The UARS microwave limb sounder version 5 data set: Theory, characterization, and validation

Nitric acid (HNO3) is a major player in processes controlling the springtime depletion of polar ozone. It is the main constituent of the Polar Stratospheric Clouds (PSCs) and a primary reservoir for reactive nitrogen. Potential variations in the stratospheric circulation and temperature may alter the extent and duration of PSCs activity, influencing the future ozone levels significantly. Monitoring HNO3 and its long-term variability, especially in polar region, is then crucial for better understanding issues related to ozone decline and expected recovery. In this study we present an intercomparison between ground based HNO3 measurements, carried out by means of the Ground-Based Millimeter-wave Spectrometer (GBMS), and two satellite data sets produced by the two NASA/JPL Microwave Limb Sounder (MLS) experiments. In particular, we compare UARS MLS measurements (1991-1999) with those carried out by the GBMS at South Pole, Antarctica (90°S), Fall of 1993 and 1995. A similar intercomparison is made between Aura MLS HNO3 observations (2004 - to date) and GBMS measurements obtained during the period February 2004 - March 2007, at the mid-latitudes/high altitudes station of Testa Grigia (45.9° N, 7.7° E, elev. 3500 m), and during polar winters 2008/09 and 2009/2010 at Thule Air Base (76.5°N 68.8°W), Greenland. We assess systematic differences between GBMS and both UARS and Aura HNO3 data sets at seven potential temperature levels (θ) spanning the range 465 – 960 K. The UARS data set advected to the South Pole shows a low bias, within 20% for all θ levels but the 960 K, with respect to GBMS measurements. A very good agreement, within 5%, is obtained between Aura and GBMS observations at Testa Grigia, while larger differences, possibly due to latitude dependent effects, are observed over Thule. These differences are under further investigations but a preliminary comparison over Thule among MLS v3, GBMS, and ACE-FTS measurements suggests that GBMS measurements carried out during winter 2009 might not be reliable. These comparisons have been performed in the framework of the NASA JPL GOZCARDS project, which is aimed at developing a long-term, global data record of the relevant stratospheric constituents in the context of ozone decline. GBMS has been selected in GOZCARDS since its HNO3 dataset, although sampling different latitudes in different years, is the only one spanning a sufficiently long time interval for cross-calibrating HNO3 measurements by the UARS and Aura MLS experiments

A linear CO chemistry parameterization in a chemistry-transport model: evaluation and application to data assimilation

This paper presents an evaluation of a new linear parameterization valid for the troposphere and the stratosphere, based on a first order approximation of the carbon monoxide (CO) continuity equation. This linear scheme (hereinafter noted LINCO) has been implemented in the 3-D Chemical Transport Model (CTM) MOCAGE (MOdèle de Chimie Atmospherique Grande Echelle). First, a one and a half years of LINCO simulation has been compared to output obtained from a detailed chemical scheme output. The mean differences between both schemes are about ±25 ppbv (part per billion by volume) or 15% in the troposphere and ±10 ppbv or 100% in the stratosphere. Second, LINCO has been compared to diverse observations from satellite instruments covering the troposphere (Measurements Of Pollution In The Troposphere: MOPITT) and the stratosphere (Microwave Limb Sounder: MLS) and also from aircraft (Measurements of ozone and water vapour by Airbus in-service aircraft: MOZAIC programme) mostly flying in the upper troposphere and lower stratosphere (UTLS). In the troposphere, the LINCO seasonal variations as well as the vertical and horizontal distributions are quite close to MOPITT CO observations. However, a bias of ~−40 ppbv is observed at 700 Pa between LINCO and MOPITT. In the stratosphere, MLS and LINCO present similar large-scale patterns, except over the poles where the CO concentration is underestimated by the model. In the UTLS, LINCO presents small biases less than 2% compared to independent MOZAIC profiles. Third, we assimilated MOPITT CO using a variational 3D-FGAT (First Guess at Appropriate Time) method in conjunction with MOCAGE for a long run of one and a half years. The data assimilation greatly improves the vertical CO distribution in the troposphere from 700 to 350 hPa compared to independent MOZAIC profiles. At 146 hPa, the assimilated CO distribution is also improved compared to MLS observations by reducing the bias up to a factor of 2 in the tropics. This study confirms that the linear scheme is able to simulate reasonably well the CO distribution in the troposphere and in the lower stratosphere. Therefore, the low computing cost of the linear scheme opens new perspectives to make free runs and CO data assimilation runs at high resolution and over periods of several years

Validation of Aura Microwave Limb Sounder O-3 and CO observations in the upper troposphere and lower stratosphere

