The Goddard Cumulus Ensemble Model (GCE): Improvements and Applications for Studying Precipitation Processes

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Lang, Stephen E.; Zeng, Xiping; Li, Xiaowen; Matsui, Toshi; Mohr, Karen; Posselt, Derek; Chern, Jiundar; Peters-Lidard, Christa; Norris, Peter M.;

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daleu, C. L.; Plant, R. S.; Woolnough, S. J.

Here, as part of an international intercomparison project, a set of single-column models (SCMs) and cloud-resolving models (CRMs) are run under the weak-temperature gradient (WTG) method and the damped gravity wave (DGW) method. For each model, the implementation of the WTG or DGW method involves a simulated column which is coupled to a reference state defined with profiles obtained from the same model in radiative-convective equilibrium. The simulated column has the same surface conditions as the reference state and is initialized with profiles from the reference state. We performed systematic comparison of the behavior of different models under a consistentmore » implementation of the WTG method and the DGW method and systematic comparison of the WTG and DGW methods in models with different physics and numerics. CRMs and SCMs produce a variety of behaviors under both WTG and DGW methods. Some of the models reproduce the reference state while others sustain a large-scale circulation which results in either substantially lower or higher precipitation compared to the value of the reference state. CRMs show a fairly linear relationship between precipitation and circulation strength. SCMs display a wider range of behaviors than CRMs. Some SCMs under the WTG method produce zero precipitation. Within an individual SCM, a DGW simulation and a corresponding WTG simulation can produce different signed circulation. When initialized with a dry troposphere, DGW simulations always result in a precipitating equilibrium state. The greatest sensitivities to the initial moisture conditions occur for multiple stable equilibria in some WTG simulations, corresponding to either a dry equilibrium state when initialized as dry or a precipitating equilibrium state when initialized as moist. Multiple equilibria are seen in more WTG simulations for higher SST. In some models, the existence of multiple equilibria is sensitive to some parameters in the WTG calculations.« less

Mean-state acceleration of cloud-resolving models and large eddy simulations

DOE PAGES

Jones, C. R.; Bretherton, C. S.; Pritchard, M. S.

2015-10-29

In this study, large eddy simulations and cloud-resolving models (CRMs) are routinely used to simulate boundary layer and deep convective cloud processes, aid in the development of moist physical parameterization for global models, study cloud-climate feedbacks and cloud-aerosol interaction, and as the heart of superparameterized climate models. These models are computationally demanding, placing practical constraints on their use in these applications, especially for long, climate-relevant simulations. In many situations, the horizontal-mean atmospheric structure evolves slowly compared to the turnover time of the most energetic turbulent eddies. We develop a simple scheme to reduce this time scale separation to accelerate themore » evolution of the mean state. Using this approach we are able to accelerate the model evolution by a factor of 2–16 or more in idealized stratocumulus, shallow and deep cumulus convection without substantial loss of accuracy in simulating mean cloud statistics and their sensitivity to climate change perturbations. As a culminating test, we apply this technique to accelerate the embedded CRMs in the Superparameterized Community Atmosphere Model by a factor of 2, thereby showing that the method is robust and stable to realistic perturbations across spatial and temporal scales typical in a GCM.« less

Progress in the Development of a Global Quasi-3-D Multiscale Modeling Framework

NASA Astrophysics Data System (ADS)

Jung, J.; Konor, C. S.; Randall, D. A.

2017-12-01

The Quasi-3-D Multiscale Modeling Framework (Q3D MMF) is a second-generation MMF, which has following advances over the first-generation MMF: 1) The cloud-resolving models (CRMs) that replace conventional parameterizations are not confined to the large-scale dynamical-core grid cells, and are seamlessly connected to each other, 2) The CRMs sense the three-dimensional large- and cloud-scale environment, 3) Two perpendicular sets of CRM channels are used, and 4) The CRMs can resolve the steep surface topography along the channel direction. The basic design of the Q3D MMF has been developed and successfully tested in a limited-area modeling framework. Currently, global versions of the Q3D MMF are being developed for both weather and climate applications. The dynamical cores governing the large-scale circulation in the global Q3D MMF are selected from two cube-based global atmospheric models. The CRM used in the model is the 3-D nonhydrostatic anelastic Vector-Vorticity Model (VVM), which has been tested with the limited-area version for its suitability for this framework. As a first step of the development, the VVM has been reconstructed on the cubed-sphere grid so that it can be applied to global channel domains and also easily fitted to the large-scale dynamical cores. We have successfully tested the new VVM by advecting a bell-shaped passive tracer and simulating the evolutions of waves resulted from idealized barotropic and baroclinic instabilities. For improvement of the model, we also modified the tracer advection scheme to yield positive-definite results and plan to implement a new physics package that includes a double-moment microphysics and an aerosol physics. The interface for coupling the large-scale dynamical core and the VVM is under development. In this presentation, we shall describe the recent progress in the development and show some test results.

A Goddard Multi-Scale Modeling System with Unified Physics

NASA Technical Reports Server (NTRS)

Tao, W.K.; Anderson, D.; Atlas, R.; Chern, J.; Houser, P.; Hou, A.; Lang, S.; Lau, W.; Peters-Lidard, C.; Kakar, R.;

Intercomparison of methods of coupling between convection and large-scale circulation. 1. Comparison over uniform surface conditions

DOE PAGES

Daleu, C. L.; Plant, R. S.; Woolnough, S. J.; ...

2015-10-24

Here, as part of an international intercomparison project, a set of single-column models (SCMs) and cloud-resolving models (CRMs) are run under the weak-temperature gradient (WTG) method and the damped gravity wave (DGW) method. For each model, the implementation of the WTG or DGW method involves a simulated column which is coupled to a reference state defined with profiles obtained from the same model in radiative-convective equilibrium. The simulated column has the same surface conditions as the reference state and is initialized with profiles from the reference state. We performed systematic comparison of the behavior of different models under a consistentmore » implementation of the WTG method and the DGW method and systematic comparison of the WTG and DGW methods in models with different physics and numerics. CRMs and SCMs produce a variety of behaviors under both WTG and DGW methods. Some of the models reproduce the reference state while others sustain a large-scale circulation which results in either substantially lower or higher precipitation compared to the value of the reference state. CRMs show a fairly linear relationship between precipitation and circulation strength. SCMs display a wider range of behaviors than CRMs. Some SCMs under the WTG method produce zero precipitation. Within an individual SCM, a DGW simulation and a corresponding WTG simulation can produce different signed circulation. When initialized with a dry troposphere, DGW simulations always result in a precipitating equilibrium state. The greatest sensitivities to the initial moisture conditions occur for multiple stable equilibria in some WTG simulations, corresponding to either a dry equilibrium state when initialized as dry or a precipitating equilibrium state when initialized as moist. Multiple equilibria are seen in more WTG simulations for higher SST. In some models, the existence of multiple equilibria is sensitive to some parameters in the WTG calculations.« less

Tropical Oceanic Precipitation Processes over Warm Pool: 2D and 3D Cloud Resolving Model Simulations

NASA Technical Reports Server (NTRS)

Tao, W.- K.; Johnson, D.

1998-01-01

Rainfall is a key link in the hydrologic cycle as well as the primary heat source for the atmosphere, The vertical distribution of convective latent-heat release modulates the large-scale circulations of the tropics, Furthermore, changes in the moisture distribution at middle and upper levels of the troposphere can affect cloud distributions and cloud liquid water and ice contents. How the incoming solar and outgoing longwave radiation respond to these changes in clouds is a major factor in assessing climate change. Present large-scale weather and climate models simulate cloud processes only crudely, reducing confidence in their predictions on both global and regional scales. One of the most promising methods to test physical parameterizations used in General Circulation Models (GCMS) and climate models is to use field observations together with Cloud Resolving Models (CRMs). The CRMs use more sophisticated and physically realistic parameterizations of cloud microphysical processes, and allow for their complex interactions with solar and infrared radiative transfer processes. The CRMs can reasonably well resolve the evolution, structure, and life cycles of individual clouds and cloud systems, The major objective of this paper is to investigate the latent heating, moisture and momenti,im budgets associated with several convective systems developed during the TOGA COARE IFA - westerly wind burst event (late December, 1992). The tool for this study is the Goddard Cumulus Ensemble (CCE) model which includes a 3-class ice-phase microphysical scheme, The model domain contains 256 x 256 grid points (using 2 km resolution) in the horizontal and 38 grid points (to a depth of 22 km depth) in the vertical, The 2D domain has 1024 grid points. The simulations are performed over a 7 day time period. We will examine (1) the precipitation processes (i.e., condensation/evaporation) and their interaction with warm pool; (2) the heating and moisture budgets in the convective and stratiform regions; (3) the cloud (upward-downward) mass fluxes in convective and stratiform regions; (4) characteristics of clouds (such as cloud size, updraft intensity and cloud lifetime) and the comparison of clouds with Radar observations. Differences and similarities in organization of convection between simulated 2D and 3D cloud systems. Preliminary results indicated that there is major differences between 2D and 3D simulated stratiform rainfall amount and convective updraft and downdraft mass fluxes.

Microphysics, Radiation and Surface Processes in the Goddard Cumulus Ensemble (GCE) Model

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Starr, David (Technical Monitor)

2002-01-01

One of the most promising methods to test the representation of cloud processes used in climate models is to use observations together with Cloud Resolving Models (CRMs). The CRMs use more sophisticated and realistic representations of cloud microphysical processes, and they can reasonably well resolve the time evolution, structure, and life cycles of clouds and cloud systems (size about 2-200 km). The CRMs also allow explicit interaction between out-going longwave (cooling) and in-coming solar (heating) radiation with clouds. Observations can provide the initial conditions and validation for CRM results. The Goddard Cumulus Ensemble (GCE) Model, a CRM, has been developed and improved at NASA/Goddard Space Flight Center over the past two decades. The GCE model has been used to understand the following: 1) water and energy cycles and their roles in the tropical climate system; 2) the vertical redistribution of ozone and trace constituents by individual clouds and well organized convective systems over various spatial scales; 3) the relationship between the vertical distribution of latent heating (phase change of water) and the large-scale (pre-storm) environment; 4) the validity of assumptions used in the representation of cloud processes in climate and global circulation models; and 5) the representation of cloud microphysical processes and their interaction with radiative forcing over tropical and midlatitude regions. Four-dimensional cloud and latent heating fields simulated from the GCE model have been provided to the TRMM Science Data and Information System (TSDIS) to develop and improve algorithms for retrieving rainfall and latent heating rates for TRMM and the NASA Earth Observing System (EOS). More than 90 referred papers using the GCE model have been published in the last two decades. Also, more than 10 national and international universities are currently using the GCE model for research and teaching. In this talk, five specific major GCE improvements: (1) ice microphysics, (2) longwave and shortwave radiative transfer processes, (3) land surface processes, (4) ocean surface fluxes and (5) ocean mixed layer processes are presented. The performance of these new GCE improvements will be examined. Observations are used for model validation.

Precipitation processes developed during TOGA COARE (1992), GATE (1974), SCSMEX (1998), and KWAJEX (1999): 3D Cloud Resolving Model Simulation

NASA Technical Reports Server (NTRS)

Tao, W.-K.

2006-01-01

Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D). A few 3D CRMs have been used to study the response of clouds to large-scale forcing. In these 3D simulations, the model domain was small, and the integration time was 6 hours. Only recently have 3D experiments been performed for multi-day periods for tropical cloud systems with large horizontal domains at the National Center for Atmospheric Research (NCAR), NOAA GFDL, the U.K. Met. Office, Colorado State University and NASA Goddard Space Flight Center. An improved 3D Goddard Cumulus Ensemble (GCE) model was recently used to simulate periods during TOGA COARE (December 19-27, 1992), GATE (september 1-7, 1974), SCSMEX (May 18-26, June 2-11, 1998) and KWAJEX (August 7-13, August 18-21, and August 29-September 12, 1999) using a 512 by 512 km domain and 41 vertical layers. The major objectives of this paper are: (1) to identify the differences and similarities in the simulated precipitation processes and their associated surface and water energy budgets in TOGA COARE, GATE, KWAJEX, and SCSMEX, and (2) to asses the impact of microphysics, radiation budget and surface fluxes on the organization of convection in tropics.

Coupled fvGCM-GCE Modeling System, 3D Cloud-Resolving Model and Cloud Library

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2005-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud-resolving models (CRMs) agree with observations better than traditional singlecolumn models in simulating various types of clouds and cloud systems from Merent geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloudscale model (termed a super-parameterization or multiscale modeling framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameteridon NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CRMs. A seed fund is available at NASA Goddard to build a MMF based on the 2D Goddard cumulus Ensemble (GCE) model and the Goddard finite volume general circulation model (fvGCM). A prototype MMF in being developed and production nms will be conducted at the beginning of 2005. In this talk, I will present: (1) A brief review on GCE model and its applications on precipitation processes, (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), (3) A cloud library generated by Goddard MMF, and 3D GCE model, and (4) A brief discussion on the GCE model on developing a global cloud simulator.

Evolution of Precipitation Structure During the November DYNAMO MJO Event: Cloud-Resolving Model Intercomparison and Cross Validation Using Radar Observations

NASA Astrophysics Data System (ADS)

Li, Xiaowen; Janiga, Matthew A.; Wang, Shuguang; Tao, Wei-Kuo; Rowe, Angela; Xu, Weixin; Liu, Chuntao; Matsui, Toshihisa; Zhang, Chidong

2018-04-01

Evolution of precipitation structures are simulated and compared with radar observations for the November Madden-Julian Oscillation (MJO) event during the DYNAmics of the MJO (DYNAMO) field campaign. Three ground-based, ship-borne, and spaceborne precipitation radars and three cloud-resolving models (CRMs) driven by observed large-scale forcing are used to study precipitation structures at different locations over the central equatorial Indian Ocean. Convective strength is represented by 0-dBZ echo-top heights, and convective organization by contiguous 17-dBZ areas. The multi-radar and multi-model framework allows for more stringent model validations. The emphasis is on testing models' ability to simulate subtle differences observed at different radar sites when the MJO event passed through. The results show that CRMs forced by site-specific large-scale forcing can reproduce not only common features in cloud populations but also subtle variations observed by different radars. The comparisons also revealed common deficiencies in CRM simulations where they underestimate radar echo-top heights for the strongest convection within large, organized precipitation features. Cross validations with multiple radars and models also enable quantitative comparisons in CRM sensitivity studies using different large-scale forcing, microphysical schemes and parameters, resolutions, and domain sizes. In terms of radar echo-top height temporal variations, many model sensitivity tests have better correlations than radar/model comparisons, indicating robustness in model performance on this aspect. It is further shown that well-validated model simulations could be used to constrain uncertainties in observed echo-top heights when the low-resolution surveillance scanning strategy is used.

Convergence behavior of idealized convection-resolving simulations of summertime deep moist convection over land

NASA Astrophysics Data System (ADS)

Panosetti, Davide; Schlemmer, Linda; Schär, Christoph

2018-05-01

Convection-resolving models (CRMs) can explicitly simulate deep convection and resolve interactions between convective updrafts. They are thus increasingly used in numerous weather and climate applications. However, the truncation of the continuous energy cascade at scales of O (1 km) poses a serious challenge, as in kilometer-scale simulations the size and properties of the simulated convective cells are often determined by the horizontal grid spacing (Δ x ).In this study, idealized simulations of deep moist convection over land are performed to assess the convergence behavior of a CRM at Δ x = 8, 4, 2, 1 km and 500 m. Two types of convergence estimates are investigated: bulk convergence addressing domain-averaged and integrated variables related to the water and energy budgets, and structural convergence addressing the statistics and scales of individual clouds and updrafts. Results show that bulk convergence generally begins at Δ x =4 km, while structural convergence is not yet fully achieved at the kilometer scale, despite some evidence that the resolution sensitivity of updraft velocities and convective mass fluxes decreases at finer resolution. In particular, at finer grid spacings the maximum updraft velocity generally increases, and the size of the smallest clouds is mostly determined by Δ x . A number of different experiments are conducted, and it is found that the presence of orography and environmental vertical wind shear yields more energetic structures at scales much larger than Δ x , sometimes reducing the resolution sensitivity. Overall the results lend support to the use of kilometer-scale resolutions in CRMs, despite the inability of these models to fully resolve the associated cloud field.

