GEOS S2S-2_1 File Specification: GMAO Seasonal and Sub-Seasonal Forecast Output

The NASA GMAO seasonal (9 months) and subseasonal (45 days) forecasts are produced with the Goddard Earth Observing System (GEOS) Atmosphere-Ocean General Circulation Model and Data Assimilation System Version S2S-2_1. The new system replaces version S2S-1.0 described in Borovikov et al (2017), and includes upgrades to many components of the system. The atmospheric model includes an upgrade from a pre-MERRA-2 version running on a latitude-longitude grid at approx. 1 degree resolution to a current version running on a cubed sphere grid at approximately 1/2 degree resolution. The important developments are related to the dynamical core (Putman et al., 2011), the moist physics (''two-moment microphysics'' of Barahona et al., 2014) and the cryosphere (Cullather et al., 2014). As in the previous GMAO S2S system, the land model is that of Koster et al (2000). GMAO S2S-2_1 now includes the Goddard Chemistry Aerosol Radiation and Transport (GOCART, Colarco et al., 2010) single moment interactive aerosol model that includes predictive aerosols including dust, sea salt and several species of carbon and sulfate. The previous version of GMAO S2S specified aerosol amounts from climatology, which were used to inform the atmospheric radiation only. The ocean model includes an upgrade from MOM4 to MOM5 (Griffies 2012), and continues to be run on the tripolar grid at approximately 1/2 degree resolution in the tropics with 40 vertical levels. As in S2S-1.0, the sea ice model is from the Los Alamos Sea Ice model (CICE4, Hunke and Lipscomb 2010). The Ocean Data Assimilation System (ODAS) has been upgraded from the one described in Borovikov et al., 2017 to one that uses a modified version of the Penny, 2014 Local Ensemble Transform Kalman Filter (LETKF), and now assimilates along-track altimetry. The ODAS also does a nudging to MERRA-2 SST and sea ice boundary conditions. The atmospheric data assimilation fields used to constrain the atmosphere in the ODAS have been upgraded from MERRA to a MERRA-2 like system. The system is initialized using a MERRA-2-like atmospheric reanalysis (Gelaro et al. 2017) and the GMAO S2S-2_1 ocean analysis. Additional ensemble members for forecasts are produced with initial states at 5-day intervals, with additional members based on perturbations of the atmospheric and ocean states. Both subseasonal and seasonal forecasts are submitted to the National MultiModel Ensemble (NMME) project, and are part of the US/Canada multimodel seasonal forecasts (http://www.cpc.ncep.noaa.gov/products/NMME/). A large suite of retrospective forecasts (''hindcasts'') have been completed, and contribute to the calculation of the model's baseline climatology and drift, anomalies from which are the basis of the seasonal forecasts

GEOS S2S Version 3: The New NASA/GMAO High Resolution Seasonal Prediction System

The NASA/Goddard Global Modeling and Assimilation Office (GMAO) released Version 2 of the Subseasonal to Seasonal (GEOS-S2S) forecast system in the fall of 2017, and it has been producing near-real time subseasonal to seasonal forecasts and a weakly coupled atmosphere-ocean data assimilation record since then. A new version of the coupled modeling and analysis system (Version 3) was released by the GMAO at the end of 2019. The new version runs at higher oceanic resolution than the previous (approximately 1/2 degree for the atmosphere, 1/4 degree for the ocean), and includes interactive earth system model components not typically present in seasonal prediction systems (two moment cloud microphysics for aerosol indirect effect and an interactive aerosol model). The weakly coupled atmosphere-ocean data assimilation system now includes assimilation of sea surface salinity, that has been shown to result in improved ocean mixed layer simulation and ENSO prediction skill

An Introduction to the NASA GMAO Coupled Atmosphere-Ocean System - GEOS-S2S Version 3

Recently NASA's Global Modeling and Assimilation Office (GMAO) has developed a new Subseasonal to Seasonal Prediction system Version 3 (GEOS-S2S-3). This upgrade replaces the GEOS-S2S-2 which is NASA's current contribution to the North American Multi-Model Experiment seasonal prediction project (Kirtman et al., 2014). The main improvements for our S2S-3 system include 1) a higher resolution MOM5 (Griffies et al., 2005) ocean model (now 0.25o x 0.25o x 50 layers), 2) an improved atmospheric/ocean interface layer (Akella and Suarez, 2018), and 3) assimilation of a long-track satellite salinity into the ocean model (Hackert et al, 2019). Atmospheric forcing is provided by the NASA MERRA-2 reanalysis (Gelaro et al., 2017). Initialization for the ocean relies on the GMAO ocean reanalysis system which assimilates all available in situ temperature and salinity, satellite sea surface salinity, and sea level using the Local Ensemble Transform Kalman Filter (LETKF) implementation of (Penny et al., 2013) on a 5 day assimilation cycle with 20 fixed ensemble members.In this presentation, we will authenticate our new S2S-3 ocean reanalysis using standard GODAE validation metrics. For example, we will compare gridded fields of mean and standard deviation of the ocean reanalysis versus observed fields. We will show correlation/RMS of model versus observations and temperature and salinity mean profiles for the various basins and latitude bands. Basin-scale volume transports, such as the Atlantic Meridional Overturning Circulation and the Indonesian Throughflow will be validated. Equatorial ocean waves will be compared by decomposing sea level into Kelvin and Rossby components. For each of these metrics, we plan to validate the results and then compare our new S2S-3 against the current production version, S2S-2. Finally, we will compare 9-month seasonal forecasts initialized from these two systems for the tropical Pacific NINO3.4 region over the period 1981-present

