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Replica Registration Service - Functional Interface Specification1.0

Description: The goal of the Replica Registration Service (RRS) is toprovide a uniform interface to various file catalogs, replica catalogs,and metadata catalogs. It can be thought of as an abstraction of theconcepts used in such systems to register files and their replicas. Someexperiments may prefer to support their own file catalogs (which may havetheir own specialized structures, semantics, and implementations) ratherthan use a standard replica catalog. Providing an RRS that can interactwith such a catalog (for example by invoking a script) can permit thatcatalog to be invoked as a service in the same way that other replicacatalogs do. If at a later time the experiment wishes to change toanother file catalog or an RLS, it is only a matter of developing an RRSfor that new catalog and replacing the existing catalog. In addition,some systems use metadata catalogs or other catalogs to manage the filename spaces. Our goal is to provide a single interface that supports theregistration of files into such name spaces as well as retrieving thisinformation.
Date: February 28, 2005
Creator: Shoshani, Arie; Sim, Alex & Stockinger, Kurt
Partner: UNT Libraries Government Documents Department

Correlation-induced anomalies and extreme sensitivity in fcc-PU1

Description: We have used GGA + U density functional theory to study the effects of correlation on the properties offcc-Pu. We found that the structural and elastic properties offcc-Pu are highly sensitive to the Hubbard U parameter. Within an interval of 0.1 eV ofthe U parameter, the equilibrium lattice constants offcc-Pu can change from 0.44 to 0.47 nm. While the bulk modulus can drop by a factor of5 to 10. The pressure derivative, dB/dp, ofthe bulk modulus can rise dramatically from 5 to 16 and then drop to a negative value before recovering to a more normal value. These observations are partially supported by existing experiments and the prediction of a negative dB/dp needs to be tested in future experiments.
Date: January 1, 2009
Creator: Chen, Shao-ping
Partner: UNT Libraries Government Documents Department

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

Description: RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.
Date: May 26, 2010
Creator: Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S. et al.
Partner: UNT Libraries Government Documents Department

Primate-Specific Evolution of an LDLR Enhancer

Description: Sequence changes in regulatory regions have often beeninvoked to explain phenotypic divergence among species, but molecularexamples of this have been difficult to obtain. In this study, weidentified an anthropoid primate specific sequence element thatcontributed to the regulatory evolution of the LDL receptor. Using acombination of close and distant species genomic sequence comparisonscoupled with in vivo and in vitro studies, we show that a functionalcholesterol-sensing sequence motif arose and was fixed within apre-existing enhancer in the common ancestor of anthropoid primates. Ourstudy demonstrates one molecular mechanism by which ancestral mammalianregulatory elements can evolve to perform new functions in the primatelineage leading to human.
Date: June 28, 2006
Creator: Wang, Qian-fei; Prabhakar, Shyam; Wang, Qianben; Moses, Alan M.; Chanan, Sumita; Brown, Myles et al.
Partner: UNT Libraries Government Documents Department

Butt Joint Tool Status: ITER-US-LLNL-NMARTOVETSKY-01312007

Description: Butt joint tool vacuum vessel has been built at C&H Enterprise, Inc. Leak checking and loading tests were taken place at the factory. The conductor could not be pumped down better than to 500 mtorr and therefore we could not check the sealing mechanism of the seal around conductor. But the rest of the vessel, including the flat gasket, one of the difficult seals worked well, no indication of leak at sensitivity 1e-7 l*torr/sec. The load test showed fully functional system of the load mechanism. The conductors were loaded up to 2200 kgf (21560 N) and the pressure between the butts was uniform with 100% of the contact proved by pressure sensitive film. The status of the butt joint tool development is reported.
Date: February 1, 2007
Creator: Martovetsky, N N
Partner: UNT Libraries Government Documents Department

Integration of Phenotypic Metadata and Protein Similarity in Archaea Using a Spectral Bipartitioning Approach