A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model

PubMed Central

2017-01-01

The discovery of cis-regulatory modules (CRMs) is the key to understanding mechanisms of transcription regulation. Since CRMs have specific regulatory structures that are the basis for the regulation of gene expression, how to model the regulatory structure of CRMs has a considerable impact on the performance of CRM identification. The paper proposes a CRM discovery algorithm called ComSPS. ComSPS builds a regulatory structure model of CRMs based on HMM by exploring the rules of CRM transcriptional grammar that governs the internal motif site arrangement of CRMs. We test ComSPS on three benchmark datasets and compare it with five existing methods. Experimental results show that ComSPS performs better than them. PMID:28497059

Performance of the Goddard Multiscale Modeling Framework with Goddard Ice Microphysical Schemes

NASA Technical Reports Server (NTRS)

Chern, Jiun-Dar; Tao, Wei-Kuo; Lang, Stephen E.; Matsui, Toshihisa; Li, J.-L.; Mohr, Karen I.; Skofronick-Jackson, Gail M.; Peters-Lidard, Christa D.

2016-01-01

The multiscale modeling framework (MMF), which replaces traditional cloud parameterizations with cloud-resolving models (CRMs) within a host atmospheric general circulation model (GCM), has become a new approach for climate modeling. The embedded CRMs make it possible to apply CRM-based cloud microphysics directly within a GCM. However, most such schemes have never been tested in a global environment for long-term climate simulation. The benefits of using an MMF to evaluate rigorously and improve microphysics schemes are here demonstrated. Four one-moment microphysical schemes are implemented into the Goddard MMF and their results validated against three CloudSat/CALIPSO cloud ice products and other satellite data. The new four-class (cloud ice, snow, graupel, and frozen drops/hail) ice scheme produces a better overall spatial distribution of cloud ice amount, total cloud fractions, net radiation, and total cloud radiative forcing than earlier three-class ice schemes, with biases within the observational uncertainties. Sensitivity experiments are conducted to examine the impact of recently upgraded microphysical processes on global hydrometeor distributions. Five processes dominate the global distributions of cloud ice and snow amount in long-term simulations: (1) allowing for ice supersaturation in the saturation adjustment, (2) three additional correction terms in the depositional growth of cloud ice to snow, (3) accounting for cloud ice fall speeds, (4) limiting cloud ice particle size, and (5) new size-mapping schemes for snow and graupel. Despite the cloud microphysics improvements, systematic errors associated with subgrid processes, cyclic lateral boundaries in the embedded CRMs, and momentum transport remain and will require future improvement.

The Diurnal Cycle in TOGA-COARE: Regional Scale Model Simulations

NASA Technical Reports Server (NTRS)

Tao, W.-K.; Jia, Y.

1999-01-01

The diurnal variation of precipitation processes over the tropics is a well-known phenomenon and has been studied using surface rainfall data, radar reflectivity data, and satellite-derived cloudiness and precipitation. Recently, analyzed observations from Tropical Oceans and Global Atmosphere Coupled Ocean-Atmosphere Response Experiment (TOGA COARE) in the tropical western Pacific ocean to study the relevant mechanisms producing diurnal variation of precipitation. They found that the diurnal Sea surface temperature (SST) cycle is important for afternoon showers in the undisturbed periods and diurnal radiative processes for nocturnal rainfall. Cloud resolving models (CRMS) have been used to determine the mechanisms associated with diurnal variation of precipitating processes. CRMs allow explicit cloud-radiation and air-sea interactive processes. However, CRMs can be only used for idealized simulations (i.e., no feedback between clouds and their embedded large-scale environments; cyclic lateral boundary conditions and idealized initial conditions). In this study, the Penn State/NCAR Mesoscale Model (MM5) with improved physics (i.e., cloud microphysics, radiation, land-soil-vegetation-surface processes, and TOGA COARE flux scheme) and a multiple level nesting technique (covers the TOGA COARE LSA/IFA with a 54 km grid and can nest down to 18, 6 and possibly even 2 km) will be adopted for studying the diurnal variations of rainfall. We will examine precipitation processes over open ocean and over land. We will also perform sensitivity tests to determine how the radiative forcing and diurnal SST cycle affects the development of convection.

Coupled fvGCM-GCE Modeling System, 3D Cloud-Resolving Model and Cloud Library

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2005-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud- resolving models (CRMs) agree with observations better than traditional single-column models in simulating various types of clouds and cloud systems from different geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a super-parameterization or multi-scale modeling framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CRMs. A seed fund is available at NASA Goddard to build a MMF based on the 2D Goddard Cumulus Ensemble (GCE) model and the Goddard finite volume general circulation model (fvGCM). A prototype MMF in being developed and production runs will be conducted at the beginning of 2005. In this talk, I will present: (1) A brief review on GCE model and its applications on precipitation processes, ( 2 ) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), (3) A cloud library generated by Goddard MMF, and 3D GCE model, and (4) A brief discussion on the GCE model on developing a global cloud simulator.

Evaluation of Intercomparisons of Four Different Types of Model Simulating TWP-ICE

NASA Technical Reports Server (NTRS)

Petch, Jon; Hill, Adrian; Davies, Laura; Fridlind, Ann; Jakob, Christian; Lin, Yanluan; Xie, Shaoecheng; Zhu, Ping

2013-01-01

Four model intercomparisons were run and evaluated using the TWP-ICE field campaign, each involving different types of atmospheric model. Here we highlight what can be learnt from having single-column model (SCM), cloud-resolving model (CRM), global atmosphere model (GAM) and limited-area model (LAM) intercomparisons all based around the same field campaign. We also make recommendations for anyone planning further large multi-model intercomparisons to ensure they are of maximum value to the model development community. CRMs tended to match observations better than other model types, although there were exceptions such as outgoing long-wave radiation. All SCMs grew large temperature and moisture biases and performed worse than other model types for many diagnostics. The GAMs produced a delayed and significantly reduced peak in domain-average rain rate when compared to the observations. While it was shown that this was in part due to the analysis used to drive these models, the LAMs were also driven by this analysis and did not have the problem to the same extent. Based on differences between the models with parametrized convection (SCMs and GAMs) and those without (CRMs and LAMs), we speculate that that having explicit convection helps to constrain liquid water whereas the ice contents are controlled more by the representation of the microphysics.

A Coupled fcGCM-GCE Modeling System: A 3D Cloud Resolving Model and a Regional Scale Model

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2005-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud-resolving models (CRMs) agree with observations better than traditional single-column models in simulating various types of clouds and cloud systems from different geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a super-parameterization or multi-scale modeling framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and ore sophisticated physical parameterization. NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CRMs. The Goddard MMF is based on the 2D Goddard Cumulus Ensemble (GCE) model and the Goddard finite volume general circulation model (fvGCM), and it has started production runs with two years results (1998 and 1999). Also, at Goddard, we have implemented several Goddard microphysical schemes (21CE, several 31CE), Goddard radiation (including explicity calculated cloud optical properties), and Goddard Land Information (LIS, that includes the CLM and NOAH land surface models) into a next generation regional scale model, WRF. In this talk, I will present: (1) A Brief review on GCE model and its applications on precipitation processes (microphysical and land processes), (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), (3) A discussion on the Goddard WRF version (its developments and applications), and (4) The characteristics of the four-dimensional cloud data sets (or cloud library) stored at Goddard.

A Coupled GCM-Cloud Resolving Modeling System, and a Regional Scale Model to Study Precipitation Processes

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2007-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud-resolving models (CRMs) agree with observations better than traditional single-column models in simulating various types of clouds and cloud systems from different geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a superparameterization or multi-scale modeling framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CRMs. The Goddard MMF is based on the 2D Goddard Cumulus Ensemble (GCE) model and the Goddard finite volume general circulation model (fvGCM), and it has started production runs with two years results (1998 and 1999). Also, at Goddard, we have implemented several Goddard microphysical schemes (2ICE, several 31CE), Goddard radiation (including explicitly calculated cloud optical properties), and Goddard Land Information (LIS, that includes the CLM and NOAH land surface models) into a next generatio11 regional scale model, WRF. In this talk, I will present: (1) A brief review on GCE model and its applications on precipitation processes (microphysical and land processes), (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications).

A Coupled GCM-Cloud Resolving Modeling System, and A Regional Scale Model to Study Precipitation Processes

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2006-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud-resolving models (CRMs) agree with observations better than traditional single-column models in simulating various types of clouds and cloud systems from different geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a super-parameterization or multi-scale modeling framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CRMs. The Goddard MMF is based on the 2D Goddard Cumulus Ensemble (GCE) model and the Goddard finite volume general circulation model (fvGCM), and it has started production runs with two years results (1998 and 1999). Also, at Goddard, we have implemented several Goddard microphysical schemes (21CE, several 31CE), Goddard radiation (including explicitly calculated cloud optical properties), and Goddard Land Information (LIS, that includes the CLM and NOAH land surface models) into a next generation regional scale model, WRF. In this talk, I will present: (1) A brief review on GCE model and its applications on precipitation processes (microphysical and land processes), (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications).

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

PubMed

Nikulova, Anna A; Favorov, Alexander V; Sutormin, Roman A; Makeev, Vsevolod J; Mironov, Andrey A

2012-07-01

Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices. Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a CRM model by revealing the conserved rules that describe the relative location of binding sites. The constructed model may be consequently used for the genome-wide prediction of similar CRMs, and thus detection of co-regulated genes, and for the investigation of the regulatory grammar of the system. Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila.

Precipitation Processes Developed During ARM (1997), TOGA COARE (1992), GATE (1974), SCSMEX (1998), and KWAJEX (1999): Consistent 2D, Semi-3D and 3D Cloud Resolving Model Simulations

NASA Technical Reports Server (NTRS)

Tao, W-K.

2003-01-01

Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D). A few 3D CRMs have been used to study the response of clouds to large-scale forcing. In these 3D simulations, the model domain was small, and the integration time was 6 hours. Only recently have 3D experiments been performed for multi-day periods for tropical cloud systems with large horizontal domains at the National Center for Atmospheric Research (NACAR) and at NASA Goddard Space Flight Center . At Goddard, a 3D Goddard Cumulus Ensemble (GCE) model was used to simulate periods during TOGA COARE, SCSMEX and KWAJEX using 512 by 512 km domain (with 2 km resolution). The results indicate that surface precipitation and latent heating profiles are very similar between the 2D and 3D GCE model simulations. The reason for the strong similarity between the 2D and 3D CRM simulations is that the same observed large-scale advective tendencies of potential temperature, water vapor mixing ratio, and horizontal momentum were used as the main focusing in both the 2D and 3D models. Interestingly, the 2D and 3D versions of the CRM used at CSU showed significant differences in the rainfall and cloud statistics for three ARM cases. The major objectives of this paper are: (1) to assess the performance of the super-parameterization technique, (2) calculate and examine the surface energy (especially radiation) and water budgets, and (3) identify the differences and similarities in the organization and entrainment rates of convection between simulated 2D and 3D cloud systems.

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

PubMed

Kazemian, Majid; Zhu, Qiyun; Halfon, Marc S; Sinha, Saurabh

2011-12-01

Despite recent advances in experimental approaches for identifying transcriptional cis-regulatory modules (CRMs, 'enhancers'), direct empirical discovery of CRMs for all genes in all cell types and environmental conditions is likely to remain an elusive goal. Effective methods for computational CRM discovery are thus a critically needed complement to empirical approaches. However, existing computational methods that search for clusters of putative binding sites are ineffective if the relevant TFs and/or their binding specificities are unknown. Here, we provide a significantly improved method for 'motif-blind' CRM discovery that does not depend on knowledge or accurate prediction of TF-binding motifs and is effective when limited knowledge of functional CRMs is available to 'supervise' the search. We propose a new statistical method, based on 'Interpolated Markov Models', for motif-blind, genome-wide CRM discovery. It captures the statistical profile of variable length words in known CRMs of a regulatory network and finds candidate CRMs that match this profile. The method also uses orthologs of the known CRMs from closely related genomes. We perform in silico evaluation of predicted CRMs by assessing whether their neighboring genes are enriched for the expected expression patterns. This assessment uses a novel statistical test that extends the widely used Hypergeometric test of gene set enrichment to account for variability in intergenic lengths. We find that the new CRM prediction method is superior to existing methods. Finally, we experimentally validate 12 new CRM predictions by examining their regulatory activity in vivo in Drosophila; 10 of the tested CRMs were found to be functional, while 6 of the top 7 predictions showed the expected activity patterns. We make our program available as downloadable source code, and as a plugin for a genome browser installed on our servers. © The Author(s) 2011. Published by Oxford University Press.

The impact of simulated mesoscale convective systems on global precipitation: A multiscale modeling study

NASA Astrophysics Data System (ADS)

Tao, Wei-Kuo; Chern, Jiun-Dar

2017-06-01

The importance of precipitating mesoscale convective systems (MCSs) has been quantified from TRMM precipitation radar and microwave imager retrievals. MCSs generate more than 50% of the rainfall in most tropical regions. MCSs usually have horizontal scales of a few hundred kilometers (km); therefore, a large domain with several hundred km is required for realistic simulations of MCSs in cloud-resolving models (CRMs). Almost all traditional global and climate models do not have adequate parameterizations to represent MCSs. Typical multiscale modeling frameworks (MMFs) may also lack the resolution (4 km grid spacing) and domain size (128 km) to realistically simulate MCSs. The impact of MCSs on precipitation is examined by conducting model simulations using the Goddard Cumulus Ensemble (GCE, a CRM) model and Goddard MMF that uses the GCEs as its embedded CRMs. Both models can realistically simulate MCSs with more grid points (i.e., 128 and 256) and higher resolutions (1 or 2 km) compared to those simulations with fewer grid points (i.e., 32 and 64) and low resolution (4 km). The modeling results also show the strengths of the Hadley circulations, mean zonal and regional vertical velocities, surface evaporation, and amount of surface rainfall are weaker or reduced in the Goddard MMF when using more CRM grid points and higher CRM resolution. In addition, the results indicate that large-scale surface evaporation and wind feedback are key processes for determining the surface rainfall amount in the GMMF. A sensitivity test with reduced sea surface temperatures shows both reduced surface rainfall and evaporation.

