The HadGEM3-GA7.1 radiative kernel: the importance of a well-resolved stratosphere

We present top-of-atmosphere and surface radiative kernels based on the atmospheric component (GA7.1) of the HadGEM3 general circulation model developed by the UK Met Office. We show that the utility of radiative kernels for forcing adjustments in idealised CO2 perturbation experiments is greatest where there is sufficiently high resolution in the stratosphere in both the target climate model and the radiative kernel. This is because stratospheric cooling to a CO2 perturbation continues to increase with height, and low-resolution or low-top kernels or climate model output are unable to fully resolve the full stratospheric temperature adjustment. In the sixth phase of the Coupled Model Intercomparison Project (CMIP6), standard atmospheric model data are available up to 1 hPa on 19 pressure levels, which is a substantial advantage compared to CMIP5. We show in the IPSL-CM6A-LR model where a full set of climate diagnostics are available that the HadGEM3-GA7.1 kernel exhibits linear behaviour and the residual error term is small, as well as from a survey of kernels available in the literature that in general low-top radiative kernels underestimate the stratospheric temperature response. The HadGEM3-GA7.1 radiative kernels are available at https://doi.org/10.5281/zenodo.3594673 (Smith, 2019)

Spud 1.0: generalising and automating the user interfaces of scientific computer models

The interfaces by which users specify the scenarios to be simulated by scientific computer models are frequently primitive, under-documented and ad-hoc text files which make using the model in question difficult and error-prone and significantly increase the development cost of the model. In this paper, we present a model-independent system, Spud, which formalises the specification of model input formats in terms of formal grammars. This is combined with an automated graphical user interface which guides users to create valid model inputs based on the grammar provided, and a generic options reading module, libspud, which minimises the development cost of adding model options. <br><br> Together, this provides a user friendly, well documented, self validating user interface which is applicable to a wide range of scientific models and which minimises the developer input required to maintain and extend the model interface

Analyzing First-Person Stories Based on Socializing, Eating and Sedentary Patterns

First-person stories can be analyzed by means of egocentric pictures acquired throughout the whole active day with wearable cameras. This manuscript presents an egocentric dataset with more than 45,000 pictures from four people in different environments such as working or studying. All the images were manually labeled to identify three patterns of interest regarding people's lifestyle: socializing, eating and sedentary. Additionally, two different approaches are proposed to classify egocentric images into one of the 12 target categories defined to characterize these three patterns. The approaches are based on machine learning and deep learning techniques, including traditional classifiers and state-of-art convolutional neural networks. The experimental results obtained when applying these methods to the egocentric dataset demonstrated their adequacy for the problem at hand.Comment: Accepted at First International Workshop on Social Signal Processing and Beyond, 19th International Conference on Image Analysis and Processing (ICIAP), September 201

Calibration, inversion and sensitivity analysis for hydro-morphodynamic models through the application of adjoint methods

The development of reliable, sophisticated hydro-morphodynamic models is essential for protecting the coastal environment against hazards such as flooding and erosion. There exists a high degree of uncertainty associated with the application of these models, in part due to incomplete knowledge of various physical, empirical and numerical closure related parameters in both the hydrodynamic and morphodynamic solvers. This uncertainty can be addressed through the application of adjoint methods. These have the notable advantage that the number and/or dimension of the uncertain parameters has almost no effect on the computational cost associated with calculating the model sensitivities. Here, we develop the first freely available and fully flexible adjoint hydro-morphodynamic model framework. This flexibility is achieved through using the pyadjoint library, which allows us to assess the uncertainty of any parameter with respect to any model functional, without further code implementation. The model is developed within the coastal ocean model Thetis constructed using the finite element code-generation library Firedrake. We present examples of how this framework can perform sensitivity analysis, inversion and calibration for a range of uncertain parameters based on the final bedlevel. These results are verified using so-called dual-twin experiments, where the ‘correct’ parameter value is used in the generation of synthetic model test data, but is unknown to the model in subsequent testing. Moreover, we show that inversion and calibration with experimental data using our framework produces physically sensible optimum parameters and that these parameters always lead to more accurate results. In particular, we demonstrate how our adjoint framework can be applied to a tsunami-like event to invert for the tsunami wave from sediment deposits

A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data

BACKGROUND: In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed. RESULTS: A number of validation experiments were performed on Lactococcus lactis IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance. CONCLUSION: Even in cases where 90 % of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days), the CV was at an acceptable 25 %. Clustering experiments showed that trends can be reliably detected also from genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality

Surface warming and wetting due to methane’s long-wave radiative effects muted by short-wave absorption

