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The limitations of self-report measures of dietary intake are well known. Novel, technology-based measures of dietary intake may provide a more accurate, less burdensome alternative to existing tools. The first objective of this study was to compare participant burden for two technology-based measures of dietary intake among school-age children: the Automated-Self Administered 24-hour Dietary Assessment Tool-2018 (ASA24-2018) and the Remote Food Photography Method (RFPM). The second objective was to compare reported energy intake for each method to the Estimated Energy Requirement for each child, as a benchmark for actual intake. Forty parent-child dyads participated in 2, 3-day dietary assessments: a parent proxy-reported version of the ASA24 and the RFPM. A parent survey was subsequently administered to compare satisfaction, ease of use and burden with each method. A linear mixed model examined differences in total daily energy intake (TDEI) between assessments, and between each assessment method and the EER. Reported energy intake was 379 kcal higher with the ASA24 than the RFPM (p=0.0002). Reported energy intake with the ASA24 was 231 kcal higher than the EER (p = 0.008). Reported energy intake with the RFPM did not differ significantly from the EER (difference in predicted means = −148 kcal, p = 0.09). Median satisfaction and ease of use scores were 5 out of 6 for both methods. A higher proportion of parents reported that the ASA24 was more time consuming than the RFPM (74.4% vs. 25.6%, p = 0.002). Utilization of both methods is warranted given their high satisfaction among parents.
Understanding place-based contributors to health requires geographically and culturally diverse study populations, but sharing location data is a significant challenge to multisite studies. Here, we describe a standardized and reproducible method to perform geospatial analyses for multisite studies. Using census tract-level information, we created software for geocoding and geospatial data linkage that was distributed to a consortium of birth cohorts located throughout the USA. Individual sites performed geospatial linkages and returned tract-level information for 8810 children to a central site for analyses. Our generalizable approach demonstrates the feasibility of geospatial analyses across study sites to promote collaborative translational research.
Studies suggest that alcohol consumption and alcohol use disorders have distinct genetic backgrounds.
We examined whether polygenic risk scores (PRS) for consumption and problem subscales of the Alcohol Use Disorders Identification Test (AUDIT-C, AUDIT-P) in the UK Biobank (UKB; N = 121 630) correlate with alcohol outcomes in four independent samples: an ascertained cohort, the Collaborative Study on the Genetics of Alcoholism (COGA; N = 6850), and population-based cohorts: Avon Longitudinal Study of Parents and Children (ALSPAC; N = 5911), Generation Scotland (GS; N = 17 461), and an independent subset of UKB (N = 245 947). Regression models and survival analyses tested whether the PRS were associated with the alcohol-related outcomes.
In COGA, AUDIT-P PRS was associated with alcohol dependence, AUD symptom count, maximum drinks (R2 = 0.47–0.68%, p = 2.0 × 10−8–1.0 × 10−10), and increased likelihood of onset of alcohol dependence (hazard ratio = 1.15, p = 4.7 × 10−8); AUDIT-C PRS was not an independent predictor of any phenotype. In ALSPAC, the AUDIT-C PRS was associated with alcohol dependence (R2 = 0.96%, p = 4.8 × 10−6). In GS, AUDIT-C PRS was a better predictor of weekly alcohol use (R2 = 0.27%, p = 5.5 × 10−11), while AUDIT-P PRS was more associated with problem drinking (R2 = 0.40%, p = 9.0 × 10−7). Lastly, AUDIT-P PRS was associated with ICD-based alcohol-related disorders in the UKB subset (R2 = 0.18%, p < 2.0 × 10−16).
AUDIT-P PRS was associated with a range of alcohol-related phenotypes across population-based and ascertained cohorts, while AUDIT-C PRS showed less utility in the ascertained cohort. We show that AUDIT-P is genetically correlated with both use and misuse and demonstrate the influence of ascertainment schemes on PRS analyses.
The objective of this study is to compare aneuploidy rates between three distinct areas of the human trophectoderm: mural, polar and a region in between these two locations termed the ‘mid’ trophectoderm. This is a cohort study on in vitro fertilization (IVF) patients undergoing comprehensive chromosome screening at the blastocyst stage at a private IVF clinic. All embryos underwent assisted hatching on day 3 with blastocyst biopsy and comprehensive chromosome screening. Biopsied blastocysts were divided into three groups depending on which area (polar, mid, or mural) of the trophectoderm was protruding from the zona pellucida and biopsied. Aneuploidy rates were significantly higher with cells from the polar region of the trophectoderm (56.2%) compared with cells removed from the mural region of the trophectoderm (30.0%; P = 0.0243). A comparison of all three areas combined also showed a decreasing trend, but this did not reach clinical significance, polar (56.2%), mid (47.4%) and mural trophectoderm (30.0%; P = 0.1859). The non-concordance demonstrated between polar and mural trophectoderm can be attributed to biological occurrences including chromosomal mosaicism or procedural differences between embryologists.
Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green® real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease.
Mercury is the only terrestrial planet other than Earth that possesses a global magnetic field, and the unique solar wind environment of the inner heliosphere has profound consequences for both the structure and dynamics of its magnetosphere. The first in situ observations of Mercury and its space environment made four decades ago by the Mariner 10 spacecraft revealed a magnetic field that is sufficiently strong to stand off the solar wind and form a magnetosphere. Many new insights into Mercury’s magnetosphere were enabled by data returned by the MESSENGER spacecraft. The extensive magnetic field and particle observations allowed detailed characterization of the magnetospheric structure and configuration. MESSENGER magnetic field observations definitively determined the orientation, moment, and location of the internal planetary magnetic dipole field. Furthermore, these observations established the configuration of the magnetopause, bow shock, and magnetospheric current systems. Plasma observations revealed the distribution and composition of plasma in the magnetosphere. We review the geometry and dominant physical processes of Mercury’s unique magnetosphere inferred from MESSENGER data, including the solar wind environment, the shape and location of magnetospheric boundaries, and the fundamental regions and configuration of the magnetosphere and transport and heating of plasma therein.
We investigate perturbations that maximize the gain of disturbance energy in a two-dimensional isolated vortex and a counter-rotating vortex pair. The optimization is carried out using the method of Lagrange multipliers. For low initial energy of the perturbation (
), the nonlinear optimal perturbation/gain is found to be the same as the linear optimal perturbation/gain. Beyond a certain threshold
, the optimal perturbation/gain obtained from linear and nonlinear computations are different. There exists a range of
for which the nonlinear optimal gain is higher than the linear optimal gain. For an isolated vortex, the higher value of nonlinear optimal gain is attributed to interaction among different azimuthal components, which is otherwise absent in a linearized system. Spiral dislocations are found in the nonlinear optimal perturbation at the radial location where the most dominant wavenumber changes. Long-time nonlinear evolution of linear and nonlinear optimal perturbations is studied. The evolution shows that, after the initial increment of perturbation energy, the vortex attains a quasi-steady state where the mean perturbation energy decreases on a slow time scale. The quasi-steady vortex state is non-axisymmetric and its shape depends on the initial perturbation. It is observed that the lifetime of a quasi-steady vortex state obtained using the nonlinear optimal perturbation is longer than that obtained using the linear optimal perturbation. For a counter-rotating vortex pair, the mechanism that maximizes the energy gain is found to be similar to that of the isolated vortex. Within the linear framework, the optimal perturbation for a vortex pair can be either symmetric or antisymmetric, whereas the structure of the nonlinear optimal perturbation, beyond the threshold
, is always asymmetric. No quasi-steady state for a counter-rotating vortex pair is observed.
In North America, the raccoon-associated variant of rabies virus (RRV) is of special concern, given its relatively rapid spread throughout the eastern USA and its potential public health impact due to high raccoon host densities in urban areas. Northward expansion of this epizootic included an outbreak in the Canadian province of Quebec in 2006–2009 due to trans-border spread from the State of Vermont. To inform a more proactive approach to future control efforts, this study uses phylogenetic analyses to explore the role of geography and alternative carnivore hosts in the dynamics of RRV spread within Vermont. Specifically, we sought to examine whether striped skunks, a species frequently infected by RRV, could be part of the maintenance host community. Whole genome sequencing of 160 RRV samples from Vermont and neighbouring US states were used for fine-scale phylogeographic analyses. Results, together with the complete surveillance record of raccoon rabies since its entry into Vermont in 1994, document incursions by two distinct viral lineages and identify topographical features of the landscape which have significantly influenced viral spread, resulting in a complex distribution pattern of viral variants throughout the state. Results of phylogenetic cluster analysis and discrete state reconstruction contained some evidence of skunk-to-skunk and skunk-to-raccoon transmission but overall failed to support a role for skunks as alternative maintenance hosts.
As part of further investigations into three linked haemorrhagic fever with renal syndrome (HFRS) cases in Wales and England, 21 rats from a breeding colony in Cherwell, and three rats from a household in Cheltenham were screened for hantavirus. Hantavirus RNA was detected in either the lungs and/or kidney of 17/21 (81%) of the Cherwell rats tested, higher than previously detected by blood testing alone (7/21, 33%), and in the kidneys of all three Cheltenham rats. The partial L gene sequences obtained from 10 of the Cherwell rats and the three Cheltenham rats were identical to each other and the previously reported UK Cherwell strain. Seoul hantavirus (SEOV) RNA was detected in the heart, kidney, lung, salivary gland and spleen (but not in the liver) of an individual rat from the Cherwell colony suspected of being the source of SEOV. Serum from 20/20 of the Cherwell rats and two associated HFRS cases had high levels of SEOV-specific antibodies (by virus neutralisation). The high prevalence of SEOV in both sites and the moderately severe disease in the pet rat owners suggest that SEOV in pet rats poses a greater public health risk than previously considered.
