Neutrino Quasielastic Scattering on Nuclear Targets: Parametrizing Transverse Enhancement (Meson Exchange Currents)

We present a parametrization of the observed enhancement in the transverse electron quasielastic (QE) response function for nucleons bound in carbon as a function of the square of the four momentum transfer ($Q^2$) in terms of a correction to the magnetic form factors of bound nucleons. The parametrization should also be applicable to the transverse cross section in neutrino scattering. If the transverse enhancement originates from meson exchange currents (MEC), then it is theoretically expected that any enhancement in the longitudinal or axial contributions is small. We present the predictions of the "Transverse Enhancement" model (which is based on electron scattering data only) for the $\nu_\mu, \bar{\nu}_\mu$ differential and total QE cross sections for nucleons bound in carbon. The $Q^2$ dependence of the transverse enhancement is observed to resolve much of the long standing discrepancy in the QE total cross sections and differential distributions between low energy and high energy neutrino experiments on nuclear targets.Comment: Revised Version- July 21, 2011: 17 pages, 20 Figures. To be published in Eur. Phys. J.

Environmental Impact of Undular Tidal Bores in Tropical Rivers

A tidal bore impacts significantly on the estuarine ecosystem, although little is known on the flow field, mixing and sediment motion beneath tidal bores. In the absence of detailed systematic field measurements, a quasi-steady flow analogy was applied to investigate undular tidal bores with inflow Froude numbers between 1.25 and 1.6. Experimental results indicated that rapid flow redistributions occur beneath the free-surface undulations, with significant variations in bed shear stress between wave crests and troughs. Dynamic similarity was used to predict detailed flow characteristics of undular tidal bores. The effects of periodic loading on river sediments, scour of river bed and flow mixing behind the bore are discussed. A better understanding of these processes will contribute to better management practices in tidal bore affected rivers, including the Styx and Daly rivers in tropical Australia

Reconstructing the accumulation history of a saltmarsh sediment core: which age-depth model is best?

Saltmarsh-based reconstructions of relative sea-level (RSL) change play a central role in current efforts seeking to quantify the relationship between climate and sea-level rise. The development of an accurate chronology is pivotal, since errors in age-depth relationships will propagate to the final record as alterations in both the timing and magnitude of reconstructed change. A range of age-depth modelling packages are available but differences in their theoretical basis and practical operation mean contrasting accumulation histories can be produced from the same dataset. We compare the performance of five age-depth modelling programs (Bacon, Bchron, Bpeat, Clam and OxCal) when applied to the kinds of data used in high resolution, saltmarsh-based RSL reconstructions. We investigate their relative performance by comparing modelled accumulation curves against known age-depth relationships generated from simulated stratigraphic sequences. Bpeat is particularly sensitive to non-linearities which, whilst maximising the detection of small rate changes, has the potential to generate spurious variations, particularly in the last 400 years. Bacon generally replicates the pattern and magnitude of change but with notable offsets in timing. Bchron and OxCal successfully constrain the known accumulation history within their error envelopes although the best-fit solutions tend to underestimate the magnitude of change. The best-fit solutions of Clam generally replicate the timing and magnitude of changes well, but are sensitive to the underlying shape of the calibration curve, performing poorly where plateaus in atmospheric 14C concentration exist. We employ an ensemble of age-depth models to reconstruct a 1500 year accumulation history for a saltmarsh core recovered from Connecticut, USA based on a composite chronology comprising 26 AMS radiocarbon dates, 210Pb, 137Cs radionuclides and an historical pollen chronohorizon. The resulting record reveals non-linear accumulation during the late Holocene with a marked increase in rate around AD1800. With the exception of the interval between AD1500 and AD1800, all modelsproduce accumulation curves that agree to within ~10 cm at the century-scale. The accumulation rate increase around AD1800 is associated with the transition from a radiocarbon-based to a 210Pb dominated chronology. Whilst repeat analysis excluding the 210Pb data alters the precise timing and magnitude of this acceleration, a shift to faster accumulation compared to the long-term rate is a robust feature of the record and not simply an artefact of the switch in dating methods. Simulation indicates that a rise of similar magnitude to the post-AD1800 increase (detrended increase of ~16 cm) is theoretically constrained and detectable within the radiocarbon-dated portion of the record. The absence of such a signal suggests that the recent rate of accumulation is unprecedented in the last 1500 years. Our results indicate that reliable (sub)century-scale age-depth models can be developed from saltmarsh sequences, and that the vertical uncertainties associated with them translate to RSL reconstruction errors that are typically smaller than those associated with the most precise microfossil-based estimates of palaeomarsh-surface elevation

