Frequentist p-values for large-scale-single step genome-wide association, with an application to birth weight in American Angus cattle.

Background: Single-step genomic best linear unbiased prediction (SSGBLUP) is a comprehensive method for genomic prediction. Point estimates of marker effects from SSGBLUP are often used for genome-wide association studies (GWAS) without a formal framework of hypothesis testing. Our objective was to implement p-values for singlemarker GWAS studies within the single-step GWAS (SSGWAS) framework by deriving computational algorithms and procedures, and by applying these to a large beef cattle population. Methods: P-values were obtained based on the prediction error (co)variances for single nucleotide polymorphisms (SNPs), which were obtained from the prediction error (co)variances of genomic predictions based on the inverse of the coefficient matrix and formulas to estimate SNP effects. Results: Computation of p-values took a negligible time for a dataset with almost 2 million animals in the pedigree and 1424 genotyped sires, and no inflation of statistics was observed. The SNPs that passed the Bonferroni threshold of 10-5.9 were the same as those that explained the highest proportion of additive genetic variance, but even at the same significance levels and effects, some of them explained less genetic variance due to lower allele frequency. Conclusions: The use of a p-value for SSGWAS is a very general and efficient strategy to identify quantitative trait loci (QTL). It can be used for complex datasets such as those used in animal breeding, where only a proportion of the pedigreed animals are genotyped

Surface Emissions Modulate Indoor SVOC Concentrations through Volatility-Dependent Partitioning.

Measurements by semivolatile thermal desorption aerosol gas chromatography (SV-TAG) were used to investigate how semivolatile organic compounds (SVOCs) partition among indoor reservoirs in (1) a manufactured test house under controlled conditions (HOMEChem campaign) and (2) a single-family residence when vacant (H2 campaign). Data for phthalate diesters and siloxanes suggest that volatility-dependent partitioning processes modulate airborne SVOC concentrations through interactions with surface-laden condensed-phase reservoirs. Airborne concentrations of SVOCs with vapor pressures in the range of C13 to C23 alkanes were observed to be correlated with indoor air temperature. Observed temperature dependencies were quantitatively similar to theoretical predictions that assumed a surface-air boundary layer with equilibrium partitioning maintained at the air-surface interface. Airborne concentrations of SVOCs with vapor pressures corresponding to C25 to C31 alkanes correlated with airborne particle mass concentration. For SVOCs with higher vapor pressures, which are expected to be predominantly gaseous, correlations with particle mass concentration were weak or nonexistent. During primary particle emission events, enhanced gas-phase emissions from condensed-phase reservoirs partitioned to airborne particles, contributing substantially to organic particulate matter. An emission event related to oven-usage was inferred to deposit siloxanes in condensed-phase reservoirs throughout the house, leading to the possibility of reemission during subsequent periods with high particle loading

Accuracy of genomic BLUP when considering a genomic relationship matrix based on the number of the largest eigenvalues: a simulation study.

International audienceAbstractBackgroundThe dimensionality of genomic information is limited by the number of independent chromosome segments (Me), which is a function of the effective population size. This dimensionality can be determined approximately by singular value decomposition of the gene content matrix, by eigenvalue decomposition of the genomic relationship matrix (GRM), or by the number of core animals in the algorithm for proven and young (APY) that maximizes the accuracy of genomic prediction. In the latter, core animals act as proxies to linear combinations of Me. Field studies indicate that a moderate accuracy of genomic selection is achieved with a small dataset, but that further improvement of the accuracy requires much more data. When only one quarter of the optimal number of core animals are used in the APY algorithm, the accuracy of genomic selection is only slightly below the optimal value. This suggests that genomic selection works on clusters of Me.ResultsThe simulation included datasets with different population sizes and amounts of phenotypic information. Computations were done by genomic best linear unbiased prediction (GBLUP) with selected eigenvalues and corresponding eigenvectors of the GRM set to zero. About four eigenvalues in the GRM explained 10% of the genomic variation, and less than 2% of the total eigenvalues explained 50% of the genomic variation. With limited phenotypic information, the accuracy of GBLUP was close to the peak where most of the smallest eigenvalues were set to zero. With a large amount of phenotypic information, accuracy increased as smaller eigenvalues were added.ConclusionsA small amount of phenotypic data is sufficient to estimate only the effects of the largest eigenvalues and the associated eigenvectors that contain a large fraction of the genomic information, and a very large amount of data is required to estimate the remaining eigenvalues that account for a limited amount of genomic information. Core animals in the APY algorithm act as proxies of almost the same number of eigenvalues. By using an eigenvalues-based approach, it was possible to explain why the moderate accuracy of genomic selection based on small datasets only increases slowly as more data are added