Passive surveillance for lyssaviruses in UK bats has been ongoing since 1987 and has identified 13 cases of EBLV-2 from a single species; Myotis daubentonii. No other lyssavirus species has been detected. Between 2005 and 2015, 10 656 bats were submitted, representing 18 species, creating a spatially and temporally uneven sample of British bat fauna. Uniquely, three UK cases originate from a roost at Stokesay Castle in Shropshire, England, where daily checks for grounded and dead bats are undertaken and bat carcasses have been submitted for testing since 2007. Twenty per cent of Daubenton's bats submitted from Stokesay Castle since surveillance began, have tested positive for EBLV-2. Phylogenetic analysis reveals geographical clustering of UK viruses. Isolates from Stokesay Castle are more closely related to one another than to viruses from other regions. Daubenton's bats from Stokesay Castle represent a unique opportunity to study a natural population that appears to maintain EBLV-2 infection and may represent endemic infection at this site. Although the risk to public health from EBLV-2 is low, consequences of infection are severe and effective communication on the need for prompt post-exposure prophylaxis for anyone that has been bitten by a bat is essential.
Data on the diets of young children in the UK are limited, despite growing evidence of the importance of early diet for long-term health. We used the largest contemporary dietary data set to describe the intake of 21-month-old children in the UK. Parents of 2336 children aged 21 months from the UK Gemini twin cohort completed 3-d diet diaries in 2008/2009. Family background information was obtained from questionnaires completed 8 months after birth. Mean total daily intakes of energy, macronutrients (g and %E) and micronutrients from food and beverages, including and excluding supplements, were derived. Comparisons with UK dietary reference values (DRV) were made using t tests and general linear regression models, respectively. Daily energy intake (kJ), protein (g) and most micronutrients exceeded DRV, except for vitamin D and Fe, where 96 or 84 % and 70 or 6 % of children did not achieve the reference nutrient intake or lower reference nutrient intake (LRNI), respectively, even with supplementation. These findings reflect similar observations in the smaller sample of children aged 18–36 months in the National Diet and Nutrition Survey. At a population level, young children in the UK are exceeding recommended daily intakes of energy and protein, potentially increasing their risk of obesity. The majority of children are not meeting the LRNI for vitamin D, largely reflecting inadequate use of the supplements recommended at this age. Parents may need more guidance on how to achieve healthy energy and nutrient intakes for young children.
The aim of this study was to examine cross-sectionally whether higher cardiorespiratory fitness (CRF) might favorably modify amyloid-β (Aβ)-related decrements in cognition in a cohort of late-middle-aged adults at risk for Alzheimer’s disease (AD). Sixty-nine enrollees in the Wisconsin Registry for Alzheimer’s Prevention participated in this study. They completed a comprehensive neuropsychological exam, underwent 11C Pittsburgh Compound B (PiB)-PET imaging, and performed a graded treadmill exercise test to volitional exhaustion. Peak oxygen consumption (VO2peak) during the exercise test was used as the index of CRF. Forty-five participants also underwent lumbar puncture for collection of cerebrospinal fluid (CSF) samples, from which Aβ42 was immunoassayed. Covariate-adjusted regression analyses were used to test whether the association between Aβ and cognition was modified by CRF. There were significant VO2peak*PiB-PET interactions for Immediate Memory (p=.041) and Verbal Learning & Memory (p=.025). There were also significant VO2peak*CSF Aβ42 interactions for Immediate Memory (p<.001) and Verbal Learning & Memory (p<.001). Specifically, in the context of high Aβ burden, that is, increased PiB-PET binding or reduced CSF Aβ42, individuals with higher CRF exhibited significantly better cognition compared with individuals with lower CRF. In a late-middle-aged, at-risk cohort, higher CRF is associated with a diminution of Aβ-related effects on cognition. These findings suggest that exercise might play an important role in the prevention of AD. (JINS, 2015, 21, 841–850)
The time series of vital signs, such as heart rate (HR) and blood pressure (BP), can exhibit complex dynamic behaviors as a result of internally and externally induced changes in the state of the underlying control systems (Peng et al. 1995; Ivanov et al. 1999; Costa et al. 2002). For instance, time series of BP can exhibit oscillations on the order of seconds (e.g., due to the variations in sympathovagal balance), to minutes (e.g., as a consequence of fever, blood loss, or behavioral factors), to hours (e.g., due to humoral variations, sleep-wake cycle, or circadian effects) (Mancia 2012; Parati et al. 2013). A question of interest is whether “similar” dynamical patterns can be automatically identified across a heterogeneous patient cohort, and be used for prognosis of patients' health and progress.
