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Knowledge of population structure and breed composition of a population can be advantageous for a number of reasons; these include designing optimal (cross)breeding strategies in order to maximise non-additive genetic effects, maintaining flockbook integrity by authenticating animals being registered and as a quality control measure in the genotyping process. The objectives of the present study were to 1) describe the population structure of 24 sheep breeds, 2) quantify the breed composition of both flockbook-recorded and crossbred animals using single nucleotide polymorphism BLUP (SNP-BLUP), and 3) quantify the accuracy of breed composition prediction from low-density genotype panels containing between 2000 and 6000 SNPs. In total, 9334 autosomal SNPs on 11 144 flockbook-recorded animals and 1172 crossbred animals were used. The population structure of all breeds was characterised by principal component analysis (PCA) as well as the pairwise breed fixation index (Fst). The total number of animals, all of which were purebred, included in the calibration population for SNP-BLUP was 2579 with the number of animals per breed ranging from 9 to 500. The remaining 9559 flockbook-recorded animals, composite breeds and crossbred animals represented the test population; three breeds were excluded from breed composition prediction. The breed composition predicted using SNP-BLUP with 9334 SNPs was considered the gold standard prediction. The pairwise breed Fst ranged from 0.040 (between the Irish Blackface and Scottish Blackface) to 0.282 (between the Border Leicester and Suffolk). Principal component analysis revealed that the Suffolk from Ireland and the Suffolk from New Zealand formed distinct, non-overlapping clusters. In contrast, the Texel from Ireland and that from New Zealand formed integrated, overlapping clusters. Composite animals such as the Belclare clustered close to its founder breeds (i.e., Finn, Galway, Lleyn and Texel). When all 9334 SNPs were used to predict breed composition, an animal that had a majority breed proportion predicted to be ≥0.90 was defined as purebred for the present study. As the panel density decreased, the predicted breed proportion threshold, used to identify animals as purebred, also decreased (≥0.85 with 6000 SNPs to ≥0.60 with 2000 SNPs). In all, results from the study suggest that breed composition for purebred and crossbred animals can be determined with SNP-BLUP using ≥5000 SNPs.
In the present study, we aimed to compare anthropometric indicators as predictors of mortality in a community-based setting.
We conducted a population-based longitudinal study nested in a cluster-randomized trial. We assessed weight, height and mid-upper arm circumference (MUAC) on children 12 months after the trial began and used the trial’s annual census and monitoring visits to assess mortality over 2 years.
Children aged 6–60 months during the study.
Of 1023 children included in the study at baseline, height-for-age Z-score, weight-for-age Z-score, weight-for-height Z-score and MUAC classified 777 (76·0 %), 630 (61·6 %), 131 (12·9 %) and eighty (7·8 %) children as moderately to severely malnourished, respectively. Over the 2-year study period, fifty-eight children (5·7 %) died. MUAC had the greatest AUC (0·68, 95 % CI 0·61, 0·75) and had the strongest association with mortality in this sample (hazard ratio = 2·21, 95 % CI 1·26, 3·89, P = 0·006).
MUAC appears to be a better predictor of mortality than other anthropometric indicators in this community-based, high-malnutrition setting in Niger.
Shiga toxin-producing Escherichia coli (STEC) infection can cause serious illness including haemolytic uraemic syndrome. The role of socio-economic status (SES) in differential clinical presentation and exposure to potential risk factors amongst STEC cases has not previously been reported in England. We conducted an observational study using a dataset of all STEC cases identified in England, 2010–2015. Odds ratios for clinical characteristics of cases and foodborne, waterborne and environmental risk factors were estimated using logistic regression, stratified by SES, adjusting for baseline demographic factors. Incidence was higher in the highest SES group compared to the lowest (RR 1.54, 95% CI 1.19–2.00). Odds of Accident and Emergency attendance (OR 1.35, 95% CI 1.10–1.75) and hospitalisation (OR 1.71, 95% CI 1.36–2.15) because of illness were higher in the most disadvantaged compared to the least, suggesting potential lower ascertainment of milder cases or delayed care-seeking behaviour in disadvantaged groups. Advantaged individuals were significantly more likely to report salad/fruit/vegetable/herb consumption (OR 1.59, 95% CI 1.16–2.17), non-UK or UK travel (OR 1.76, 95% CI 1.40–2.27; OR 1.85, 95% CI 1.35–2.56) and environmental exposures (walking in a paddock, OR 1.82, 95% CI 1.22–2.70; soil contact, OR 1.52, 95% CI 2.13–1.09) suggesting other unmeasured risks, such as person-to-person transmission, could be more important in the most disadvantaged group.
