We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human ...microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.
This paper describes the development of a technically robust climate modelling system, HadGEM3, which couples the Met Office Unified Model atmosphere component, the NEMO ocean model and the Los ...Alamos sea ice model (CICE) using the OASIS coupler. Details of the coupling and technical solutions of the physical model (HadGEM3-AO) are documented, in addition to a description of the configurations of the individual submodels. The paper demonstrates that the implementation of the model has resulted in accurate conservation of heat and freshwater across the model components. The model performance in early versions of this climate model is briefly described to demonstrate that the results are scientifically credible. HadGEM3-AO is the basis for a number of modelling efforts outside of the Met Office, both within the UK and internationally. This documentation of the HadGEM3-AO system provides a detailed reference for developers of HadGEM3-based climate configurations.
The Transiting Exoplanet Survey Satellite (TESS) recently observed 18 transits of the hot Jupiter WASP-4b. The sequence of transits occurred 81.6 11.7 s earlier than had been predicted, based on data ...stretching back to 2007. This is unlikely to be the result of a clock error, because TESS observations of other hot Jupiters (WASP-6b, 18b, and 46b) are compatible with a constant period, ruling out an 81.6 s offset at the 6.4 level. The 1.3 day orbital period of WASP-4b appears to be decreasing at a rate of ms per year. The apparent period change might be caused by tidal orbital decay or apsidal precession, although both interpretations have shortcomings. The gravitational influence of a third body is another possibility, though at present there is minimal evidence for such a body. Further observations are needed to confirm and understand the timing variation.
ABSTRACT We present post-cryogenic Spitzer imaging at 3.6 and 4.5 m with the Infrared Array Camera (IRAC) of the Spitzer/HETDEX Exploratory Large-Area (SHELA) survey. SHELA covers 24 deg2 of the ...Sloan Digital Sky Survey "Stripe 82" region, and falls within the footprints of the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) and the Dark Energy Survey. The HETDEX blind R ∼ 800 spectroscopy will produce ∼200,000 redshifts from the Ly emission for galaxies in the range 1.9 < z < 3.5, and an additional ∼200,000 redshifts from the O ii emission for galaxies at z < 0.5. When combined with deep ugriz images from the Dark Energy Camera, K-band images from NEWFIRM, and other ancillary data, the IRAC photometry from Spitzer will enable a broad range of scientific studies of the relationship between structure formation, galaxy stellar mass, halo mass, the presence of active galactic nuclei, and environment over a co-moving volume of ∼0.5 Gpc3 at 1.9 < z < 3.5. Here, we discuss the properties of the SHELA IRAC data set, including the data acquisition, reduction, validation, and source catalogs. Our tests show that the images and catalogs are 80% (50%) complete to limiting magnitudes of 22.0 (22.6) AB mag in the detection image, which is constructed from the weighted sum of the IRAC 3.6 and 4.5 m images. The catalogs reach limiting sensitivities of 1.1 Jy at both 3.6 and 4.5 m (1 , for R = 2″ circular apertures). As a demonstration of the science, we present IRAC number counts, examples of highly temporally variable sources, and galaxy surface density profiles of rich galaxy clusters. In the spirit of the Spitzer Exploratory programs, we provide all of the images and catalogs as part of the publication.
The Integrated Science Investigation of the Sun (ISIS) is a complete science investigation on the Solar Probe Plus (SPP) mission, which flies to within nine solar radii of the Sun’s surface. ISIS ...comprises a two-instrument suite to measure energetic particles over a very broad energy range, as well as coordinated management, science operations, data processing, and scientific analysis. Together, ISIS observations allow us to explore the mechanisms of energetic particles dynamics, including their: (1) Origins—defining the seed populations and physical conditions necessary for energetic particle acceleration; (2) Acceleration—determining the roles of shocks, reconnection, waves, and turbulence in accelerating energetic particles; and (3) Transport—revealing how energetic particles propagate from the corona out into the heliosphere. The two ISIS Energetic Particle Instruments measure lower (EPI-Lo) and higher (EPI-Hi) energy particles. EPI-Lo measures ions and ion composition from ∼20 keV/nucleon–15 MeV total energy and electrons from ∼25–1000 keV. EPI-Hi measures ions from ∼1–200 MeV/nucleon and electrons from ∼0.5–6 MeV. EPI-Lo comprises 80 tiny apertures with fields-of-view (FOVs) that sample over nearly a complete hemisphere, while EPI-Hi combines three telescopes that together provide five large-FOV apertures. ISIS observes continuously inside of 0.25 AU with a high data collection rate and burst data (EPI-Lo) coordinated with the rest of the SPP payload; outside of 0.25 AU, ISIS runs in low-rate science mode whenever feasible to capture as complete a record as possible of the solar energetic particle environment and provide calibration and continuity for measurements closer in to the Sun. The ISIS Science Operations Center plans and executes commanding, receives and analyzes all ISIS data, and coordinates science observations and analyses with the rest of the SPP science investigations. Together, ISIS’ unique observations on SPP will enable the discovery, untangling, and understanding of the important physical processes that govern energetic particles in the innermost regions of our heliosphere, for the first time. This paper summarizes the ISIS investigation at the time of the SPP mission Preliminary Design Review in January 2014.