In this work, we present a Bayesian nonparametric switching Markov processes framework with conditionally linear dynamics to learn phenotypic dynamic behaviors from vital sign time series of a patient cohort, and use the learned dynamics to characterize the changing physiological states of patients for critical-care bed-side monitoring (Lehman et al. 2012, 2013, 2014a; Nemati 2012). We assume that although the underlying dynamical system may be nonlinear and nonstationary and the stochastic noise components can be non-Gaussian, the dynamics can be approximated by a collection of linear dynamical systems (Nemati 2012; Nemati et al. 2012). Each such linear “dynamic” (or mode) is a time-dependent rule that describes how the future state of the system evolves from its current state, centered around a given system equilibrium point. Therefore, an ideal algorithm would be able to identify time series segments that follow a “similar” dynamic, and would switch to a different mode upon a change in the state of the underlying system.
We explore several variants of the Bayesian nonparametric approach to discovery of shared dynamics among patients via switching Markov processes: hierarchical Dirichlet process (HDP) autoregressive hidden Markov model (HDP-AR-HMM) (Teh et al. 2006; Fox et al. 2008), an explicit-duration HDP-based hidden semi-Markov model (HDP-AR-HSMM) (Johnson & Willsky 2013a), and the beta process autoregressive HMM (BP-AR-HMM) (Fox 2009; Fox et al. 2009, 2014).
Experimental data are presented showing maximum carbon C6+ ion energies obtained from nm-scaled targets in the relativistic transparent regime for laser intensities between 9 × 1019 and 2 × 1021 W/cm2. When combined with two-dimensional particle-in-cell simulations, these results show a steep linear scaling for carbon ions with the normalized laser amplitude a0 (
$a_0 \propto \sqrt ( I)$
). The results are in good agreement with a semi-analytic model that allows one to calculate the optimum thickness and the maximum ion energies as functions of a0 and the laser pulse duration τλ for ion acceleration in the relativistic-induced transparency regime. Following our results, ion energies exceeding 100 MeV/amu may be accessible with currently available laser systems.
Vertebrate pigmentation provides an ideal system for studying the intersections between evolution, genetics, and developmental biology. Teleost fish, with their accessible developmental stages and intense and diverse colours produced by chromatophores, are an ideal group for study. We set out to test whether Betta splendens is a good model organism for studying the evolution and development of diverse pigmentation. Our results demonstrate that B. splendens can be bred to produce large numbers of offspring with easily visualized pigment cells. Depending on the colour of the parents, there was variation in larval pigmentation patterns both within and between breeding events. In juveniles the developing adult pigmentation patterns showed even greater variation. These results suggest that B. splendens has great potential as a model organism for pigmentation studies.
Infants in the neonatal intensive care unit (NICU) are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) acquisition. Outbreaks may be difficult to identify due in part to limitations in current molecular genotyping available in clinical practice. Comparison of genome-wide single nucleotide polymorphisms (SNPs) may identify epidemiologically distinct isolates among a population sample that appears homogenous when evaluated using conventional typing methods.
To investigate a putative MRSA outbreak in a NICU utilizing whole-genome sequencing and phylogenetic analysis to identify recent transmission events.
Clinical and surveillance specimens collected during clinical care and outbreak investigation.
A total of 17 neonates hospitalized in a 43-bed level III NICU in northeastern Florida from December 2010 to October 2011 were included in this study.
We assessed epidemiological data in conjunction with 4 typing methods: antibiograms, PFGE, spa types, and phylogenetic analysis of genome-wide SNPs.
Among the 17 type USA300 isolates, 4 different spa types were identified using pulsed-field gel electrophoresis. Phylogenetic analysis identified 5 infants as belonging to 2 clusters of epidemiologically linked cases and excluded 10 unlinked cases from putative transmission events. The availability of these results during the initial investigation would have improved infection control interventions.
Whole-genome sequencing and phylogenetic analysis are invaluable tools for epidemic investigation; they identify transmission events and exclude cases mistakenly implicated by traditional typing methods. When routinely applied to surveillance and investigation in the clinical setting, this approach may provide actionable intelligence for measured, appropriate, and effective interventions.
Infect. Control Hosp. Epidemiol. 2015;36(7):777–785