Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium

As technology advances, whole genome sequencing (WGS) is likely to supersede other genotyping technologies. The rate of this change depends on its relative cost and utility. Variants identified uniquely through WGS may reveal novel biological pathways underlying complex disorders and provide high-resolution insight into when, where, and in which cell type these pathways are affected. Alternatively, cheaper and less computationally intensive approaches may yield equivalent insights. Understanding the role of rare variants in the noncoding gene-regulating genome, through pilot WGS projects, will be critical to determine which of these two extremes best represents reality. With large cohorts, well-defined risk loci, and a compelling need to understand the underlying biology, psychiatric disorders have a role to play in this preliminary WGS assessment. The WGSPD consortium will integrate data for 18,000 individuals with psychiatric disorders, beginning with autism spectrum disorder, schizophrenia, bipolar disorder, and major depressive disorder, along with over 150,000 controls

Tower and Aircraft Eddy Covariance Measurements of Water Vapor, Energy, and Carbon Dioxide Fluxes during SMACEX

Abstract A network of eddy covariance (EC) and micrometeorological flux (METFLUX) stations over corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] canopies was established as part of the Soil Moisture–Atmosphere Coupling Experiment (SMACEX) in central Iowa during the summer of 2002 to measure fluxes of heat, water vapor, and carbon dioxide (CO2) during the growing season. Additionally, EC measurements of water vapor and CO2 fluxes from an aircraft platform complemented the tower-based measurements. Sensible heat, water vapor, and CO2 fluxes showed the greatest spatial and temporal variability during the early crop growth stage. Differences in all of the energy balance components were detectable between corn and soybean as well as within similar crops throughout the study period. Tower network–averaged fluxes of sensible heat, water vapor, and CO2 were observed to be in good agreement with area-averaged aircraft flux measurements

Mapping evapotranspiration with high-resolution aircraft imagery over vineyards using one- and two-source modeling schemes

Thermal and multispectral remote sensing data from low-altitude aircraft can provide high spatial resolution necessary for sub-field ( 10 m) and plant canopy (1 m) scale evapotranspiration (ET) monitoring. In this study, highresolution (sub-meter-scale) thermal infrared and multispectral shortwave data from aircraft are used to map ET over vineyards in central California with the two-source energy balance (TSEB) model and with a simple model having operational immediate capabilities called DATTUTDUT (Deriving Atmosphere Turbulent Transport Useful To Dummies Using Temperature). The latter uses contextual information within the image to scale between radiometric land surface temperature (TR) values representing hydrologic limits of potential ET and a non-evaporative surface. Imagery from 5 days throughout the growing season is used for mapping ET at the sub-field scale. The performance of the two models is evaluated using tower-based measurements of sensible (H) and latent heat (LE) flux or ET. The comparison indicates that TSEB was able to derive reasonable ET estimates under varying conditions, likely due to the physically based treatment of the energy and the surface temperature partitioning between the soil/cover crop inter-row and vine canopy elements. On the other hand, DATTUTDUT performance was somewhat degraded presumably because the simple scaling scheme does not consider differences in the two sources (vine and inter-row) of heat and temperature contributions or the effect of surface roughness on the efficiency of heat exchange. Maps of the evaporative fraction (EFDLE/(H CLE)) from the two models had similar spatial patterns but different magnitudes in some areas within the fields on certain days. Large EF discrepancies between the models were found on 2 of the 5 days (DOY 162 and 219) when there were significant differences with the tower-based ET measurements, particularly using the DATTUTDUT model. These differences in EF between the models translate to significant variations in daily water use estimates for these 2 days for the vineyards. Model sensitivity analysis demonstrated the high degree of sensitivity of the TSEB model to the accuracy of the TR data, while the DATTUTDUT model was insensitive to systematic errors in TR as is the case with contextual-based models. However, it is shown that the study domain and spatial resolution will significantly influence the ET estimation from the DATTUTDUT model. Future work is planned for developing a hybrid approach that leverages the strengths of both modeling schemes and is simple enough to be used operationally with high-resolution imagery