People's differences in cognitive functions are partly heritable and are associated with important life outcomes. Previous genome-wide association (GWA) studies of cognitive functions have found ...evidence for polygenic effects yet, to date, there are few replicated genetic associations. Here we use data from the UK Biobank sample to investigate the genetic contributions to variation in tests of three cognitive functions and in educational attainment. GWA analyses were performed for verbal-numerical reasoning (N=36 035), memory (N=112 067), reaction time (N=111 483) and for the attainment of a college or a university degree (N=111 114). We report genome-wide significant single-nucleotide polymorphism (SNP)-based associations in 20 genomic regions, and significant gene-based findings in 46 regions. These include findings in the ATXN2, CYP2DG, APBA1 and CADM2 genes. We report replication of these hits in published GWA studies of cognitive function, educational attainment and childhood intelligence. There is also replication, in UK Biobank, of SNP hits reported previously in GWA studies of educational attainment and cognitive function. GCTA-GREML analyses, using common SNPs (minor allele frequency>0.01), indicated significant SNP-based heritabilities of 31% (s.e.m.=1.8%) for verbal-numerical reasoning, 5% (s.e.m.=0.6%) for memory, 11% (s.e.m.=0.6%) for reaction time and 21% (s.e.m.=0.6%) for educational attainment. Polygenic score analyses indicate that up to 5% of the variance in cognitive test scores can be predicted in an independent cohort. The genomic regions identified include several novel loci, some of which have been associated with intracranial volume, neurodegeneration, Alzheimer's disease and schizophrenia.
Fast radio bursts (FRBs) are bright, millisecond-duration radio transients originating from sources at extragalactic distances
, the origin of which is unknown. Some FRB sources emit repeat bursts, ...ruling out cataclysmic origins for those events
. Despite searches for periodicity in repeat burst arrival times on timescales from milliseconds to many days
, these bursts have hitherto been observed to appear sporadically and-although clustered
-without a regular pattern. Here we report observations of a 16.35 ± 0.15 day periodicity (or possibly a higher-frequency alias of that periodicity) from the repeating FRB 180916.J0158+65 detected by the Canadian Hydrogen Intensity Mapping Experiment Fast Radio Burst Project
. In 38 bursts recorded from 16 September 2018 to 4 February 2020 UTC, we find that all bursts arrive in a five-day phase window, and 50 per cent of the bursts arrive in a 0.6-day phase window. Our results suggest a mechanism for periodic modulation either of the burst emission itself or through external amplification or absorption, and disfavour models invoking purely sporadic processes.
Static strain in complex oxide heterostructures has been extensively used to engineer electronic and magnetic properties at equilibrium. In the same spirit, deformations of the crystal lattice with ...light may be used to achieve functional control across heterointerfaces dynamically. Here, by exciting large-amplitude infrared-active vibrations in a LaAlO3 substrate we induce magnetic order melting in a NdNiO3 film across a heterointerface. Femtosecond resonant soft X-ray diffraction is used to determine the spatiotemporal evolution of the magnetic disordering. We observe a magnetic melt front that propagates from the substrate interface into the film, at a speed that suggests electronically driven motion. Light control and ultrafast phase front propagation at heterointerfaces may lead to new opportunities in optomagnetism, for example by driving domain wall motion to transport information across suitably designed devices.
