Leveraging population admixture to characterize the heritability of complex traits.

Despite recent progress on estimating the heritability explained by genotyped SNPs (h(2)g), a large gap between h(2)g and estimates of total narrow-sense heritability (h(2)) remains. Explanations for this gap include rare variants or upward bias in family-based estimates of h(2) due to shared environment or epistasis. We estimate h(2) from unrelated individuals in admixed populations by first estimating the heritability explained by local ancestry (h(2)γ). We show that h(2)γ = 2FSTCθ(1 - θ)h(2), where FSTC measures frequency differences between populations at causal loci and θ is the genome-wide ancestry proportion. Our approach is not susceptible to biases caused by epistasis or shared environment. We applied this approach to the analysis of 13 phenotypes in 21,497 African-American individuals from 3 cohorts. For height and body mass index (BMI), we obtained h(2) estimates of 0.55 ± 0.09 and 0.23 ± 0.06, respectively, which are larger than estimates of h(2)g in these and other data but smaller than family-based estimates of h(2)

Yield Strength of Transparent MgAl2O4 Nano-Ceramic at High Pressure and Temperature

We report here experimental results of yield strength and stress relaxation measurements of transparent MgAl2O4 nano-ceramics at high pressure and temperature. During compression at ambient temperature, the differential strain deduced from peak broadening increased significantly with pressure up to 2 GPa, with no clear indication of strain saturation. However, by then, warming the sample above 400°C under 4 GPa, stress relaxation was obviously observed, and all subsequent plastic deformation cycles are characterized again by peak broadening. Our results reveal a remarkable reduction in yield strength as the sintering temperature increases from 400 to 900°C. The low temperature for the onset of stress relaxation has attracted attention regarding the performance of transparent MgAl2O4 nano-ceramics as an engineering material

Leveraging population admixture to explain missing heritability of complex traits

Despite recent progress on estimating the heritability explained by genotyped SNPs (hg2), a large gap between hg2 and estimates of total narrow-sense heritability (h2) remains. Explanations for this gap include rare variants, or upward bias in family-based estimates of h2 due to shared environment or epistasis. We estimate h2 from unrelated individuals in admixed populations by first estimating the heritability explained by local ancestry (hγ2). We show that hγ2 = 2FSTCθ(1−θ)h2, where FSTC measures frequency differences between populations at causal loci and θ is the genome-wide ancestry proportion. Our approach is not susceptible to biases caused by epistasis or shared environment. We examined 21,497 African Americans from three cohorts, analyzing 13 phenotypes. For height and BMI, we obtained h2 estimates of 0.55 ± 0.09 and 0.23 ± 0.06, respectively, which are larger than estimates of hg2 in these and other data, but smaller than family-based estimates of h2

Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults

Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious

Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults

Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious

Global, regional, and national burden of disorders affecting the nervous system, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BackgroundDisorders affecting the nervous system are diverse and include neurodevelopmental disorders, late-life neurodegeneration, and newly emergent conditions, such as cognitive impairment following COVID-19. Previous publications from the Global Burden of Disease, Injuries, and Risk Factor Study estimated the burden of 15 neurological conditions in 2015 and 2016, but these analyses did not include neurodevelopmental disorders, as defined by the International Classification of Diseases (ICD)-11, or a subset of cases of congenital, neonatal, and infectious conditions that cause neurological damage. Here, we estimate nervous system health loss caused by 37 unique conditions and their associated risk factors globally, regionally, and nationally from 1990 to 2021.MethodsWe estimated mortality, prevalence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs), with corresponding 95% uncertainty intervals (UIs), by age and sex in 204 countries and territories, from 1990 to 2021. We included morbidity and deaths due to neurological conditions, for which health loss is directly due to damage to the CNS or peripheral nervous system. We also isolated neurological health loss from conditions for which nervous system morbidity is a consequence, but not the primary feature, including a subset of congenital conditions (ie, chromosomal anomalies and congenital birth defects), neonatal conditions (ie, jaundice, preterm birth, and sepsis), infectious diseases (ie, COVID-19, cystic echinococcosis, malaria, syphilis, and Zika virus disease), and diabetic neuropathy. By conducting a sequela-level analysis of the health outcomes for these conditions, only cases where nervous system damage occurred were included, and YLDs were recalculated to isolate the non-fatal burden directly attributable to nervous system health loss. A comorbidity correction was used to calculate total prevalence of all conditions that affect the nervous system combined.FindingsGlobally, the 37 conditions affecting the nervous system were collectively ranked as the leading group cause of DALYs in 2021 (443 million, 95% UI 378–521), affecting 3·40 billion (3·20–3·62) individuals (43·1%, 40·5–45·9 of the global population); global DALY counts attributed to these conditions increased by 18·2% (8·7–26·7) between 1990 and 2021. Age-standardised rates of deaths per 100 000 people attributed to these conditions decreased from 1990 to 2021 by 33·6% (27·6–38·8), and age-standardised rates of DALYs attributed to these conditions decreased by 27·0% (21·5–32·4). Age-standardised prevalence was almost stable, with a change of 1·5% (0·7–2·4). The ten conditions with the highest age-standardised DALYs in 2021 were stroke, neonatal encephalopathy, migraine, Alzheimer's disease and other dementias, diabetic neuropathy, meningitis, epilepsy, neurological complications due to preterm birth, autism spectrum disorder, and nervous system cancer.InterpretationAs the leading cause of overall disease burden in the world, with increasing global DALY counts, effective prevention, treatment, and rehabilitation strategies for disorders affecting the nervous system are needed