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Global, regional, and national under-5 mortality, adult mortality, age-specific mortality, and life expectancy, 1970–2016: a systematic analysis for the Global Burden of Disease Study 2016

BACKGROUND: Detailed assessments of mortality patterns, particularly age-specific mortality, represent a crucial input that enables health systems to target interventions to specific populations. Understanding how all-cause mortality has changed with respect to development status can identify exemplars for best practice. To accomplish this, the Global Burden of Diseases, Injuries, and Risk Factors Study 2016 (GBD 2016) estimated age-specific and sex-specific all-cause mortality between 1970 and 2016 for 195 countries and territories and at the subnational level for the five countries with a population greater than 200 million in 2016. METHODS: We have evaluated how well civil registration systems captured deaths using a set of demographic methods called death distribution methods for adults and from consideration of survey and census data for children younger than 5 years. We generated an overall assessment of completeness of registration of deaths by dividing registered deaths in each location-year by our estimate of all-age deaths generated from our overall estimation process. For 163 locations, including subnational units in countries with a population greater than 200 million with complete vital registration (VR) systems, our estimates were largely driven by the observed data, with corrections for small fluctuations in numbers and estimation for recent years where there were lags in data reporting (lags were variable by location, generally between 1 year and 6 years). For other locations, we took advantage of different data sources available to measure under-5 mortality rates (U5MR) using complete birth histories, summary birth histories, and incomplete VR with adjustments; we measured adult mortality rate (the probability of death in individuals aged 15-60 years) using adjusted incomplete VR, sibling histories, and household death recall. We used the U5MR and adult mortality rate, together with crude death rate due to HIV in the GBD model life table system, to estimate age-specific and sex-specific death rates for each location-year. Using various international databases, we identified fatal discontinuities, which we defined as increases in the death rate of more than one death per million, resulting from conflict and terrorism, natural disasters, major transport or technological accidents, and a subset of epidemic infectious diseases; these were added to estimates in the relevant years. In 47 countries with an identified peak adult prevalence for HIV/AIDS of more than 0·5% and where VR systems were less than 65% complete, we informed our estimates of age-sex-specific mortality using the Estimation and Projection Package (EPP)-Spectrum model fitted to national HIV/AIDS prevalence surveys and antenatal clinic serosurveillance systems. We estimated stillbirths, early neonatal, late neonatal, and childhood mortality using both survey and VR data in spatiotemporal Gaussian process regression models. We estimated abridged life tables for all location-years using age-specific death rates. We grouped locations into development quintiles based on the Socio-demographic Index (SDI) and analysed mortality trends by quintile. Using spline regression, we estimated the expected mortality rate for each age-sex group as a function of SDI. We identified countries with higher life expectancy than expected by comparing observed life expectancy to anticipated life expectancy on the basis of development status alone. FINDINGS: Completeness in the registration of deaths increased from 28% in 1970 to a peak of 45% in 2013; completeness was lower after 2013 because of lags in reporting. Total deaths in children younger than 5 years decreased from 1970 to 2016, and slower decreases occurred at ages 5-24 years. By contrast, numbers of adult deaths increased in each 5-year age bracket above the age of 25 years. The distribution of annualised rates of change in age-specific mortality rate differed over the period 2000 to 2016 compared with earlier decades: increasing annualised rates of change were less frequent, although rising annualised rates of change still occurred in some locations, particularly for adolescent and younger adult age groups. Rates of stillbirths and under-5 mortality both decreased globally from 1970. Evidence for global convergence of death rates was mixed; although the absolute difference between age-standardised death rates narrowed between countries at the lowest and highest levels of SDI, the ratio of these death rates-a measure of relative inequality-increased slightly. There was a strong shift between 1970 and 2016 toward higher life expectancy, most noticeably at higher levels of SDI. Among countries with populations greater than 1 million in 2016, life expectancy at birth was highest for women in Japan, at 86·9 years (95% UI 86·7-87·2), and for men in Singapore, at 81·3 years (78·8-83·7) in 2016. Male life expectancy was generally lower than female life expectancy between 1970 and 2016, an

Global, regional, and national age-sex-specific mortality and life expectancy, 1950–2017: a systematic analysis for the Global Burden of Disease Study 2017