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison

PubMed Central

Kazemian, Majid; Zhu, Qiyun; Halfon, Marc S.; Sinha, Saurabh

2011-01-01

Despite recent advances in experimental approaches for identifying transcriptional cis-regulatory modules (CRMs, ‘enhancers’), direct empirical discovery of CRMs for all genes in all cell types and environmental conditions is likely to remain an elusive goal. Effective methods for computational CRM discovery are thus a critically needed complement to empirical approaches. However, existing computational methods that search for clusters of putative binding sites are ineffective if the relevant TFs and/or their binding specificities are unknown. Here, we provide a significantly improved method for ‘motif-blind’ CRM discovery that does not depend on knowledge or accurate prediction of TF-binding motifs and is effective when limited knowledge of functional CRMs is available to ‘supervise’ the search. We propose a new statistical method, based on ‘Interpolated Markov Models’, for motif-blind, genome-wide CRM discovery. It captures the statistical profile of variable length words in known CRMs of a regulatory network and finds candidate CRMs that match this profile. The method also uses orthologs of the known CRMs from closely related genomes. We perform in silico evaluation of predicted CRMs by assessing whether their neighboring genes are enriched for the expected expression patterns. This assessment uses a novel statistical test that extends the widely used Hypergeometric test of gene set enrichment to account for variability in intergenic lengths. We find that the new CRM prediction method is superior to existing methods. Finally, we experimentally validate 12 new CRM predictions by examining their regulatory activity in vivo in Drosophila; 10 of the tested CRMs were found to be functional, while 6 of the top 7 predictions showed the expected activity patterns. We make our program available as downloadable source code, and as a plugin for a genome browser installed on our servers. PMID:21821659

Validation of Model Simulations of Anvil Cirrus Properties During TWP-ICE: Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zipser, Edward J.

2013-05-20

This 3-year grant, with two extensions, resulted in a successful 5-year effort, led by Ph.D. student Adam Varble, to compare cloud resolving model (CRM) simulations with the excellent database obtained during the TWP-ICE field campaign. The objective, largely achieved, is to undertake these comparisons comprehensively and quantitatively, informing the community in ways that goes beyond pointing out errors in the models, but points out ways to improve both cloud dynamics and microphysics parameterizations in future modeling efforts. Under DOE support, Adam Varble, with considerable assistance from Dr. Ann Fridlind and others, entrained scientists who ran some 10 different CRMs andmore » 4 different limited area models (LAMs) using a variety of microphysics parameterizations, to ensure that the conclusions of the study will have considerable generality.« less

Coupled fvGCM-GCE Modeling System, TRMM Latent Heating and Cloud Library

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2004-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud-resolving models (CRMs) agree with observations better than traditional single-column models in simulating various types of clouds and cloud systems from different geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a super-parameterization or multi-scale modeling framework, MMF) to use these satellite data to imiprove the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CRMs. A seed fund is available at NASA Goddard to build a MMF based on the 2D GCE model and the Goddard finite volume general circulation model (fvGCM). A prototype MMF will be developed by the end of 2004 and production runs will be conducted at the beginning of 2005. The purpose of this proposal is to augment the current Goddard MMF and other cloud modeling activities. I this talk, I will present: (1) A summary of the second Cloud Modeling Workshop took place at NASA Goddard, (2) A summary of the third TRMM Latent Heating Workshop took place at Nara Japan, (3) A brief discussion on the Goddard research plan of using Weather Research Forecast (WRF) model, and (4) A brief discussion on the GCE model on developing a global cloud simulator.

Evaluation of Cloud-Resolving and Limited Area Model Intercomparison Simulations Using TWP-ICE Observations. Part 2 ; Precipitation Microphysics

NASA Technical Reports Server (NTRS)

Varble, Adam; Zipser, Edward J.; Fridland, Ann M.; Zhu, Ping; Ackerman, Andrew S.; Chaboureau, Jean-Pierre; Fan, Jiwen; Hill, Adrian; Shipway, Ben; Williams, Christopher

2014-01-01

Ten 3-D cloud-resolving model (CRM) simulations and four 3-D limited area model (LAM) simulations of an intense mesoscale convective system observed on 23-24 January 2006 during the Tropical Warm Pool-International Cloud Experiment (TWP-ICE) are compared with each other and with observations and retrievals from a scanning polarimetric radar, colocated UHF and VHF vertical profilers, and a Joss-Waldvogel disdrometer in an attempt to explain a low bias in simulated stratiform rainfall. Despite different forcing methodologies, similar precipitation microphysics errors appear in CRMs and LAMs with differences that depend on the details of the bulk microphysics scheme used. One-moment schemes produce too many small raindrops, which biases Doppler velocities low, but produces rainwater contents (RWCs) that are similar to observed. Two-moment rain schemes with a gamma shape parameter (mu) of 0 produce excessive size sorting, which leads to larger Doppler velocities than those produced in one-moment schemes but lower RWCs. Two-moment schemes also produce a convective median volume diameter distribution that is too broad relative to observations and, thus, may have issues balancing raindrop formation, collision-coalescence, and raindrop breakup. Assuming a mu of 2.5 rather than 0 for the raindrop size distribution improves one-moment scheme biases, and allowing mu to have values greater than 0 may improve excessive size sorting in two-moment schemes. Underpredicted stratiform rain rates are associated with underpredicted ice water contents at the melting level rather than excessive rain evaporation, in turn likely associated with convective detrainment that is too high in the troposphere and mesoscale circulations that are too weak. A limited domain size also prevents a large, well-developed stratiform region like the one observed from developing in CRMs, although LAMs also fail to produce such a region.

Coupled fvGCM-GCE Modeling System: TRMM Latent Heating and Cloud Library

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2005-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud-resolving models (CRMs) agree with observations better than traditional single-column models in simulating various types of clouds and cloud systems from different geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a super-parameterization or multi-scale modeling framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CRMs. A seed fund is available at NASA Goddard to build a MMF based on the 2D GCE model and the Goddard finite volume general circulation model (fvGCM). A prototype MMF will be developed by the end of 2004 and production runs will be conducted at the beginning of 2005. The purpose of this proposal is to augment the current Goddard MMF and other cloud modeling activities. In this talk, I will present: (1) A summary of the second Cloud Modeling Workshop took place at NASA Goddard, (2) A summary of the third TRMM Latent Heating Workshop took place at Nara Japan, (3) A brief discussion on the GCE model on developing a global cloud simulator.

Precipitation Processes developed during ARM (1997), TOGA COARE(1992), GATE(1 974), SCSMEX(1998) and KWAJEX(1999): Consistent 2D and 3D Cloud Resolving Model Simulations

NASA Technical Reports Server (NTRS)

Tao, W.-K.; Shie, C.-H.; Simpson, J.; Starr, D.; Johnson, D.; Sud, Y.

2003-01-01

Real clouds and clouds systems are inherently three dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D). A few 3D CRMs have been used to study the response of clouds to large-scale forcing. In these 3D simulations, the model domain was small, and the integration time was 6 hours. Only recently have 3D experiments been performed for multi-day periods for tropical cloud system with large horizontal domains at the National Center for Atmospheric Research. The results indicate that surface precipitation and latent heating profiles are very similar between the 2D and 3D simulations of these same cases. The reason for the strong similarity between the 2D and 3D CRM simulations is that the observed large-scale advective tendencies of potential temperature, water vapor mixing ratio, and horizontal momentum were used as the main forcing in both the 2D and 3D models. Interestingly, the 2D and 3D versions of the CRM used in CSU and U.K. Met Office showed significant differences in the rainfall and cloud statistics for three ARM cases. The major objectives of this project are to calculate and axamine: (1)the surface energy and water budgets, (2) the precipitation processes in the convective and stratiform regions, (3) the cloud upward and downward mass fluxes in the convective and stratiform regions; (4) cloud characteristics such as size, updraft intensity and lifetime, and (5) the entrainment and detrainment rates associated with clouds and cloud systems that developed in TOGA COARE, GATE, SCSMEX, ARM and KWAJEX. Of special note is that the analyzed (model generated) data sets are all produced by the same current version of the GCE model, i.e. consistent model physics and configurations. Trajectory analyse and inert tracer calculation will be conducted to identify the differences and similarities in the organization of convection between simulated 2D and 3D cloud systems.

Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parishani, Hossein; Pritchard, Michael S.; Bretherton, Christopher S.

Systematic biases in the representation of boundary layer (BL) clouds are a leading source of uncertainty in climate projections. A variation on superparameterization (SP) called “ultraparameterization” (UP) is developed, in which the grid spacing of the cloud-resolving models (CRMs) is fine enough (250 × 20 m) to explicitly capture the BL turbulence, associated clouds, and entrainment in a global climate model capable of multiyear simulations. UP is implemented within the Community Atmosphere Model using 2° resolution (~14,000 embedded CRMs) with one-moment microphysics. By using a small domain and mean-state acceleration, UP is computationally feasible today and promising for exascale computers.more » Short-duration global UP hindcasts are compared with SP and satellite observations of top-of-atmosphere radiation and cloud vertical structure. The most encouraging improvement is a deeper BL and more realistic vertical structure of subtropical stratocumulus (Sc) clouds, due to stronger vertical eddy motions that promote entrainment. Results from 90 day integrations show climatological errors that are competitive with SP, with a significant improvement in the diurnal cycle of offshore Sc liquid water. Ongoing concerns with the current UP implementation include a dim bias for near-coastal Sc that also occurs less prominently in SP and a bright bias over tropical continental deep convection zones. Nevertheless, UP makes global eddy-permitting simulation a feasible and interesting alternative to conventionally parameterized GCMs or SP-GCMs with turbulence parameterizations for studying BL cloud-climate and cloud-aerosol feedback.« less

Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence

DOE PAGES

Parishani, Hossein; Pritchard, Michael S.; Bretherton, Christopher S.; ...

2017-06-19

Systematic biases in the representation of boundary layer (BL) clouds are a leading source of uncertainty in climate projections. A variation on superparameterization (SP) called “ultraparameterization” (UP) is developed, in which the grid spacing of the cloud-resolving models (CRMs) is fine enough (250 × 20 m) to explicitly capture the BL turbulence, associated clouds, and entrainment in a global climate model capable of multiyear simulations. UP is implemented within the Community Atmosphere Model using 2° resolution (~14,000 embedded CRMs) with one-moment microphysics. By using a small domain and mean-state acceleration, UP is computationally feasible today and promising for exascale computers.more » Short-duration global UP hindcasts are compared with SP and satellite observations of top-of-atmosphere radiation and cloud vertical structure. The most encouraging improvement is a deeper BL and more realistic vertical structure of subtropical stratocumulus (Sc) clouds, due to stronger vertical eddy motions that promote entrainment. Results from 90 day integrations show climatological errors that are competitive with SP, with a significant improvement in the diurnal cycle of offshore Sc liquid water. Ongoing concerns with the current UP implementation include a dim bias for near-coastal Sc that also occurs less prominently in SP and a bright bias over tropical continental deep convection zones. Nevertheless, UP makes global eddy-permitting simulation a feasible and interesting alternative to conventionally parameterized GCMs or SP-GCMs with turbulence parameterizations for studying BL cloud-climate and cloud-aerosol feedback.« less

Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence

NASA Astrophysics Data System (ADS)

Parishani, Hossein; Pritchard, Michael S.; Bretherton, Christopher S.; Wyant, Matthew C.; Khairoutdinov, Marat

2017-07-01

Systematic biases in the representation of boundary layer (BL) clouds are a leading source of uncertainty in climate projections. A variation on superparameterization (SP) called "ultraparameterization" (UP) is developed, in which the grid spacing of the cloud-resolving models (CRMs) is fine enough (250 × 20 m) to explicitly capture the BL turbulence, associated clouds, and entrainment in a global climate model capable of multiyear simulations. UP is implemented within the Community Atmosphere Model using 2° resolution (˜14,000 embedded CRMs) with one-moment microphysics. By using a small domain and mean-state acceleration, UP is computationally feasible today and promising for exascale computers. Short-duration global UP hindcasts are compared with SP and satellite observations of top-of-atmosphere radiation and cloud vertical structure. The most encouraging improvement is a deeper BL and more realistic vertical structure of subtropical stratocumulus (Sc) clouds, due to stronger vertical eddy motions that promote entrainment. Results from 90 day integrations show climatological errors that are competitive with SP, with a significant improvement in the diurnal cycle of offshore Sc liquid water. Ongoing concerns with the current UP implementation include a dim bias for near-coastal Sc that also occurs less prominently in SP and a bright bias over tropical continental deep convection zones. Nevertheless, UP makes global eddy-permitting simulation a feasible and interesting alternative to conventionally parameterized GCMs or SP-GCMs with turbulence parameterizations for studying BL cloud-climate and cloud-aerosol feedback.

On polarimetric radar signatures of deep convection for model evaluation: columns of specific differential phase observed during MC3E

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Lier-Walqui, Marcus; Fridlind, Ann; Ackerman, Andrew S

2016-02-01

The representation of deep convection in general circulation models is in part informed by cloud-resolving models (CRMs) that function at higher spatial and temporal resolution; however, recent studies have shown that CRMs often fail at capturing the details of deep convection updrafts. With the goal of providing constraint on CRM simulation of deep convection updrafts, ground-based remote sensing observations are analyzed and statistically correlated for four deep convection events observed during the Midlatitude Continental Convective Clouds Experiment (MC3E). Since positive values of specific differential phase observed above the melting level are associated with deep convection updraft cells, so-called columns aremore » analyzed using two scanning polarimetric radars in Oklahoma: the National Weather Service Vance WSR-88D (KVNX) and the Department of Energy C-band Scanning Atmospheric Radiation Measurement (ARM) Precipitation Radar (C-SAPR). KVNX and C-SAPR volumes and columns are then statistically correlated with vertical winds retrieved via multi-Doppler wind analysis, lightning flash activity derived from the Oklahoma Lightning Mapping Array, and KVNX differential reflectivity . Results indicate strong correlations of volume above the melting level with updraft mass flux, lightning flash activity, and intense rainfall. Analysis of columns reveals signatures of changing updraft properties from one storm event to another as well as during event evolution. Comparison of to shows commonalities in information content of each, as well as potential problems with associated with observational artifacts.« less

Outcomes of infants with indeterminate diagnosis detected by cystic fibrosis newborn screening.

PubMed

Ren, Clement L; Fink, Aliza K; Petren, Kristofer; Borowitz, Drucy S; McColley, Susanna A; Sanders, Don B; Rosenfeld, Margaret; Marshall, Bruce C

2015-06-01

Cystic fibrosis transmembrane conductance regulator-related metabolic syndrome (CRMS) describes asymptomatic infants with a positive cystic fibrosis (CF) newborn screen (NBS) but inconclusive diagnostic testing for CF. Little is known about the epidemiology and outcomes of CRMS. The goal of this study was to determine the prevalence, clinical features, and short-term outcomes of infants with CRMS. We analyzed data from the US CF Foundation Patient Registry (CFFPR) from 2010 to 2012. We compared demographic, diagnostic, anthropometric, health care utilization, microbiology, and treatment characteristics between infants with CF and infants with CRMS. There were 1983 infants diagnosed via NBS between 2010 and 2012 reported to the CFFPR. By using the CF Foundation guideline definitions, 1540 and 309 infants met the criteria for CF and CRMS, respectively (CF:CRMS ratio = 5.0:1.0). Of note, 40.8% of infants with CRMS were entered into the registry with a clinical diagnosis of CF. Infants with CRMS tended to have normal nutritional indices. However, 11% of infants with CRMS had a positive Pseudomonas aeruginosa respiratory tract culture in the first year of life. CRMS is a common outcome of CF NBS, and some infants with CRMS may develop features concerning for CF disease. A substantial proportion of infants with CRMS were assigned a clinical diagnosis of CF, which may reflect misclassification or clinical features not collected in the CFFPR. Copyright © 2015 by the American Academy of Pediatrics.