International audienceGlobal satellite observations of ozone and carbon monoxide from the Microwave Limb Sounder (MLS) on the EOS Aura spacecraft are discussed with emphasis on those observations in the 215–100 hPa region (the upper troposphere and lower stratosphere). The precision, resolution and accuracy of the data produced by the MLS “version 2.2” processing algorithms are discussed and quantified. O3 accuracy is estimated at ~40 ppbv +5% (~20 ppbv +20% at 215 hPa) while the CO accuracy is estimated at ~30 ppbv +30% for pressures of 147 hPa and less. Comparisons with expectations and other observations show good agreements for the O3 product, generally consistent with the systematic errors quoted above. In the case of CO, a persistent factor of ~2 high bias is seen at 215 hPa. However, the morphology is shown to be realistic, consistent with raw MLS radiance data, and useful for scientific study. The MLS CO data at higher altitudes are shown to be consistent with other observations

2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size.

Variation in cerebral cortex size and complexity is thought to contribute to differences in cognitive ability between humans and other animals. Here we compare cortical progenitor cell output in humans and three nonhuman primates using directed differentiation of pluripotent stem cells (PSCs) in adherent two-dimensional (2D) and organoid three-dimensional (3D) culture systems. Clonal lineage analysis showed that primate cortical progenitors proliferate for a protracted period of time, during which they generate early-born neurons, in contrast to rodents, where this expansion phase largely ceases before neurogenesis begins. The extent of this additional cortical progenitor expansion differs among primates, leading to differences in the number of neurons generated by each progenitor cell. We found that this mechanism for controlling cortical size is regulated cell autonomously in culture, suggesting that primate cerebral cortex size is regulated at least in part at the level of individual cortical progenitor cell clonal output.T.O. was supported by the Wellcome Trust PhD Programme in Developmental Biology at the University of Cambridge. F.J.L. and B.D.S. are Wellcome Trust Investigators. This research was supported by core funding to the Gurdon Institute by the Wellcome Trust and Cancer Research UK. F.H.G. was supported by the Helmsley, Mathers, and JPB Foundations.This is the final version of the article. It first appeared from Elsevier via https://doi.org/10.1016/j.stem.2016.03.00

Analysis of CO in the tropical troposphere using Aura satellite data and the GEOS-Chem model: insights into transport characteristics of the GEOS meteorological products

We use the GEOS-Chem chemistry-transport model (CTM) to interpret the spatial and temporal variations of tropical tropospheric CO observed by the Microwave Limb Sounder (MLS) and the Tropospheric Emission Spectrometer (TES). In so doing, we diagnose and evaluate transport in the GEOS-4 and GEOS-5 assimilated meteorological fields that drive the model, with a particular focus on vertical mixing at the end of the dry season when convection moves over the source regions. The results indicate that over South America, deep convection in both GEOS-4 and GEOS-5 decays at too low an altitude early in the wet season, and the source of CO from isoprene in the model (MEGAN v2.1) is too large, causing a lag in the model's seasonal maximum of CO compared to MLS CO in the upper troposphere (UT). TES and MLS data reveal problems with excessive transport of CO to the eastern equatorial Pacific and lofting in the ITCZ in August and September, particularly in GEOS-4. Over southern Africa, GEOS-4 and GEOS-5 simulations match the phase of the observed CO variation from the lower troposphere (LT) to the UT fairly well, although the magnitude of the seasonal maximum is underestimated considerably due to low emissions in the model. A sensitivity run with increased emissions leads to improved agreement with observed CO in the LT and middle troposphere (MT), but the amplitude of the seasonal variation is too high in the UT in GEOS-4. Difficulty in matching CO in the LT and UT implies there may be overly vigorous vertical mixing in GEOS-4 early in the wet season. Both simulations and observations show a time lag between the peak in fire emissions (July and August) and in CO (September and October). We argue that it is caused by the prevailing subsidence in the LT until convection moves south in September, as well as the low sensitivity of TES data in the LT over the African Plateau. The MLS data suggest that too much CO has been transported from fires in northern Africa to the UT in the model during the burning season, as does MOZAIC aircraft data, perhaps as a result of the combined influence of too strong Harmattan winds in the LT and too strong vertical mixing over the Gulf of Guinea in the model

Novel biallelic USH2A variants in a patient with usher syndrome type IIA- a case report

