Radiation transport in the atmosphere - sea ice - ocean system

Thesis (Ph.D.) University of Alaska Fairbanks, 1995A comprehensive radiative transfer model for the coupled atmosphere-sea ice-ocean system has been developed. The theoretical work required for constructing such a coupled model is described first. This work extends the discrete ordinate method, which has been proven to be effective in studies of radiative transfer in the atmosphere, to solve the radiative transfer problem pertaining to a system consisting of two strata with different indices of refraction, such as the atmosphere-ocean system and the atmosphere-sea ice-ocean system. The relevant changes (as compared to the standard problem with constant index of refraction throughout the medium) in formulation and solution of the radiative transfer equation, including the proper application of interface and boundary conditions, are presented. This solution is then applied to the atmosphere-sea ice-ocean system to study the solar energy balance in this coupled system. The input parameters required by the model are observable physical properties (e.g., the profiles of temperature and gas concentrations in the atmosphere, and the profiles of temperature, density, and salinity in the ice). The atmosphere, sea ice and ocean are each divided into a sufficient number of layers in the vertical to adequately resolve changes in their optical properties. This model rigorously accounts for the multiple scattering and absorption by atmospheric molecules, clouds, snow and sea water, as well as inclusions in the sea ice, such as brine pockets and air bubbles. The effects of various factors on the solar energy distribution in the entire system have been studied quantitatively. These factors include the ice salinity and density variations, cloud microphysics as well as variations in melt ponds and snow cover on the ice surface. Finally, the coupled radiative transfer model is used to study the impacts of clouds, snow and ice algae on the light transport in sea ice and in the ocean, as well as to simulate spectral irradiance and extinction measurements in sea ice

An Analytical Solution of Radiative Transfer in the Coupled Atmosphere-Ocean System with Rough Surface

Using the efficient discrete-ordinate method, we present an analytical solution for radiative transfer in the coupled atmosphere-ocean system with rough air-water interface. The theoretical formulations of the radiative transfer equation and solution are described. The effects of surface roughness on radiation field in the atmosphere and ocean are studied and compared with measurements. The results show that ocean surface roughness has significant effects on the upwelling radiation in the atmosphere and the downwelling radiation in the ocean. As wind speed increases, the angular domain of sunglint broadens, the surface albedo decreases, and the transmission to ocean increases. The downward radiance field in the upper ocean is highly anisotropic, but this anisotropy decreases rapidly as surface wind increases and as depth in ocean increases. The effects of surface roughness on radiation also depend greatly on both wavelength and angle of incidence (i.e., solar elevation); these effects are significantly smaller throughout the spectrum at high sun. The model-observation discrepancies may indicate that the Cox-Munk surface roughness model is not sufficient for high wind conditions

LSD: a leaf senescence database

By broad literature survey, we have developed a leaf senescence database (LSD, http://www.eplantsenescence.org/) that contains a total of 1145 senescence associated genes (SAGs) from 21 species. These SAGs were retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and were classified into different categories according to their functions in leaf senescence or morphological phenotypes when mutated. We made extensive annotations for these SAGs by both manual and computational approaches, and users can either browse or search the database to obtain information including literatures, mutants, phenotypes, expression profiles, miRNA interactions, orthologs in other plants and cross links to other databases. We have also integrated a bioinformatics analysis platform WebLab into LSD, which allows users to perform extensive sequence analysis of their interested SAGs. The SAG sequences in LSD can also be downloaded readily for bulk analysis. We believe that the LSD contains the largest number of SAGs to date and represents the most comprehensive and informative plant senescence-related database, which would facilitate the systems biology research and comparative studies on plant aging

The Continual Intercomparison of Radiation Codes: Results from Phase I

The computer codes that calculate the energy budget of solar and thermal radiation in Global Climate Models (GCMs), our most advanced tools for predicting climate change, have to be computationally efficient in order to not impose undue computational burden to climate simulations. By using approximations to gain execution speed, these codes sacrifice accuracy compared to more accurate, but also much slower, alternatives. International efforts to evaluate the approximate schemes have taken place in the past, but they have suffered from the drawback that the accurate standards were not validated themselves for performance. The manuscript summarizes the main results of the first phase of an effort called "Continual Intercomparison of Radiation Codes" (CIRC) where the cases chosen to evaluate the approximate models are based on observations and where we have ensured that the accurate models perform well when compared to solar and thermal radiation measurements. The effort is endorsed by international organizations such as the GEWEX Radiation Panel and the International Radiation Commission and has a dedicated website (i.e., http://circ.gsfc.nasa.gov) where interested scientists can freely download data and obtain more information about the effort's modus operandi and objectives. In a paper published in the March 2010 issue of the Bulletin of the American Meteorological Society only a brief overview of CIRC was provided with some sample results. In this paper the analysis of submissions of 11 solar and 13 thermal infrared codes relative to accurate reference calculations obtained by so-called "line-by-line" radiation codes is much more detailed. We demonstrate that, while performance of the approximate codes continues to improve, significant issues still remain to be addressed for satisfactory performance within GCMs. We hope that by identifying and quantifying shortcomings, the paper will help establish performance standards to objectively assess radiation code quality, and will guide the development of future phases of CIR