Memory, space and time: Researching children's lives

This article discusses the research approach in 'Pathways through Childhood', a small qualitative study drawing on memories of childhood. The research explores how wider social arrangements and social change influence children's everyday lives.The article discusses the way that the concepts of social memory, space and time have been drawn on to access and analyse children's experiences, arguing that attention to the temporal and spatial complexity of childhood reveals less visible yet formative influences and connections. Children's everyday engagements involve connections between past and present time, between children, families, communities and nations, and between different places. Children carve out space and time for themselves from these complex relations. © The Author(s) 2010

Seasonal analysis of submicron aerosol in Old Delhi using high-resolution aerosol mass spectrometry: chemical characterisation, source apportionment and new marker identification

We present the first real-time composition of submicron particulate matter (PM1) in Old Delhi using high-resolution aerosol mass spectrometry (HR-AMS). Old Delhi is one of the most polluted locations in the world, and PM1 concentrations reached ∼ 750 µg m−3 during the most polluted period, the post-monsoon period, where PM1 increased by 188 % over the pre-monsoon period. Sulfate contributes the largest inorganic PM1 mass fraction during the pre-monsoon (24 %) and monsoon (24 %) periods, with nitrate contributing most during the post-monsoon period (8 %). The organics dominate the mass fraction (54 %–68 %) throughout the three periods, and, using positive matrix factorisation (PMF) to perform source apportionment analysis of organic mass, two burning-related factors were found to contribute the most (35 %) to the post-monsoon increase. The first PMF factor, semi-volatility biomass burning organic aerosol (SVBBOA), shows a high correlation with Earth observation fire counts in surrounding states, which links its origin to crop residue burning. The second is a solid fuel OA (SFOA) factor with links to local open burning due to its high composition of polyaromatic hydrocarbons (PAHs) and novel AMS-measured marker species for polychlorinated dibenzodioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs). Two traffic factors were resolved: one hydrocarbon-like OA (HOA) factor and another nitrogen-rich HOA (NHOA) factor. The N compounds within NHOA were mainly nitrile species which have not previously been identified within AMS measurements. Their PAH composition suggests that NHOA is linked to diesel and HOA to compressed natural gas and petrol. These factors combined make the largest relative contribution to primary PM1 mass during the pre-monsoon and monsoon periods while contributing the second highest in the post-monsoon period. A cooking OA (COA) factor shows strong links to the secondary factor, semi-volatility oxygenated OA (SVOOA). Correlations with co-located volatile organic compound (VOC) measurements and AMS-measured organic nitrogen oxides (OrgNO) suggest SVOOA is formed from aged COA. It is also found that a significant increase in chloride concentrations (522 %) from pre-monsoon to post-monsoon correlates well with SVBBOA and SFOA, suggesting that crop residue burning and open waste burning are responsible. A reduction in traffic emissions would effectively reduce concentrations across most of the year. In order to reduce the post-monsoon peak, sources such as funeral pyres, solid waste burning and crop residue burning should be considered when developing new air quality policy

Genomic selection for tick resistance in Braford and Hereford cattle using single-step methodology.

