Documentation of the GLAS fourth order general calculation model. Volume 3: Vectorized code for the Cyber 205

Volume 3 of a 3-volume technical memoranda which contains documentation of the GLAS fourth order genera circulation model is presented. The volume contains the CYBER 205 scalar and vector codes of the model, list of variables, and cross references. A dictionary of FORTRAN variables used in the Scalar Version, and listings of the FORTRAN Code compiled with the C-option, are included. Cross reference maps of local variables are included for each subroutine

Documentation of the GLAS fourth order general circulation model. Volume 1: Model documentation

The volume 1, of a 3 volume technical memoranda which contains a documentation of the GLAS Fourth Order General Circulation Model is presented. Volume 1 contains the documentation, description of the stratospheric/tropospheric extension, user's guide, climatological boundary data, and some climate simulation studies

Documentation of the GLAS fourth order general circulation model. Volume 2: Scalar code

Volume 2, of a 3 volume technical memoranda contains a detailed documentation of the GLAS fourth order general circulation model. Volume 2 contains the CYBER 205 scalar and vector codes of the model, list of variables, and cross references. A variable name dictionary for the scalar code, and code listings are outlined

Improved representation of underwater light field and its impact on ecosystem dynamics: a study in the North Sea

Understanding ecosystem state on the North-West European (NWE) Shelf is of major im18 portance for both economy and climate research. The purpose of this work is to advance our modelling of in-water optics on the NWE Shelf, with important implications for how we model primary productivity, as well as for assimilation of water-leaving radiances. We implement a stand-alone bio-optical module into the existing coupled physical-biogeo-chemical model configuration. The advantage of the bio-optical module, when compared to the pre-existing light scheme is that it resolves the underwater light spectrally and distinguishes between direct and diffuse downwelling streams. The changed underwater light compares better with both satellite and in-situ observations. The module lowered the underwater Photosynthetically Active Radiation, decreasing the simulated primary productivity, but overall the improved underwater light had relatively limited impact on the phyto plankton seasonal dynamics. We showed that the model skill in representing phytoplankton seasonal cycle (e.g phytoplankton bloom) can be substantially improved either by assimilation of satellite Phytoplankton Functional Type (PFT) chlorophyll, or by assimilating a novel PFT absorption product. Assimilation of the two PFT products yields similar results, with an important difference in the PFT community structure. Both assimilative runs lead to lower plankton biomass and increase the nutrient concentrations. We discuss some future directions on how to improve our model skill in biogeochemistry without using as similation, e.g. by improving nutrient forcing, re-tuning the model parameters and using the bio-optical module to provide a two-way physical-biogeochemical coupling, improving the consistency between model physical and biogeochemical components

Data assimilation insights on selecting the most valuable atmospheric measurements

We discuss how objective guidance on selecting the most valuable atmospheric measurements on future Mars spacecraft missions can be provided through already developed Martian atmospheric data assimilation systems, and in particular through Observing System Simulation Experiments (OSSEs) which are widely used to design instruments for the Earth’s atmosphere

Potential and Actual impacts of deforestation and afforestation on land surface temperature

Forests are undergoing significant changes throughout the globe. These changes can modify water, energy, and carbon balance of the land surface, which can ultimately affect climate. We utilize satellite data to quantify the potential and actual impacts of forest change on land surface temperature (LST) from 2003 to 2013. The potential effect of forest change on temperature is calculated by the LST difference between forest and nearby nonforest land, whereas the actual impact on temperature is quantified by the LST trend difference between deforested (afforested) and nearby unchanged forest (nonforest land) over several years. The good agreement found between potential and actual impacts both at annual and seasonal levels indicates that forest change can have detectable impacts on surface temperature trends. That impact, however, is different for maximum and minimum temperatures. Overall, deforestation caused a significant warming up to 0.28 K/decade on average temperature trends in tropical regions, a cooling up to -0.55 K/decade in boreal regions, a weak impact in the northern temperate regions, and strong warming (up to 0.32 K/decade) in the southern temperate regions. Afforestation induced an opposite impact on temperature trends. The magnitude of the estimated temperature impacts depends on both the threshold and the data set (Moderate Resolution Imaging Spectroradiometer and Landsat) by which forest cover change is defined. Such a latitudinal pattern in temperature impact is mainly caused by the competing effects of albedo and evapotranspiration on temperature. The methodology developed here can be used to evaluate the temperature change induced by forest cover change around the globe.Maryland Council on the Environment [1357928]; National Natural Science Foundation of China [41371096, 41130534]; China Scholar Council fellowship [201306010169]; National Socio-Environmental Synthesis Center-NSF [DBI-1052875]SCI(E)[email protected]

