of prisoners of war that emerged after 1945. It focuses on one of the key elements of the post-war prisoner of war (POW) regime, the role of neutral bodies – state authorities acting as ‘protecting powers’ or humanitarian agencies such as the International Committee of the Red Cross – in supervising the implementation of the 1949 POW convention. It examines the importance of neutral supervision for the POW regime, and shows how the events of the Korean War affected the willingness of states to comply with their obligations under the new convention

Examining public service motivation in the voluntary sector: implications for public management

Building on research about the nature of Public Service Motivation (PSM) and its application outside the public sector, the authors provide a qualitative based examination of PSM's relevance to voluntary sector employees. In doing so, they explore how far their motivations extend beyond those encompassed within current conceptualisations of PSM and whether PSM research can be enriched through the adoption of qualitative methodologies. The findings suggest that PSM accounts for some, but not all, of the motives of voluntary sector employees and indicate that public sector managers involved in outsourcing public services need to be sensitive to their distinctive features

The “Majestic Equality” of the Law: Conservatism, Radicalism, and Reform of the Civil Courts in Upper Canada, 1841-1853

The mid-nineteenth century was an age of reform in the civil courts of the common-law world. Why, in spite of the clamour for change within Upper Canada and the introduction of reforms in adjacent common-law jurisdictions, were Upper Canada’s leading lawyers and politicians so reluctant to act? The answer is found in the conservatism of the province’s leaders, which stemmed not only from the legal training of the lawyers, but also from the moderate conservative ideology of the Upper Canadian leadership as a whole. At an almost unprecedented time of public debate, when resentment to lawyers and the courts was being expressed and a radical critique of the courts and the profession was emerging, Upper Canada’s most influential residents managed to maintain political control and steadfastly refused to act in advance of the mother country

Development and evaluation of an enterovirus D68 real-time reverse transcriptase PCR assay

We have developed and evaluated a real-time reverse transcriptase PCR (RT-PCR) assay for the detection of human enterovirus D68 (EV-D68) in clinical specimens. This assay was developed in response to the unprecedented 2014 nationwide EV-D68 outbreak in the United States associated with severe respiratory illness. As part of our evaluation of the outbreak, we sequenced and published the genome sequence of the EV-D68 virus circulating in St. Louis, MO. This sequence, along with other GenBank sequences from past EV-D68 occurrences, was used to computationally select a region of EV-D68 appropriate for targeting in a strain-specific RT-PCR assay. The RT-PCR assay amplifies a segment of the VP1 gene, with an analytic limit of detection of 4 copies per reaction, and it was more sensitive than commercially available assays that detect enteroviruses and rhinoviruses without distinguishing between the two, including three multiplex respiratory panels approved for clinical use by the FDA. The assay did not detect any other enteroviruses or rhinoviruses tested and did detect divergent strains of EV-D68, including the first EV-D68 strain (Fermon) identified in California in 1962. This assay should be useful for identifying and studying current and future outbreaks of EV-D68 viruses

Experiential Factors Affect Red and Blue Preferences in Neonatal Chickens (Gallus gallus)

White leghorn chickens (Gallus Gallus) were isolated and reared in either white, half red and half blue, red, or blue cages, and at 60 hrs. and 120 hrs. were given a preference test for either a red or blue stationary object. Chicks housed in white cages were exposed to white throughout the experiment, and chicks housed in half red and half blue were exposed to red and blue in the same manner. Subjects housed in red cages for the first 60 hrs. were reversed to blue cages for the second 60 hrs. and subjects initially housed in blue cages were reversed to red cages. Subjects exposed to white, red and blue or red, showed a preference for red at 60 hrs. while subjects initially exposed to blue showed a tendency to prefer blue. At 120 hrs. subjects exposed to white showed no preference, while the subjects exposed to red and blue continued to display a red preference. Subjects initially exposed to red and reversed to blue showed no preference but subjects reversed from blue to red showed a red preference. This suggests that color preferences in chicks may be affected by an interaction between the initial attractiveness of a color and the amount of experience with that color at an early age

Extreme-scaling Applications 24/7 on JUQUEEN Blue Gene/Q

Jülich Supercomputing Centre has offered Extreme Scaling Workshops since 2009, with the latest edition in February 2015 giving seven international code teams an opportunity to (im)prove the scaling of their applications to all 458752 cores of the JUQUEEN IBM BlueGene/Q. Each of them successfully adapted their application codes and datasets to the restricted compute-node memory and exploit the massive parallelism with up to 1.8 million processes or threads. They thereby qualified to become members of the High-Q Club which now has over 24 codes demonstrating extreme scalability. Achievements in both strong and weak scaling are compared, and complemented with a review of program languages and parallelisation paradigms, exploitation of hardware threads, and file I/O requirements