Description: In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes clear that the sequence flexibility allowed a given protein varies significantly among different protein families. The degree to which sequences are conserved not only differs for each protein family, but also is affected by the phylogenetic divergence of the source organisms. Clustering techniques that use similarity thresholds for protein families do not always allow for these variations and thus cannot be confidently used for applications such as automated annotation and phylogenetic profiling. In this work, we applied a spectral bipartitioning technique to all proteins from 53 archaeal genomes. Comparisons between different taxonomic levels allowed us to study the effects of phylogenetic distances on cluster structure. Likewise, by associating functional annotations and phenotypic metadata with each protein, we could compare our protein similarity clusters with both protein function and associated phenotype. Our clusters can be analyzed graphically and interactively online.
Date: January 1, 2009
Creator: Hooper, Sean D.; Anderson, Iain J; Pati, Amrita; Dalevi, Daniel; Mavromatis, Konstantinos & Kyrpides, Nikos C
Partner: UNT Libraries Government Documents Department

Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections

Description: We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, {omega}B97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, {omega}B97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as {omega}B97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.
Date: June 14, 2008
Creator: Chai, Jeng-Da & Head-Gordon, Martin
Partner: UNT Libraries Government Documents Department

Advanced Lost Foam Casting Technology - Phase V

Description: Previous research, conducted under DOE Contracts DE-FC07-89ID12869, DE-FC07-93ID12230 and DE-FC07-95ID113358 made significant advances in understanding the Lost Foam Casting (LFC) Process and clearly identified areas where additional developments were needed to improve the process and make it more functional in industrial environments. The current project focused on eight tasks listed as follows: Task 1--Computational Model for the Process and Data Base to Support the Model; Task 2--Casting Dimensional Accuracy; Task 3--Pattern Production; Task 4--Improved Pattern Materials; Task 5--Coating Control; Task 6--In-Plant Case Studies; Task 7--Energy and the Environmental Data; and Task 8--Technology Transfer. This report summarizes the work done on all tasks in the period of October 1, 1999 through September 30, 2004. The results obtained in each task and subtask are summarized in this Executive Summary and details are provided in subsequent sections of the report.
Date: April 29, 2004
Creator: Sun, Wanliang; Littleton, Harry E. & Bates, Charles E.
Partner: UNT Libraries Government Documents Department

Primate-specific evolution of an LDLR enhancer

Description: Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study we identified an anthropoid primate-specific sequence element that contributed to the regulatory evolution of the low-density lipoprotein receptor. Using a combination of close and distant species genomic sequence comparisons coupled with in vivo and in vitro studies, we found that a functional cholesterol-sensing sequence motif arose and was fixed within a pre-existing enhancer in the common ancestor of anthropoid primates. Our study demonstrates one molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions in the primate lineage leading to human.
Date: December 1, 2005
Creator: Wang, Qian-Fei; Prabhakar, Shyam; Wang, Qianben; Moses, Alan M.; Chanan, Sumita; Brown, Myles et al.
Partner: UNT Libraries Government Documents Department

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Description: Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.
Date: September 1, 2006
Creator: Kunin, Victor; Sorek, Rotem & Hugenholtz, Philip
Partner: UNT Libraries Government Documents Department

Transitive closure and metric inequality of weighted graphs:detecting protein interaction modules using cliques

Description: We study transitivity properties of edge weights in complex networks. We show that enforcing transitivity leads to a transitivity inequality which is equivalent to ultra-metric inequality. This can be used to define transitive closure on weighted undirected graphs, which can be computed using a modified Floyd-Warshall algorithm. We outline several applications and present results of detecting protein functional modules in a protein interaction network.
Date: June 2, 2006
Creator: Ding, Chris; He, Xiaofeng; Xiong, Hui; Peng, Hanchuan & Holbrook,Stephen R.
Partner: UNT Libraries Government Documents Department

