Direct retrieval of isoprene from satellite-based infrared measurements.

Isoprene is the atmosphere's most important non-methane organic compound, with key impacts on atmospheric oxidation, ozone, and organic aerosols. In-situ isoprene measurements are sparse, and satellite-based constraints have employed an indirect approach using its oxidation product formaldehyde, which is affected by non-isoprene sources plus uncertainty and spatial smearing in the isoprene-formaldehyde relationship. Direct global isoprene measurements are therefore needed to better understand its sources, sinks, and atmospheric impacts. Here we show that the isoprene spectral signatures are detectable from space using the satellite-borne Cross-track Infrared Sounder (CrIS), develop a full-physics retrieval methodology for quantifying isoprene abundances from these spectral features, and apply the algorithm to CrIS measurements over Amazonia. The results are consistent with model output and in-situ data, and establish the feasibility of direct global space-based isoprene measurements. Finally, we demonstrate the potential for combining space-based measurements of isoprene and formaldehyde to constrain atmospheric oxidation over isoprene source regions

Modeling Study of the Air Quality Impact of Record-Breaking Southern California Wildfires in December 2017

We investigate the air quality impact of record‐breaking wildfires in Southern California during 5–18 December 2017 using the Weather Research and Forecasting model with Chemistry in combination with satellite and surface observations. This wildfire event was driven by dry and strong offshore Santa Ana winds, which played a critical role in fire formation and air pollutant transport. By utilizing fire emissions derived from the high‐resolution (375 × 375 m²) Visible Infrared Imaging Radiometer Suite active fire detections, the simulated magnitude and temporal evolution of fine particulate matter (PM_(2.5)) concentrations agree reasonably well with surface observations (normalized mean bias = 4.0%). Meanwhile, the model could generally capture the spatial pattern of aerosol optical depth from satellite observations. Sensitivity tests reveal that using a high spatial resolution for fire emissions and a reasonable treatment of plume rise (a fair split between emissions injected at surface and those lifted to upper levels) is important for achieving decent PM_(2.5) simulation results. Biases in PM_(2.5) simulation are relatively large (about 50%) during the period with the strongest Santa Ana wind, due to a possible underestimation of burning area and uncertainty in wind field variation. The 2017 December fire event increases the 14‐day averaged PM_(2.5) concentrations by up to 231.2 μg/m³ over the downwind regions, which substantially exceeds the U.S. air quality standards, potentially leading to adverse health impacts. The human exposure to fire‐induced PM_(2.5) accounts for 14–42% of the annual total PM_(2.5) exposure in areas impacted by the fire plumes

Satellite measurements of peroxyacetyl nitrate from the Cross-Track Infrared Sounder: comparison with ATom aircraft measurements

We present an overview of an optimal estimation algorithm to retrieve peroxyacetyl nitrate (PAN) from single-field-of-view Level 1B radiances measured by the Cross-Track Infrared Sounder (CrIS). CrIS PAN retrievals show peak sensitivity in the mid-troposphere, with degrees of freedom for signal less than or equal to 1.0. We show comparisons with two sets of aircraft measurements from the Atmospheric Tomography Mission (ATom), the PAN and Trace Hydrohalocarbon ExpeRiment (PANTHER) and the Georgia Tech chemical ionization mass spectrometer (GT-CIMS). We find a systematic difference between the two aircraft datasets, with vertically averaged mid-tropospheric values from the GT-CIMS around 14 % lower than equivalent values from PANTHER. However, the two sets of aircraft measurements are strongly correlated (R2 value of 0.92) and do provide a consistent view of the large-scale variation of PAN. We demonstrate that the retrievals of PAN from CrIS show skill in measurement of these large-scale PAN distributions in the remote mid-troposphere compared to the retrieval prior. The standard deviation of individual CrIS–aircraft differences is 0.08 ppbv, which we take as an estimate of the uncertainty of the CrIS mid-tropospheric PAN for a single satellite field of view. The standard deviation of the CrIS–aircraft comparisons for averaged CrIS retrievals (median of 20 satellite coincidences with each aircraft profile) is lower at 0.05 ppbv. This would suggest that the retrieval error is reduced with averaging, although not with the square root of the number of observations. We find a negative bias of the order of 0.1 ppbv in the CrIS PAN results with respect to the aircraft measurements. This bias shows a dependence on column water vapor. We provide a water-vapor-dependent bias correction for use with the CrIS PAN data.</p

Absorption Coefficient (ABSCO) Tables for the Orbiting Carbon Observatories: Version 5.1

The accuracy of atmospheric trace gas retrievals depends directly on the accuracy of the molecular absorption model used within the retrieval algorithm. For remote sensing of well-mixed gases, such as carbon dioxide (CO₂), where the atmospheric variability is small compared to the background, the quality of the molecular absorption model is key. Recent updates to oxygen (O₂) absorption coefficients (ABSCO) for the 0.76 μm A-band and the water vapor (H₂O) continuum model within the 1.6 μm and 2.06 μm CO₂ bands used within the Orbiting Carbon Observatory (OCO-2 and OCO-3) algorithm are described here. Updates in the O₂ A-band involve the inclusion of new laboratory measurements within multispectrum fits to improve relative consistency between O₂ line shapes and collision-induced absorption (CIA). The H₂O continuum model has been updated to MTCKD v3.2, which has benefited from information from a range of laboratory studies relative to the model utilized in the previous ABSCO version. Impacts of these spectroscopy updates have been evaluated against ground-based atmospheric spectra from the Total Carbon Column Observing Network (TCCON) and within the framework of the OCO-2 algorithm, using OCO-2 soundings covering a range of atmospheric and surface conditions. The updated absorption coefficients (ABSCO version 5.1) are found to offer improved fitting residuals and reduced biases in retrieved surface pressure relative to the previous version (ABSCO v5.0) used within B8 and B9 of the OCO-2 retrieval algorithm and have been adopted for the OCO B10 Level 2 algorithm