The Rhipicephalus microplus tick is one of the main sources of losses in tropical cattle production, causing decreased performance, hide devaluation, and increased costs with treatments and transmission of infectious agents. The aim of this work was to evaluate the utility of genomic evaluation of Braford and Hereford cattle for genetic resistance to ticks.ISAG, 2012

Dimensionality of genomic information and performance of the Algorithm for Proven and Young for different livestock species

International audienceAbstractBackgroundA genomic relationship matrix (GRM) can be inverted efficiently with the Algorithm for Proven and Young (APY) through recursion on a small number of core animals. The number of core animals is theoretically linked to effective population size (Ne). In a simulation study, the optimal number of core animals was equal to the number of largest eigenvalues of GRM that explained 98% of its variation. The purpose of this study was to find the optimal number of core animals and estimate Ne for different species.MethodsDatasets included phenotypes, pedigrees, and genotypes for populations of Holstein, Jersey, and Angus cattle, pigs, and broiler chickens. The number of genotyped animals varied from 15,000 for broiler chickens to 77,000 for Holsteins, and the number of single-nucleotide polymorphisms used for genomic prediction varied from 37,000 to 61,000. Eigenvalue decomposition of the GRM for each population determined numbers of largest eigenvalues corresponding to 90, 95, 98, and 99% of variation.ResultsThe number of eigenvalues corresponding to 90% (98%) of variation was 4527 (14,026) for Holstein, 3325 (11,500) for Jersey, 3654 (10,605) for Angus, 1239 (4103) for pig, and 1655 (4171) for broiler chicken. Each trait in each species was analyzed using the APY inverse of the GRM with randomly selected core animals, and their number was equal to the number of largest eigenvalues. Realized accuracies peaked with the number of core animals corresponding to 98% of variation for Holstein and Jersey and closer to 99% for other breed/species. Ne was estimated based on comparisons of eigenvalue decomposition in a simulation study. Assuming a genome length of 30 Morgan, Ne was equal to 149 for Holsteins, 101 for Jerseys, 113 for Angus, 32 for pigs, and 44 for broilers.ConclusionsEigenvalue profiles of GRM for common species are similar to those in simulation studies although they are affected by number of genotyped animals and genotyping quality. For all investigated species, the APY required less than 15,000 core animals. Realized accuracies were equal or greater with the APY inverse than with regular inversion. Eigenvalue analysis of GRM can provide a realistic estimate of Ne

New times, new politics: history and memory during the final years of the CPGB

This article examines the relationship between collective memory, historical interpretation and political identity. It focuses on the dissolution of the Communist Party of Great Britain (CPGB) as constructed through collective narrative memory, and on Marxist interpretations of history. The divisions within the party and the wider Marxist community, stretching from 1956 until 1991, were often framed around questions of historical interpretation. The events of 1989–1991 created an historical and mnemonic crisis for CPGB members who struggled to reconcile their past identities with their present situation. Unlike the outward-facing revisionism of other political parties, this was an intensely personal affair. The solution for many was to emphasise the need to find new ways to progress socialist aims, without relying on a discredited grand narrative. In contrast, other Communist parties, such as the Communist Party of Britain, which had been established (or ‘re-established’) in 1988, fared rather better. By adhering to the international party line of renewal and continued struggle, the party was able to hold its narrative together, condemning the excesses of totalitarian regimes, while reaffirming the need for international class struggle

On handling urban informality in southern Africa

In this article I reconsider the handling of urban informality by urban planning and management systems in southern Africa. I argue that authorities have a fetish about formality and that this is fuelled by an obsession with urban modernity. I stress that the desired city, largely inspired by Western notions of modernity, has not been and cannot be realized. Using illustrative cases of top–down interventions, I highlight and interrogate three strategies that authorities have deployed to handle informality in an effort to create or defend the modern city. I suggest that the fetish is built upon a desire for an urban modernity based on a concept of formal order that the authorities believe cannot coexist with the “disorder” and spatial “unruliness” of informality. I question the authorities' conviction that informality is an abomination that needs to be “converted”, dislocated or annihilated. I conclude that the very configuration of urban governance and socio-economic systems in the region, like the rest of sub-Saharan Africa, renders informality inevitable and its eradication impossible