Introduction: Simulation has assumed an integral role in the Canadian healthcare system with applications in quality improvement, systems development, and medical education. High quality simulation-based research (SBR) is required to ensure the effective and efficient use of this tool. This study sought to establish national SBR priorities and describe the barriers and facilitators of SBR in Emergency Medicine (EM) in Canada. Methods: Simulation leads (SLs) from all fourteen Canadian Departments or Divisions of EM associated with an adult FRCP-EM training program were invited to participate in three surveys and a final consensus meeting. The first survey documented active EM SBR projects. Rounds two and three established and ranked priorities for SBR and identified the perceived barriers and facilitators to SBR at each site. Surveys were completed by SLs at each participating institution, and priority research themes were reviewed by senior faculty for broad input and review. Results: Twenty SLs representing all 14 invited institutions participated in all three rounds of the study. 60 active SBR projects were identified, an average of 4.3 per institution (range 0-17). 49 priorities for SBR in Canada were defined and summarized into seven priority research themes. An additional theme was identified by the senior reviewing faculty. 41 barriers and 34 facilitators of SBR were identified and grouped by theme. Fourteen SLs representing 12 institutions attended the consensus meeting and vetted the final list of eight priority research themes for SBR in Canada: simulation in CBME, simulation for interdisciplinary and inter-professional learning, simulation for summative assessment, simulation for continuing professional development, national curricular development, best practices in simulation-based education, simulation-based education outcomes, and simulation as an investigative methodology. Conclusion: Conclusion: This study has summarized the current SBR activity in EM in Canada, as well as its perceived barriers and facilitators. We also provide a consensus on priority research themes in SBR in EM from the perspective of Canadian simulation leaders. This group of SLs has formed a national simulation-based research group which aims to address these identified priorities with multicenter collaborative studies.
Important Bird and Biodiversity Areas (IBAs) are sites identified as being globally important for the conservation of bird populations on the basis of an internationally agreed set of criteria. We present the first review of the development and spread of the IBA concept since it was launched by BirdLife International (then ICBP) in 1979 and examine some of the characteristics of the resulting inventory. Over 13,000 global and regional IBAs have so far been identified and documented in terrestrial, freshwater and marine ecosystems in almost all of the world’s countries and territories, making this the largest global network of sites of significance for biodiversity. IBAs have been identified using standardised, data-driven criteria that have been developed and applied at global and regional levels. These criteria capture multiple dimensions of a site’s significance for avian biodiversity and relate to populations of globally threatened species (68.6% of the 10,746 IBAs that meet global criteria), restricted-range species (25.4%), biome-restricted species (27.5%) and congregatory species (50.3%); many global IBAs (52.7%) trigger two or more of these criteria. IBAs range in size from < 1 km2 to over 300,000 km2 and have an approximately log-normal size distribution (median = 125.0 km2, mean = 1,202.6 km2). They cover approximately 6.7% of the terrestrial, 1.6% of the marine and 3.1% of the total surface area of the Earth. The launch in 2016 of the KBA Global Standard, which aims to identify, document and conserve sites that contribute to the global persistence of wider biodiversity, and whose criteria for site identification build on those developed for IBAs, is a logical evolution of the IBA concept. The role of IBAs in conservation planning, policy and practice is reviewed elsewhere. Future technical priorities for the IBA initiative include completion of the global inventory, particularly in the marine environment, keeping the dataset up to date, and improving the systematic monitoring of these sites.
Mycobacterium ulcerans is recognised as the third most common mycobacterial infection worldwide. It causes necrotising infections of skin and soft tissue and is classified as a neglected tropical disease by the World Health Organization (WHO). However, despite extensive research, the environmental reservoir of the organism and mode of transmission of the infection to humans remain unknown. This limits the ability to design and implement public health interventions to effectively and consistently prevent the spread and reduce the incidence of this disease. In recent years, the epidemiology of the disease has changed. In most endemic regions of the world, the number of cases reported to the WHO are reducing, with a 64% reduction in cases reported worldwide in the last 9 years. Conversely, in a smaller number of countries including Australia and Nigeria, reported cases are increasing at a rapid rate, new endemic areas continue to appear, and in Australia cases are becoming more severe. The reasons for this changing epidemiology are unknown. We review the epidemiology of M. ulcerans disease worldwide, and document recent changes. We also outline and discuss the current state of knowledge on the ecology of M. ulcerans, possible transmission mechanisms to humans and what may be enabling the spread of M. ulcerans into new endemic areas.
