Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism.

Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology

Computational fluid dynamics modelling of residence times in vegetated stormwater ponds

Experimental data characterising dispersion within Typha latifolia were previously collected in a laboratory setting. This mixing characterisation was combined with previously proposed computational fluid dynamics modelling approaches to predict residence time distributions for vegetated stormwater treatment pond layouts (including a wetland) derived from Highways England design guidance. The results showed that the presence of vegetation resulted in residence times closer to plug flow, indicating significant improvements in stormwater treatment capability. The new modelling approach reflects changes in residence time due to mixing within the vegetation, but it also suggests that it is more important to include vegetation within the model in the correct location than it is to accurately characterise it. Estimates of hydraulic efficiency suggest that fully vegetated stormwater ponds such as wetlands should function well as a treatment device, but more typical ponds with clear water need to be designed to be between 50% and 100% larger than their nominal residence times would suggest when designed against treatment criteria

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

A preliminary study of the effect of closed incision management with negative pressure wound therapy over high-risk incisions

Background Certain postoperative wounds are recognised to be associated with more complications than others and may be termed high-risk. Wound healing can be particularly challenging following high-energy trauma where wound necrosis and infection rates are high. Surgical incision for joint arthrodesis can also be considered high-risk as it requires extensive and invasive surgery and postoperative distal limb swelling and wound dehiscence are common. Recent human literature has investigated the use of negative pressure wound therapy (NPWT) over high-risk closed surgical incisions and beneficial effects have been noted including decreased drainage, decreased dehiscence and decreased infection rates. In a randomised, controlled study twenty cases undergoing distal limb high-energy fracture stabilisation or arthrodesis were randomised to NPWT or control groups. All cases had a modified Robert-Jones dressing applied for 72 h postoperatively and NPWT was applied for 24 h in the NPWT group. Morphometric assessment of limb circumference was performed at six sites preoperatively, 24 and 72 h postoperatively. Wound discharge was assessed at 24 and 72 h. Postoperative analgesia protocol was standardised and a Glasgow Composite Measure Pain Score (GCPS) carried out at 24, 48 and 72 h. Complications were noted and differences between groups were assessed. Results Percentage change in limb circumference between preoperative and 24 and 72 h postoperative measurements was significantly less at all sites for the NPWT group with exception of the joint proximal to the surgical site and the centre of the operated bone at 72 h. Median discharge score was lower in the NPWT group than the control group at 24 h. No significant differences in GCPS or complication rates were noted. Conclusions Digital swelling and wound discharge were reduced when NPWT was employed for closed incision management. Larger studies are required to evaluate whether this will result in reduced discomfort and complication rates postoperatively

Effect of Geographical Access to Health Facilities on Child Mortality in Rural Ethiopia: A Community Based Cross Sectional Study

BACKGROUND: There have been few studies that have examined associations between access to health care and child health outcomes in remote populations most in need of health services. This study assessed the effect of travel time and distance to health facilities on mortality in children under five years in a remote area of rural north-western Ethiopia. METHODS AND FINDINGS: This study involved a randomly selected cross sectional survey of 2,058 households. Data were collected during home visits to all resident women of reproductive age (15-49 years). A geographic information system (GIS) was used to map all households and the only health centre in the district. The analysis was restricted to 2,206 rural children who were under the age of five years during the five years before the survey. Data were analysed using random effects Poisson regression. 90.4% (1,996/2,206) of children lived more than 1.5 hours walk from the health centre. Children who lived ≥1.5 hrs from the health centre had a two to three fold greater risk of death than children who lived <1.5 hours from the health centre (children with travel time 1.5-<2.5 hrs adjusted relative risk [adjRR] 2.3[0.95-5.6], travel time 2.5-<3.5 hrs adjRR 3.1[1.3-7.4] and travel time 3.5-<6.5 hrs adjRR 2.5[1.1-6.2]). CONCLUSION: Distance to a health centre had a marked influence on under five mortality in a poor, rural, remote area of Ethiopia. This study provides important information for policy makers on the likely impact of new health centres and their most effective location in remote areas

Hydraulic & Design Parameters in Full-Scale Constructed Wetland & Treatment Units: Six Case Studies

The efficiency of pond and constructed wetland (CW) treatment systems, is influenced by the internal hydrodynamics and mixing interactions between water and aquatic vegetation. In order to contribute to current knowledge of how emergent real vegetation affects solute mixing, and on what the shape and size effects are on the mixing characteristics, an understanding and quantification of those physical processes and interactions was evaluated. This paper presents results from tracer tests conducted during 2015-2016 in six full-scale systems in the UK under different flow regimes, operational depths, shapes and sizes, and in-/outlet configurations. The aim is to quantify the hydraulic performance and mixing characteristics of the treatment units, and to investigate the effect of size and shape on the mixing processes. Relative comparison of outlet configuration, inflow conditions, and internal features between the six different treatment units showed variations in residence times of up to a factor of 3. A key outcome of this study, demonstrated that the width is a more important dimension for the efficiency of the unit compared to the depth. Results underlined the importance of investigating hydrodynamics and physics of flow in full-size units to enhance treatment efficiency and predictions of water quality models

Association between Proximity to a Health Center and Early Childhood Mortality in Madagascar

Objective: To evaluate the association between proximity to a health center and early childhood mortality in Madagascar, and to assess the influence of household wealth, maternal educational attainment, and maternal health on the effects of distance. Methods: From birth records of subjects in the Demographic and Health Survey, we identified 12565 singleton births from January 2004 to August 2009. After excluding 220 births that lacked global positioning system information for exposure assessment, odds ratios (ORs) and their 95% confidence intervals (CIs) for neonatal mortality and infant mortality were estimated using multilevel logistic regression models, with 12345 subjects (level 1), nested within 584 village locations (level 2), and in turn nested within 22 regions (level 3). We additionally stratified the subjects by the birth order. We estimated predicted probabilities of each outcome by a three-level model including cross-level interactions between proximity to a health center and household wealth, maternal educational attainment, and maternal anemia. Results: Compared with those who lived >1.5–3.0 km from a health center, the risks for neonatal mortality and infant mortality tended to increase among those who lived further than 5.0 km from a health center; the adjusted ORs for neonatal mortality and infant mortality for those who lived >5.0–10.0 km away from a health center were 1.36 (95% CI: 0.92–2.01) and 1.42 (95% CI: 1.06–1.90), respectively. The positive associations were more pronounced among the second or later child. The distance effects were not modified by household wealth status, maternal educational attainment, or maternal health status. Conclusions: Our study suggests that distance from a health center is a risk factor for early childhood mortality (primarily, infant mortality) in Madagascar by using a large-scale nationally representative dataset. The accessibility to health care in remote areas would be a key factor to achieve better infant health

Origin of the Spin-Orbital Liquid State in a Nearly J=0 Iridate Ba3ZnIr2O9

We show using detailed magnetic and thermodynamic studies and theoretical calculations that the ground state of Ba3ZnIr2O9 is a realization of a novel spin-orbital liquid state. Our results reveal that Ba3ZnIr2O9 with Ir5+ (5d(4)) ions and strong spin-orbit coupling (SOC) arrives very close to the elusive J = 0 state but each Ir ion still possesses a weak moment. Ab initio density functional calculations indicate that this moment is developed due to superexchange, mediated by a strong intradimer hopping mechanism. While the Ir spins within the structural Ir2O9 dimer are expected to form a spin-orbit singlet state (SOS) with no resultant moment, substantial frustration arising from interdimer exchange interactions induce quantum fluctuations in these possible SOS states favoring a spin-orbital liquid phase down to at least 100 mK