199 research outputs found
Recommended from our members
Evaluation of Open Geospatial Consortium Standards fur Use In LLNL Geographic Information Systems (GIS)
The objective of this project is to evaluate existing and emerging Open Geospatial Consortium (OGC) standards for use in LLNL programs that rely heavily on geographic data. OGC standards are intended to facilitate interoperability between geospatial processing systems to avoid duplication of effort, lower development costs, and encourage competition based on improved capability and performance rather than vendor lock-in. Some of these standards appear to be gaining traction in the geospatial data community, the Federal government, DOE and DHS. A serious evaluation of this technology is appropriate at this time due to increasing interest and mandated compliance in the Federal government in some situations. A subset of OGC standards is identified and reviewed with a focus on applications to LLNL programs. Each standard or recommendation reviewed was evaluated in general terms. In addition, for specific programs such as Gen&SIS and NARAC, a specific evaluation was made of several of the standards and how they could be used most effectively. It is also important to evaluate the acceptance of these standards in the commercial arena. The implementation of OGC standards by the largest GIS vendor (ESRI) was reviewed. At present, OGC standards are primary useful in specific situations. More generally, many of the standards are immature and their impact on the government and commercial sectors is unclear. Consequently, OGC and related developments need to be observed. As specific standards or groups of standards mature and establish their relevance, these can also be incorporated in LLNL programs as requirements dictate, especially if open implementations and commercial products are available
Recommended from our members
Evaluation of OGC Standards for Use in LLNL GIS
Over the summer of 2005, the Lawrence Livermore National Laboratory (LLNL) Computer Applications and Research Department conducted a small project that examined whether Open Geospatial Consortium (OGC) standards might be useful in meeting program mission requirements more effectively. OGC standards are intended to facilitate interoperability between geospatial processing systems to lower development costs and to avoid duplication of effort and vendor lock-in. Some OGC standards appear to be gaining traction in the geospatial data community, the Federal government, Department of Energy (DOE) and Department of Homeland Security (DHS) and so an evaluation was deemed appropriate
Quantitative image analysis identifies pVHL as a key regulator of microtubule dynamic instability
The product of the von Hippel-Lindau tumor suppressor gene stabilizes microtubules by inhibiting GTPase activity
Naturally Embedded Query Languages
We investigate the properties of a simple programming language whose main computational engine is structural recursion on sets. We describe a progression of sublanguages in this paradigm that (1) have increasing expressive power, and (2) illustrate robust conceptual restrictions thus exhibiting interesting additional properties. These properties suggest that we consider our sublanguages as candidates for "query languages". Viewing query languages as restrictions of our more general programming language has several advantages. First, there is no "impedance mismatch" problem; the query languages are already there, so they share common semantic foundation with the general language. Second, we suggest a uniform characterization of nested relational and complex-object algebras in terms of some surprisingly simple operators; and we can make comparisons of expressiveness in a general framework. Third, we exhibit differences in expressive power that are not always based on complexity arguments..
Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer
BACKGROUND: In real-time RT quantitative PCR (qPCR) the accuracy of normalized data is highly dependent on the reliability of the reference genes (RGs). Failure to use an appropriate control gene for normalization of qPCR data may result in biased gene expression profiles, as well as low precision, so that only gross changes in expression level are declared statistically significant or patterns of expression are erroneously characterized. Therefore, it is essential to determine whether potential RGs are appropriate for specific experimental purposes. Aim of this study was to identify and validate RGs for use in the differentiation of normal and tumor lung expression profiles. METHODS: A meta-analysis of lung cancer transcription profiles generated with the GeneChip technology was used to identify five putative RGs. Their consistency and that of seven commonly used RGs was tested by using Taqman probes on 18 paired normal-tumor lung snap-frozen specimens obtained from non-small-cell lung cancer (NSCLC) patients during primary curative resection. RESULTS: The 12 RGs displayed showed a wide range of Ct values: except for rRNA18S (mean 9.8), the mean values of all the commercial RGs and ESD ranged from 19 to 26, whereas those of the microarray-selected RGs (BTF-3, YAP1, HIST1H2BC, RPL30) exceeded 26. RG expression stability within sample populations and under the experimental conditions (tumour versus normal lung specimens) was evaluated by: (1) descriptive statistic; (2) equivalence test; (3) GeNorm applet. All these approaches indicated that the most stable RGs were POLR2A, rRNA18S, YAP1 and ESD. CONCLUSION: These data suggest that POLR2A, rRNA18S, YAP1 and ESD are the most suitable RGs for gene expression profile studies in NSCLC. Furthermore, they highlight the limitations of commercial RGs and indicate that meta-data analysis of genome-wide transcription profiling studies may identify new RGs
18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells
Background: One requisite of quantitative reverse transcription PCR (qRT-PCR) is to normalise the data with an
internal reference gene that is invariant regardless of treatment, such as virus infection. Several studies have found
variability in the expression of commonly used housekeeping genes, such as beta-actin (ACTB) and
glyceraldehyde-3-phosphate dehydrogenase (GAPDH), under different experimental settings. However, ACTB and
GAPDH remain widely used in the studies of host gene response to virus infections, including influenza viruses. To
date no detailed study has been described that compares the suitability of commonly used housekeeping genes in
influenza virus infections. The present study evaluated several commonly used housekeeping genes [ACTB, GAPDH,
18S ribosomal RNA (18S rRNA), ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide (ATP5B)
and ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) (ATP5G1)] to identify the most
stably expressed gene in human, pig, chicken and duck cells infected with a range of influenza A virus subtypes.
Results: The relative expression stability of commonly used housekeeping genes were determined in primary
human bronchial epithelial cells (HBECs), pig tracheal epithelial cells (PTECs), and chicken and duck primary
lung-derived cells infected with five influenza A virus subtypes. Analysis of qRT-PCR data from virus and mock
infected cells using NormFinder and BestKeeper software programmes found that 18S rRNA was the most stable
gene in HBECs, PTECs and avian lung cells.
Conclusions: Based on the presented data from cell culture models (HBECs, PTECs, chicken and duck lung cells)
infected with a range of influenza viruses, we found that 18S rRNA is the most stable reference gene for normalising
qRT-PCR data. Expression levels of the other housekeeping genes evaluated in this study (including ACTB and
GPADH) were highly affected by influenza virus infection and hence are not reliable as reference genes for RNA
normalisation
Fabrication and properties of acellular porcine anulus fibrosus for tissue engineering in spine surgery
Molecular association of glucose-6- phosphate isomerase and pyruvate kinase M2 with glyceraldehyde-3-phosphate dehydrogenase in cancer cells
Background: For a long time cancer cells are known for increased uptake of glucose and its metabolization through
glycolysis. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key regulatory enzyme of this pathway and can
produce ATP through oxidative level of phosphorylation. Previously, we reported that GAPDH purified from a variety of malignant tissues, but not from normal tissues, was strongly inactivated by a normal metabolite, methylglyoxal (MG).Molecular mechanism behind MG mediated GAPDH inhibition in cancer cells is not well understood.
Methods: GAPDH was purified from Ehrlich ascites carcinoma (EAC) cells based on its enzymatic activity. GAPDH
associated proteins in EAC cells and 3-methylcholanthrene (3MC) induced mouse tumor tissue were detected by mass spectrometry analysis and immunoprecipitation (IP) experiment, respectively. Interacting domains of GAPDH
and its associated proteins were assessed by in silico molecular docking analysis. Mechanism of MG mediated GAPDH
inactivation in cancer cells was evaluated by measuring enzyme activity, Circular dichroism (CD) spectroscopy, IP and mass spectrometry analyses.
Result: Here, we report that GAPDH is associated with glucose-6-phosphate isomerase (GPI) and pyruvate kinase M2
(PKM2) in Ehrlich ascites carcinoma (EAC) cells and also in 3-methylcholanthrene (3MC) induced mouse tumor tissue.
Molecular docking analyses suggest C-terminal domain preference for the interaction between GAPDH and GPI.
However, both C and N termini of PKM2 might be interacting with the C terminal domain of GAPDH. Expression of both PKM2 and GPI is increased in 3MC induced tumor compared with the normal tissue. In presence of 1 mM MG,association of GAPDH with PKM2 or GPI is not perturbed, but the enzymatic activity of GAPDH is reduced to 26.8 ± 5 % in 3MC induced tumor and 57.8 ± 2.3 % in EAC cells. Treatment of MG to purified GAPDH complex leads to glycation at R399 residue of PKM2 only, and changes the secondary structure of the protein complex.
Conclusion: PKM2 may regulate the enzymatic activity of GAPDH. Increased enzymatic activity of GAPDH in tumor cells may be attributed to its association with PKM2 and GPI. Association of GAPDH with PKM2 and GPI could be a signature for cancer cells. Glycation at R399 of PKM2 and changes in the secondary structure of GAPDH complex could be one of the mechanisms by which GAPDH activity is inhibited in tumor cells by MG
Morphological characteristics of cartilage-bone transitional structures in the human knee joint and CAD design of an osteochondral scaffold
Mechanochemical modeling of dynamic microtubule growth involving sheet-to-tube transition
Microtubule dynamics is largely influenced by nucleotide hydrolysis and the
resultant tubulin configuration changes. The GTP cap model has been proposed to
interpret the stabilizing mechanism of microtubule growth from the view of
hydrolysis effects. Besides, the microtubule growth involves the closure of a
curved sheet at its growing end. The curvature conversion also helps to
stabilize the successive growth, and the curved sheet is referred to as the
conformational cap. However, there still lacks theoretical investigation on the
mechanical-chemical coupling growth process of microtubules. In this paper, we
study the growth mechanisms of microtubules by using a coarse-grained molecular
method. Firstly, the closure process involving a sheet-to-tube transition is
simulated. The results verify the stabilizing effect of the sheet structure,
and the minimum conformational cap length that can stabilize the growth is
demonstrated to be two dimers. Then, we show that the conformational cap can
function independently of the GTP cap, signifying the pivotal role of
mechanical factors. Furthermore, based on our theoretical results, we describe
a Tetris-like growth style of microtubules: the stochastic tubulin assembly is
regulated by energy and harmonized with the seam zipping such that the sheet
keeps a practically constant length during growth.Comment: 23 pages, 7 figures. 2 supporting movies have not been uploaded due
to the file type restriction
- …