Low-temperature gas opacity - AESOPUS: a versatile and quick computational tool

We introduce a new tool - AESOPUS: Accurate Equation of State and OPacity Utility Software - for computing the equation of state and the Rosseland mean (RM) opacities of matter in the ideal gas phase. Results are given as a function of one pair of state variables, (i.e. temperature T in the range 3.2 <= log(T) <= 4.5, and parameter R= rho/(T/10^6 K)^3 in the range -8 <= log(R) <= 1), and arbitrary chemical mixture. The chemistry is presently solved for about 800 species, consisting of almost 300 atomic and 500 molecular species. The gas opacities account for many continuum and discrete sources, including atomic opacities, molecular absorption bands, and collision-induced absorption. Several tests made on AESOPUS have proved that the new opacity tool is accurate in the results,flexible in the management of the input prescriptions, and agile in terms of computational time requirement. We set up a web-interface (http://stev.oapd.inaf.it/aesopus) which enables the user to compute and shortly retrieve RM opacity tables according to his/her specific needs, allowing a full degree of freedom in specifying the chemical composition of the gas. Useful applications may regard RM opacities of gas mixtures with i) scaled-solar abundances of metals, choosing among various solar mixture compilations available in the literature; ii) varying CNO abundances, suitable for evolutionary models of red and asymptotic giant branch stars and massive stars in the Wolf-Rayet stages; iii) various degrees of enhancement in alpha-elements, and C-N, Na-O and Mg-Al abundance anti-correlations, necessary to properly describe the properties of stars in early-type galaxies and Galactic globular clusters; iv) zero-metal abundances appropriate for studies of gas opacity in primordial conditions.Comment: 32 pages, 34 postscript figures, A&A in press; new section 4.1.2 showing first tests with stellar models, sections 2.2, 2.2.2 and 5 expanded; interactive web-page at http://stev.oapd.inaf.it/aesopu

Transmission spectroscopy with VLT FORS2 : a featureless spectrum for the low-density transiting exoplanet WASP-88b

PS was supported by a UK Science and Technology Facilities Council (STFC) studentship. CH acknowledges funding from the European Union H2020-MSCA-ITN2019 under grant agreement no. 860470 (CHAMELEON). NM acknowledges funding from the UKRI Future Leaders Scheme (MR/T040866/1), Science and Technology Facilities Council Consolidated Grant (ST/R000395/1), and Leverhulme Trust research project grant (RPG-2020-82).We present ground-based optical transmission spectroscopy of the low-density hot Jupiter WASP-88b covering the wavelength range of 4413−8333  Å with the FOcal Reducer Spectrograph (FORS2) on the Very Large Telescope. The FORS2 white light curves exhibit a significant time-correlated noise that we model using a Gaussian process and remove as a wavelength-independent component from the spectroscopic light curves. We analyse complementary photometric observations from the Transiting Exoplanet Survey Satellite and refine the system properties and ephemeris. We find a featureless transmission spectrum with increased absorption towards shorter wavelengths. We perform an atmospheric retrieval analysis with the aura code, finding tentative evidence for haze in the upper atmospheric layers and a lower likelihood for a dense cloud deck. While our retrieval analysis results point towards clouds and hazes, further evidence is needed to definitively reject a clear-sky scenario.Publisher PDFPeer reviewe

Evaluating the two-source energy balance model using local thermal and surface flux observations in a strongly advective irrigated agricultural area

Application and validation of many thermal remote sensing-based energy balance models involve the use of local meteorological inputs of incoming solar radiation, wind speed and air temperature as well as accurate land surface temperature (LST), vegetation cover and surface flux measurements. For operational applications at large scales, such local information is not routinely available. In addition, the uncertainty in LST estimates can be several degrees due to sensor calibration issues, atmospheric effects and spatial variations in surface emissivity. Time differencing techniques using multi-temporal thermal remote sensing observations have been developed to reduce errors associated with deriving the surface- air temperature gradient, particularly in complex landscapes. The Dual-Temperature-Difference (DTD) method addresses these issues by utilizing the Two-Source Energy Balance (TSEB) model of Norman et al. (1995) [1], and is a relatively simple scheme requiring meteorological input from standard synoptic weather station networks or mesoscale modeling. A comparison of the TSEB and DTD schemes is performed using LST and flux observations from eddy covariance (EC) flux towers and large weighing lysimeters (LYs) in irrigated cotton fields collected during BEAREX08, a large-scale field experiment conducted in the semi-arid climate of the Texas High Plains as described by Evett et al. (2012) [2]. Model output of the energy fluxes (i.e., net radiation, soil heat flux, sensible and latent heat flux) generated with DTD and TSEB using local and remote meteorological observations are compared with EC and LY observations. The DTD method is found to be significantly more robust in flux estimation compared to the TSEB using the remote meteorological observations. However, discrepancies between model and measured fluxes are also found to be significantly affected by the local inputs of LST and vegetation cover and the representativeness of the remote sensing observations with the local flux measurement footprint