The Wilkinson Microwave Anisotropy Probe (WMAP) 5-year data provide stringent limits on deviations from the minimal, six-parameter Lambda cold dark matter model. We report these limits and use them ...to constrain the physics of cosmic inflation via Gaussianity, adiabaticity, the power spectrum of primordial fluctuations, gravitational waves, and spatial curvature. We also constrain models of dark energy via its equation of state, parity-violating interaction, and neutrino properties, such as mass and the number of species. We detect no convincing deviations from the minimal model. The six parameters and the corresponding 68% uncertainties, derived from the WMAP data combined with the distance measurements from the Type Ia supernovae (SN) and the Baryon Acoustic Oscillations (BAO) in the distribution of galaxies, are: Omega b h 2 = 0.02267+0.00058 -0.00059, Omega c h 2 = 0.1131 ± 0.0034, Omega Lambda = 0.726 ± 0.015, ns = 0.960 ± 0.013, tau = 0.084 ± 0.016, and at k = 0.002 Mpc-1. From these, we derive sigma 8 = 0.812 ± 0.026, H 0 = 70.5 ± 1.3 km s-1 Mpc-1, Omega b = 0.0456 ± 0.0015, Omega c = 0.228 ± 0.013, Omega m h 2 = 0.1358+0.0037 -0.0036, z reion = 10.9 ± 1.4, and t 0 = 13.72 ± 0.12 Gyr. With the WMAP data combined with BAO and SN, we find the limit on the tensor-to-scalar ratio of r < 0.22(95%CL), and that ns > 1 is disfavored even when gravitational waves are included, which constrains the models of inflation that can produce significant gravitational waves, such as chaotic or power-law inflation models, or a blue spectrum, such as hybrid inflation models. We obtain tight, simultaneous limits on the (constant) equation of state of dark energy and the spatial curvature of the universe: -0.14 < 1 + w < 0.12(95%CL) and -0.0179 < Omega k < 0.0081(95%CL). We provide a set of 'WMAP distance priors,' to test a variety of dark energy models with spatial curvature. We test a time-dependent w with a present value constrained as -0.33 < 1 + w 0 < 0.21 (95% CL). Temperature and dark matter fluctuations are found to obey the adiabatic relation to within 8.9% and 2.1% for the axion-type and curvaton-type dark matter, respectively. The power spectra of TB and EB correlations constrain a parity-violating interaction, which rotates the polarization angle and converts E to B. The polarization angle could not be rotated more than -59 < Delta alpha < 24 (95% CL) between the decoupling and the present epoch. We find the limit on the total mass of massive neutrinos of capital sigma m Delta < 0.67 eV(95%CL), which is free from the uncertainty in the normalization of the large-scale structure data. The number of relativistic degrees of freedom (dof), expressed in units of the effective number of neutrino species, is constrained as N eff = 4.4 ± 1.5 (68%), consistent with the standard value of 3.04. Finally, quantitative limits on physically-motivated primordial non-Gaussianity parameters are -9 < f local NL < 111 (95% CL) and -151 < f equil NL < 253 (95% CL) for the local and equilateral models, respectively.
Observations and ocean state estimates are used to investigate the nature and mechanism of decadal variability in the East Australian Current (EAC) system and South Pacific subtropical gyre. A 62 ...year record on the Tasmanian continental shelf shows decadal variations of temperature and salinity, as well as a long‐term trend, which has been related to wind‐driven variations in the poleward extension of the EAC. Repeat expendable bathythermograph lines spanning the last 15 years suggest that low‐frequency variations in the transport of the EAC extension and Tasman Front are anticorrelated, but the time series are too short to draw firm conclusions. Here we use two ocean state estimates spanning the past 50 years to diagnose the physical mechanisms and spatial structure of the decadal variability of the South Pacific subtropical gyre. The observations and state estimates paint a consistent picture of the decadal variability of the gyre and EAC system. Strengthening of the basin‐wide wind stress curl drives a southward expansion of the subtropical gyre. As the gyre shifts south, the EAC extension pathway is favored at the expense of the Tasman Front, resulting in the observed anticorrelation of the these two major currents. The results suggest that the subtropical gyre and western boundary current respond to decadal variability in basin‐scale wind stress curl, consistent with Island Rule dynamics; that strong decadal variability of the South Pacific gyre complicates efforts to infer trends from short‐term records; and that wind stress curl changes over the South Pacific basin drive changes in the EAC system that are likely to have implications for marine ecosystems and regional climate.
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