BACKGROUND: Assessments of age-specific mortality and life expectancy have been done by the UN Population Division, Department of Economics and Social Affairs (UNPOP), the United States Census Bureau, WHO, and as part of previous iterations of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD). Previous iterations of the GBD used population estimates from UNPOP, which were not derived in a way that was internally consistent with the estimates of the numbers of deaths in the GBD. The present iteration of the GBD, GBD 2017, improves on previous assessments and provides timely estimates of the mortality experience of populations globally. METHODS: The GBD uses all available data to produce estimates of mortality rates between 1950 and 2017 for 23 age groups, both sexes, and 918 locations, including 195 countries and territories and subnational locations for 16 countries. Data used include vital registration systems, sample registration systems, household surveys (complete birth histories, summary birth histories, sibling histories), censuses (summary birth histories, household deaths), and Demographic Surveillance Sites. In total, this analysis used 8259 data sources. Estimates of the probability of death between birth and the age of 5 years and between ages 15 and 60 years are generated and then input into a model life table system to produce complete life tables for all locations and years. Fatal discontinuities and mortality due to HIV/AIDS are analysed separately and then incorporated into the estimation. We analyse the relationship between age-specific mortality and development status using the Socio-demographic Index, a composite measure based on fertility under the age of 25 years, education, and income. There are four main methodological improvements in GBD 2017 compared with GBD 2016: 622 additional data sources have been incorporated; new estimates of population, generated by the GBD study, are used; statistical methods used in different components of the analysis have been further standardised and improved; and the analysis has been extended backwards in time by two decades to start in 1950. FINDINGS: Globally, 18·7% (95% uncertainty interval 18·4–19·0) of deaths were registered in 1950 and that proportion has been steadily increasing since, with 58·8% (58·2–59·3) of all deaths being registered in 2015. At the global level, between 1950 and 2017, life expectancy increased from 48·1 years (46·5–49·6) to 70·5 years (70·1–70·8) for men and from 52·9 years (51·7–54·0) to 75·6 years (75·3–75·9) for women. Despite this overall progress, there remains substantial variation in life expectancy at birth in 2017, which ranges from 49·1 years (46·5–51·7) for men in the Central African Republic to 87·6 years (86·9–88·1) among women in Singapore. The greatest progress across age groups was for children younger than 5 years; under-5 mortality dropped from 216·0 deaths (196·3–238·1) per 1000 livebirths in 1950 to 38·9 deaths (35·6–42·83) per 1000 livebirths in 2017, with huge reductions across countries. Nevertheless, there were still 5·4 million (5·2–5·6) deaths among children younger than 5 years in the world in 2017. Progress has been less pronounced and more variable for adults, especially for adult males, who had stagnant or increasing mortality rates in several countries. The gap between male and female life expectancy between 1950 and 2017, while relatively stable at the global level, shows distinctive patterns across super-regions and has consistently been the largest in central Europe, eastern Europe, and central Asia, and smallest in south Asia. Performance was also variable across countries and time in observed mortality rates compared with those expected on the basis of development. INTERPRETATION: This analysis of age-sex-specific mortality shows that there are remarkably complex patterns in population mortality across countries. The findings of this study highlight global successes, such as the large decline in under-5 mortality, which reflects significant local, national, and global commitment and investment over several decades. However, they also bring attention to mortality patterns that are a cause for concern, particularly among adult men and, to a lesser extent, women, whose mortality rates have stagnated in many countries over the time period of this study, and in some cases are increasing

Assessing the Influence of a Range of Spring Meteorological Parameters on Tree Phenology

The timing of phenological phases, such as leaf unfolding of trees, is partly driven by the weather. The impact of weather on the spring phenology of a selection of tree species in the phenological garden at Valentia Observatory, Caherciveen, County Kerry, Ireland, for the period 1967-2004 was assessed. In particular, the beginning of the growing season (BGS), as determined by the date of leaf unfolding, was considered. The impact on BGS of a range of meteorological parameters and derived parameters, including minimum, maximum and mean air temperature (°C), soil temperature (°C), rainfall (mm), sunshine (hours), number of air frost days and number of rain days was investigated. These parameters were averaged or summed over the months of February, March and April and linear regression analysis with BGS was carried out for several tree species. The results showed that the regression coefficients of BGS on minimum air and soil temperature were highest, with Populus canescens and Populus tremula showing the strongest relationships. Temperature parameters were found to be more important in driving advancing phenology than any other meteorological parameter tested