Time-periodic solutions of the Benjamin-Ono equation

Description: We present a spectrally accurate numerical method for finding non-trivial time-periodic solutions of non-linear partial differential equations. The method is based on minimizing a functional (of the initial condition and the period) that is positive unless the solution is periodic, in which case it is zero. We solve an adjoint PDE to compute the gradient of this functional with respect to the initial condition. We include additional terms in the functional to specify the free parameters, which, in the case of the Benjamin-Ono equation, are the mean, a spatial phase, a temporal phase and the real part of one of the Fourier modes at t = 0. We use our method to study global paths of non-trivial time-periodic solutions connecting stationary and traveling waves of the Benjamin-Ono equation. As a starting guess for each path, we compute periodic solutions of the linearized problem by solving an infinite dimensional eigenvalue problem in closed form. We then use our numerical method to continue these solutions beyond the realm of linear theory until another traveling wave is reached (or until the solution blows up). By experimentation with data fitting, we identify the analytical form of the solutions on the path connecting the one-hump stationary solution to the two-hump traveling wave. We then derive exact formulas for these solutions by explicitly solving the system of ODE's governing the evolution of solitons using the ansatz suggested by the numerical simulations.
Date: April 1, 2008
Creator: Ambrose , D.M. & Wilkening, Jon
Partner: UNT Libraries Government Documents Department

Gaining analytic control of parton showers

Description: Parton showers are widely used to generate fully exclusive final states needed to compare theoretical models to experimental observations. While, in general, parton showers give a good description of the experimental data, the precise functional form of the probability distribution underlying the event generation is generally not known. The reason is that realistic parton showers are required to conserve four-momentum at each vertex. In this paper we investigate in detail how four-momentum conservation is enforced in a standard parton shower and why this destroysthe analytic control of the probability distribution. We show how to modify a parton shower algorithm such that it conserves four-momentum at each vertex, but for which the full analytic form of the probability distribution is known. We then comment how this analytic control can be used to match matrix element calculations with parton showers, and to estimate effects of power corrections and other uncertainties in parton showers.
Date: May 14, 2007
Creator: Tackmann, Frank; Bauer, Christian W. & Tackmann, Frank J.
Partner: UNT Libraries Government Documents Department

The Riesz Representation Theorem

Description: In 1909, F. Riesz succeeded in giving an integral represntation for continuous linear functionals on C[0,1]. Although other authors, notably Hadamard and Frechet, had given representations for continuous linear functionals on C[0,1], their results lacked the clarity, elegance, and some of the substance (uniqueness) of Riesz's theorem. Subsequently, the integral representation of continuous linear functionals has been known as the Riesz Representation Theorem. In this paper, three different proofs of the Riesz Representation Theorem are presented. The first approach uses the denseness of the Bernstein polynomials in C[0,1] along with results of Helly to write the continuous linear functionals as Stieltjes integrals. The second approach makes use of the Hahn-Banach Theorem in order to write the functional as an integral. The paper concludes with a detailed presentation of a Daniell integral development of the Riesz Representation Theorem.
Date: August 1980
Creator: Williams, Stanley C. (Stanley Carl)
Partner: UNT Libraries


Description: The primary changes that have been made to this revision reflect the relocation of the Waste Certification Official (WCO) organizationally from the Quality Services Division (QSD) into the Laboratory Waste Services (LWS) Organization. Additionally, the responsibilities for program oversight have been differentiated between the QSD and LWS. The intent of this effort is to ensure that those oversight functions, which properly belonged to the WCO, moved with that function; but retain an independent oversight function outside of the LWS Organization ensuring the potential for introduction of organizational bias, regarding programmatic and technical issues, is minimized. The Waste Certification Program (WCP) itself has been modified to allow the waste certification function to be performed by any of the personnel within the LWS Waste Acceptance/Certification functional area. However, a single individual may not perform both the technical waste acceptance review and the final certification review on the same 2109 data package. Those reviews must be performed by separate individuals in a peer review process. There will continue to be a designated WCO who will have lead programmatic responsibility for the WCP and will exercise overall program operational oversite as well as determine the overall requirements of the certification program. The quality assurance organization will perform independent, outside oversight to ensure that any organizational bias does not degrade the integrity of the waste certification process. The core elements of the previous WCP have been retained, however, the terms and process structure have been modified.. There are now two ''control points,'' (1) the data package enters the waste certification process with the signature of the Generator Interface/Generator Interface Equivalent (GI/GIE), (2) the package is ''certified'', thus exiting the process. The WCP contains three steps, (1) the technical review for waste acceptance, (2) a review of the packaging and labeling (the old Control Point 3), ...
Date: January 8, 2002
Creator: MORGAN, LK
Partner: UNT Libraries Government Documents Department


