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Bioinformatics for Diagnostics, Forensics, and Virulence Characterization and Detection
We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently >1000 probes …
Date:
April 5, 2005
Creator:
Gardner, S & Slezak, T
Object Type:
Article
System:
The UNT Digital Library
ACCELERATING CLOSURE AT DOE SITES WITH EM'S SCIENCE AND TECHNOLOGY PROGRAM
Technical support is important for all U.S. Department of Energy (DOE) facilities facing difficult technical issues, aggressive remediation schedules, and tight budgets. It is especially vital for closure sites, which typically are smaller and have fewer resources available to apply to remediation activities. In many cases, closure sites and other small sites no longer have staff with the expertise required to overcome technical barriers on their own. As closure deadlines approach, special technical expertise is needed to identify, evaluate, and implement new and innovative approaches that will result in significant cost and schedule improvement for the waste disposition pathway. Site ''problem holders'' must have access to world-class scientific and engineering expertise from DOE national laboratories and research facilities, private industry, and universities to address immediate critical problems. In order to have confidence in the feasibility and results of innovative approaches, site contractors need to have the benefit of the valuable experiences of technicians who have faced similar problems and found solutions. The DOE Environmental Management (EM) Science and Technology (S&T) program recognizes the need of the closure sites to solve problems aggressively and is highly responsive to this need. Technical support from the S&T program can take many forms, such …
Date:
February 27, 2003
Creator:
Walker, J. S.; Toussaint, Craig R., (info: Ph.D.) & Gardner, E. J.
Object Type:
Article
System:
The UNT Digital Library
Drift waves in stellarator geometry
Drift waves are investigated in a real three-dimensional stellarator geometry. A linear system, based on the cold ion fluid model and a ballooning mode formalism, is solved numerically in the geometry of the stellarator H1-NF. The spectra of stable and unstable modes, as well as localization, are discussed. The dependence of the spectrum of the unstable modes on the wavevector, plasma density variation, and the location in the plasma is presented.
Date:
February 7, 2000
Creator:
Persson, M.; Nadeem, M.; Lewandowski, J.L.V. & Gardner, H.J.
Object Type:
Report
System:
The UNT Digital Library
The Rapid Cycling Medical Synchrotron RCMS.
Thirteen hadron beam therapy facilities began operation between 1990 and 2001 - 5 in Europe, 4 in North America, 3 in Japan, and 1 in South Africa [l]. Ten of them irradiate tumors with protons, 2 with Carbon- 12 ions, and 1 with both protons and Carbon-12. The facility with the highest patient throughput - a total of 6 174 patients in 11 years and as many as 150 patient treatments per day -is the Loma Linda University Medical Center, which uses a weak focusing slow cycling synchrotron to accelerate beam for delivery to passive scattering nozzles at the end of rotatable gantries [2, 3,4]. The Rapid Cycling Medical Synchrotron (RCMS) is a second generation synchrotron that, by contrast with the Loma Linda synchrotron, is strong focusing and rapid cycling, with a repetition rate of 30 Hz. Primary parameters for the RCMS are listed in Table 1.
Date:
June 2, 2002
Creator:
Peggs, S.; Barton, D.; Beebe-Wang, J.; Cardona, J.; Brennan, M.; Fischer, W. et al.
Object Type:
Article
System:
The UNT Digital Library
A search for W+- H ---> muon-neutrino b anti-b production at the Tevatron
All known experimental results on fundamental particles and their interactions can be described to great accuracy by a theory called the Standard Model. In the Standard Model of particle physics, the masses of particles are explained through the Higgs mechanism. The Higgs boson is the only Standard Model particle not discovered yet, and its observation or exclusion is an important test of the Standard Model. While the Standard Model predicts that a Higgs boson should exist, it does not exactly predict its mass. Direct searches have excluded a Higgs with m{sub H} < 114.4 GeV at 95% confidence level, while indirect measurements indicate that the mass should be less than 144 GeV. This analysis looks for W{sup {+-}}H {yields} {mu}{nu}{sub {mu}}b{bar b} in 1 fb{sup -1} of data collected with the D0 detector in p{bar p} collisions with {radical}s = 1.96 TeV. The analysis strategy relies on the tracking, calorimetry and muon reconstruction of the D0 experiment. The signature is a muon, missing transverse energy (E{sub T}) to account for the neutrino and two b-jets. The Higgs mass is reconstructed using the invariant mass of the two jets. Backgrounds are W{sup {+-}}b{bar b}, W{sup {+-}} c{bar c}, W{sup {+-}} + …
Date:
February 1, 2008
Creator:
Anastasoaie, Carmen Miruna & U., /Nijmegen
Object Type:
Thesis or Dissertation
System:
The UNT Digital Library
Coincidence Prompt Gamma-Ray Neutron Activation Analysis
The normal prompt gamma-ray neutron activation analysis for either bulk or small beam samples inherently has a small signal-to-noise (S/N) ratio due primarily to the neutron source being present while the sample signal is being obtained. Coincidence counting offers the possibility of greatly reducing or eliminating the noise generated by the neutron source. The present report presents our results to date on implementing the coincidence counting PGNAA approach. We conclude that coincidence PGNAA yields: (1) a larger signal-to-noise (S/N) ratio, (2) more information (and therefore better accuracy) from essentially the same experiment when sophisticated coincidence electronics are used that can yield singles and coincidences simultaneously, and (3) a reduced (one or two orders of magnitude) signal from essentially the same experiment. In future work we will concentrate on: (1) modifying the existing CEARPGS Monte Carlo code to incorporate coincidence counting, (2) obtaining coincidence schemes for 18 or 20 of the common elements in coal and cement, and (3) optimizing the design of a PGNAA coincidence system for the bulk analysis of coal.