OBJECTIVES/SPECIFIC AIMS: Incomplete spinal cord injury typically results in life-long disability, often in the form of profound loss of locomotion capability. Individuals who have experienced incomplete spinal cord injury exhibit persistent eccentric motor deficits, which are particularly prevalent in the weight acceptance phase of gait and emphasized in sagittal plane knee motion and frontal plane hip motion. METHODS/STUDY POPULATION: Motion analysis can capture the kinematic and joint-level deficits of these individuals, but it is impossible to directly calculate the contributions of individual muscles to weight acceptance due to the complexity of the musculoskeletal system. Instead, those muscle contributions must be simulated in order to approximate muscle power during locomotion. RESULTS/ANTICIPATED RESULTS: The traditional method for driving these simulations with electromyography readings is unavailable for individuals who have neuromuscular deficits (e.g., spasticity or paralysis), due to the need to generate reliable maximum voluntary isometric contractions for baseline purposes. Instead, this research develops a novel method for using resting electromyography data to drive musculoskeletal simulations using a muscle activation threshold paradigm. DISCUSSION/SIGNIFICANCE OF IMPACT: The simulation results of this method more closely resemble experimental results, but further simulation refinement is needed to fully capture the true muscle activity.
To date, Ireland has been a leading light in the provision of youth mental health services. However, cognisant of the efforts of governmental and non-governmental agencies working in youth mental health, there is much to be done. Barriers into care as well as discontinuity of care across the spectrum of services remain key challenges. This editorial provides guidance for the next stage of development in youth mental care and support that will require significant national engagement and resource investment.
Introduction: Head injury is a common presentation to all emergency departments. Previous research has shown that such injuries may be complicated by delayed intracranial hemorrhage (D-ICH) after the initial scan is negative. Exposure to anticoagulant or anti-platelet medications (ACAP) may be a risk factor for D-ICH. We have conducted a systematic review and meta-analysis to determine the incidence of delayed traumatic intracranial hemorrhage in patients taking anticoagulants, anti-platelets or both. Methods: The literature search was conducted in March 2017 with an update in April 2017. Keyword and MeSH terms were used to search OVID Medline, Embase and the Cochrane database as well as grey literature sources. All cohort and experimental studies were eligible for selection. Inclusion criteria included pre-injury exposure to oral anticoagulant and / or anti-platelet medication and a negative initial CT scan of the brain (CT1). The primary outcome was delayed intracranial hemorrhage present on repeat CT scan (CT2) within 48 hours of the presentation. Only patients who were rescanned or observed minimally were included. Clinically significant D-ICH were those that required neurosurgery, caused death or necessitated a change in management strategy, such as admission. Results: Fifteen primary studies were ultimately identified, comprising a total of 3801 patients. Of this number, 2111 had a control CT scan. 39 cases of D-ICH were identified, with the incidence of D-ICH calculated to be 1.31% (95% CI [0.56, 2.27]). No more than 12 of these patients had a clinically significant D-ICH representing 0.09% (95% CI [0.00, 0.31]). 10 of them were on warfarin and two on aspirin. There were three deaths recorded and three patients needed neurosurgery. Conclusion: The relatively low incidence suggests that repeat CT should not be mandatory for patients without ICH on first CT. This is further supported by the negligibly low rate of clinically significant D-ICH. Evidence-based assessments should be utilised to indicate the appropriate discharge plan, with further research required to guide the balance between clinical observation and repeat CT.
We present a multi-frequency study of the intermediate spiral SAB(r)bc type galaxy NGC 6744, using available data from the Chandra X-Ray telescope, radio continuum data from the Australia Telescope Compact Array and Murchison Widefield Array, and Wide-field Infrared Survey Explorer infrared observations. We identify 117 X-ray sources and 280 radio sources. Of these, we find nine sources in common between the X-ray and radio catalogues, one of which is a faint central black hole with a bolometric radio luminosity similar to the Milky Way’s central black hole. We classify 5 objects as supernova remnant (SNR) candidates, 2 objects as likely SNRs, 17 as H ii regions, 1 source as an AGN; the remaining 255 radio sources are categorised as background objects and one X-ray source is classified as a foreground star. We find the star-formation rate (SFR) of NGC 6744 to be in the range 2.8–4.7 M⊙~yr − 1 signifying the galaxy is still actively forming stars. The specific SFR of NGC 6744 is greater than that of late-type spirals such as the Milky Way, but considerably less that that of a typical starburst galaxy.
Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 autosomal and 68 X-chromosome SNPs) on 383 female sheep. Genotype allele intensity values, either as their original raw values or transformed to logarithm intensity ratio (LRR), were used to accurately diagnose two dizygotic (i.e. fraternal) twin 53,X sheep, both of which received their single X chromosome from their sire. This is the first reported case of 53,X dizygotic twins in any species. Relative to the X-chromosome SNP genotype mean allele intensity values of normal females, the mean allele intensity value of SNP genotypes on the X chromosome of the two females monosomic for the X chromosome was 7.45 to 12.4 standard deviations less, and were easily detectable using either the AxiomTM or Illumina genotype platform; the next lowest mean allele intensity value of a female was 4.71 or 3.3 standard deviations less than the population mean depending on the platform used. Both 53,X females could also be detected based on the genotype LRR although this was more easily detectable when comparing the mean LRR of the X chromosome of each female to the mean LRR of their respective autosomes. On autopsy, the ovaries of the two sheep were small for their age and evidence of prior ovulation was not appreciated. In both sheep, the density of primordial follicles in the ovarian cortex was lower than normally found in ovine ovaries and primary follicle development was not observed. Mammary gland development was very limited. Results substantiate previous studies in other species that aneuploidy can be readily detected using SNP genotype allele intensity values generally already available, and the approach proposed in the present study was agnostic to genotype platform.
This paper will review a new technique of detecting companion stars in LMXBs and X-ray transients in outburst using the Bowen fluorescence NIII lines at 4634-4640. These lines are very efficiently reprocessed in the atmospheres of the companion stars and, thereby, provide estimates of the K2 velocities and mass functions. The method has been applied to Sco X-1, X1822-371 and GX339-4 which, in the latter case, provides dynamical evidence for the presence of an accreting black hole. Preliminary results from a VLT campaign on V801 Ara, V926 Sco and XTE J1814-338 are also presented.
We present first results from a coordinated multiwavelength study of the neutron star low-mass X-ray binary EXO 0748 676. Fast UV, X-ray, and optical data were obtained including both spectral and timing information. We discuss how this study allows us to probe the temperature distribution within the binary and hence the geometry and efficiency of X-ray irradiation.
An adolescent male with a recent history of streptococcal pharyngitis presented with severe substernal chest pain, troponin leak, and ST-segment elevation, which are suggestive of acute inferolateral myocardial infarction. The coronary angiogram was normal. The patient was subsequently diagnosed with non-rheumatic streptococcal myocarditis. He was treated with amoxicillin and had excellent recovery. Non-rheumatic streptococcal myocarditis is an important mimic of acute myocardial infarction in young adults.
In the context of water use for agricultural production, water footprints (WFs) have become an important sustainability indicator. To understand better the water demand for beef and sheep meat produced on pasture-based systems, a WF of individual farms is required. The main objective of this study was to determine the primary contributors to freshwater consumption up to the farm gate expressed as a volumetric WF and associated impacts for the production of 1 kg of beef and 1 kg of sheep meat from a selection of pasture-based farms for 2 consecutive years, 2014 and 2015. The WF included green water, from the consumption of soil moisture due to evapotranspiration, and blue water, from the consumption of ground and surface waters. The impact of freshwater consumption on global water stress from the production of beef and sheep meat in Ireland was also computed. The average WF of the beef farms was 8391 l/kg carcass weight (CW) of which 8222 l/kg CW was green water and 169 l/kg CW was blue water; water for the production of pasture (including silage and grass) contributed 88% to the WF, concentrate production – 10% and on-farm water use – 1%. The average stress-weighted WF of beef was 91 l H2O eq/kg CW, implying that each kg of beef produced in Ireland contributed to freshwater scarcity equivalent to the consumption of 91 l of freshwater by an average world citizen. The average WF of the sheep farms was 7672 l/kg CW of which 7635 l/kg CW was green water and 37 l/kg CW was blue water; water for the production of pasture contributed 87% to the WF, concentrate production – 12% and on-farm water use – 1%. The average stress-weighted WF was 2 l H2O eq/kg CW for sheep. This study also evaluated the sustainability of recent intensification initiatives in Ireland and found that increases in productivity were supported through an increase in green water use and higher grass yields per hectare on both beef and sheep farms.