BACKGROUND: Usher Syndrome is the commonest cause of inherited blindness and deafness. The condition is clinically and genetically heterogeneous, with no current treatment. We report a case carrying novel biallelic variants in USH2A causing progressive early adolescent onset visual and hearing impairment consistent with Usher Syndrome Type IIA. CASE PRESENTATION: Our patient presented at age 13 with progressive visual field loss and hearing loss, associated with early onset of cataract in her 40s requiring lens extraction. Now 52 years old, latest best corrected visual acuity (BCVA) stands at Logmar Right Eye (RE) 0.8 and Left Eye (LE) 0.2, with significantly constricted visual fields bilaterally. She was registered partially sighted age 46. Clinical and molecular genetic assessment of the proband was consistent with a diagnosis of Usher Syndrome Type IIA. Genetic testing identified two novel USH2A variants, resulting in the premature termination codon p.Leu30Ter and a missense mutation p.Cys3251Tyr. Segregation analysis confirmed that these variants were biallelic in the affected case. Comprehensive in silico analysis confirmed that these mutations are the probable cause of Usher Syndrome Type IIA in this individual. CONCLUSIONS: The identification of novel mutations in USH2A increases the spectrum of genetic variations that lead to Usher Syndrome, aiding genetic diagnosis, assessment of patient prognosis, and emphasising the importance of genetic testing to identify new mutations in patients with undiagnosed progressive visual loss. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12886-022-02353-7

The methyl binding domain 3/nucleosome remodelling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex.

BACKGROUND: Chromatin-modifying complexes have key roles in regulating various aspects of neural stem cell biology, including self-renewal and neurogenesis. The methyl binding domain 3/nucleosome remodelling and deacetylation (MBD3/NuRD) co-repressor complex facilitates lineage commitment of pluripotent cells in early mouse embryos and is important for stem cell homeostasis in blood and skin, but its function in neurogenesis had not been described. Here, we show for the first time that MBD3/NuRD function is essential for normal neurogenesis in mice. RESULTS: Deletion of MBD3, a structural component of the NuRD complex, in the developing mouse central nervous system resulted in reduced cortical thickness, defects in the proper specification of cortical projection neuron subtypes and neonatal lethality. These phenotypes are due to alterations in PAX6+ apical progenitor cell outputs, as well as aberrant terminal neuronal differentiation programmes of cortical plate neurons. Normal numbers of PAX6+ apical neural progenitor cells were generated in the MBD3/NuRD-mutant cortex; however, the PAX6+ apical progenitor cells generate EOMES+ basal progenitor cells in reduced numbers. Cortical progenitor cells lacking MBD3/NuRD activity generate neurons that express both deep- and upper-layer markers. Using laser capture microdissection, gene expression profiling and chromatin immunoprecipitation, we provide evidence that MBD3/NuRD functions to control gene expression patterns during neural development. CONCLUSIONS: Our data suggest that although MBD3/NuRD is not required for neural stem cell lineage commitment, it is required to repress inappropriate transcription in both progenitor cells and neurons to facilitate appropriate cell lineage choice and differentiation programmes.We wish to thank Nicola Reynolds for the help with figures; Aoife O’Shaughnessy for the critical reading of the manuscript; Peter Humphreys, the SCI Biofacility staff and Margaret McLeish for technical assistance; Stephanie Hall and Gerard Evan for access to the Laser Capture Microscope and Nathalie Saurat and members of the BH lab for useful discussions. This work was supported by a Wellcome Trust Senior Fellowship in the Basic Biomedical Sciences awarded to BH and a bourse de formation from the Fonds de la Recherche en Santé Québec awarded to EK.This is the final published version of the article. It was originally published in Neural Development (Knock E, et al., Neural Development, 2015, 10:13, doi:10.1186/s13064-015-0040-z). The final version is available at http://dx.doi.org/10.1186/s13064-015-0040-

The roles of convection, extratropical mixing, and in-situ freeze-drying in the Tropical Tropopause Layer

Mechanisms for transporting and dehydrating air across the tropical tropopause layer (TTL) are investigated with a conceptual two dimensional (2-D) model. The 2-D TTL model combines the Holton and Gettelman cold trap dehydration mechanism (Holton and Gettelman, 2001) with the two column convection model of Folkins and Martin (2005). We investigate 3 possible transport scenarios through the TTL: 1) slow uniform ascent across the level of zero radiative heating without direct convective mixing, 2) convective mixing of H<sub>2</sub>O vapor at 100% relative humidity with respect to ice (RHi) with no ice retention, and 3) convective mixing of extremely subsaturated air (100% RHi following the moist adiabatic temperature above the level of neutral buoyancy) with sufficient ice retention such that total H<sub>2</sub>O is 100%RHi. The three mechanisms produce similar seasonal cycles for H<sub>2</sub>O that are in good quantitative agreement with the Aura Microwave Limb Sounder (MLS) measurements. We use Aura MLS measurement of CO and Atmospheric Chemistry Experiment-Fourier Transform Spectrometer measurement of HDO to distinguish among the transport mechanisms. Model comparisons with the observations support the view that H<sub>2</sub>O is predominantly controlled by regions having the lowest cold point tropopause temperature but the trace species CO and HDO support the convective mixing of dry air and lofted ice. The model provides some insight into the processes affecting the long term trends observed in stratospheric H<sub>2</sub>O