WMAP constraints on scalar-tensor cosmology and the variation of the gravitational constant

We present observational constraints on a scalar-tensor gravity theory by $\chi^2$ test for CMB anisotropy spectrum. We compare the WMAP temperature power spectrum with the harmonic attractor model, in which the scalar field has its harmonic effective potential with curvature $\beta$ in the Einstein conformal frame and the theory relaxes toward Einstein gravity with time. We found that the present value of the scalar coupling, i.e. the present level of deviation from Einstein gravity $(\alpha_0^2)$, is bounded to be smaller than $5\times 10^{-4-7\beta}$ ($2\sigma$), and $10^{-2-7\beta}$ ($4\sigma$) for $0< \beta<0.45$. This constraint is much stronger than the bound from the solar system experiments for large $\beta$ models, i.e., $\beta> 0.2$ and 0.3 in $2\sigma$ and $4\sigma$ limits, respectively. Furthermore, within the framework of this model, the variation of the gravitational constant at the recombination epoch is constrained as $|G(z=z_{rec})-G_0|/G_0 < 0.05(2\sigma)$, and $0.23(4\sigma)$.Comment: 7 page

Genomic adaptations of Campylobacter jejuni to long-term human colonization

Background Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. Results There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. Conclusions This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment

Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor

Scale issues in soil moisture modelling: problems and prospects

Soil moisture storage is an important component of the hydrological cycle and plays a key role in land-surface-atmosphere interaction. The soil-moisture storage equation in this study considers precipitation as an input and soil moisture as a residual term for runoff and evapotranspiration. A number of models have been developed to estimate soil moisture storage and the components of the soil-moisture storage equation. A detailed discussion of the impli cation of the scale of application of these models reports that it is not possible to extrapolate processes and their estimates from the small to the large scale. It is also noted that physically based models for small-scale applications are sufficiently detailed to reproduce land-surface- atmosphere interactions. On the other hand, models for large-scale applications oversimplify the processes. Recently developed physically based models for large-scale applications can only be applied to limited uses because of data restrictions and the problems associated with land surface characterization. It is reported that remote sensing can play an important role in over coming the problems related to the unavailability of data and the land surface characterization of large-scale applications of these physically based models when estimating soil moisture storage.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

The Theory of Brown Dwarfs and Extrasolar Giant Planets

Straddling the traditional realms of the planets and the stars, objects below the edge of the main sequence have such unique properties, and are being discovered in such quantities, that one can rightly claim that a new field at the interface of planetary science and and astronomy is being born. In this review, we explore the essential elements of the theory of brown dwarfs and giant planets, as well as of the new spectroscopic classes L and T. To this end, we describe their evolution, spectra, atmospheric compositions, chemistry, physics, and nuclear phases and explain the basic systematics of substellar-mass objects across three orders of magnitude in both mass and age and a factor of 30 in effective temperature. Moreover, we discuss the distinctive features of those extrasolar giant planets that are irradiated by a central primary, in particular their reflection spectra, albedos, and transits. Aspects of the latest theory of Jupiter and Saturn are also presented. Throughout, we highlight the effects of condensates, clouds, molecular abundances, and molecular/atomic opacities in brown dwarf and giant planet atmospheres and summarize the resulting spectral diagnostics. Where possible, the theory is put in its current observational context.Comment: 67 pages (including 36 figures), RMP RevTeX LaTeX, accepted for publication in the Reviews of Modern Physics. 30 figures are color. Most of the figures are in GIF format to reduce the overall size. The full version with figures can also be found at: http://jupiter.as.arizona.edu/~burrows/papers/rm

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

The genetic architecture of the human cerebral cortex

INTRODUCTION The cerebral cortex underlies our complex cognitive capabilities. Variations in human cortical surface area and thickness are associated with neurological, psychological, and behavioral traits and can be measured in vivo by magnetic resonance imaging (MRI). Studies in model organisms have identified genes that influence cortical structure, but little is known about common genetic variants that affect human cortical structure. RATIONALE To identify genetic variants associated with human cortical structure at both global and regional levels, we conducted a genome-wide association meta-analysis of brain MRI data from 51,665 individuals across 60 cohorts. We analyzed the surface area and average thickness of the whole cortex and 34 cortical regions with known functional specializations. RESULTS We identified 306 nominally genome-wide significant loci (P < 5 × 10−8) associated with cortical structure in a discovery sample of 33,992 participants of European ancestry. Of the 299 loci for which replication data were available, 241 loci influencing surface area and 14 influencing thickness remained significant after replication, with 199 loci passing multiple testing correction (P < 8.3 × 10−10; 187 influencing surface area and 12 influencing thickness). Common genetic variants explained 34% (SE = 3%) of the variation in total surface area and 26% (SE = 2%) in average thickness; surface area and thickness showed a negative genetic correlation (rG = −0.32, SE = 0.05, P = 6.5 × 10−12), which suggests that genetic influences have opposing effects on surface area and thickness. Bioinformatic analyses showed that total surface area is influenced by genetic variants that alter gene regulatory activity in neural progenitor cells during fetal development. By contrast, average thickness is influenced by active regulatory elements in adult brain samples, which may reflect processes that occur after mid-fetal development, such as myelination, branching, or pruning. When considered together, these results support the radial unit hypothesis that different developmental mechanisms promote surface area expansion and increases in thickness. To identify specific genetic influences on individual cortical regions, we controlled for global measures (total surface area or average thickness) in the regional analyses. After multiple testing correction, we identified 175 loci that influence regional surface area and 10 that influence regional thickness. Loci that affect regional surface area cluster near genes involved in the Wnt signaling pathway, which is known to influence areal identity. We observed significant positive genetic correlations and evidence of bidirectional causation of total surface area with both general cognitive functioning and educational attainment. We found additional positive genetic correlations between total surface area and Parkinson’s disease but did not find evidence of causation. Negative genetic correlations were evident between total surface area and insomnia, attention deficit hyperactivity disorder, depressive symptoms, major depressive disorder, and neuroticism. CONCLUSION This large-scale collaborative work enhances our understanding of the genetic architecture of the human cerebral cortex and its regional patterning. The highly polygenic architecture of the cortex suggests that distinct genes are involved in the development of specific cortical areas. Moreover, we find evidence that brain structure is a key phenotype along the causal pathway that leads from genetic variation to differences in general cognitive function

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe