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

Plug and Play: Interoperability in Concert

In order to make database systems interoperate with systems beyond traditional application areas a new paradigm called "exporting database functionality" as a radical departure from traditional thinking has been proposed in research anddevelopment. Traditionally, all data is loaded into and owned by the database, whereas according to the new paradigm data may reside outside the database in external repositories or archives. Nevertheless, database functionality, such as query processing, and indexing, is provided exploiting interoperability ofthe DBMS with the external repositories. Obviously, there is an overhead involved having the DBMS interoperate with external repositories instead of a priori loading all data into the DBMS. In this paper we discuss alternatives for interoperability at di erent levels of abstraction, and we report on evaluations performed using the Concert prototype system making these cost factors explicit

Kondo resonance behavior of heavy fermion f-electron materials (invited)

The Kondo properties of the impurity Anderson model provide a theoretical framework for relating thermodynamic and angle integrated electron spectroscopy data in many heavy fermion materials. We describe the success and the challenges of this approach, summarize a detailed analysis of CeSi2,CeSi2, and give a perspective on the relation to the lattice Anderson model. © 2000 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71136/2/JAPIAU-87-9-6088-1.pd

Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes [preprint]

Known chemoproteomic probes generally use warheads that tag a single type of amino acid or modified form thereof to identify cases in which its hyper-reactivity underpins function. Much important biochemistry derives from electron-poor enzyme cofactors, transient intermediates and chemically-labile regulatory modifications, but probes for such species are underdeveloped. Here, we have innovated a versatile class of chemoproteomic probes for this less charted hemisphere of the proteome by using hydrazine as the common chemical warhead. Its electron-rich nature allows it to react by both polar and radicaloid mechanisms and to target multiple, pharmacologically important functional classes of enzymes bearing diverse organic and inorganic cofactors. Probe attachment can be blocked by active-site-directed inhibitors, and elaboration of the warhead supports connection of a target to a lead compound. The capacity of substituted hydrazines to profile, discover and inhibit diverse cofactor-dependent enzymes enables cell and tissue imaging and makes this platform useful for enzyme and drug discovery

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..

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

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