Spectrodirectional Investigation of a Geometric-Optical Canopy Reflectance Model by Laboratory Simulation

NASA Astrophysics Data System (ADS)

Stanford, Adam Christopher

Canopy reflectance models (CRMs) can accurately estimate vegetation canopy biophysical-structural information such as Leaf Area Index (LAI) inexpensively using satellite imagery. The strict physical basis which geometric-optical CRMs employ to mathematically link canopy bidirectional reflectance and structure allows for the tangible replication of a CRM's geometric abstraction of a canopy in the laboratory, enabling robust CRM validation studies. To this end, the ULGS-2 goniometer was used to obtain multiangle, hyperspectral (Spectrodirectional) measurements of a specially-designed tangible physical model forest, developed based upon the Geometric-Optical Mutual Shadowing (GOMS) CRM, at three different canopy cover densities. GOMS forward-modelled reflectance values had high levels of agreement with ULGS-2 measurements, with obtained reflectance RMSE values ranging from 0.03% to 0.1%. Canopy structure modelled via GOMS Multiple-Forward-Mode (MFM) inversion had varying levels of success. The methods developed in this thesis can potentially be extended to more complex CRMs through the implementation of 3D printing.

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila

PubMed Central

2014-01-01

Background Cis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs. Description It is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality. Conclusions cisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable hypotheses for the molecular mechanisms of metazoan gene regulation. We believe that the information deposited in cisMEP will greatly facilitate the comparative usage of different CRM prediction tools and will help biologists to study the modular regulatory mechanisms between different TFs and their target genes. PMID:25521507

Simulation of Shallow Cumuli and Their Transition to Deep Convective Clouds by Cloud-resolving Models with Different Third-order Turbulence Closures

NASA Technical Reports Server (NTRS)

Cheng, Anning; Xu, Kuan-Man

2006-01-01

The abilities of cloud-resolving models (CRMs) with the double-Gaussian based and the single-Gaussian based third-order closures (TOCs) to simulate the shallow cumuli and their transition to deep convective clouds are compared in this study. The single-Gaussian based TOC is fully prognostic (FP), while the double-Gaussian based TOC is partially prognostic (PP). The latter only predicts three important third-order moments while the former predicts all the thirdorder moments. A shallow cumulus case is simulated by single-column versions of the FP and PP TOC models. The PP TOC improves the simulation of shallow cumulus greatly over the FP TOC by producing more realistic cloud structures. Large differences between the FP and PP TOC simulations appear in the cloud layer of the second- and third-order moments, which are related mainly to the underestimate of the cloud height in the FP TOC simulation. Sensitivity experiments and analysis of probability density functions (PDFs) used in the TOCs show that both the turbulence-scale condensation and higher-order moments are important to realistic simulations of the boundary-layer shallow cumuli. A shallow to deep convective cloud transition case is also simulated by the 2-D versions of the FP and PP TOC models. Both CRMs can capture the transition from the shallow cumuli to deep convective clouds. The PP simulations produce more and deeper shallow cumuli than the FP simulations, but the FP simulations produce larger and wider convective clouds than the PP simulations. The temporal evolutions of cloud and precipitation are closely related to the turbulent transport, the cold pool and the cloud-scale circulation. The large amount of turbulent mixing associated with the shallow cumuli slows down the increase of the convective available potential energy and inhibits the early transition to deep convective clouds in the PP simulation. When the deep convective clouds fully develop and the precipitation is produced, the cold pools produced by the evaporation of the precipitation are not favorable to the formation of shallow cumuli.

A Robust Multi-Scale Modeling System for the Study of Cloud and Precipitation Processes

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2012-01-01

During the past decade, numerical weather and global non-hydrostatic models have started using more complex microphysical schemes originally developed for high resolution cloud resolving models (CRMs) with 1-2 km or less horizontal resolutions. These microphysical schemes affect the dynamic through the release of latent heat (buoyancy loading and pressure gradient) the radiation through the cloud coverage (vertical distribution of cloud species), and surface processes through rainfall (both amount and intensity). Recently, several major improvements of ice microphysical processes (or schemes) have been developed for cloud-resolving model (Goddard Cumulus Ensemble, GCE, model) and regional scale (Weather Research and Forecast, WRF) model. These improvements include an improved 3-ICE (cloud ice, snow and graupel) scheme (Lang et al. 2010); a 4-ICE (cloud ice, snow, graupel and hail) scheme and a spectral bin microphysics scheme and two different two-moment microphysics schemes. The performance of these schemes has been evaluated by using observational data from TRMM and other major field campaigns. In this talk, we will present the high-resolution (1 km) GeE and WRF model simulations and compared the simulated model results with observation from recent field campaigns [i.e., midlatitude continental spring season (MC3E; 2010), high latitude cold-season (C3VP, 2007; GCPEx, 2012), and tropical oceanic (TWP-ICE, 2006)].

On polarimetric radar signatures of deep convection for model evaluation: columns of specific differential phase observed during MC3E

PubMed Central

van Lier-Walqui, Marcus; Fridlind, Ann M.; Ackerman, Andrew S.; Collis, Scott; Helmus, Jonathan; MacGorman, Donald R.; North, Kirk; Kollias, Pavlos; Posselt, Derek J.

2017-01-01

The representation of deep convection in general circulation models is in part informed by cloud-resolving models (CRMs) that function at higher spatial and temporal resolution; however, recent studies have shown that CRMs often fail at capturing the details of deep convection updrafts. With the goal of providing constraint on CRM simulation of deep convection updrafts, ground-based remote-sensing observations are analyzed and statistically correlated for four deep convection events observed during the Midlatitude Continental Convective Clouds Experiment (MC3E). Since positive values of specific differential phase (KDP) observed above the melting level are associated with deep convection updraft cells, so-called “KDP columns” are analyzed using two scanning polarimetric radars in Oklahoma: the National Weather Service Vance WSR-88D (KVNX) and the Department of Energy C-band Scanning Atmospheric Radiation Measurement (ARM) Precipitation Radar (C-SAPR). KVNX and C-SAPR KDP volumes and columns are then statistically correlated with vertical winds retrieved via multi-Doppler wind analysis, lightning flash activity derived from the Oklahoma Lightning Mapping Array, and KVNX differential reflectivity (ZDR). Results indicate strong correlations of KDP volume above the melting level with updraft mass flux, lightning flash activity, and intense rainfall. Analysis of KDP columns reveals signatures of changing updraft properties from one storm event to another as well as during event evolution. Comparison of ZDR to KDP shows commonalities in information content of each, as well as potential problems with ZDR associated with observational artifacts. PMID:29503466

On polarimetric radar signatures of deep convection for model evaluation: columns of specific differential phase observed during MC3E.

PubMed

van Lier-Walqui, Marcus; Fridlind, Ann M; Ackerman, Andrew S; Collis, Scott; Helmus, Jonathan; MacGorman, Donald R; North, Kirk; Kollias, Pavlos; Posselt, Derek J

2016-02-01

The representation of deep convection in general circulation models is in part informed by cloud-resolving models (CRMs) that function at higher spatial and temporal resolution; however, recent studies have shown that CRMs often fail at capturing the details of deep convection updrafts. With the goal of providing constraint on CRM simulation of deep convection updrafts, ground-based remote-sensing observations are analyzed and statistically correlated for four deep convection events observed during the Midlatitude Continental Convective Clouds Experiment (MC3E). Since positive values of specific differential phase ( K DP ) observed above the melting level are associated with deep convection updraft cells, so-called " K DP columns" are analyzed using two scanning polarimetric radars in Oklahoma: the National Weather Service Vance WSR-88D (KVNX) and the Department of Energy C-band Scanning Atmospheric Radiation Measurement (ARM) Precipitation Radar (C-SAPR). KVNX and C-SAPR K DP volumes and columns are then statistically correlated with vertical winds retrieved via multi-Doppler wind analysis, lightning flash activity derived from the Oklahoma Lightning Mapping Array, and KVNX differential reflectivity ( Z DR ). Results indicate strong correlations of K DP volume above the melting level with updraft mass flux, lightning flash activity, and intense rainfall. Analysis of K DP columns reveals signatures of changing updraft properties from one storm event to another as well as during event evolution. Comparison of Z DR to K DP shows commonalities in information content of each, as well as potential problems with Z DR associated with observational artifacts.

Various Numerical Applications on Tropical Convective Systems Using a Cloud Resolving Model

NASA Technical Reports Server (NTRS)

Shie, C.-L.; Tao, W.-K.; Simpson, J.

2003-01-01

In recent years, increasing attention has been given to cloud resolving models (CRMs or cloud ensemble models-CEMs) for their ability to simulate the radiative-convective system, which plays a significant role in determining the regional heat and moisture budgets in the Tropics. The growing popularity of CRM usage can be credited to its inclusion of crucial and physically relatively realistic features such as explicit cloud-scale dynamics, sophisticated microphysical processes, and explicit cloud-radiation interaction. On the other hand, impacts of the environmental conditions (for example, the large-scale wind fields, heat and moisture advections as well as sea surface temperature) on the convective system can also be plausibly investigated using the CRMs with imposed explicit forcing. In this paper, by basically using a Goddard Cumulus Ensemble (GCE) model, three different studies on tropical convective systems are briefly presented. Each of these studies serves a different goal as well as uses a different approach. In the first study, which uses more of an idealized approach, the respective impacts of the large-scale horizontal wind shear and surface fluxes on the modeled tropical quasi-equilibrium states of temperature and water vapor are examined. In this 2-D study, the imposed large-scale horizontal wind shear is ideally either nudged (wind shear maintained strong) or mixed (wind shear weakened), while the minimum surface wind speed used for computing surface fluxes varies among various numerical experiments. For the second study, a handful of real tropical episodes (TRMM Kwajalein Experiment - KWAJEX, 1999; TRMM South China Sea Monsoon Experiment - SCSMEX, 1998) have been simulated such that several major atmospheric characteristics such as the rainfall amount and its associated stratiform contribution, the Qlheat and Q2/moisture budgets are investigated. In this study, the observed large-scale heat and moisture advections are continuously applied to the 2-D model. The modeled cloud generated from such an approach is termed continuously forced convection or continuous large-scale forced convection. A third study, which focuses on the respective impact of atmospheric components on upper Ocean heat and salt budgets, will be presented in the end. Unlike the two previous 2-D studies, this study employs the 3-D GCE-simulated diabatic source terms (using TOGA COARE observations) - radiation (longwave and shortwave), surface fluxes (sensible and latent heat, and wind stress), and precipitation as input for the Ocean mixed-layer (OML) model.

Cystic Fibrosis Transmembrane Conductance Regulator-Related Metabolic Syndrome and Cystic Fibrosis Screen Positive, Inconclusive Diagnosis.

PubMed

Ren, Clement L; Borowitz, Drucy S; Gonska, Tanja; Howenstine, Michelle S; Levy, Hara; Massie, John; Milla, Carlos; Munck, Anne; Southern, Kevin W

2017-02-01

An unintended consequence of cystic fibrosis (CF) newborn screening (NBS) is the identification of infants with a positive NBS test but inconclusive diagnostic testing. These infants are classified as CF transmembrane conductance regulator-related metabolic syndrome (CRMS) in the US and CF screen positive, inconclusive diagnosis (CFSPID) in other countries. Diagnostic and management decisions of these infants are challenges for CF healthcare professionals and stressful situations for families. As CF NBS has become more widespread across the world, increased information about the epidemiology and outcomes of these infants is becoming available. These data were reviewed at the 2015 CF Foundation Diagnosis Consensus Conference, and a harmonized definition of CRMS and CFSPID was developed. At the consensus conference, participants reviewed published and unpublished studies of CRMS/CFSPID and used a modified Delphi methodology to develop a harmonized approach to the definition of CRMS/CFSPID. Several studies of CRMS/CFSPID from populations around the world have been published in the past year. Although the studies vary in the number of infants studied, study design, and outcome measures, there have been some consistent findings. CRMS/CFSPID occurs relatively frequently, with CF:CRMS that ranges from 3 to 5 cases of CF for every 1 case of CRMS/CFSPID in regions where gene sequencing is not used. The incidence varies by NBS protocol used, and in some regions more cases of CRMS/CFSPID are detected than cases of CF. The majority of individuals with CRMS/CFSPID do not develop CF disease or progress to a diagnosis of CF. However, between 10% and 20% of asymptomatic infants can develop clinical features concerning for CF, such as a respiratory culture positive for Pseudomonas aeruginosa. Most studies have only reported short-term outcomes in the first 1-3 years of life; the long-term outcomes of CRMS/CFSPID remain unknown. The European CF Society definition of CFSPID and the CF Foundation definition of CRMS differ only slightly, and the consensus conference was able to create a unified definition of CRMS/CFSPID. CRMS/CFSPID is a relatively common outcome of CF NBS, and clinicians need to be prepared to counsel families whose NBS test falls into this classification. The vast majority of infants with CRMS/CFSPID will remain free from disease manifestations early in life. However, a small proportion may develop clinical features concerning for CF or demonstrate progression to a clinical phenotype compatible with a CF diagnosis, and their long-term outcomes are not known. A consistent international definition of CRMS/CFSPID will allow for better data collection for study of outcomes and result in improved patient care. Copyright © 2016 Elsevier Inc. All rights reserved.

Overview Article: Identifying transcriptional cis-regulatory modules in animal genomes

PubMed Central

Suryamohan, Kushal; Halfon, Marc S.

2014-01-01

Gene expression is regulated through the activity of transcription factors and chromatin modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional enhancers. Because regulated gene expression is fundamental to cell differentiation and acquisition of new cell fates, identifying, characterizing, and understanding the mechanisms of action of CRMs is critical for understanding development. CRM discovery has historically been challenging, as CRMs can be located far from the genes they regulate, have few readily-identifiable sequence characteristics, and for many years were not amenable to high-throughput discovery methods. However, the recent availability of complete genome sequences and the development of next-generation sequencing methods has led to an explosion of both computational and empirical methods for CRM discovery in model and non-model organisms alike. Experimentally, CRMs can be identified through chromatin immunoprecipitation directed against transcription factors or histone post-translational modifications, identification of nucleosome-depleted “open” chromatin regions, or sequencing-based high-throughput functional screening. Computational methods include comparative genomics, clustering of known or predicted transcription factor binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each is subject to a greater or lesser number of false-positive identifications. Experimental confirmation of predictions is essential, although shortcomings in current methods suggest that additional means of validation need to be developed. PMID:25704908

Short Communication: Comparative Susceptibility of Rhesus Macaques of Indian and Chinese Origin to Vaginal Simian-Human Immunodeficiency Virus Transmission as Models for HIV Prevention Research.

PubMed

Veazey, Ronald S; Ling, Binhua

2017-12-01

Historically, Indian rhesus macaques (iRMs) have been preferred for simian immunodeficiency virus (SIV)/HIV prevention, pathogenesis, and treatment studies, yet their supply is limited. Chinese rhesus macaques (cRMs) are currently more available, yet little is known regarding the relative susceptibility of this subspecies to vaginal transmission of SIV or simian-human immunodeficiency virus (SHIV). In this study, we compared the susceptibility of 40 cRMs and 21 iRMs with a single vaginal challenge with SHIVsf162P. Our results showed that cRMs have comparable primary SHIV infection as iRMs, underscoring their equal importance in studies of HIV transmission and prevention.

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation

PubMed Central

O'Connor, Timothy R.; Bailey, Timothy L.

2014-01-01

Predicting which genomic regions control the transcription of a given gene is a challenge. We present a novel computational approach for creating and validating maps that associate genomic regions (cis-regulatory modules–CRMs) with genes. The method infers regulatory relationships that explain gene expression observed in a test tissue using widely available genomic data for ‘other’ tissues. To predict the regulatory targets of a CRM, we use cross-tissue correlation between histone modifications present at the CRM and expression at genes within 1 Mbp of it. To validate cis-regulatory maps, we show that they yield more accurate models of gene expression than carefully constructed control maps. These gene expression models predict observed gene expression from transcription factor binding in the CRMs linked to that gene. We show that our maps are able to identify long-range regulatory interactions and improve substantially over maps linking genes and CRMs based on either the control maps or a ‘nearest neighbor’ heuristic. Our results also show that it is essential to include CRMs predicted in multiple tissues during map-building, that H3K27ac is the most informative histone modification, and that CAGE is the most informative measure of gene expression for creating cis-regulatory maps. PMID:25200088

Distinct Endothelial Cell Responses in the Heart and Kidney Microvasculature Characterize the Progression of Heart Failure With Preserved Ejection Fraction in the Obese ZSF1 Rat With Cardiorenal Metabolic Syndrome.