The objective of this experiment was to establish the effect of low-concentrate (LC) and high-concentrate (HC) supplementation in the early and late periods of lactation on milk production and cow traffic in a pasture-based automatic milking (AM) system. In total, 40 cows (10 primiparous and 30 multiparous) were randomly assigned to one of the two treatments. The experimental periods for the early and late lactation trials extended from 23 February to 12 April 2015 and 31 August to 18 October 2015, respectively (49 days in each trial period). The early lactation supplement levels were 2.3 and 4.4 kg/cow per day for LC and HC, respectively, whereas the late lactation supplement levels were 0.5 and 2.7 kg/cow per day for LC and HC, respectively. Variables measured included milking frequency, milking interval, milking outcome and milking characteristics, milk yield/visit and per day, wait time/visit and per day, return time/visit and the distribution of gate passes. As the herd was seasonal (spring) calving, the experimental periods could not run concurrently and as a result no statistical comparison between the periods was conducted. There was no significant effect of treatment in the early lactation period on any of the milk production, milking characteristics or cow traffic variables. However, treatment did significantly affect the distribution of gate passes, with the HC cows recording significantly more gate passes in the hours preceding the gate time change such as hours 7 (P<0.01), 15 (P<0.05), 20, 21 (P<0.001), and 22 (P<0.05), whereas the LC treatment recorded significantly more gate passes in the hours succeeding the gate time change, such as time points 2 (P<0.01) and 10 (P<0.05). There was a significant effect of treatment in late lactation, with HC having a greater milk yield (P<0.01), milking duration and activity/day (P<0.05), while also having a significantly shorter milking interval (P<0.05) and return time/visit (P<0.01). The distribution of gate passes were similar to the early lactation period, with HC also recording a significantly greater number of gate passes during the early morning period (P<0.01) when visitations were at their lowest. Any decision regarding the supplementing of dairy cows with concentrates needs to be examined from an economic perspective, to establish if the milk production and cow traffic benefits displayed in late lactation outweigh the cost of the concentrate; thereby ensuring that the decision to supplement is financially prudent.
Synthesis of Ni and Zn substituted nano-greigite,
Fe3S4, is achieved from single source
diethyldithiocarbamato precursor compounds, producing particles typically
50–100 nm in diameter with plate-like pseudohexagonal morphologies. Up to 12
wt.% Ni is incorporated into the greigite structure, and there is evidence
that Zn is also incorporated but Co is not substituted into the lattice. The
Fe L3 X-ray absorption spectra for these materials have a narrow
single peak at 707.7 eV and the resulting main X-ray magnetic circular
dichroism (XMCD) has the same sign at 708.75 eV. All XMCD spectra also have
a broad positive feature at 711 eV, a characteristic of covalent mixing. The
greigite XMCD spectra contrast with the three clearly defined XMCD site
specific peaks found in the ferrite spinel, magnetite. The Fe
L2,3X-ray absorption spectra and XMCD spectra of the
greigite reflect and reveal the high conductivity of greigite and the very
strong covalency of the Fe–S bonding. The electron hopping between
Fe3+ and Fe2+ on octahedral sites results in an
intermediate oxidation state of the Fe in the Oh site of
Fe2.5+ producing an effective formula of [Fe3+
↑]A-site[2Fe2.5+ ↓]B-siteS42–]. The Ni L2,3 X-ray absorption spectra and XMCD reveal substitution on the
Oh site with a strongly covalent character and an
oxidation state <Ni1.5+ in a representative formula
[Fe3+ ↑]A[[(2 – x)Fe2.5+
Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys’ dams (i.e. mates of the sire to be imputed). The impact on the accuracy of genotype imputation by including more progeny (and their dams’) genotypes in the imputation reference population was also quantified. When genotypes of the dams were not available, genotypes of 41 sires with at least 15 genotyped progeny were used for the imputation; when genotypes of the dams were available, genotypes of 21 sires with at least 10 genotyped progeny were used for the imputation. Imputation was undertaken exploiting family and population level information. The mean and variability in the proportion of genotypes per individual that could not be imputed reduced as the number of progeny genotypes used per individual increased. Little improvement in the proportion of genotypes that could not be imputed was achieved once genotypes of seven progeny and their dams were used or genotypes of 11 progeny without their respective dam’s genotypes were used. Mean imputation accuracy per individual (depicted by both concordance rates and correlation between true and imputed) increased with increasing progeny group size. Moreover, the range in mean imputation accuracy per individual reduced as more progeny genotypes were used in the imputation. If the genotype of the mate of the sire was also used, high accuracy of imputation (mean genotype concordance rate per individual of 0.988), with little additional benefit thereafter, was achieved with seven genotyped progeny. In the absence of genotypes on the dam, similar imputation accuracy could not be achieved even using genotypes on up to 15 progeny. Results therefore suggest, at least for the SNP density used in the present study, that it is possible to accurately impute the genotypes of a non-genotyped parent from the genotypes of its progeny and there is a benefit of also including the genotype of the sire’s mate (i.e. dam of the progeny).