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Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005–2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.
Few studies have used genomic epidemiology to understand tuberculosis (TB) transmission in rural and remote settings – regions often unique in history, geography and demographics. To improve our understanding of TB transmission dynamics in Yukon Territory (YT), a circumpolar Canadian territory, we conducted a retrospective analysis in which we combined epidemiological data collected through routine contact investigations with clinical and laboratory results. Mycobacterium tuberculosis isolates from all culture-confirmed TB cases in YT (2005–2014) were genotyped using 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) and compared to each other and to those from the neighbouring province of British Columbia (BC). Whole genome sequencing (WGS) of genotypically clustered isolates revealed three sustained transmission networks within YT, two of which also involved BC isolates. While each network had distinct characteristics, all had at least one individual acting as the probable source of three or more culture-positive cases. Overall, WGS revealed that TB transmission dynamics in YT are distinct from patterns of spread in other, more remote Northern Canadian regions, and that the combination of WGS and epidemiological data can provide actionable information to local public health teams.
Objectives: Studies of neurocognitively elite older adults, termed SuperAgers, have identified clinical predictors and neurobiological indicators of resilience against age-related neurocognitive decline. Despite rising rates of older persons living with HIV (PLWH), SuperAging (SA) in PLWH remains undefined. We aimed to establish neuropsychological criteria for SA in PLWH and examined clinically relevant correlates of SA. Methods: 734 PLWH and 123 HIV-uninfected participants between 50 and 64 years of age underwent neuropsychological and neuromedical evaluations. SA was defined as demographically corrected (i.e., sex, race/ethnicity, education) global neurocognitive performance within normal range for 25-year-olds. Remaining participants were labeled cognitively normal (CN) or impaired (CI) based on actual age. Chi-square and analysis of variance tests examined HIV group differences on neurocognitive status and demographics. Within PLWH, neurocognitive status differences were tested on HIV disease characteristics, medical comorbidities, and everyday functioning. Multinomial logistic regression explored independent predictors of neurocognitive status. Results: Neurocognitive status rates and demographic characteristics differed between PLWH (SA=17%; CN=38%; CI=45%) and HIV-uninfected participants (SA=35%; CN=55%; CI=11%). In PLWH, neurocognitive groups were comparable on demographic and HIV disease characteristics. Younger age, higher verbal IQ, absence of diabetes, fewer depressive symptoms, and lifetime cannabis use disorder increased likelihood of SA. SA reported increased independence in everyday functioning, employment, and health-related quality of life than non-SA. Conclusions: Despite combined neurological risk of aging and HIV, youthful neurocognitive performance is possible for older PLWH. SA relates to improved real-world functioning and may be better explained by cognitive reserve and maintenance of cardiometabolic and mental health than HIV disease severity. Future research investigating biomarker and lifestyle (e.g., physical activity) correlates of SA may help identify modifiable neuroprotective factors against HIV-related neurobiological aging. (JINS, 2019, 25, 507–519)
The Zika virus was largely unknown to many health care systems before the outbreak of 2015. The unique public health threat posed by the Zika virus and the evolving understanding of its pathology required continuous communication between a health care delivery system and a local public health department. By leveraging an existing relationship, NYC Health+Hospitals worked closely with New York City Department of Health and Mental Hygiene to ensure that Zika-related processes and procedures within NYC Health+Hospitals facilities aligned with the most current Zika virus guidance. Support given by the public health department included prenatal clinical and laboratory support and the sharing of data on NYC Health+Hospitals Zika virus screening and testing rates, thus enabling this health care delivery system to make informed decisions and practices. The close coordination, collaboration, and communication between the health care delivery system and the local public health department examined in this article demonstrate the importance of working together to combat a complex public health emergency and how this relationship can serve as a guide for other jurisdictions to optimize collaboration between external partners during major outbreaks, emerging threats, and disasters that affect public health. (Disaster Med Public Health Preparedness. 2018;12:689-691)