PubMed

van Dijk, Christian G M; Oosterhuis, Nynke R; Xu, Yan Juan; Brandt, Maarten; Paulus, Walter J; van Heerebeek, Loek; Duncker, Dirk J; Verhaar, Marianne C; Fontoura, Dulce; Lourenço, André P; Leite-Moreira, Adelino F; Falcão-Pires, Inês; Joles, Jaap A; Cheng, Caroline

2016-04-01

The combination of cardiac and renal disease driven by metabolic risk factors, referred to as cardiorenal metabolic syndrome (CRMS), is increasingly recognized as a critical pathological entity. The contribution of (micro)vascular injury to CRMS is considered to be substantial. However, mechanistic studies are hampered by lack of in vivo models that mimic the natural onset of the disease. Here, we evaluated the coronary and renal microvasculature during CRMS development in obese diabetic Zucker fatty/Spontaneously hypertensive heart failure F1 hybrid (ZSF1) rats. Echocardiographic, urine, and blood evaluations were conducted in 3 groups (Wistar-Kyoto, lean ZSF1, and obese ZSF1) at 20 and 25 weeks of age. Immunohistological evaluation of renal and cardiac tissues was conducted at both time points. At 20 and 25 weeks, obese ZSF1 rats showed higher body weight, significant left ventricular hypertrophy, and impaired diastolic function compared with all other groups. Indices of systolic function did not differ between groups. Obese ZSF1 rats developed hyperproliferative vascular foci in the subendocardium, which lacked microvascular organization and were predilection sites of inflammation and fibrosis. In the kidney, obese ZSF1 animals showed regression of the peritubular and glomerular microvasculature, accompanied by tubulointerstitial damage, glomerulosclerosis, and proteinuria. The obese ZSF1 rat strain is a suitable in vivo model for CRMS, sharing characteristics with the human syndrome during the earliest onset of disease. In these rats, CRMS induces microvascular fibrotic responses in heart and kidneys, associated with functional impairment of both organs. © 2016 American Heart Association, Inc.

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann–Mangold organizer

PubMed Central

Sudou, Norihiro; Yamamoto, Shinji; Ogino, Hajime; Taira, Masanori

2012-01-01

How multiple developmental cues are integrated on cis-regulatory modules (CRMs) for cell fate decisions remains uncertain. The Spemann–Mangold organizer in Xenopus embryos expresses the transcription factors Lim1/Lhx1, Otx2, Mix1, Siamois (Sia) and VegT. Reporter analyses using sperm nuclear transplantation and DNA injection showed that cerberus (cer) and goosecoid (gsc) are activated by the aforementioned transcription factors through CRMs conserved between X. laevis and X. tropicalis. ChIP-qPCR analysis for the five transcription factors revealed that cer and gsc CRMs are initially bound by both Sia and VegT at the late blastula stage, and subsequently bound by all five factors at the gastrula stage. At the neurula stage, only binding of Lim1 and Otx2 to the gsc CRM, among others, persists, which corresponds to their co-expression in the prechordal plate. Based on these data, together with detailed expression pattern analysis, we propose a new model of stepwise formation of the organizer, in which (1) maternal VegT and Wnt-induced Sia first bind to CRMs at the blastula stage; then (2) Nodal-inducible Lim1, Otx2, Mix1 and zygotic VegT are bound to CRMs in the dorsal endodermal and mesodermal regions where all these genes are co-expressed; and (3) these two regions are combined at the gastrula stage to form the organizer. Thus, the in vivo dynamics of multiple transcription factors highlight their roles in the initiation and maintenance of gene expression, and also reveal the stepwise integration of maternal, Nodal and Wnt signaling on CRMs of organizer genes to generate the organizer. PMID:22492356

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer.

PubMed

Sudou, Norihiro; Yamamoto, Shinji; Ogino, Hajime; Taira, Masanori

2012-05-01

How multiple developmental cues are integrated on cis-regulatory modules (CRMs) for cell fate decisions remains uncertain. The Spemann-Mangold organizer in Xenopus embryos expresses the transcription factors Lim1/Lhx1, Otx2, Mix1, Siamois (Sia) and VegT. Reporter analyses using sperm nuclear transplantation and DNA injection showed that cerberus (cer) and goosecoid (gsc) are activated by the aforementioned transcription factors through CRMs conserved between X. laevis and X. tropicalis. ChIP-qPCR analysis for the five transcription factors revealed that cer and gsc CRMs are initially bound by both Sia and VegT at the late blastula stage, and subsequently bound by all five factors at the gastrula stage. At the neurula stage, only binding of Lim1 and Otx2 to the gsc CRM, among others, persists, which corresponds to their co-expression in the prechordal plate. Based on these data, together with detailed expression pattern analysis, we propose a new model of stepwise formation of the organizer, in which (1) maternal VegT and Wnt-induced Sia first bind to CRMs at the blastula stage; then (2) Nodal-inducible Lim1, Otx2, Mix1 and zygotic VegT are bound to CRMs in the dorsal endodermal and mesodermal regions where all these genes are co-expressed; and (3) these two regions are combined at the gastrula stage to form the organizer. Thus, the in vivo dynamics of multiple transcription factors highlight their roles in the initiation and maintenance of gene expression, and also reveal the stepwise integration of maternal, Nodal and Wnt signaling on CRMs of organizer genes to generate the organizer.

Diagnosing the Ice Crystal Enhancement Factor in the Tropics

NASA Technical Reports Server (NTRS)

Zeng, Xiping; Tao, Wei-Kuo; Matsui, Toshihisa; Xie, Shaocheng; Lang, Stephen; Zhang, Minghua; Starr, David O'C; Li, Xiaowen; Simpson, Joanne

2009-01-01

Recent modeling studies have revealed that ice crystal number concentration is one of the dominant factors in the effect of clouds on radiation. Since the ice crystal enhancement factor and ice nuclei concentration determine the concentration, they are both important in quantifying the contribution of increased ice nuclei to global warming. In this study, long-term cloud-resolving model (CRM) simulations are compared with field observations to estimate the ice crystal enhancement factor in tropical and midlatitudinal clouds, respectively. It is found that the factor in tropical clouds is 10 3-104 times larger than that of mid-latitudinal ones, which makes physical sense because entrainment and detrainment in the Tropics are much stronger than in middle latitudes. The effect of entrainment/detrainment on the enhancement factor, especially in tropical clouds, suggests that cloud microphysical parameterizations should be coupled with subgrid turbulence parameterizations within CRMs to obtain a more accurate depiction of cloud-radiative forcing.

Precipitation Processes Developed During ARM (1997), TOGA COARE (1992) GATE (1974), SCSMEX (1998), and KWAJEX (1999): Consistent 3D, Semi-3D and 3D Cloud Resolving Model Simulations

NASA Technical Reports Server (NTRS)

Tao, W.-K.; Hou, A.; Atlas, R.; Starr, D.; Sud, Y.

2003-01-01

Real clouds and cloud systems are inherently three-dimensional (3D). Because of the limitations in computer resources, however, most cloud-resolving models (CRMs) today are still two-dimensional (2D) have been used to study the response of clouds to large-scale forcing. IN these 3D simulators, the model domain was small, and the integration time was 6 hours. Only recently have 3D experiments been performed for multi-day periods for tropical clouds systems with large horizontal domains at the National Center of Atmospheric Research (NCAR) and at NASA Goddard Space Center. At Goddard, a 3D cumulus Ensemble (GCE) model was used to simulate periods during TOGA COARE, GATE, SCSMEX, ARM, and KWAJEX using a 512 by 512 km domain (with 2-km resolution). The result indicate that surface precipitation and latent heating profiles are very similar between the 2D and 3D GCE model simulation. The major objective of this paper are: (1) to assess the performance of the super-parametrization technique, (2) calculate and examine the surface energy (especially radiation) and water budget, and (3) identify the differences and similarities in the organization and entrainment rates of convection between simulated 2D and 3D cloud systems.

Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

PubMed

Kang, Keunsoo; Kim, Joomyeong; Chung, Jae Hoon; Lee, Daeyoup

2011-09-01

The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available information to identify and characterize genome-wide CRMs in a species of interest. CCD first defines a set of the epigenetic features which is significantly associated with a set of known CRMs as a code called 'trace code', and subsequently uses the trace code to pinpoint putative CRMs throughout the genome. Using 61 genome-wide data sets obtained from 17 independent mouse studies, CCD successfully catalogued ∼12 600 CRMs (five distinct classes) including polycomb repressive complex 2 target sites as well as imprinting control regions. Interestingly, we discovered that ∼4% of the identified CRMs belong to at least two different classes named 'multi-functional CRM', suggesting their functional importance for regulating spatiotemporal gene expression. From these examples, we show that CCD can be applied to any potential genome-wide datasets and therefore will shed light on unveiling genome-wide CRMs in various species.

Convective Systems Over the Japan Sea: Cloud-Resolving Model Simulations

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Yoshizaki, Masanori; Shie, Chung-Lin; Kato, Teryuki

2002-01-01

Wintertime observations of MCSs (Mesoscale Convective Systems) over the Sea of Japan - 2001 (WMO-01) were collected from January 12 to February 1, 2001. One of the major objectives is to better understand and forecast snow systems and accompanying disturbances and the associated key physical processes involved in the formation and development of these disturbances. Multiple observation platforms (e.g., upper-air soundings, Doppler radar, wind profilers, radiometers, etc.) during WMO-01 provided a first attempt at investigating the detailed characteristics of convective storms and air pattern changes associated with winter storms over the Sea of Japan region. WMO-01 also provided estimates of the apparent heat source (Q1) and apparent moisture sink (Q2). The vertical integrals of Q1 and Q2 are equal to the surface precipitation rates. The horizontal and vertical adjective components of Q1 and Q2 can be used as large-scale forcing for the Cloud Resolving Models (CRMs). The Goddard Cumulus Ensemble (GCE) model is a CRM (typically run with a 1-km grid size). The GCE model has sophisticated microphysics and allows explicit interactions between clouds, radiation, and surface processes. It will be used to understand and quantify precipitation processes associated with wintertime convective systems over the Sea of Japan (using data collected during the WMO-01). This is the first cloud-resolving model used to simulate precipitation processes in this particular region. The GCE model-simulated WMO-01 results will also be compared to other GCE model-simulated weather systems that developed during other field campaigns (i.e., South China Sea, west Pacific warm pool region, eastern Atlantic region and central USA).

Simulation of Boundary-Layer Cumulus and Stratocumulus Clouds using a Cloud-Resolving Model With Low- and Third-Order Turbulence Closures

NASA Technical Reports Server (NTRS)

Xu, Kuan-Man; Cheng, Anning

2007-01-01

The effects of subgrid-scale condensation and transport become more important as the grid spacings increase from those typically used in large-eddy simulation (LES) to those typically used in cloud-resolving models (CRMs). Incorporation of these effects can be achieved by a joint probability density function approach that utilizes higher-order moments of thermodynamic and dynamic variables. This study examines how well shallow cumulus and stratocumulus clouds are simulated by two versions of a CRM that is implemented with low-order and third-order turbulence closures (LOC and TOC) when a typical CRM horizontal resolution is used and what roles the subgrid-scale and resolved-scale processes play as the horizontal grid spacing of the CRM becomes finer. Cumulus clouds were mostly produced through subgrid-scale transport processes while stratocumulus clouds were produced through both subgrid-scale and resolved-scale processes in the TOC version of the CRM when a typical CRM grid spacing is used. The LOC version of the CRM relied upon resolved-scale circulations to produce both cumulus and stratocumulus clouds, due to small subgrid-scale transports. The mean profiles of thermodynamic variables, cloud fraction and liquid water content exhibit significant differences between the two versions of the CRM, with the TOC results agreeing better with the LES than the LOC results. The characteristics, temporal evolution and mean profiles of shallow cumulus and stratocumulus clouds are weakly dependent upon the horizontal grid spacing used in the TOC CRM. However, the ratio of the subgrid-scale to resolved-scale fluxes becomes smaller as the horizontal grid spacing decreases. The subcloud-layer fluxes are mostly due to the resolved scales when a grid spacing less than or equal to 1 km is used. The overall results of the TOC simulations suggest that a 1-km grid spacing is a good choice for CRM simulation of shallow cumulus and stratocumulus.

Continuous Evaluation of Fast Processes in Climate Models Using ARM Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhijin; Sha, Feng; Liu, Yangang

2016-02-02

This five-year award supports the project “Continuous Evaluation of Fast Processes in Climate Models Using ARM Measurements (FASTER)”. The goal of this project is to produce accurate, consistent and comprehensive data sets for initializing both single column models (SCMs) and cloud resolving models (CRMs) using data assimilation. A multi-scale three-dimensional variational data assimilation scheme (MS-3DVAR) has been implemented. This MS-3DVAR system is built on top of WRF/GSI. The Community Gridpoint Statistical Interpolation (GSI) system is an operational data assimilation system at the National Centers for Environmental Prediction (NCEP) and has been implemented in the Weather Research and Forecast (WRF) model.more » This MS-3DVAR is further enhanced by the incorporation of a land surface 3DVAR scheme and a comprehensive aerosol 3DVAR scheme. The data assimilation implementation focuses in the ARM SGP region. ARM measurements are assimilated along with other available satellite and radar data. Reanalyses are then generated for a few selected period of time. This comprehensive data assimilation system has also been employed for other ARM-related applications.« less

Reference materials for the monitoring of the aquatic environment--a review with special emphasis on organic priority pollutants.

PubMed

Bercaru, Ofelia; Gawlik, Bernd Manfred; Ulberth, Franz; Vandecasteele, Carlo

2003-08-01

During recent years, the awareness of quality assurance and quality control in environmental analyses has constantly increased, especially due to the implementation of new guidelines and regulations at both the national and international level. Achieving comparable results by using certified reference materials is one of the primary concerns of the scientific community. As a result, there is a growing demand for certified reference materials to cover different matrices and pollutants. Moreover, these CRMs should be in close relationship to the determinants and target concentrations required by environmental bodies and European Directives as well. Supplementary information to this paper presents an inventory of reference materials available on the market from different suppliers against the priority pollutants listed in the Water Framework Directive. These CRMs cover matrices such as water, sediment and biota. The use of CRMs in relationship to appropriate analytical methods and relevant determinants is discussed and the need for matrix-CRMs, particularly for organic pollutants is emphasised. The use of proficiency testing schemes as an alternative for the lack of appropriate CRMs and future trends in the production of CRMs within the BCR framework are also discussed.

A Coupled GCM-Cloud Resolving Modeling System, and a Regional Scale Model to Study Precipitation Processes

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2006-01-01

Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that cloud-resolving models (CRMs) agree with observations better than traditional single-column models in simulating various types of clouds and cloud systems from different geographic locations. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a super-parameterization or multi-scale modeling framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign cloud related datasets can provide initial conditions as well as validation for both the MMF and CFWs. The Goddard MMF is based on the 2D Goddard Cumulus Ensemble (GCE) model and the Goddard finite volume general circulation model (fvGCM), and it has started production runs with two years results (1 998 and 1999). In this talk, I will present: (1) A brief review on GCE model and its applications on precipitation processes (microphysical and land processes), (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications).