Temporally adaptive classifier for multispectral imagery, A

Includes bibliographical references.This paper presents a new temporally adaptive classification system for multispectral images. A spatial-temporal adaptation mechanism is devised to account for the changes in the feature space as a result of environmental variations. Classification based upon spatial features is performed using Bayesian framework or probabilistic neural networks (PNNs) while the temporal updating takes place using a spatial-temporal predictor. A simple iterative updating mechanism is also introduced for adjusting the parameters of these systems. The proposed methodology is used to develop a pixel-based cloud classification system. Experimental results on cloud classification from satellite imagery are provided to show the usefulness of this system.This work was supported by the DoD Center for Geoscience Atmospheric Research at Colorado State University under the Cooperative Agreement (#DAAL01-98-2-0078) with the Army Research Laboratory

Novel sparseness-inducing dual Kalman filter and its application to tracking time-varying spatially-sparse structural stiffness changes and inputs

While the theory of Bayesian system identification provides a probabilistic means for reliably and robustly inferring models of a dynamic system and their parameters based on measured dynamic response, exploiting sparseness during online tracking of changing model parameters is not well understood. The focus in this study is to implement the dual Kalman filter for real-time Bayesian sequential state and parameter identification based on noisy sensor signals while incorporating sparse Bayesian learning to impose sparse model parameter changes from their initial reference values. We also want out model to be able to capture the evolution of sparse model parameter changes between two successive time instants. To this end, we present a hierarchical Bayesian model for tracking the joint posterior distribution of the state and model parameter vectors for a monitored dynamical system, where the two afore-mentioned sparseness constraints (sparse changes from reference values and with time) are also effectively incorporated for each time. We show our stochastic model of the structural dynamical system can be represented as a coupled conditionally-linear Gaussian state space model for the state and model parameter vectors, leading to some interesting analytical properties of the method that allow quantities of interest to be calculated in real time by using Kalman filtering equations. The parameters for the measurement and state prediction errors are learned solely from the available data up to the current time and so our method resolves the well-known instability problem in Kalman filtering due to arbitrary assignment of the error-distribution parameters. Finally, two illustrative applications are presented, one for identification of stiffness degradation and the other for input time–history identification where both are based on noisy dynamic response measurements from a structure

Novel sparseness-inducing dual Kalman filter and its application to tracking time-varying spatially-sparse structural stiffness changes and inputs

While the theory of Bayesian system identification provides a probabilistic means for reliably and robustly inferring models of a dynamic system and their parameters based on measured dynamic response, exploiting sparseness during online tracking of changing model parameters is not well understood. The focus in this study is to implement the dual Kalman filter for real-time Bayesian sequential state and parameter identification based on noisy sensor signals while incorporating sparse Bayesian learning to impose sparse model parameter changes from their initial reference values. We also want out model to be able to capture the evolution of sparse model parameter changes between two successive time instants. To this end, we present a hierarchical Bayesian model for tracking the joint posterior distribution of the state and model parameter vectors for a monitored dynamical system, where the two afore-mentioned sparseness constraints (sparse changes from reference values and with time) are also effectively incorporated for each time. We show our stochastic model of the structural dynamical system can be represented as a coupled conditionally-linear Gaussian state space model for the state and model parameter vectors, leading to some interesting analytical properties of the method that allow quantities of interest to be calculated in real time by using Kalman filtering equations. The parameters for the measurement and state prediction errors are learned solely from the available data up to the current time and so our method resolves the well-known instability problem in Kalman filtering due to arbitrary assignment of the error-distribution parameters. Finally, two illustrative applications are presented, one for identification of stiffness degradation and the other for input time–history identification where both are based on noisy dynamic response measurements from a structure