In several species, adult metabolic phenotype is influenced by the intrauterine environment, often in a sex-linked manner. In horses, there is also a window of susceptibility to programming immediately after birth but whether adult glucose–insulin dynamics are altered by neonatal conditions remains unknown. Thus, this study investigated the effects of birth weight, sex and neonatal glucocorticoid overexposure on glucose–insulin dynamics of young adult horses. For the first 5 days after birth, term foals were treated with saline as a control or ACTH to raise cortisol levels to those of stressed neonates. At 1 and 2 years of age, insulin secretion and sensitivity were measured by exogenous glucose administration and hyperinsulinaemic–euglycaemic clamp, respectively. Glucose-stimulated insulin secretion was less in males than females at both ages, although there were no sex-linked differences in glucose tolerance. Insulin sensitivity was greater in females than males at 1 year but not 2 years of age. Birth weight was inversely related to the area under the glucose curve and positively correlated to insulin sensitivity at 2 years but not 1 year of age. In contrast, neonatal glucocorticoid overexposure induced by adrenocorticotropic hormone (ACTH) treatment had no effect on whole body glucose tolerance, insulin secretion or insulin sensitivity at either age, although this treatment altered insulin receptor abundance in specific skeletal muscles of the 2-year-old horses. These findings show that glucose–insulin dynamics in young adult horses are sexually dimorphic and determined by a combination of genetic and environmental factors acting during early life.
Our knowledge of the universe comes from recording the photon and particle fluxes incident on the Earth from space. We thus require sensitive measurement across the entire energy spectrum, using large telescopes with efficient instrumentation located on superb sites. Technological advances and engineering constraints are nearing the point where we are recording as many photons arriving at a site as is possible. Major advances in the future will come from improving the quality of the site. The ultimate site is, of course, beyond the Earth’s atmosphere, such as on the Moon, but economic limitations prevent our exploiting this avenue to the degree that the scientific community desires. Here we describe an alternative, which offers many of the advantages of space for a fraction of the cost: the Antarctic Plateau.
BOUT++ is a 3D nonlinear finite-difference plasma simulation code, capable of solving quite general systems of Partial Differential Equations (PDEs), but targeted particularly on studies of the edge region of tokamak plasmas. BOUT++ is publicly available, and has been adopted by a growing number of researchers worldwide. Here we present improvements which have been made to the code since its original release, both in terms of structure and its capabilities. Some recent applications of these methods are reviewed, and areas of active development are discussed. We also present algorithms and tools which have been developed to enable creation of inputs from analytic expressions and experimental data, and for processing and visualisation of output results. This includes a new tool Hypnotoad for the creation of meshes from experimental equilibria. Algorithms have been implemented in BOUT++ to solve a range of linear algebraic problems encountered in the simulation of reduced Magnetohydrodynamics (MHD) and gyro-fluid models: A preconditioning scheme is presented which enables the plasma potential to be calculated efficiently using iterative methods supplied by the PETSc library (the Portable, Extensible Toolkit for Scientific Computation) (Balay et al. 2014), without invoking the Boussinesq approximation. Scaling studies are also performed of a linear solver used as part of physics-based preconditioning to accelerate the convergence of implicit time-integration schemes.
Campylobacter is a common cause of intestinal disease in humans and is often linked to the consumption of contaminated poultry meat. Despite considerable research on the topic there is a large amount of uncertainty associated with Campylobacter epidemiology. A Bayesian model framework was applied to multiple longitudinal datasets on Campylobacter infection in UK broiler flocks to estimate the time at which each flock was first infected with Campylobacter. The model results suggest that the day of first infection ranges from 10 to 45 days; however, over half had a time of infection between 30 and 35 days. When considering only those flocks which were thinned, 48% had an estimated day of infection within 2 days of the day of thinning, thus suggesting an association between thinning and Campylobacter infection. These results demonstrate how knowledge of the time of infection can be correlated to known events to identify potential risk factors for infection.