Dynamic micro- and macrovascular remodeling in coronary circulation of obese Ossabaw pigs with metabolic syndrome

PubMed Central

Katz, Paige S.; Kelly, Amy P.; Galantowicz, Maarten L.; Cismowski, Mary J.; West, T. Aaron; Neeb, Zachary P.; Berwick, Zachary C.; Goodwill, Adam G.; Alloosh, Mouhamad; Tune, Johnathan D.; Sturek, Michael; Lucchesi, Pamela A.

2012-01-01

Previous studies from our laboratory showed that coronary arterioles from type 2 diabetic mice undergo inward hypertrophic remodeling and reduced stiffness. The aim of the current study was to determine if coronary resistance microvessels (CRMs) in Ossabaw swine with metabolic syndrome (MetS) undergo remodeling distinct from coronary conduit arteries. Male Ossabaw swine were fed normal (n = 7, Lean) or hypercaloric high-fat (n = 7, MetS) diets for 6 mo, and then CRMs were isolated and mounted on a pressure myograph. CRMs isolated from MetS swine exhibited decreased luminal diameters (126 ± 5 and 105 ± 9 μm in Lean and MetS, respectively, P < 0.05) with thicker walls (18 ± 3 and 31 ± 3 μm in Lean and MetS, respectively, P < 0.05), which doubled the wall-to-lumen ratio (14 ± 2 and 30 ± 2 in Lean and MetS, respectively, P < 0.01). Incremental modulus of elasticity (IME) and beta stiffness index (BSI) were reduced in CRMs isolated from MetS pigs (IME: 3.6 × 106 ± 0.7 × 106 and 1.1 × 106 ± 0.2 × 106 dyn/cm2 in Lean and MetS, respectively, P < 0.001; BSI: 10.3 ± 0.4 and 7.3 ± 1.8 in Lean and MetS, respectively, P < 0.001). BSI in the left anterior descending coronary artery was augmented in pigs with MetS. Structural changes were associated with capillary rarefaction, decreased hyperemic-to-basal coronary flow velocity ratio, and augmented myogenic tone. MetS CRMs showed a reduced collagen-to-elastin ratio, while immunostaining for the receptor for advanced glycation end products was selectively increased in the left anterior descending coronary artery. These data suggest that MetS causes hypertrophic inward remodeling of CRMs and capillary rarefaction, which contribute to decreased coronary flow and myocardial ischemia. Moreover, our data demonstrate novel differential remodeling between coronary micro- and macrovessels in a clinically relevant model of MetS. PMID:22837170

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

PubMed Central

Dunipace, Leslie; Ozdemir, Anil; Stathopoulos, Angelike

2011-01-01

It has been shown in several organisms that multiple cis-regulatory modules (CRMs) of a gene locus can be active concurrently to support similar spatiotemporal expression. To understand the functional importance of such seemingly redundant CRMs, we examined two CRMs from the Drosophila snail gene locus, which are both active in the ventral region of pre-gastrulation embryos. By performing a deletion series in a ∼25 kb DNA rescue construct using BAC recombineering and site-directed transgenesis, we demonstrate that the two CRMs are not redundant. The distal CRM is absolutely required for viability, whereas the proximal CRM is required only under extreme conditions such as high temperature. Consistent with their distinct requirements, the CRMs support distinct expression patterns: the proximal CRM exhibits an expanded expression domain relative to endogenous snail, whereas the distal CRM exhibits almost complete overlap with snail except at the anterior-most pole. We further show that the distal CRM normally limits the increased expression domain of the proximal CRM and that the proximal CRM serves as a `damper' for the expression levels driven by the distal CRM. Thus, the two CRMs interact in cis in a non-additive fashion and these interactions may be important for fine-tuning the domains and levels of gene expression. PMID:21813571

Suitability of customer relationship management systems for the management of study participants in biomedical research.

PubMed

Schwanke, J; Rienhoff, O; Schulze, T G; Nussbeck, S Y

2013-01-01

Longitudinal biomedical research projects study patients or participants over a course of time. No IT solution is known that can manage study participants, enhance quality of data, support re-contacting of participants, plan study visits, and keep track of informed consent procedures and recruitments that may be subject to change over time. In business settings management of personal is one of the major aspects of customer relationship management systems (CRMS). To evaluate whether CRMS are suitable IT solutions for study participant management in biomedical research. Three boards of experts in the field of biomedical research were consulted to get an insight into recent IT developments regarding study participant management systems (SPMS). Subsequently, a requirements analysis was performed with stakeholders of a major biomedical research project. The successive suitability evaluation was based on the comparison of the identified requirements with the features of six CRMS. Independently of each other, the interviewed expert boards confirmed that there is no generic IT solution for the management of participants. Sixty-four requirements were identified and prioritized in a requirements analysis. The best CRMS was able to fulfill forty-two of these requirements. The non-fulfilled requirements demand an adaption of the CRMS, consuming time and resources, reducing the update compatibility, the system's suitability, and the security of the CRMS. A specific solution for the SPMS is favored instead of a generic and commercially-oriented CRMS. Therefore, the development of a small and specific SPMS solution was commenced and is currently on the way to completion.

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord

PubMed Central

José-Edwards, Diana S.; Oda-Ishii, Izumi; Kugler, Jamie E.; Passamaneck, Yale J.; Katikala, Lavanya; Nibu, Yutaka; Di Gregorio, Anna

2015-01-01

A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs. PMID:26684323

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.

PubMed

José-Edwards, Diana S; Oda-Ishii, Izumi; Kugler, Jamie E; Passamaneck, Yale J; Katikala, Lavanya; Nibu, Yutaka; Di Gregorio, Anna

2015-12-01

A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.

Avian collision risk models for wind energy impact assessments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Masden, E.A., E-mail: elizabeth.masden@uhi.ac.uk; Cook, A.S.C.P.

2016-01-15

With the increasing global development of wind energy, collision risk models (CRMs) are routinely used to assess the potential impacts of wind turbines on birds. We reviewed and compared the avian collision risk models currently available in the scientific literature, exploring aspects such as the calculation of a collision probability, inclusion of stationary components e.g. the tower, angle of approach and uncertainty. 10 models were cited in the literature and of these, all included a probability of collision of a single bird colliding with a wind turbine during passage through the rotor swept area, and the majority included a measuremore » of the number of birds at risk. 7 out of the 10 models calculated the probability of birds colliding, whilst the remainder used a constant. We identified four approaches to calculate the probability of collision and these were used by others. 6 of the 10 models were deterministic and included the most frequently used models in the UK, with only 4 including variation or uncertainty in some way, the most recent using Bayesian methods. Despite their appeal, CRMs have their limitations and can be ‘data hungry’ as well as assuming much about bird movement and behaviour. As data become available, these assumptions should be tested to ensure that CRMs are functioning to adequately answer the questions posed by the wind energy sector. - Highlights: • We highlighted ten models available to assess avian collision risk. • Only 4 of the models included variability or uncertainty. • Collision risk models have limitations and can be ‘data hungry’. • It is vital that the most appropriate model is used for a given task.« less

Mineral oil certified reference materials for the determination of polychlorinated biphenyls from the National Metrology Institute of Japan (NMIJ)

PubMed Central

Aoyagi, Yoshie; Matsuo, Mayumi; Ishikawa, Keiichiro; Hanari, Nobuyasu; Otsuka, Satoko; Tsuda, Yoko; Yarita, Takashi

2008-01-01

Four mineral oil certified reference materials (CRMs), NMIJ CRM 7902-a, CRM 7903-a, CRM 7904-a, and CRM 7905-a, have been issued by the National Metrology Institute of Japan, which is part of the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST), for the determination of polychlorinated biphenyls (PCBs). The raw materials for the CRMs were an insulation oil (CRM 7902-a and CRM 7903-a) and a fuel oil (CRM7904-a and CRM 7905-a). A solution of PCB3, PCB8, and technical PCB products, comprising four types of Kaneclor, was added to the oil matrices. The total PCB concentrations in the PCB-fortified oils (CRM 7902-a and CRM 7904-a) are approximately 6 mg kg−1. In addition, the mineral oils which were not fortified with PCBs were also distributed as CRMs (CRM 7903-a and CRM 7905-a). Characterization of these CRMs was conducted by the NMIJ/AIST, where the mineral oils and the PCB solution were analyzed using multiple analytical methods such as dimethylsulfoxide extraction, normal-phase liquid chromatography, gel permeation chromatography, reversed-phase liquid chromatography, and chromatography using sulfoxide-bonded silica; and/or various capillary columns for gas chromatography, and two ionization modes for mass spectrometry. The target compounds in the mineral oils and those in the PCB solution were determined by one of the primary methods of measurement, isotope dilution–mass spectrometry (ID-MS). Certified values have been provided for 11 PCB congeners (PCB3, 8, 28, 52, 101, 118, 138, 153, 180, 194, and 206) in the CRMs. These CRMs have information values for PCB homologue concentrations determined by using a Japanese official method for determination of PCBs in wastes and densities determined with an oscillational density meter. Because oil samples having arbitrary PCB concentrations between respective property values of the PCB-fortified and nonfortified CRMs can be prepared by gravimetric mixing of the CRM pairs, these CRMs can be used for validation of PCB analyses using various instruments which have different sensitivities. Figure Preparation and certification processes of the mineral oil CRMs (example shown is polychlorinated biphenyls in insulation oil, high/low concentrations) Electronic supplementary material The online version of this article (doi:10.1007/s00216-008-2010-3) contains supplementary material, which is available to authorized users. PMID:18415091

Sensitivity simulations of superparameterised convection in a general circulation model

NASA Astrophysics Data System (ADS)

Rybka, Harald; Tost, Holger

2015-04-01

Cloud Resolving Models (CRMs) covering a horizontal grid spacing from a few hundred meters up to a few kilometers have been used to explicitly resolve small-scale and mesoscale processes. Special attention has been paid to realistically represent cloud dynamics and cloud microphysics involving cloud droplets, ice crystals, graupel and aerosols. The entire variety of physical processes on the small-scale interacts with the larger-scale circulation and has to be parameterised on the coarse grid of a general circulation model (GCM). Since more than a decade an approach to connect these two types of models which act on different scales has been developed to resolve cloud processes and their interactions with the large-scale flow. The concept is to use an ensemble of CRM grid cells in a 2D or 3D configuration in each grid cell of the GCM to explicitly represent small-scale processes avoiding the use of convection and large-scale cloud parameterisations which are a major source for uncertainties regarding clouds. The idea is commonly known as superparameterisation or cloud-resolving convection parameterisation. This study presents different simulations of an adapted Earth System Model (ESM) connected to a CRM which acts as a superparameterisation. Simulations have been performed with the ECHAM/MESSy atmospheric chemistry (EMAC) model comparing conventional GCM runs (including convection and large-scale cloud parameterisations) with the improved superparameterised EMAC (SP-EMAC) modeling one year with prescribed sea surface temperatures and sea ice content. The sensitivity of atmospheric temperature, precipiation patterns, cloud amount and types is observed changing the embedded CRM represenation (orientation, width, no. of CRM cells, 2D vs. 3D). Additionally, we also evaluate the radiation balance with the new model configuration, and systematically analyse the impact of tunable parameters on the radiation budget and hydrological cycle. Furthermore, the subgrid variability (individual CRM cell output) is analysed in order to illustrate the importance of a highly varying atmospheric structure inside a single GCM grid box. Finally, the convective transport of Radon is observed comparing different transport procedures and their influence on the vertical tracer distribution.

Sustainable in situ remediation of recalcitrant organic pollutants in groundwater with controlled release materials: A review.

PubMed

O'Connor, David; Hou, Deyi; Ok, Yong Sik; Song, Yinan; Sarmah, Ajit K; Li, Xuanru; Tack, Filip M G

2018-06-06

The removal of recalcitrant organic pollutants in groundwater is a challenge being faced around the world. Achieving effective long-term remediation of contaminated aquifers faces a variety of significant issues such as back diffusion, tailing, and rebound. In recent years, some researchers have proposed the use of controlled release materials (CRMs) as a new approach to counteracting such issues. The novelty of CRMs lies in that they release their active products slowly, over prolonged periods of time, in order to sustain in situ treatments and long-term effectiveness. Here we review the main constituents of CRMs, analyze their production, characterization, and applications, with a focus on reaction mechanisms, effectiveness, and secondary effects. This review shows that the reactive components of CRMs most commonly involve either: (i) chemical oxidants to treat contaminants such as TCE, PCE, BTEX, and 1,4-Dioxane; (ii) sources of dissolved oxygen to stimulate aerobic biodegradation of contaminants such as BTEX and 1,4-Dioxane; or, (iii) substrates that stimulate reductive dechlorination of contaminants such as TCE and 1,2-DCA. It was found that in some studies, CRMs provided sustained delivery of CRM treatment reagents over several years, and achieved complete contaminant removal. However, lower removal rates were apparent in other cases, which may be ascribed to insufficient dispersion in the subsurface. There are a relatively limited number of field-scale applications of CRMs in contaminated land remediation. Those conducted to date suggest that CRMs could prove to be an effective future remediation strategy. Lessons learned from field applications, suggestions for future research directions, and conclusions are put forward in this review. Copyright © 2018 Elsevier B.V. All rights reserved.

CF and School

MedlinePlus

... Testing for Cystic Fibrosis CFTR-Related Metabolic Syndrome (CRMS) How Babies Are Screened in IRT-Only vs. ... Guidelines Infant Care Clinical Care Guidelines Management of CRMS in First 2 Years and Beyond Clinical Care ...

About Cystic Fibrosis

MedlinePlus

... Testing for Cystic Fibrosis CFTR-Related Metabolic Syndrome (CRMS) How Babies Are Screened in IRT-Only vs. ... Guidelines Infant Care Clinical Care Guidelines Management of CRMS in First 2 Years and Beyond Clinical Care ...

Allergic Bronchopulmonary Aspergillosis

MedlinePlus

... Testing for Cystic Fibrosis CFTR-Related Metabolic Syndrome (CRMS) How Babies Are Screened in IRT-Only vs. ... Guidelines Infant Care Clinical Care Guidelines Management of CRMS in First 2 Years and Beyond Clinical Care ...

Therapies for Cystic Fibrosis

MedlinePlus

... Testing for Cystic Fibrosis CFTR-Related Metabolic Syndrome (CRMS) How Babies Are Screened in IRT-Only vs. ... Guidelines Infant Care Clinical Care Guidelines Management of CRMS in First 2 Years and Beyond Clinical Care ...

Germs and Staying Healthy

MedlinePlus

... Testing for Cystic Fibrosis CFTR-Related Metabolic Syndrome (CRMS) How Babies Are Screened in IRT-Only vs. ... Guidelines Infant Care Clinical Care Guidelines Management of CRMS in First 2 Years and Beyond Clinical Care ...

Newborn Screening for CF

MedlinePlus

... Testing for Cystic Fibrosis CFTR-Related Metabolic Syndrome (CRMS) How Babies Are Screened in IRT-Only vs. ... Guidelines Infant Care Clinical Care Guidelines Management of CRMS in First 2 Years and Beyond Clinical Care ...

Methicillin-Resistant Staphylococcus aureus (MRSA)

MedlinePlus

... Testing for Cystic Fibrosis CFTR-Related Metabolic Syndrome (CRMS) How Babies Are Screened in IRT-Only vs. ... Guidelines Infant Care Clinical Care Guidelines Management of CRMS in First 2 Years and Beyond Clinical Care ...