Transiting Exoplanet Studies and Community Targets for JWST's Early Release Science Program

The James Webb Space Telescope will revolutionize transiting exoplanet atmospheric science due to its capability for continuous, long-duration observations and its larger collecting area, spectral coverage, and spectral resolution compared to existing space-based facilities. However, it is unclear precisely how well JWST will perform and which of its myriad instruments and observing modes will be best suited for transiting exoplanet studies. In this article, we describe a prefatory JWST Early Release Science (ERS) program that focuses on testing specific observing modes to quickly give the community the data and experience it needs to plan more efficient and successful future transiting exoplanet characterization programs. We propose a multi-pronged approach wherein one aspect of the program focuses on observing transits of a single target with all of the recommended observing modes to identify and understand potential systematics, compare transmission spectra at overlapping and neighboring wavelength regions, confirm throughputs, and determine overall performances. In our search for transiting exoplanets that are well suited to achieving these goals, we identify 12 objects (dubbed "community targets") that meet our defined criteria. Currently, the most favorable target is WASP-62b because of its large predicted signal size, relatively bright host star, and location in JWST's continuous viewing zone. Since most of the community targets do not have well-characterized atmospheres, we recommend initiating preparatory observing programs to determine the presence of obscuring clouds/hazes within their atmospheres. Measurable spectroscopic features are needed to establish the optimal resolution and wavelength regions for exoplanet characterization. Other initiatives from our proposed ERS program include testing the instrument brightness limits and performing phase-curve observations.(Abridged)Comment: This is a white paper that originated from an open discussion at the Enabling Transiting Exoplanet Science with JWST workshop held November 16 - 18, 2015 at STScI (http://www.stsci.edu/jwst/science/exoplanets). Accepted for publication in PAS

Rare deleterious mutations of the gene EFR3A in autism spectrum disorders

Background: Whole-exome sequencing studies in autism spectrum disorder (ASD) have identified de novo mutations in novel candidate genes, including the synaptic gene Eighty-five Requiring 3A (EFR3A). EFR3A is a critical component of a protein complex required for the synthesis of the phosphoinositide PtdIns4P, which has a variety of functions at the neural synapse. We hypothesized that deleterious mutations in EFR3A would be significantly associated with ASD. Methods: We conducted a large case/control association study by deep resequencing and analysis of whole-exome data for coding and splice site variants in EFR3A. We determined the potential impact of these variants on protein structure and function by a variety of conservation measures and analysis of the Saccharomyces cerevisiae Efr3 crystal structure. We also analyzed the expression pattern of EFR3A in human brain tissue. Results: Rare nonsynonymous mutations in EFR3A were more common among cases (16 / 2,196 = 0.73%) than matched controls (12 / 3,389 = 0.35%) and were statistically more common at conserved nucleotides based on an experiment-wide significance threshold (P = 0.0077, permutation test). Crystal structure analysis revealed that mutations likely to be deleterious were also statistically more common in cases than controls (P = 0.017, Fisher exact test). Furthermore, EFR3A is expressed in cortical neurons, including pyramidal neurons, during human fetal brain development in a pattern consistent with ASD-related genes, and it is strongly co-expressed (P < 2.2 × 10−16, Wilcoxon test) with a module of genes significantly associated with ASD. Conclusions: Rare deleterious mutations in EFR3A were found to be associated with ASD using an experiment-wide significance threshold. Synaptic phosphoinositide metabolism has been strongly implicated in syndromic forms of ASD. These data for EFR3A strengthen the evidence for the involvement of this pathway in idiopathic autism

Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

This corrects the article DOI: 10.1038/sdata.2017.179