Although greenhouse gases absorb primarily long-wave radiation, they also absorb short-wave radiation. Recent studies have highlighted the importance of methane short-wave absorption, which enhances its stratospherically adjusted radiative forcing by up to ~ 15%. The corresponding climate impacts, however, have been only indirectly evaluated and thus remain largely unquantified. Here we present a systematic, unambiguous analysis using one model and separate simulations with and without methane short-wave absorption. We find that methane short-wave absorption counteracts ~30% of the surface warming associated with its long-wave radiative effects. An even larger impact occurs for precipitation as methane short-wave absorption offsets ~60% of the precipitation increase relative to its long-wave radiative effects. The methane short-wave-induced cooling is due largely to cloud rapid adjustments, including increased low-level clouds, which enhance the reflection of incoming short-wave radiation, and decreased high-level clouds, which enhance outgoing long-wave radiation. The cloud responses, in turn, are related to the profile of atmospheric solar heating and corresponding changes in temperature and relative humidity. Despite our findings, methane remains a potent contributor to global warming, and efforts to reduce methane emissions are vital for keeping global warming well below 2 °C above preindustrial values

Physics of Neutron Star Kicks

It is no longer necessary to `sell' the idea of pulsar kicks, the notion that neutron stars receive a large velocity (a few hundred to a thousand km s$^{-1}$) at birth. However, the origin of the kicks remains mysterious. We review the physics of different kick mechanisms, including hydrodynamically driven, neutrino and magnetically driven kicks.Comment: 8 pages including 1 figure. To be published in "Stellar Astrophysics" (Pacific Rim Conference Proceedings), (Kluwer Pub.

Breastfeeding patterns and exposure to suboptimal breastfeeding among children in developing countries: review and analysis of nationally representative surveys

BACKGROUND: Suboptimal breastfeeding is associated with higher mortality among infants and young children in the developing world. We describe patterns in 'exclusive breastfeeding' and 'any breastfeeding' rates and quantify exposure to suboptimal breastfeeding among children aged two years or younger in developing countries. METHODS: We reviewed nationally representative surveys that collected data on breastfeeding rates in 94 developing countries. Surveys were categorized by completeness and comprehensiveness of data. Complete and comprehensive data were analysed with minimum chi-square regression. With a fitting procedure, estimated parameters were used to impute missing observations for incomplete or non-comprehensive surveys. Breastfeeding indicators were calculated and are reported for 135 developing countries by UN region. RESULTS: Amongst infants aged six months or younger in the developing world, the prevalence of exclusive breastfeeding is 39% and the prevalence of no breastfeeding is 5.6%. The prevalence of continued breastfeeding is 86% and 68% for infants and children aged 6–11 and 12–23 months, respectively, in the developing world. Imputation expands population coverage of indicators, especially for infants. Breastfeeding trends are highly linear and estimated parameters defining the age-specific attrition hazard are robust. Survey-reported rates, particularly for exclusive breastfeeding, appear to have systematic upward bias, and exposure estimates must be considered conservative. CONCLUSIONS: Compliance with breastfeeding recommendations in developing countries is low, and more attention should be given to increasing breastfeeding – especially exclusive breastfeeding – and to monitoring trends. Although the introduction of more standardized and better validated survey instruments is desirable, since data coverage, completeness and comprehensiveness are extensive, global exposure assessment is relatively robust. Moreover, the regularity of breastfeeding patterns show existing survey data capture real biological and social phenomena. Our method for the analysis of breastfeeding rates provides a potent tool for summarizing trends, validating observations, translating and extrapolating indicators (as well as projecting and imputing estimates when necessary) and should support more effective child health monitoring

Experimental Passage of St. Louis Encephalitis Virus In Vivo in Mosquitoes and Chickens Reveals Evolutionarily Significant Virus Characteristics

St. Louis encephalitis virus (SLEV; Flaviviridae, flavivirus) was the major cause of epidemic flaviviral encephalitis in the U.S. prior to the introduction of West Nile virus (WNV) in 1999. However, outbreaks of SLEV have been significantly more limited then WNV in terms of levels of activity and geographic dispersal. One possible explanation for these variable levels of activity is that differences in the potential for each virus to adapt to its host cycle exist. The need for arboviruses to replicate in disparate hosts is thought to result in constraints on both evolution and host-specific adaptation. If cycling is the cause of genetic stability observed in nature and arboviruses lack host specialization, then sequential passage should result in both the accumulation of mutations and specialized viruses better suited for replication in that host. Previous studies suggest that WNV and SLEV differ in capacity for both genetic change and host specialization, and in the costs each accrues from specializing. In an attempt to clarify how selective pressures contribute to epidemiological patterns of WNV and SLEV, we evaluated mutant spectra size, consensus genetic change, and phenotypic changes for SLEV in vivo following 20 sequential passages via inoculation in either Culex pipiens mosquitoes or chickens. Results demonstrate that the capacity for genetic change is large for SLEV and that the size of the mutant spectrum is host-dependent using our passage methodology. Despite this, a general lack of consensus change resulted from passage in either host, a result that contrasts with the idea that constraints on evolution in nature result from host cycling alone. Results also suggest that a high level of adaptation to both hosts already exists, despite host cycling. A strain significantly more infectious in chickens did emerge from one lineage of chicken passage, yet other lineages and all mosquito passage strains did not display measurable host-specific fitness gains. In addition, increased infectivity in chickens did not decrease infectivity in mosquitoes, which further contrasts the concept of fitness trade-offs for arboviruses