Three-dimensional constrained variational analysis: Approach and application to analysis of atmospheric diabatic heating and derivative fields during an ARM SGP intensive observational period

NASA Astrophysics Data System (ADS)

Tang, Shuaiqi; Zhang, Minghua

2015-08-01

Atmospheric vertical velocities and advective tendencies are essential large-scale forcing data to drive single-column models (SCMs), cloud-resolving models (CRMs), and large-eddy simulations (LESs). However, they cannot be directly measured from field measurements or easily calculated with great accuracy. In the Atmospheric Radiation Measurement Program (ARM), a constrained variational algorithm (1-D constrained variational analysis (1DCVA)) has been used to derive large-scale forcing data over a sounding network domain with the aid of flux measurements at the surface and top of the atmosphere (TOA). The 1DCVA algorithm is now extended into three dimensions (3DCVA) along with other improvements to calculate gridded large-scale forcing data, diabatic heating sources (Q1), and moisture sinks (Q2). Results are presented for a midlatitude cyclone case study on 3 March 2000 at the ARM Southern Great Plains site. These results are used to evaluate the diabatic heating fields in the available products such as Rapid Update Cycle, ERA-Interim, National Centers for Environmental Prediction Climate Forecast System Reanalysis, Modern-Era Retrospective Analysis for Research and Applications, Japanese 55-year Reanalysis, and North American Regional Reanalysis. We show that although the analysis/reanalysis generally captures the atmospheric state of the cyclone, their biases in the derivative terms (Q1 and Q2) at regional scale of a few hundred kilometers are large and all analyses/reanalyses tend to underestimate the subgrid-scale upward transport of moist static energy in the lower troposphere. The 3DCVA-gridded large-scale forcing data are physically consistent with the spatial distribution of surface and TOA measurements of radiation, precipitation, latent and sensible heat fluxes, and clouds that are better suited to force SCMs, CRMs, and LESs. Possible applications of the 3DCVA are discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varble, Adam; Zipser, Edward J.; Fridlind, Ann

Ten 3D cloud-resolving model (CRM) simulations and four 3D limited area model (LAM) simulations of an intense mesoscale convective system observed on January 23-24, 2006 during the Tropical Warm Pool – International Cloud Experiment (TWP-ICE) are compared with each other and with observations and retrievals from a scanning polarimetric radar, co-located UHF and VHF vertical profilers, and a Joss-Waldvogel disdrometer in an attempt to explain published results showing a low bias in simulated stratiform rainfall. Despite different forcing methodologies, similar precipitation microphysics errors appear in CRMs and LAMs with differences that depend on the details of the bulk microphysics schememore » used. One-moment schemes produce too many small raindrops, which biases Doppler velocities low, but produces rain water contents (RWCs) that are similar to observed. Two-moment rain schemes with a gamma shape parameter (μ) of 0 produce excessive size sorting, which leads to larger Doppler velocities than those produced in one-moment schemes, but lower RWCs than observed. Two moment schemes also produce a convective median volume diameter distribution that is too broad relative to observations and thus, may have issues balancing raindrop formation, collision coalescence, and raindrop breakup. Assuming a μ of 2.5 rather than 0 for the raindrop size distribution improves one-moment scheme biases, and allowing μ to have values greater than 0 may improve two-moment schemes. Under-predicted stratiform rain rates are associated with under-predicted ice water contents at the melting level rather than excessive rain evaporation, in turn likely associated with convective detrainment that is too high in the troposphere and mesoscale circulations that are too weak. In addition to stronger convective updrafts than observed, limited domain size prevents a large, well-developed stratiform region from developing in CRMs, while a dry bias in ECMWF analyses does the same to the LAMs.« less

Contrasting self-aggregation over land and ocean surfaces

NASA Astrophysics Data System (ADS)

Inda Diaz, H. A.; O'Brien, T. A.

2017-12-01

The spontaneous organization of convection into clusters, or self-aggregation, demonstrably changes the nature and statistics of precipitation. While there has been much recent progress in this area, the processes that control self-aggregation are still poorly understood. Most of the work to date has focused on self-aggregation over ocean-like surfaces, but it is particularly pressing to understand what controls convective aggregation over land, since the associated change in precipitation statistics—between non-aggregated and aggregated convection—could have huge impacts on society and infrastructure. Radiative-convective equilibrium (RCE), has been extensively used as an idealized framework to study the tropical atmosphere. Self-aggregation manifests in numerous numerical models of RCE, nevertheless, there is still a lack of understanding in how it relates to convective organization in the observed world. Numerous studies have examined self-aggregation using idealized Cloud Resolving Models (CRMs) and General Circulation Models over the ocean, however very little work has been done on RCE and self-aggregation over land. Idealized models of RCE over ocean have shown that aggregation is sensitive to sea surface temperature (SST), more intense precipitation occurs in aggregated systems, and a variety of feedbacks—such as surface flux, cloud radiative, and upgradient moisture transport— contribute to the maintenance of aggregation, however it is not clear if these results apply over land. Progress in this area could help relate understanding of self-aggregation in idealized simulations to observations. In order to explore the behavior of self-aggregation over land, we use a CRM to simulate idealized RCE over land. In particular, we examine the aggregation of convection and how it compares with aggregation over ocean. Based on previous studies, where a variety of different CRMs exhibit a SST threshold below which self-aggregation does not occur, we hypothesize that idealized land simulations will exhibit similar threshold behavior when there is an adequate surface moisture supply. We systematically explore this by varying parameters that exert strong control on the surface enthalpy and moisture budget, such as type of land, surface albedo, and greenhouse gas concentration.

CRYSTAL-FACE Analysis and Simulations of the July 23rd Extended Anvil Case

NASA Technical Reports Server (NTRS)

Starr, David

2003-01-01

A key focus of CRYSTAL-FACE (Cirrus Regional Study of Tropical Anvils and cirrus Layers - Florida Area Cirrus Experiment) was the generation and subsequent evolution of cirrus outflow from deep convective cloud systems. Present theoretical background and motivations will be discussed. An integrated look at the observations of an extended cirrus anvil cloud system observed on 23 July 2002 will be presented, including lidar and millimeter radar observation; from NASA s ER-2 and in-situ observations from NASA s WB-57 and University of North Dakota Citation. The observations will be compared to results of simulations using 1-D and 2-D high-resolution (100 meter) cloud resolving models. The CRMs explicitly account for cirrus microphysical development by resolving the evolving ice crystal size distribution (bin model) in time and space. Both homogeneous and heterogeneous nucleation are allowed in the model. The CRM simulations are driven using the output of regional simulations using MM5 that produces deep convection similar to what was observed. The MM5 model employs a 2 km inner grid (32 layers) over a 360 km domain, nested within a 6-km grid over a 600-km domain. Initial and boundary conditions for the 36-hour MM5 simulation are taken from NCEP Eta model analysis at 32 km resolution. Key issues to be explored are the settling of the observed anvil versus the model simulations, and comparisons of dynamical properties, such as vertical motions, occurring in the observations and models. The former provides an integrated measure of the validity of the model microphysics (fallspeed) while the latter is the key factor in forcing continued ice generation.

Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome.

PubMed

Dresch, Jacqueline M; Zellers, Rowan G; Bork, Daniel K; Drewell, Robert A

2016-01-01

A long-standing objective in modern biology is to characterize the molecular components that drive the development of an organism. At the heart of eukaryotic development lies gene regulation. On the molecular level, much of the research in this field has focused on the binding of transcription factors (TFs) to regulatory regions in the genome known as cis-regulatory modules (CRMs). However, relatively little is known about the sequence-specific binding preferences of many TFs, especially with respect to the possible interdependencies between the nucleotides that make up binding sites. A particular limitation of many existing algorithms that aim to predict binding site sequences is that they do not allow for dependencies between nonadjacent nucleotides. In this study, we use a recently developed computational algorithm, MARZ, to compare binding site sequences using 32 distinct models in a systematic and unbiased approach to explore nucleotide dependencies within binding sites for 15 distinct TFs known to be critical to Drosophila development. Our results indicate that many of these proteins have varying levels of nucleotide interdependencies within their DNA recognition sequences, and that, in some cases, models that account for these dependencies greatly outperform traditional models that are used to predict binding sites. We also directly compare the ability of different models to identify the known KRUPPEL TF binding sites in CRMs and demonstrate that a more complex model that accounts for nucleotide interdependencies performs better when compared with simple models. This ability to identify TFs with critical nucleotide interdependencies in their binding sites will lead to a deeper understanding of how these molecular characteristics contribute to the architecture of CRMs and the precise regulation of transcription during organismal development.

Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome

PubMed Central

Dresch, Jacqueline M.; Zellers, Rowan G.; Bork, Daniel K.; Drewell, Robert A.

2016-01-01

A long-standing objective in modern biology is to characterize the molecular components that drive the development of an organism. At the heart of eukaryotic development lies gene regulation. On the molecular level, much of the research in this field has focused on the binding of transcription factors (TFs) to regulatory regions in the genome known as cis-regulatory modules (CRMs). However, relatively little is known about the sequence-specific binding preferences of many TFs, especially with respect to the possible interdependencies between the nucleotides that make up binding sites. A particular limitation of many existing algorithms that aim to predict binding site sequences is that they do not allow for dependencies between nonadjacent nucleotides. In this study, we use a recently developed computational algorithm, MARZ, to compare binding site sequences using 32 distinct models in a systematic and unbiased approach to explore nucleotide dependencies within binding sites for 15 distinct TFs known to be critical to Drosophila development. Our results indicate that many of these proteins have varying levels of nucleotide interdependencies within their DNA recognition sequences, and that, in some cases, models that account for these dependencies greatly outperform traditional models that are used to predict binding sites. We also directly compare the ability of different models to identify the known KRUPPEL TF binding sites in CRMs and demonstrate that a more complex model that accounts for nucleotide interdependencies performs better when compared with simple models. This ability to identify TFs with critical nucleotide interdependencies in their binding sites will lead to a deeper understanding of how these molecular characteristics contribute to the architecture of CRMs and the precise regulation of transcription during organismal development. PMID:27330274

A Model for Estimating the Reliability and Validity of Criterion-Referenced Measures.

ERIC Educational Resources Information Center

Edmonston, Leon P.; Randall, Robert S.

A decision model designed to determine the reliability and validity of criterion referenced measures (CRMs) is presented. General procedures which pertain to the model are discussed as to: Measures of relationship, Reliability, Validity (content, criterion-oriented, and construct validation), and Item Analysis. The decision model is presented in…

A certified urea reference material (NMIJ CRM 6006-a) as a reliable calibrant for the elemental analyses of amino acids and food samples.

PubMed

Itoh, Nobuyasu; Yamazaki, Taichi; Sato, Ayako; Numata, Masahiko; Takatsu, Akiko

2014-01-01

We examined the reliability of a certified reference material (CRM) for urea (NMIJ CRM 6006-a) as a calibrant for N, C, and H in elemental analyzers. Only the N content for this CRM is provided as an indicative value. To estimate the C and H contents of the urea CRM, we took into account the purity of the urea and the presence of other identified impurities. When we examined the use of various masses of the calibrant (0.2 to 2 mg), we unexpectedly observed low signal intensities for small masses of H and N, but these plateaued at about 2 mg. We therefore analyzed four amino acid CRMs and four food CRMs on a 2-mg scale with the urea CRM as the calibrant. For the amino acid CRMs, the differences in the analytical and theoretical contents (≤0.0026 kg/kg) were acceptable with good repeatability (≤0.0013 kg/kg in standard deviation; n = 4). For food CRMs, comparable repeatabilities to those obtained with amino acid CRMs (≤0.0025 kg/kg in standard deviation; n = 4) were obtained. The urea CRM can therefore be used as a reliable calibrant for C, H, and N in an elemental analyzer.

Dynamics and functions of CD4⁺CD25 (high) regulatory T lymphocytes in Chinese rhesus macaques during the early stage of infection with SIVmac239.

PubMed

Li, Shao-You; Xia, Hou-Jun; Dai, Zheng-Xi; Zhang, Gao-Hong; Fan, Bo; Li, Ming-Hua; Wang, Rui-Rui; Zheng, Yong-Tang

2012-05-01

CD4(+)CD25(high) regulatory T cells (Treg), which are a specialized subset of T cells, play an important role in the prevention of autoimmune diseases, maintenance of immune system homeostasis and tolerance to self-antigens. Chinese rhesus macaques (CRMs) are widely used in preclinical research on potential therapeutic drugs, vaccines and mechanisms of human diseases. However, the basic immunological characterization of Treg cells of CRMs has not been well established. To characterize Treg cells, peripheral blood of 43 adult CRMs was analyzed for CD4+ T lymphocytes by flow cytometry. It was found that Treg cells ranged from 1.52% to 11.1% of CD4+ T cells, and the average value was 5.7%. With our SIV-infected CRM model, through further studies, it was found that Treg cells in peripheral blood increased both in relative and absolute quantities. Moreover, Treg cells maintained their functions by suppressing Th1 cytokine secretion of their target cells. The results show that Treg cells might render cellular immunity against SIV viruses dysfunctional during the early stage after infection.

Robust EM Continual Reassessment Method in Oncology Dose Finding

PubMed Central

Yuan, Ying; Yin, Guosheng

2012-01-01

The continual reassessment method (CRM) is a commonly used dose-finding design for phase I clinical trials. Practical applications of this method have been restricted by two limitations: (1) the requirement that the toxicity outcome needs to be observed shortly after the initiation of the treatment; and (2) the potential sensitivity to the prespecified toxicity probability at each dose. To overcome these limitations, we naturally treat the unobserved toxicity outcomes as missing data, and use the expectation-maximization (EM) algorithm to estimate the dose toxicity probabilities based on the incomplete data to direct dose assignment. To enhance the robustness of the design, we propose prespecifying multiple sets of toxicity probabilities, each set corresponding to an individual CRM model. We carry out these multiple CRMs in parallel, across which model selection and model averaging procedures are used to make more robust inference. We evaluate the operating characteristics of the proposed robust EM-CRM designs through simulation studies and show that the proposed methods satisfactorily resolve both limitations of the CRM. Besides improving the MTD selection percentage, the new designs dramatically shorten the duration of the trial, and are robust to the prespecification of the toxicity probabilities. PMID:22375092

An ensemble constrained variational analysis of atmospheric forcing data and its application to evaluate clouds in CAM5: Ensemble 3DCVA and Its Application

DOE PAGES

Tang, Shuaiqi; Zhang, Minghua; Xie, Shaocheng

2016-01-05

Large-scale atmospheric forcing data can greatly impact the simulations of atmospheric process models including Large Eddy Simulations (LES), Cloud Resolving Models (CRMs) and Single-Column Models (SCMs), and impact the development of physical parameterizations in global climate models. This study describes the development of an ensemble variationally constrained objective analysis of atmospheric large-scale forcing data and its application to evaluate the cloud biases in the Community Atmospheric Model (CAM5). Sensitivities of the variational objective analysis to background data, error covariance matrix and constraint variables are described and used to quantify the uncertainties in the large-scale forcing data. Application of the ensemblemore » forcing in the CAM5 SCM during March 2000 intensive operational period (IOP) at the Southern Great Plains (SGP) of the Atmospheric Radiation Measurement (ARM) program shows systematic biases in the model simulations that cannot be explained by the uncertainty of large-scale forcing data, which points to the deficiencies of physical parameterizations. The SCM is shown to overestimate high clouds and underestimate low clouds. These biases are found to also exist in the global simulation of CAM5 when it is compared with satellite data.« less

An ensemble constrained variational analysis of atmospheric forcing data and its application to evaluate clouds in CAM5: Ensemble 3DCVA and Its Application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Shuaiqi; Zhang, Minghua; Xie, Shaocheng

Large-scale atmospheric forcing data can greatly impact the simulations of atmospheric process models including Large Eddy Simulations (LES), Cloud Resolving Models (CRMs) and Single-Column Models (SCMs), and impact the development of physical parameterizations in global climate models. This study describes the development of an ensemble variationally constrained objective analysis of atmospheric large-scale forcing data and its application to evaluate the cloud biases in the Community Atmospheric Model (CAM5). Sensitivities of the variational objective analysis to background data, error covariance matrix and constraint variables are described and used to quantify the uncertainties in the large-scale forcing data. Application of the ensemblemore » forcing in the CAM5 SCM during March 2000 intensive operational period (IOP) at the Southern Great Plains (SGP) of the Atmospheric Radiation Measurement (ARM) program shows systematic biases in the model simulations that cannot be explained by the uncertainty of large-scale forcing data, which points to the deficiencies of physical parameterizations. The SCM is shown to overestimate high clouds and underestimate low clouds. These biases are found to also exist in the global simulation of CAM5 when it is compared with satellite data.« less

High-Tech Roof Management.

