Evaluation of three lidar scanning strategies for turbulence measurements

Several errors occur when a traditional Doppler beam swinging (DBS) or velocity–azimuth display (VAD) strategy is used to measure turbulence with a lidar. To mitigate some of these errors, a scanning strategy was recently developed which employs six beam positions to independently estimate the <i>u</i>, <i>v</i>, and <i>w</i> velocity variances and covariances. In order to assess the ability of these different scanning techniques to measure turbulence, a Halo scanning lidar, WindCube v2 pulsed lidar, and ZephIR continuous wave lidar were deployed at field sites in Oklahoma and Colorado with collocated sonic anemometers.</br></br>Results indicate that the six-beam strategy mitigates some of the errors caused by VAD and DBS scans, but the strategy is strongly affected by errors in the variance measured at the different beam positions. The ZephIR and WindCube lidars overestimated horizontal variance values by over 60 % under unstable conditions as a result of variance contamination, where additional variance components contaminate the true value of the variance. A correction method was developed for the WindCube lidar that uses variance calculated from the vertical beam position to reduce variance contamination in the <i>u</i> and <i>v</i> variance components. The correction method reduced WindCube variance estimates by over 20 % at both the Oklahoma and Colorado sites under unstable conditions, when variance contamination is largest. This correction method can be easily applied to other lidars that contain a vertical beam position and is a promising method for accurately estimating turbulence with commercially available lidars

Capturing plume behavior in complex terrain: an overview of the Nevada National Security Site Meteorological Experiment (METEX21)

METEX21 was an atmospheric tracer release experiment executed at the Department of Energy’s Nevada National Security Site (NNSS) in the southwestern U.S to study terrain-induced wind and thermodynamic conditions that influence local-scale (&lt;5-km) plume transport under varying atmospheric forcing conditions. Meteorological observations were collected using 10-m tall meteorological towers, 2-m tall tripods with 3-d sonic anemometers, a 3-m tall eddy covariance flux tower, Doppler profiling lidars, Doppler scanning lidars, weather-balloon launched radiosondes, and a tethered balloon equipped with wind, temperature, and aerosol sensors at heights up to 800 m. A smoke tracer was released along three transects in the horizontal and vertical directions and observed with video cameras, aerosol sensors and lidars (via aerosol backscatter). The observations showed evidence of large-scale/synoptic transience as well as local-scale upslope and downslope flows, along-axis valley flows, recirculation eddies on leeward slopes, and periods of strong shear and veer aloft. The release days were classified as either synoptically-driven or locally-driven, and a single case day is presented in detail for each. Synoptically-forced days show relatively narrow smoke plumes traveling down the valley from north to south (with the predominant wind direction), with little deviation in transport direction regardless of the elevation or ground locations of the smoke releases, except near the presence of leeside recirculation eddies. Locally-forced days exhibit a wider range of plume behavior due to the combination of thermally-induced valley and slope flows, which are often flowing in different cardinal directions, and wind shear found aloft at higher altitudes and elevations. We saw evidence of smoke lofting on top of the mesas due to strong upslope flows on these days. A major finding of this experiment was the effectiveness of scanning lidars to measure 2-dimensional plume transport out to a 2–3 km distance; much farther than could be visibly observed. METEX21 was the first of three planned tracer experiments at NNSS, and future experiments will incorporate multiple tracers to improve individual plume identification so that finer resolution flow details can be attained from these measurements, as well as deploy a larger suite of meteorological instrumentation, including more temperature profiling data

Trends and Controls on Water-Use Efficiency of an Old-Growth Coniferous Forest in the Pacific Northwest

At the ecosystem scale, water-use efficiency (WUE) is defined broadly as the ratio of carbon assimilated to water evaporated by an ecosystem. WUE is an important aspect of carbon and water cycling and has been used to assess forest ecosystem responses to climate change and rising atmospheric CO2 concentrations. This study investigates the influence of meteorological and radiation variables on forest WUE by analyzing an 18 year (1998–2015) half-hourly time series of carbon and water fluxes measured with the eddy covariance technique in an old-growth conifer forest in the Pacific Northwest, USA. Three different metrics of WUE exhibit an overall increase over the period 1998–2007 mainly due to an increase in gross primary productivity (GPP) and a decrease in evapotranspiration (ET). However, the WUE metrics did not exhibit an increase across the period from 2008 to 2015 due to a greater reduction in GPP relative to ET. The strength of associations among particular meteorological variables and WUE varied with the scale of temporal aggregation used. In general, vapor pressure deficit and air temperature appear to control WUE at half-hourly and daily time scales, whereas atmospheric CO2 concentration was identified as the most important factor controlling monthly WUE. Carbon and water fluxes and the consequent WUE showed a weak correlation to the Standard Precipitation Index, while carbon fluxes were strongly dependent on the combined effect of multiple climate factors. The inferred patterns and controls on forest WUE highlighted have implications for improved understanding and prediction of possible adaptive adjustments of forest physiology in response to climate change and rising atmospheric CO2 concentrations

Radiocarbon-Based Partitioning of Soil Respiration in an Old-Growth Coniferous Forest

Temperate forests play an important role in the global carbon cycle, and are thought to currently be a sink for atmospheric CO₂. However, we lack understanding of the drivers of forest carbon accumulation and loss, hampering our ability to predict carbon cycle responses to global change. In this study, we used CO₂ flux and radiocarbon (¹⁴C) measurements to investigate the role of seasonal drivers on soil respiration. Radiocarbon measurements of CO₂ evolved during incubation of fine roots and root-free soils at the beginning and end of the growing season (April and August) showed that these two soil respiration sources (fine roots vis-a`-vis soils) have different mean residence times that stayed constant between seasons. Radiocarbon measurements show that root respiration was made up of carbon fixed 3–5 years prior to sampling, and that heterotrophic respiration was made up of carbon fixed 7–10 years prior. The difference in radiocarbon signature between the two sources allowed us to partition autotrophic and heterotrophic respiration sources for soil respiration measurements in the field. We observed a small but significant increase in Δ¹⁴C of soil respiration between April and August, suggesting an increase in heterotrophic respiration sources over the growing season. Using a two end-member mixing model, we estimate that 55 ± 22% of soil respiration originated from autotrophic (root) sources in April, but their contribution dropped to 38 ± 21% in August. These findings suggest that the contribution of root respiration increases at a time of high productivity and/or as a result of relatively low microbial respiration in the early spring in this old-growth coniferous forest.Keywords: root respiration, stored carbon, residence time of soil carbon, photosynthates, soil CO₂ flux, radiocarbo

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Phenotypic Characterization of <i>EIF2AK4</i> Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension

Background: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 ( BMPR2 ) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene ( EIF2AK4 ) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. Methods: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource–Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of &lt;1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. Results: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (K co ; 33% [interquartile range, 30%–35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23–38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. Conclusions: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low K co and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation. </jats:sec

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in $\textit{CHM}$ in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.This work was supported by The National Institute for Health Research England (NIHR) for the NIHR BioResource – Rare Diseases project (grant number RG65966). The Moorfields Eye Hospital cohort of patients and clinical and imaging data were ascertained and collected with the support of grants from the National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, National Health Service Foundation Trust, and UCL Institute of Ophthalmology, Moorfields Eye Hospital Special Trustees, Moorfields Eye Charity, the Foundation Fighting Blindness (USA), and Retinitis Pigmentosa Fighting Blindness. M.M. is a recipient of an FFB Career Development Award. E.M. is supported by UCLH/UCL NIHR Biomedical Research Centre. F.L.R. and D.G. are supported by Cambridge NIHR Biomedical Research Centre