Description: The major objective of this study was to relate the results of a series of functional tests to the compositional and structural alterations in the rat lung induced by subchronic exposure to silica dust. Fischer-344 rats were exposed for 6 hours/day, 5 days/week for 6 months to either 0, 2, 10, or 20 mg SiO{sub 2}/m{sup 3}. The general appearance of the exposed rats was not different from that of the controls. Interestingly, female rats exposed to silica dust, at all tested concentrations, gained more weight than the controls. The lung weight and the lung-to-body weight ratio was greater in the male rats exposed to the highest concentration of silica dust.
Date: February 1, 1984
Creator: KUTZMAN,R.S.
Partner: UNT Libraries Government Documents Department

Activities of Human Gene Nomenclature Committee

Description: The objective of this project, shared between NIH and DOE, has been and remains to enable the medical genetics communities to use common names for genes that are discovered by different gene hunting groups, in different species. This effort provides consistent gene nomenclature and approved gene symbols to the community at large. This contributes to a uniform and consistent understanding of genomes, particularly the human as well as functional genomics based on comparisons between homologous genes in related species (human and mice).
Date: July 16, 2002
Partner: UNT Libraries Government Documents Department

Combined approach to the inverse protein folding problem. Final report

Description: The main scientific contribution of the project ''Combined approach to the inverse protein folding problem'' submitted in 1996 and funded by the Department of Energy in 1997 is the formulation and development of the idea of the multilink recognition method for identification of functional and structural homologues of newly discovered genes. This idea became very popular after they first announced it and used it in prediction of the threading targets for the CASP2 competition (Critical Assessment of Structure Prediction).
Date: June 1, 2000
Creator: Abagyan, Ruben A.
Partner: UNT Libraries Government Documents Department

Functional Materials for Microsystems: Smart Self-Assembled Photochromic Films: Final Report

Description: This project set out to scientifically-tailor ''smart'' interfacial films and 3-D composite nanostructures to exhibit photochromic responses to specific, highly-localized chemical and/or mechanical stimuli, and to integrate them into optical microsystems. The project involved the design of functionalized chromophoric self-assembled materials that possessed intense and environmentally-sensitive optical properties (absorbance, fluorescence) enabling their use as detectors of specific stimuli and transducers when interfaced with optical probes. The conjugated polymer polydiacetylene (PDA) proved to be the most promising material in many respects, although it had some drawbacks concerning reversibility. Throughout his work we used multi-task scanning probes (AFM, NSOM), offering simultaneous optical and interfacial force capabilities, to actuate and characterize the PDA with localized and specific interactions for detailed characterization of physical mechanisms and parameters. In addition to forming high quality mono-, bi-, and tri-layers of PDA via Langmuir-Blodgett deposition, we were successful in using the diacetylene monomer precursor as a surfactant that directed the self-assembly of an ordered, mesostructured inorganic host matrix. Remarkably, the diacetylene was polymerized in the matrix, thus providing a PDA-silica composite. The inorganic matrix serves as a perm-selective barrier to chemical and biological agents and provides structural support for improved material durability in microsystems. Our original goal was to use the composite films as a direct interface with microscale devices as optical elements (e.g., intracavity mirrors, diffraction gratings), taking advantage of the very high sensitivity of device performance to real-time dielectric changes in the films. However, our optical physics colleagues (M. Crawford and S. Kemme) were unsuccessful in these efforts, mainly due to the poor optical quality of the composite films.
Date: November 1, 2001
Partner: UNT Libraries Government Documents Department

Effective field theory for the small-x evolution

Description: The small-x behavior of structure functions in the saturation region is determined by the non-linear generalization of the BFKL equation. I suggest the effective field theory for the small-x evolution which solves formally this equation. The result is the 2+1 functional integral for the structure functions at small x.
Date: May 1, 2001
Creator: Balitsky, Ian
Partner: UNT Libraries Government Documents Department