ERIC Educational Resources Information Center

Benzie, Tim

1997-01-01

Describes the use of a computerized roof management system (CRMS) for school districts to foster multiple roof maintenance efficiency and cost effectiveness. Highlights CRMS software manufacturer choices, as well as the types of nondestructive testing equipment tools that can be used to evaluate roof conditions. (GR)

Disentangling the many layers of eukaryotic transcriptional regulation.

PubMed

Lelli, Katherine M; Slattery, Matthew; Mann, Richard S

2012-01-01

Regulation of gene expression in eukaryotes is an extremely complex process. In this review, we break down several critical steps, emphasizing new data and techniques that have expanded current gene regulatory models. We begin at the level of DNA sequence where cis-regulatory modules (CRMs) provide important regulatory information in the form of transcription factor (TF) binding sites. In this respect, CRMs function as instructional platforms for the assembly of gene regulatory complexes. We discuss multiple mechanisms controlling complex assembly, including cooperative DNA binding, combinatorial codes, and CRM architecture. The second section of this review places CRM assembly in the context of nucleosomes and condensed chromatin. We discuss how DNA accessibility and histone modifications contribute to TF function. Lastly, new advances in chromosomal mapping techniques have provided increased understanding of intra- and interchromosomal interactions. We discuss how these topological maps influence gene regulatory models.

CRMS vegetation analytical team framework: Methods for collection, development, and use of vegetation response variables

USGS Publications Warehouse

Cretini, Kari F.; Visser, Jenneke M.; Krauss, Ken W.; Steyer, Gregory D.

2011-01-01

This document identifies the main objectives of the Coastwide Reference Monitoring System (CRMS) vegetation analytical team, which are to provide (1) collection and development methods for vegetation response variables and (2) the ways in which these response variables will be used to evaluate restoration project effectiveness. The vegetation parameters (that is, response variables) collected in CRMS and other coastal restoration projects funded under the Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) are identified, and the field collection methods for these parameters are summarized. Existing knowledge on community and plant responses to changes in environmental drivers (for example, flooding and salinity) from published literature and from the CRMS and CWPPRA monitoring dataset are used to develop a suite of indices to assess wetland condition in coastal Louisiana. Two indices, the floristic quality index (FQI) and a productivity index, are described for herbaceous and forested vegetation. The FQI for herbaceous vegetation is tested with a long-term dataset from a CWPPRA marsh creation project. Example graphics for this index are provided and discussed. The other indices, an FQI for forest vegetation (that is, trees and shrubs) and productivity indices for herbaceous and forest vegetation, are proposed but not tested. New response variables may be added or current response variables removed as data become available and as our understanding of restoration success indicators develops. Once indices are fully developed, each will be used by the vegetation analytical team to assess and evaluate CRMS/CWPPRA project and program effectiveness. The vegetation analytical teams plan to summarize their results in the form of written reports and/or graphics and present these items to CRMS Federal and State sponsors, restoration project managers, landowners, and other data users for their input.

Coastwide Reference Monitoring System (CRMS)

USGS Publications Warehouse

2010-01-01

In 1990, the U.S. Congress enacted the Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) in response to growing awareness of a land loss crisis in Louisiana. Projects funded by CWPPRA require monitoring and evaluation of project effectiveness, and there is also a need to assess the cumulative effects of all projects to achieve a sustainable coastal environment. In 2003, the Louisiana Office of Coastal Protection and Restoration (OCPR) and the U.S. Geological Survey (USGS) received approval from the CWPPRA Task Force to implement the Coastwide Reference Monitoring System (CRMS) as a mechanism to monitor and evaluate the effectiveness of CWPPRA projects at the project, region, and coastwide levels. The CRMS design implements a multiple reference approach by using aspects of hydrogeomorphic functional assessments and probabilistic sampling. The CRMS program is as dynamic as the coastal habitats it monitors. The program is currently funded through CWPPRA and provides data for a variety of user groups, including resource managers, academics, landowners, and researchers.

Using inductively coupled plasma-mass spectrometry for calibration transfer between environmental CRMs.

PubMed

Turk, G C; Yu, L L; Salit, M L; Guthrie, W F

2001-06-01

Multielement analyses of environmental reference materials have been performed using existing certified reference materials (CRMs) as calibration standards for inductively coupled plasma-mass spectrometry. The analyses have been performed using a high-performance methodology that results in comparison measurement uncertainties that are significantly less than the uncertainties of the certified values of the calibration CRM. Consequently, the determined values have uncertainties that are very nearly equivalent to the uncertainties of the calibration CRM. Several uses of this calibration transfer are proposed, including, re-certification measurements of replacement CRMs, establishing traceability of one CRM to another, and demonstrating the equivalence of two CRMs. RM 8704, a river sediment, was analyzed using SRM 2704, Buffalo River Sediment, as the calibration standard. SRM 1632c, Trace Elements in Bituminous Coal, which is a replacement for SRM 1632b, was analyzed using SRM 1632b as the standard. SRM 1635, Trace Elements in Subbituminous Coal, was also analyzed using SRM 1632b as the standard.

Land-Atmosphere Coupling in the Multi-Scale Modelling Framework

NASA Astrophysics Data System (ADS)

Kraus, P. M.; Denning, S.

2015-12-01

The Multi-Scale Modeling Framework (MMF), in which cloud-resolving models (CRMs) are embedded within general circulation model (GCM) gridcells to serve as the model's cloud parameterization, has offered a number of benefits to GCM simulations. The coupling of these cloud-resolving models directly to land surface model instances, rather than passing averaged atmospheric variables to a single instance of a land surface model, the logical next step in model development, has recently been accomplished. This new configuration offers conspicuous improvements to estimates of precipitation and canopy through-fall, but overall the model exhibits warm surface temperature biases and low productivity.This work presents modifications to a land-surface model that take advantage of the new multi-scale modeling framework, and accommodate the change in spatial scale from a typical GCM range of ~200 km to the CRM grid-scale of 4 km.A parameterization is introduced to apportion modeled surface radiation into direct-beam and diffuse components. The diffuse component is then distributed among the land-surface model instances within each GCM cell domain. This substantially reduces the number excessively low light values provided to the land-surface model when cloudy conditions are modeled in the CRM, associated with its 1-D radiation scheme. The small spatial scale of the CRM, ~4 km, as compared with the typical ~200 km GCM scale, provides much more realistic estimates of precipitation intensity, this permits the elimination of a model parameterization of canopy through-fall. However, runoff at such scales can no longer be considered as an immediate flow to the ocean. Allowing sub-surface water flow between land-surface instances within the GCM domain affords better realism and also reduces temperature and productivity biases.The MMF affords a number of opportunities to land-surface modelers, providing both the advantages of direct simulation at the 4 km scale and a much reduced conceptual gap between model resolution and parameterized processes.

Sediment certified reference materials for the determination of polychlorinated biphenyls and organochlorine pesticides from the National Metrology Institute of Japan (NMIJ).

PubMed

Numata, Masahiko; Yarita, Takashi; Aoyagi, Yoshie; Tsuda, Yoko; Yamazaki, Misako; Takatsu, Akiko; Ishikawa, Keiichiro; Chiba, Koichi; Okamaoto, Kensaku

2007-04-01

Two marine sediment certified reference materials, NMIJ CRM 7304-a and 7305-a, have been issued by the National Metrology Institute of Japan in the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST) for the determination of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs). The raw materials of the CRMs were collected from a bay near industrial activity in Japan. Characterization of these CRMs was conducted by NMIJ, where the sediments were analyzed using multiple analytical methods such as pressurized liquid extraction (PLE), microwave-assisted extraction (MAE), saponification, Soxhlet extraction, supercritical fluid extraction (SFE), and ultrasonic extraction; the target compounds were determined by one of the primary methods of measurements, isotope dilution-mass spectrometry (ID-MS). Certified values have been provided for 14 PCB congeners (PCB numbers 3, 15, 28, 31, 70, 101, 105, 138, 153, 170, 180, 194, 206, 209) and 4 OCPs (gamma-HCH, 4,4'-DDT, 4,4'-DDE, 4,4'-DDD) in both CRMs. NMIJ CRM 7304-a has concentrations of the contaminants that are a factor of 2-15 greater than in CRM 7305-a. Both CRMs have information values for PCB homolog concentrations determined by collaborative analysis using a Japanese official method for determination of PCBs. The total PCB concentrations in the CRMs are approximately 920 and 86 microg kg(-1) dry mass respectively.

NBS/EPA (NATIONAL BUREAU OF STANDARDS/ENVIRONMENTAL PROTECTION AGENCY) CERTIFIED REFERENCE MATERIAL PERFORMANCE AUDIT PROGRAM: STATUS REPORT 1

EPA Science Inventory

A traceability procedure has been established which allows specialty gas producers to prepare gaseous pollutant Certified Reference Materials (CRMs). The accuracy, stability and homogeneity of the CRMs approach those of NBS Standard Reference Materials (SRMs). Part of this proced...

Sensitivity of summer ensembles of fledgling superparameterized U.S. mesoscale convective systems to cloud resolving model microphysics and grid configuration

DOE PAGES

Elliott, Elizabeth J.; Yu, Sungduk; Kooperman, Gabriel J.; ...

2016-05-01

The sensitivities of simulated mesoscale convective systems (MCSs) in the central U.S. to microphysics and grid configuration are evaluated here in a global climate model (GCM) that also permits global-scale feedbacks and variability. Since conventional GCMs do not simulate MCSs, studying their sensitivities in a global framework useful for climate change simulations has not previously been possible. To date, MCS sensitivity experiments have relied on controlled cloud resolving model (CRM) studies with limited domains, which avoid internal variability and neglect feedbacks between local convection and larger-scale dynamics. However, recent work with superparameterized (SP) GCMs has shown that eastward propagating MCS-likemore » events are captured when embedded CRMs replace convective parameterizations. This study uses a SP version of the Community Atmosphere Model version 5 (SP-CAM5) to evaluate MCS sensitivities, applying an objective empirical orthogonal function algorithm to identify MCS-like events, and harmonizing composite storms to account for seasonal and spatial heterogeneity. A five-summer control simulation is used to assess the magnitude of internal and interannual variability relative to 10 sensitivity experiments with varied CRM parameters, including ice fall speed, one-moment and two-moment microphysics, and grid spacing. MCS sensitivities were found to be subtle with respect to internal variability, and indicate that ensembles of over 100 storms may be necessary to detect robust differences in SP-GCMs. Furthermore, these results emphasize that the properties of MCSs can vary widely across individual events, and improving their representation in global simulations with significant internal variability may require comparison to long (multidecadal) time series of observed events rather than single season field campaigns.« less

Offline GCSS Intercomparison of Cloud-Radiation Interaction and Surface Fluxes

NASA Technical Reports Server (NTRS)

Tao, W.-K.; Johnson, D.; Krueger, S.; Zulauf, M.; Donner, L.; Seman, C.; Petch, J.; Gregory, J.

2004-01-01

Simulations of deep tropical clouds by both cloud-resolving models (CRMs) and single-column models (SCMs) in the GEWEX Cloud System Study (GCSS) Working Group 4 (WG4; Precipitating Convective Cloud Systems), Case 2 (19-27 December 1992, TOGA-COARE IFA) have produced large differences in the mean heating and moistening rates (-1 to -5 K and -2 to 2 grams per kilogram respectively). Since the large-scale advective temperature and moisture "forcing" are prescribed for this case, a closer examination of two of the remaining external types of "forcing", namely radiative heating and air/sea hear and moisture transfer, are warranted. This paper examines the current radiation and surface flux of parameterizations used in the cloud models participating in the GCSS WG4, be executing the models "offline" for one time step (12 s) for a prescribed atmospheric state, then examining the surface and radiation fluxes from each model. The dynamic, thermodynamic, and microphysical fluids are provided by the GCE-derived model output for Case 2 during a period of very active deep convection (westerly wind burst). The surface and radiation fluxes produced from the models are then divided into prescribed convective, stratiform, and clear regions in order to examine the role that clouds play in the flux parameterizations. The results suggest that the differences between the models are attributed more to the surface flux parameterizations than the radiation schemes.

The effects of film thickness on the electrical, optical, and structural properties of cylindrical, rotating, magnetron-sputtered ITO films

NASA Astrophysics Data System (ADS)

Kim, Jae-Ho; Seong, Tae-Yeon; Ahn, Kyung-Jun; Chung, Kwun-Bum; Seok, Hae-Jun; Seo, Hyeong-Jin; Kim, Han-Ki

2018-05-01

We report the characteristics of Sn-doped In2O3 (ITO) films intended for use as transparent conducting electrodes; the films were prepared via a five-generation, in-line type, cylindrical, rotating magnetron sputtering (CRMS) system as a function of film thickness. By using a rotating cylindrical ITO target with high usage (∼80%), we prepared high conductivity, transparent ITO films on five-generation size glass. The effects of film thickness on the electrical, optical, morphological, and structural properties of CRMS-grown ITO films are investigated in detail to correlate the thickness and performance of ITO films. The preferred orientation changed from the (2 2 2) to the (4 0 0) plane with increasing thickness of ITO is attributed to the stability of the (4 0 0) plane against resputtering during the CRMS process. Based on X-ray diffraction, surface field emission scanning electron microscopy, and cross-sectional transmission electron microscopy, we suggest a possible mechanism to explain the preferred orientation and effects of film thickness on the performance of CRMS-grown ITO films.

Ensemble superparameterization versus stochastic parameterization: A comparison of model uncertainty representation in tropical weather prediction

NASA Astrophysics Data System (ADS)

Subramanian, Aneesh C.; Palmer, Tim N.

2017-06-01

Stochastic schemes to represent model uncertainty in the European Centre for Medium-Range Weather Forecasts (ECMWF) ensemble prediction system has helped improve its probabilistic forecast skill over the past decade by both improving its reliability and reducing the ensemble mean error. The largest uncertainties in the model arise from the model physics parameterizations. In the tropics, the parameterization of moist convection presents a major challenge for the accurate prediction of weather and climate. Superparameterization is a promising alternative strategy for including the effects of moist convection through explicit turbulent fluxes calculated from a cloud-resolving model (CRM) embedded within a global climate model (GCM). In this paper, we compare the impact of initial random perturbations in embedded CRMs, within the ECMWF ensemble prediction system, with stochastically perturbed physical tendency (SPPT) scheme as a way to represent model uncertainty in medium-range tropical weather forecasts. We especially focus on forecasts of tropical convection and dynamics during MJO events in October-November 2011. These are well-studied events for MJO dynamics as they were also heavily observed during the DYNAMO field campaign. We show that a multiscale ensemble modeling approach helps improve forecasts of certain aspects of tropical convection during the MJO events, while it also tends to deteriorate certain large-scale dynamic fields with respect to stochastically perturbed physical tendencies approach that is used operationally at ECMWF.