Absorption Coefficient (ABSCO) Tables for the Orbiting Carbon Observatories: Version 5.1

The accuracy of atmospheric trace gas retrievals depends directly on the accuracy of the molecular absorption model used within the retrieval algorithm. For remote sensing of well-mixed gases, such as carbon dioxide (CO₂), where the atmospheric variability is small compared to the background, the quality of the molecular absorption model is key. Recent updates to oxygen (O₂) absorption coefficients (ABSCO) for the 0.76 μm A-band and the water vapor (H₂O) continuum model within the 1.6 μm and 2.06 μm CO₂ bands used within the Orbiting Carbon Observatory (OCO-2 and OCO-3) algorithm are described here. Updates in the O₂ A-band involve the inclusion of new laboratory measurements within multispectrum fits to improve relative consistency between O₂ line shapes and collision-induced absorption (CIA). The H₂O continuum model has been updated to MTCKD v3.2, which has benefited from information from a range of laboratory studies relative to the model utilized in the previous ABSCO version. Impacts of these spectroscopy updates have been evaluated against ground-based atmospheric spectra from the Total Carbon Column Observing Network (TCCON) and within the framework of the OCO-2 algorithm, using OCO-2 soundings covering a range of atmospheric and surface conditions. The updated absorption coefficients (ABSCO version 5.1) are found to offer improved fitting residuals and reduced biases in retrieved surface pressure relative to the previous version (ABSCO v5.0) used within B8 and B9 of the OCO-2 retrieval algorithm and have been adopted for the OCO B10 Level 2 algorithm

Evaluation of single-footprint AIRS CH4 profile retrieval uncertainties using aircraft profile measurements

We evaluate the uncertainties of methane optimal estimation retrievals from single-footprint thermal infrared observations from the Atmospheric Infrared Sounder (AIRS). These retrievals are primarily sensitive to atmospheric methane in the mid-troposphere through the lower stratosphere (&sim;2 to &sim;17&thinsp;km). We compare them to in situ observations made from aircraft during the HIAPER Pole to Pole Observations (HIPPO) and Atmospheric Tomography Mission (ATom) campaigns, and from the NOAA GML aircraft network, between the surface and 5&ndash;13&thinsp;km, across a range of years, latitudes between 60∘&thinsp;S to 80∘&thinsp;N, and over land and ocean. After a global, pressure-dependent bias correction, we find that the land and ocean have similar biases and that the reported observation error (combined measurement and interference errors) of &sim;27&thinsp;ppb is consistent with the SD between aircraft and individual AIRS observations. A single observation has measurement (noise related) uncertainty of &sim;17&thinsp;ppb, a &sim;20&thinsp;ppb uncertainty from radiative interferences (e.g., from water or temperature), and &sim;30&thinsp;ppb due to &ldquo;smoothing error&rdquo;, which is partially removed when making comparisons to in situ measurements or models in a way that accounts for this regularization. We estimate a 10&thinsp;ppb validation uncertainty because the aircraft typically did not measure methane at altitudes where the AIRS measurements have some sensitivity, e.g., the stratosphere, and there is uncertainty in the truth that we validate against. Daily averaging only partly reduces the difference between aircraft and satellite observation, likely because of correlated errors introduced into the retrieval from temperature and water vapor. For example, averaging nine observations only reduces the aircraft&ndash;model difference to &sim;17&thinsp;ppb vs. the expected &sim;10&thinsp;ppb. Seasonal averages can reduce this &sim;17&thinsp;ppb uncertainty further to &sim;10&thinsp;ppb, as determined through comparison with NOAA aircraft, likely because uncertainties related to radiative effects of temperature and water vapor are reduced when averaged over a season. &nbsp;</p

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Data associated with the manuscript Using TES retrievals to investigate PAN in North American biomass burning plumes

The attached dataset contains the latitude, longitude, time, HMS smoke overlap status, and tropospheric average and maximum TES PAN and TES CO used in Fischer et al. [2018]. See abstract and publication related to this dataset.Peroxyacyl nitrate (PAN) is a critical atmospheric reservoir for nitrogen oxide radicals, and it plays a lead role in their redistribution in the troposphere. We analyze new Tropospheric Emission Spectrometer (TES) PAN observations over North America during July 2006 to 2009. Using aircraft observations from the Colorado Front Range, we demonstrate that TES can be sensitive to elevated PAN in the boundary layer (~750 hPa) even in the presence of clouds. In situ observations have shown that wildfire emissions can rapidly produce PAN, and PAN decomposition is an important component of ozone production in smoke plumes. We identify smoke-impacted TES PAN retrievals by co-location with NOAA Hazard Mapping System (HMS) smoke plumes. Depending on the year, 15 – 32 % of cases where elevated PAN is identified in TES observations (retrievals with DOF > 0.6) overlap smoke plumes during July. Of all the retrievals attempted in July 2006 to July 2009, the percent associated with smoke is 18%. A case study of smoke transport in July 2007 illustrates that PAN enhancements associated with HMS smoke plumes can be connected to fire complexes, providing evidence that TES is sufficiently sensitive to measure elevated PAN several days downwind of major fires. Using a subset of retrievals with TES 510 hPa carbon monoxide (CO) > 150 ppbv, and multiple estimates of background PAN, we calculate enhancement ratios for tropospheric average PAN relative to CO in smoke-impacted retrievals. Most of the TES-based enhancement ratios fall within the range calculated from in situ measurements.This work was supported by NASA Award Number NNX14AF14G