Protein tyrosine phosphatases: the problems of a growing family

Protein tyrosine phosphorylation is now recognized as an important component of the control of many fundamental aspects of cellular function, including growth and differentiation, cell cycle and cytoskeletal integrity. In vivo, the net level of phosphorylation of tyrosyl residues in a target substrate reflects the balance between the competing action of kinases and phosphatases. We are examining physiological roles for protein tyrosine phosphorylation, pursuing the problem from the perspective of the enzymes that catalyze the dephosphorylation reaction, the protein tyrosine phosphatases (PTPases). The PTPases have, until recently, been somewhat neglected relative to the protein tyrosine kinases (PTKs). However, considerable progress has been made in identifying new members of the PTPase family, and it appears that they constitute a novel class of signal transducing molecules that rival the PTKs in their structural diversity and complexity. One of the principal reasons that the study of PTPases has lagged behind that of the..

Predicting flow reversals in chaotic natural convection using data assimilation

A simplified model of natural convection, similar to the Lorenz (1963) system, is compared to computational fluid dynamics simulations in order to test data assimilation methods and better understand the dynamics of convection. The thermosyphon is represented by a long time flow simulation, which serves as a reference "truth". Forecasts are then made using the Lorenz-like model and synchronized to noisy and limited observations of the truth using data assimilation. The resulting analysis is observed to infer dynamics absent from the model when using short assimilation windows. Furthermore, chaotic flow reversal occurrence and residency times in each rotational state are forecast using analysis data. Flow reversals have been successfully forecast in the related Lorenz system, as part of a perfect model experiment, but never in the presence of significant model error or unobserved variables. Finally, we provide new details concerning the fluid dynamical processes present in the thermosyphon during these flow reversals

Multiple causes of interannual sea surface temperature variability in the equatorial Atlantic Ocean

The eastern equatorial Atlantic Ocean is subject to interannual fluctuations of sea surface temperatures, with climatic impacts on the surrounding continents. The dynamic mechanism underlying Atlantic temperature variability is thought to be similar to that of the El Nino/Southern Oscillation (ENSO) in the equatorial Pacific, where air-sea coupling leads to a positive feedback between surface winds in the western basin, sea surface temperature in the eastern basin, and equatorial oceanic heat content. Here we use a suite of observational data, climate reanalysis products, and general circulation model simulations to reassess the factors driving the interannual variability. We show that some of the warm events can not be explained by previously identified equatorial wind stress forcing and ENSO-like dynamics. Instead, these events are driven by a mechanism in which surface wind forcing just north of the equator induces warm ocean temperature anomalies that are subsequently advected toward the equator. We find the surface wind patterns are associated with long-lived subtropical sea surface temperature anomalies and suggest they therefore reflect a link between equatorial and subtropical Atlantic variability

Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPκ, μ, ρ and PCP-2)

BACKGROUND: Four genes designated as PTPRK (PTPκ), PTPRL/U (PCP-2), PTPRM (PTPμ) and PTPRT (PTPρ) code for a subfamily (type R2B) of receptor protein tyrosine phosphatases (RPTPs) uniquely characterized by the presence of an N-terminal MAM domain. These transmembrane molecules have been implicated in homophilic cell adhesion. In the human, the PTPRK gene is located on chromosome 6, PTPRL/U on 1, PTPRM on 18 and PTPRT on 20. In the mouse, the four genes ptprk, ptprl, ptprm and ptprt are located in syntenic regions of chromosomes 10, 4, 17 and 2, respectively. RESULTS: The genomic organization of murine R2B RPTP genes is described. The four genes varied greatly in size ranging from ~64 kb to ~1 Mb, primarily due to proportional differences in intron lengths. Although there were also minor variations in exon length, the number of exons and the phases of exon/intron junctions were highly conserved. In situ hybridization with digoxigenin-labeled cRNA probes was used to localize each of the four R2B transcripts to specific cell types within the murine central nervous system. Phylogenetic analysis of complete sequences indicated that PTPρ and PTPμ were most closely related, followed by PTPκ. The most distant family member was PCP-2. Alignment of RPTP polypeptide sequences predicted putative alternatively spliced exons. PCR experiments revealed that five of these exons were alternatively spliced, and that each of the four phosphatases incorporated them differently. The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction. CONCLUSIONS: Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length. Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing