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  • 1
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    The Community Climate System Model version 3 (CCSM3) (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society 2006. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 19 (2006): 2122–2143, doi:10.1175/JCLI3761.1.
    Description: The Community Climate System Model version 3 (CCSM3) has recently been developed and released to the climate community. CCSM3 is a coupled climate model with components representing the atmosphere, ocean, sea ice, and land surface connected by a flux coupler. CCSM3 is designed to produce realistic simulations over a wide range of spatial resolutions, enabling inexpensive simulations lasting several millennia or detailed studies of continental-scale dynamics, variability, and climate change. This paper will show results from the configuration used for climate-change simulations with a T85 grid for the atmosphere and land and a grid with approximately 1° resolution for the ocean and sea ice. The new system incorporates several significant improvements in the physical parameterizations. The enhancements in the model physics are designed to reduce or eliminate several systematic biases in the mean climate produced by previous editions of CCSM. These include new treatments of cloud processes, aerosol radiative forcing, land–atmosphere fluxes, ocean mixed layer processes, and sea ice dynamics. There are significant improvements in the sea ice thickness, polar radiation budgets, tropical sea surface temperatures, and cloud radiative effects. CCSM3 can produce stable climate simulations of millennial duration without ad hoc adjustments to the fluxes exchanged among the component models. Nonetheless, there are still systematic biases in the ocean–atmosphere fluxes in coastal regions west of continents, the spectrum of ENSO variability, the spatial distribution of precipitation in the tropical oceans, and continental precipitation and surface air temperatures. Work is under way to extend CCSM to a more accurate and comprehensive model of the earth's climate system.
    Description: We would like to acknowledge the substantial contributions to and support for the CCSM project from the National Science Foundation (NSF), the Department of Energy (DOE), the National Oceanic and Atmospheric Administration, and the National Aeronautics and Space Administration.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 2
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    Challenges and prospects for reducing coupled climate model SST biases in the eastern tropical Atlantic and Pacific Oceans : the U.S. CLIVAR Eastern Tropical Oceans Synthesis Working Group (2017)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 97 (2016): 2305-2327, doi:10.1175/BAMS-D-15-00274.1.
    Description: Well-known problems trouble coupled general circulation models of the eastern Atlantic and Pacific Ocean basins. Model climates are significantly more symmetric about the equator than is observed. Model sea surface temperatures are biased warm south and southeast of the equator, and the atmosphere is too rainy within a band south of the equator. Near-coastal eastern equatorial SSTs are too warm, producing a zonal SST gradient in the Atlantic opposite in sign to that observed. The U.S. Climate Variability and Predictability Program (CLIVAR) Eastern Tropical Ocean Synthesis Working Group (WG) has pursued an updated assessment of coupled model SST biases, focusing on the surface energy balance components, on regional error sources from clouds, deep convection, winds, and ocean eddies; on the sensitivity to model resolution; and on remote impacts. Motivated by the assessment, the WG makes the following recommendations: 1) encourage identification of the specific parameterizations contributing to the biases in individual models, as these can be model dependent; 2) restrict multimodel intercomparisons to specific processes; 3) encourage development of high-resolution coupled models with a concurrent emphasis on parameterization development of finer-scale ocean and atmosphere features, including low clouds; 4) encourage further availability of all surface flux components from buoys, for longer continuous time periods, in persistently cloudy regions; and 5) focus on the eastern basin coastal oceanic upwelling regions, where further opportunities for observational–modeling synergism exist.
    Description: PZ, BK, and RM acknowledge support from NOAA Grant NA14OAR4310278, and PZ acknowledges support from NSF AGS-1233874. BM acknowledges support from the Regional and Global Climate Modeling Program of the U.S. Department of Energy’s Office of Science, Cooperative Agreement DE-FC02-97ER62402. PC acknowledges support from U.S. NSF Grants OCE-1334707 and AGS-1462127, and NOAA Grant NA11OAR4310154. PC also acknowledges support from China’s National Basic Research Priorities Programme (2013CB956204) and the Natural Science Foundation of China (41222037 and 41221063). TF acknowledges support from NSF Grant OCE-0745508 and NASA Grant NNX14AM71G. PB acknowledges support from the BMBF SACUS (03G0837A) project. TT and PB acknowledge support from the European Union Seventh Framework Programme (FP7 20072013) under Grant Agreement 603521 for the PREFACE Project. ES and ZW acknowledge support from NSF AGS-1338427, NOAA NA14OAR4310160, and NASA NNX14AM19G; and ES is grateful for further support from the National Monsoon Mission, Ministry of Earth Sciences, India.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment (2016)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2016-07-27
    Description: Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment The ISME Journal 10, 1967 (August 2016). doi:10.1038/ismej.2015.255 Authors: Fu-Chun Yang, Yi-Lung Chen, Sen-Lin Tang, Chang-Ping Yu, Po-Hsiang Wang, Wael Ismail, Chia-Hsiang Wang, Jiun-Yan Ding, Cheng-Yu Yang, Chia-Ying Yang & Yin-Ru Chiang
    Print ISSN: 1751-7362
    Electronic ISSN: 1751-7370
    Topics: Biology
    Published by Nature Publishing Group (NPG) on behalf of The International Society for Microbial Ecology (ISME).
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  • 4
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    Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-08-28
    Description: Nature Genetics 47, 1061 (2015). doi:10.1038/ng.3358 Authors: Lu Jiang, Zhao-Hui Gu, Zi-Xun Yan, Xia Zhao, Yin-Yin Xie, Zi-Guan Zhang, Chun-Ming Pan, Yuan Hu, Chang-Ping Cai, Ying Dong, Jin-Yan Huang, Li Wang, Yang Shen, Guoyu Meng, Jian-Feng Zhou, Jian-Da Hu, Jin-Fen Wang, Yuan-Hua Liu, Lin-Hua Yang, Feng Zhang, Jian-Min Wang, Zhao Wang, Zhi-Gang Peng, Fang-Yuan Chen, Zi-Min Sun, Hao Ding, Ju-Mei Shi, Jian Hou, Jin-Song Yan, Jing-Yi Shi, Lan Xu, Yang Li, Jing Lu, Zhong Zheng, Wen Xue, Wei-Li Zhao, Zhu Chen & Sai-Juan Chen Natural killer/T-cell lymphoma (NKTCL) is a malignant proliferation of CD56+ and cytoCD3+ lymphocytes with aggressive clinical course, which is prevalent in Asian and South American populations. The molecular pathogenesis of NKTCL has largely remained elusive. We identified somatic gene mutations in 25 people with NKTCL by whole-exome sequencing and confirmed them in an extended validation group of 80 people by targeted sequencing. Recurrent mutations were most frequently located in the RNA helicase gene DDX3X (21/105 subjects, 20.0%), tumor suppressors (TP53 and MGA), JAK-STAT-pathway molecules (STAT3 and STAT5B) and epigenetic modifiers (MLL2, ARID1A, EP300 and ASXL3). As compared to wild-type protein, DDX3X mutants exhibited decreased RNA-unwinding activity, loss of suppressive effects on cell-cycle progression in NK cells and transcriptional activation of NF-κB and MAPK pathways. Clinically, patients with DDX3X mutations presented a poor prognosis. Our work thus contributes to the understanding of the disease mechanism of NKTCL.
    Print ISSN: 1061-4036
    Electronic ISSN: 1546-1718
    Topics: Biology , Medicine
    Published by Nature Publishing Group (NPG)
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