In Ontario, Canada, the number of Salmonella Enteritidis (SE) cases increased over the years 2005–2010. A population-based case-control study was undertaken from January to August 2011 for the purpose of identifying risk factors for acquiring illness due to SE within Ontario. A total of 199 cases and 241 controls were enrolled. After adjustment for confounders, consuming any poultry meat [adjusted odds ratio (aOR) 2·24, 95% confidence interval (CI) 1·31–3·83], processed chicken (aOR 3·32, 95% CI 1·26–8·76) and not washing hands following handling of raw eggs (OR 2·82, 95% CI 1·48–5·37) were significantly associated with SE infection. The population attributable fraction was 46% for any poultry meat consumption and 10% for processed chicken. Poultry meat continues to be identified as a risk factor for SE illness. Control of SE at source, as well as proper food handling practices, are required to reduce the number of SE cases.
Mg@ZnO thin films were prepared by DC/RF magnetron co-sputtering in (N2+O2) ambient conditions using metallic Mg and Zn targets. We present a comprehensive study of the effects of film thickness, variation of O2 content in the working gas and annealing temperature on the structural, optical and magnetic properties. The band gap energy of the films is found to increase from 4.1 to 4.24 eV with the increase of O2 partial pressures from 5 to 20 % in the working gas. The films are found to be ferromagnetic at room temperature and the saturation magnetization increases initially with the film’s thickness reaching a maximum value of 14.6 emu/cm3 and then decreases to finally become diamagnetic beyond 95 nm thickness. Intrinsic strain seems to play an important role in the observed structural and magnetic properties of the Mg@ZnO films. On annealing, the as-obtained ‘mostly amorphous’ films in the temperature range 600 to 800°C become more crystalline and consequently the saturation magnetization values reduce.
Herpes virus infections can cause cognitive impairment during and after acute encephalitis. Although chronic, latent/persistent infection is considered to be relatively benign, some studies have documented cognitive impairment in exposed persons that is untraceable to encephalitis. These studies were conducted among schizophrenia (SZ) patients or older community dwellers, among whom it is difficult to control for the effects of co-morbid illness and medications. To determine whether the associations can be generalized to other groups, we examined a large sample of younger control individuals, SZ patients and their non-psychotic relatives (n=1852).
Using multivariate models, cognitive performance was evaluated in relation to exposures to herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2) and cytomegalovirus (CMV), controlling for familial and diagnostic status and sociodemographic variables, including occupation and educational status. Composite cognitive measures were derived from nine cognitive domains using principal components of heritability (PCH). Exposure was indexed by antibodies to viral antigens.
PCH1, the most heritable component of cognitive performance, declines with exposure to CMV or HSV-1 regardless of case/relative/control group status (p = 1.09 × 10−5 and 0.01 respectively), with stronger association with exposure to multiple herpes viruses (β = −0.25, p = 7.28 × 10−10). There were no significant interactions between exposure and group status.
Latent/persistent herpes virus infections can be associated with cognitive impairments regardless of other health status.
PLATO is a 6 tonne completely self-contained robotic observatory that provides its own heat, electricity, and satellite communications. It was deployed to Dome A in Antarctica in January 2008 by the Chinese expedition team, and is now in its second year of operation. PLATO is operating four 14.5cm optical telescopes with 1k × 1k CCDs, a wide-field sky camera with a 2k × 2k CCD and Sloan g, r, i filters, a fibre-fed spectrograph to measure the UV to near-IR sky spectrum, a 0.2m terahertz telescope, two sonic radars giving 1m resolution data on the boundary layer to a height of 180m, a 15m tower, meteorological sensors, and 8 web cameras. Beginning in 2010/11 PLATO will be upgraded to support a Multi Aperture Scintillation Sensor and three AST3 0.5m schmidt telescopes, with 10k × 10 CCDs and 100TB/annum data requirements.