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The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry. With the rapid advancements in higher-throughput and lower-cost sequencing technologies and accordingly the huge volume of multi-omics data generated at exponential scales and rates, NGDC is continually expanding, updating and enriching its core database resources through big data integration and value-added curation. In the past year, efforts for update have been mainly devoted to BioProject, BioSample, GSA, GWH, GVM, NONCODE, LncBook, EWAS Atlas and IC4R. Newly released resources include three human genome databases (PGG.SNV, PGG.Han and CGVD), eLMSG, EWAS Data Hub, GWAS Atlas, iSheep and PADS Arsenal. In addition, four web services, namely, eGPS Cloud, BIG Search, BIG Submission and BIG SSO, have been significantly improved and enhanced. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.

In jurisdictions including the US and the EU ground transportation and marine fuels have recently been required to contain lower concentrations of sulfur, which has resulted in reduced atmospheric SO(x) emissions. In contrast, the maximum sulfur content of aviation fuel has remained unchanged at 3000 ppm (although sulfur levels average 600 ppm in practice). We assess the costs and benefits of a potential ultra-low sulfur (15 ppm) jet fuel standard ("ULSJ"). We estimate that global implementation of ULSJ will cost US$1-4bn per year and prevent 900-4000 air quality-related premature mortalities per year. Radiative forcing associated with reduction in atmospheric sulfate, nitrate, and ammonium loading is estimated at +3.4 mW/m(2) (equivalent to about 1/10th of the warming due to CO(2) emissions from aviation) and ULSJ increases life cycle CO(2) emissions by approximately 2%. The public health benefits are dominated by the reduction in cruise SO(x) emissions, so a key uncertainty is the atmospheric modeling of vertical transport of pollution from cruise altitudes to the ground. Comparisons of modeled and measured vertical profiles of CO, PAN, O(3), and (7)Be indicate that this uncertainty is low relative to uncertainties regarding the value of statistical life and the toxicity of fine particulate matter.

A statistical downscaling approach is developed for generating regional temperature change predictions from GCM results. The approach utilizes GCM free atmosphere output and surface observations in a framework conceptually similar to the model output statistics approach common in the forecasting community. The appropriateness of this approach is demonstrated through a comparison of GCM and observed free atmosphere variables. Seasonal downscaling models are presented for eight sites within four community climate model (CCM) grid cells in the United States. The majority of these models are capable of explaining more than 90% of the variance in the temperature time series. The results indicate a wide range of differences between downscaled climate change predictions and grid cell–level CCM predictions.

Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA–mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.

[1] Air quality simulations were performed for the Houston-Galveston-Brazoria area for springtime conditions in May and June of 2009. Meteorological parameters predicted by Weather Research and Forecasting (WRF) model, for which data assimilation with recursive objective analysis was performed, are well simulated most of the time. The Community Multiscale Air Quality (CMAQ) model driven by meteorology from WRF simulates ozone and many other trace species, including radical precursors such as HCHO and HONO, with a satisfactory agreement with observations. While CMAQ satisfactorily captures the daily variations of the OH radical, it sometimes underestimates its high daytime values. Concentrations of HO 2 are often underpredicted in polluted air masses and persistently severely underpredicted at low NO x conditions, when the Houston air is affected by marine air masses. In contrast, concentrations of H 2 O 2 and CH 3 OOH are almost always overpredicted by the model, the overprediction occurs frequently in the polluted air and occurs always when marine air is encountered. Those mispredictions are consistent despite day-to-day variations in meteorological conditions and emissions and bring into question current representation of radical-related chemistry in the model as radical production and recirculation in the model is overtaken by termination processes and creation of more stable compounds, such as H 2 O 2 and CH 3 OOH. Smaller model biases of H 2 O 2 and peroxides are associated with lower humidity. The relative importance of various photolysis processes as radical sources in the Houston atmosphere was also elucidated. Morning HO x formation is dominated by HONO while ozone contributes the most during midday. HONO contribution to HO x formation is more pronounced at the surface layer where most of it is formed, radical production from ozone is more important at elevated levels where higher concentrations of ozone are observed. Formaldehyde contributes up to 40% and also peaks during midday, but on days when high morning concentrations of formaldehyde are observed, its contribution to HO x in the morning exceeds that of ozone. Photolysis of H 2 O 2 is a minor contributor to radical levels.Citation: Czader, B. H., X. Li, and B. Rappenglueck (2013), CMAQ modeling and analysis of radicals, radical precursors, and chemical transformations,

No abstract

Abstract. Accurate meteorological fields are imperative for correct chemical transport modeling. Observation nudging, along with objective analysis, is generally considered a lowcost and effective technique to improve meteorological simulations. However, the meteorological impact of observation nudging on chemistry has not been well characterized. This study involved two simulations to analyze the impact of observation nudging on simulated meteorology and ozone concentrations during the 2013 Deriving Information on Surface conditions from Column and Vertically Resolved Observations Relevant to Air Quality (DISCOVER-AQ) Texas campaign period, using the Weather Research and Forecasting (WRF) and Community Multiscale Air Quality (CMAQ) models. The results showed improved correlations between observed and simulated parameters. For example, the index of agreement (IOA) improved by about 9 % for surface temperature and 6-11 % for surface zonal (U-WIND) and meridional (V-WIND) winds when observation nudging was employed. Analysis of a cold front event indicated that nudging improved the timing of wind transition during the front passage. Observation nudging also reduced the model biases for the planetary boundary layer height predictions. Additionally, the IOA for CMAQ simulated surface ozone improved by 6 % during the simulation period. The high-ozone episode on 25 September was a post-front ozone event in Houston. The small-scale morning wind shifts near the Houston Ship Channel combined with higher aloft ozone early morning likely caused the day's ozone exceedance. While observation nudging did not recreate the wind shifts on that day and failed to reproduce the observed high ozone, analyses of surface and aircraft data found that observation nudging helped the model yield improved ozone predictions. In a 2 h period during the event, substantially better winds in the sensitivity case noticeably improved the ozone. The average IOA for ozone in the period increased from just over 0.4 to near 0.7. Further work on improving the capability of nudging to reproduce local meteorological events such as stagnations and wind reversals could enhance a chemical transport model's skill for predicting high-ozone events.