Comparison of Clouds and Cloud Feedback between AMIP5 and AMIP6

We examine the changes in clouds and cloud feedback between Phase 5 (AMIP5) and Phase 6 (AMIP6) of the Atmospheric Model Intercomparison Project. Each model is perturbed by uniformly increasing the sea surface temperature by 4 K. The simulated cloud fraction, the perturbed states and cloud radiative kernels are used to derive cloud feedback in the shortwave (SW), longwave (LW) and their sum (Net). Compared to AMIP5, the cloud fraction in AMIP6 increases by 9.1%, while the perturbation leads to a 0.25% decrease. The Net cloud feedback at the top of the atmosphere (TOA) is almost double (174%). Statistical tests support that this change is mainly due to an increase in the surface SW cloud feedback caused by optically thick, middle and low clouds. The contribution of the atmospheric Net component (12%) stems from the increase in the atmospheric LW cloud feedback, likely to play a role in weakening (strengthening) the northward (southward) meridional atmospheric energy transport, while the opposite is true for the surface LW and Net cloud feedback in the meridional oceanic energy transport. The substantial increase in cloud feedback at the TOA primarily contributes to the higher climate sensitivity. The cloud feedback spread in AMIP6 is comparable to that in AMIP5

Effect of chondroitin sulfate proteoglycans on neuronal cell adhesion, spreading and neurite growth in culture

As one major component of extracellular matrix (ECM) in the central nervous system, chondroitin sulfate proteoglycans (CSPGs) have long been known as inhibitors enriched in the glial scar that prevent axon regeneration after injury. Although many studies have shown that CSPGs inhibited neurite outgrowth in vitro using different types of neurons, the mechanism by which CSPGs inhibit axonal growth remains poorly understood. Using cerebellar granule neuron (CGN) culture, in this study, we evaluated the effects of different concentrations of both immobilized and soluble CSPGs on neuronal growth, including cell adhesion, spreading and neurite growth. Neurite length decreased while CSPGs concentration arised, meanwhile, a decrease in cell density accompanied by an increase in cell aggregates formation was observed. Soluble CSPGs also showed an inhibition on neurite outgrowth, but it required a higher concentration to induce cell aggregates formation than coated CSPGs. We also found that growth cone size was significantly reduced on CSPGs and neuronal cell spreading was restrained by CSPGs, attributing to an inhibition on lamellipodial extension. The effect of CSPGs on neuron adhesion was further evidenced by interference reflection microscopy (IRM) which directly demonstrated that both CGNs and cerebral cortical neurons were more loosely adherent to a CSPG substrate. These data demonstrate that CSPGs have an effect on cell adhesion and spreading in addition to neurite outgrowth

Spectral Kernel Approach to Study Radiative Response of Climate Variables and Interannual Variability of Reflected Solar Spectrum

The radiative kernel approach provides a simple way to separate the radiative response to different climate parameters and to decompose the feedback into radiative and climate response components. Using CERES/MODIS/Geostationary data, we calculated and analyzed the solar spectral reflectance kernels for various climate parameters on zonal, regional, and global spatial scales. The kernel linearity is tested. Errors in the kernel due to nonlinearity can vary strongly depending on climate parameter, wavelength, surface, and solar elevation; they are large in some absorption bands for some parameters but are negligible in most conditions. The spectral kernels are used to calculate the radiative responses to different climate parameter changes in different latitudes. The results show that the radiative response in high latitudes is sensitive to the coverage of snow and sea ice. The radiative response in low latitudes is contributed mainly by cloud property changes, especially cloud fraction and optical depth. The large cloud height effect is confined to absorption bands, while the cloud particle size effect is found mainly in the near infrared. The kernel approach, which is based on calculations using CERES retrievals, is then tested by direct comparison with spectral measurements from Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY) (a different instrument on a different spacecraft). The monthly mean interannual variability of spectral reflectance based on the kernel technique is consistent with satellite observations over the ocean, but not over land, where both model and data have large uncertainty. RMS errors in kernel ]derived monthly global mean reflectance over the ocean compared to observations are about 0.001, and the sampling error is likely a major component

TRIM14 promotes colorectal cancer cell migration and invasion through the SPHK1/STAT3 pathway

Abstract Background Colorectal cancer (CRC) is one of the most lethal malignancies. Tripartite Motif Containing 14 (TRIM14) is a member of TRIM family proteins, which are involved in the pathogenesis of various cancers. This study aimed to investigate TRIM14 expression in CRC tissues, and its effects on the migration and invasion of CRC cell lines. Methods TRIM14 mRNA expression was detected by real-time PCR analysis. Cell migration and invasion were measured by Transwell assays. Protein expression was assessed by western blot analysis. Results The expression of TRIM14 was significantly higher in CRC tissues than in matched non-cancerous tissues. TRIM14 knockdown by specific short hairpin RNA (shRNA) attenuated CRC cell migration and invasion, whereas TRIM14 overexpression caused reverse effect. Moreover, TRIM14 positively regulated the protein levels of sphingosine kinase 1 (SPHK1) and phosphorylated STAT3 (p-STAT3), as well as the mRNA and protein expression of matrix metalloproteinase 2, MMP9 and vascular endothelial growth factor, which are transcriptional targets of the STAT3 signaling pathway. Importantly, the blockage of the SPHK1/STAT3 signaling pathway by SKI-II or AG490 could reverse the TRIM14-promoted CRC cell migration and invasion. Conclusions Our results reveal a critical role for TRIM14 in promoting migration and invasion of CRC cells, and suggest TRIM14 may serve as a potential molecular target to prevent CRC metastasis