GEOS S2S-2_1: The GMAO High Resolution Seasonal Prediction System

A new version of the coupled modeling and analysis system used to produce near real time subseasonal to seasonal forecasts was recently released by the NASA/Goddard Global Modeling and Assimilation Office. The new version runs at higher atmospheric resolution than the previous, (approximately 1/2 degree globally), contains a substantially improved model description of the cryosphere, and includes additional interactive earth system model components (aerosol model). In addition, the Ocean data assimilation system has been replaced with a Local Ensemble Transform Kalman Filter, and now includes the assimilation of along-track sea surface height. Here will describe the new system, along with the plans for the future (GEOS S2S-3_0) which will include a higher resolution ocean model and more interactive earth system model components (interactive vegetation, biomass burning from fires). We will also present results from a series of retrospective seasonal forecasts. Results show significant improvements in surface temperatures over much of the northern hemisphere and a much improved prediction of sea ice extent in both hemispheres. Analysis of the ensemble spread shows improvements relative to the previous system, including generally better reliability. The precipitation forecast skill is comparable to previous S2S systems, and the only tradeoff is an increased "double ITCZ", which is expected as we go to higher atmospheric resolution

Vascular RAGE transports oxytocin into the brain to elicit its maternal bonding behaviour in mice

金沢大学医薬保健研究域医学系Oxytocin sets the stage for childbirth by initiating uterine contractions, lactation and maternal bonding behaviours. Mice lacking secreted oxcytocin (Oxt -/-, Cd38 -/-) or its receptor (Oxtr -/-) fail to nurture. Normal maternal behaviour is restored by peripheral oxcytocin replacement in Oxt -/- and Cd38 -/-, but not Oxtr -/- mice, implying that circulating oxcytocin crosses the blood-brain barrier. Exogenous oxcytocin also has behavioural effects in humans. However, circulating polypeptides are typically excluded from the brain. We show that oxcytocin is transported into the brain by receptor for advanced glycation end-products (RAGE) on brain capillary endothelial cells. The increases in oxcytocin in the brain which follow exogenous administration are lost in Ager -/- male mice lacking RAGE, and behaviours characteristic to abnormalities in oxcytocin signalling are recapitulated in Ager -/- mice, including deficits in maternal bonding and hyperactivity. Our findings show that RAGE-mediated transport is critical to the behavioural actions of oxcytocin associated with parenting and social bonding.3082047

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Vascular RAGE transports oxytocin into the brain to elicit its maternal bonding behaviour in mice

Yasuhiko Yamamoto et al. show that oxytocin is transported into the brain by the receptor for advanced glycation end-products (RAGE) on the blood-brain barrier. This study explains how circulating oxytocin crosses the blood-brain barrier, which is important to manifest oxytocin’s maternal bonding effects

National trends in the outcomes of subarachnoid haemorrhage and the prognostic influence of stroke centre capability in Japan: retrospective cohort study

Objectives To examine the national, 6-year trends in in-hospital clinical outcomes of patients with subarachnoid haemorrhage (SAH) who underwent clipping or coiling and the prognostic influence of temporal trends in the Comprehensive Stroke Center (CSC) capabilities on patient outcomes in Japan.Design Retrospective study.Setting Six hundred and thirty-one primary care institutions in Japan.Participants Forty-five thousand and eleven patients with SAH who were urgently hospitalised, identified using the J-ASPECT Diagnosis Procedure Combination database.Primary and secondary outcome measures Annual number of patients with SAH who remained untreated, or who received clipping or coiling, in-hospital mortality and poor functional outcomes (modified Rankin Scale: 3–6) at discharge. Each CSC was assessed using a validated scoring system (CSC score: 1–25 points).Results In the overall cohort, in-hospital mortality decreased (year for trend, OR (95% CI): 0.97 (0.96 to 0.99)), while the proportion of poor functional outcomes remained unchanged (1.00 (0.98 to 1.02)). The proportion of patients who underwent clipping gradually decreased from 46.6% to 38.5%, while that of those who received coiling and those left untreated gradually increased from 16.9% to 22.6% and 35.4% to 38%, respectively. In-hospital mortality of coiled (0.94 (0.89 to 0.98)) and untreated (0.93 (0.90 to 0.96)) patients decreased, whereas that of clipped patients remained stable. CSC score improvement was associated with increased use of coiling (per 1-point increase, 1.14 (1.08 to 1.20)) but not with short-term patient outcomes regardless of treatment modality.Conclusions The 6-year trends indicated lower in-hospital mortality for patients with SAH (attributable to better outcomes), increased use of coiling and multidisciplinary care for untreated patients. Further increasing CSC capabilities may improve overall outcomes, mainly by increasing the use of coiling. Additional studies are necessary to determine the effect of confounders such as aneurysm complexity on outcomes of clipped patients in the modern endovascular era