Date:
November 10, 2002
Creator:
Gardner, R. P.; Mayo, C. W.; Metwally, W. A.; Zhang, W.; Guo, W. & Shehata, A.
Object Type:
Report
System:
The UNT Digital Library
Booster Fault Study No. 16: Deuteron Beam on the B6 Dump
A report on the booster fault study carried out on January 22, 2003.
Date:
October 2003
Creator:
Ahrens, L. A.; Brown, K. A. & Gardner, C. J.
Object Type:
Report
System:
The UNT Digital Library
FODO/Doublet Lattice for the SNS Accumulator Ring.
Requirements of minimum beam loss for hand-on maintenance and flexibility for future operations are essential for the lattice design of the Spallation Neutron Source (SNS) accumulator ring. In this paper, we present a hybrid lattice that consists of FODO arcs and doublet straights, emphasizing injection and collimation optimization and flexibility, split tunes for coupling control, sextupole families for chromaticity control, and compatibility to future upgrades.
Date:
June 30, 2000
Creator:
Wei, J.; Gardner, C.; Lee, Y. Y. & Tsoupas, N.
Object Type:
Article
System:
The UNT Digital Library
Predicting cancer outcome
We read with interest the paper by Michiels et al on the prediction of cancer with microarrays and the commentary by Ioannidis listing the potential as well as the limitations of this approach (February 5, p 488 and 454). Cancer is a disease characterized by complex, heterogeneous mechanisms and studies to define factors that can direct new drug discovery and use should be encouraged. However, this is easier said than done. Casti teaches that a better understanding does not necessarily extrapolate to better prediction, and that useful prediction is possible without complete understanding (1). To attempt both, explanation and prediction, in a single nonmathematical construct, is a tall order (Figure 1).
Date:
March 24, 2005
Creator:
Gardner, S N & Fernandes, M
Object Type:
Article
System:
The UNT Digital Library
Characterization of Vadose Zone Sediment: Borehole 299-W23-19 [SX-115] in the S-SX Waste Management Area
This report was revised in September 2008 to remove acid-extractable sodium data from Tables 4.15 and 4.19. The sodium data was removed due to potential contamination introduced during the acid extraction process. The rest of the text remains unchanged from the original report issued in February 2002. The Tank Farm Vadose Zone Project is led by CH2M HILL Hanford Group, Inc. Their goals include defining risks from past and future single-shell tank farm activities, identifying and evaluating the efficacy of interim measures, and collecting geotechnical information and data. The purpose of these activities is to support future decisions made by the U.S. Department of Energy (DOE) regarding near-term operations, future waste retrieval, and final closure activities for the single-shell tank Waste Management Areas. To help in this effort, CH2M HILL Hanford Group, Inc. contracted with scientists at Pacific Northwest National Laboratory to analyze sediment samples collected from borehole 299-W23-19.
Date:
September 11, 2008
Creator:
Serne, R. Jeffrey; Bjornstad, Bruce N.; Lanigan, David C.; Gee, Glendon W.; Lindenmeier, Clark W.; Clayton, Ray E. et al.
Object Type:
Report
System:
The UNT Digital Library
Setup and Performance of the Rhic Injector Accelerators for the 2007 Run With Gold Ions
Gold ions for the 2007 run of the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory (BNL) are accelerated in the Tandem, Booster and AGS prior to injection into RHIC. The setup and performance of this chain of accelerators is reviewed with a focus on improvements in the quality of beam delivered to RHIC. In particular, more uniform stripping foils between Booster and AGS7 and a new bunch merging scheme in AGS have provided beam bunches with reduced longitudinal emittance for RHIC.
Date:
June 25, 2007
Creator:
Gardner, C.; Ahrens, L.; Alessi, J.; Benjamin, J.; Blaskiewicz, M. & Al., Et
Object Type:
Article
System:
The UNT Digital Library
Characterization of Vadose Zone Sediment: Borehole 299-W23-19 [SX -115] in the S-SX Waste Management Area.
The Tank Farm Vadose Zone Project is led by CH2M HILL Hanford Group, Inc. Their goals include defining risks from past and future single-shell tank farm activities, identifying and evaluating the efficacy of interim measures, and collecting geo-technical information and data. The purpose of these activities is to support future decisions made by the U.S. Department of Energy regarding near-term operations, future waste retrieval, and final closure activities for the single-shell tank Waste Management Areas. To help in this effort, CH2M HILL contracted with scientists at Pacific Northwest National Laboratory to analyze sediment samples collected from borehole 299-W23-19. The conclusions reached from this study support specific mechanisms influencing subsurface migration of contaminants. The mechanisms are supported by the distributions of contaminants beneath tank farms. These observations will help DOE and CH2M HILL identify and implement viable remediation and closure activities.
Date:
February 12, 2002
Creator:
Serne, R. Jeffrey; Schaef, Herbert T.; Bjornstad, Bruce N.; Lanigan, David C.; Gee, Glendon W.; Lindenmeier, Clark W. et al.
Object Type:
Report
System:
The UNT Digital Library
MAGNeT : Monitor for Application-Generated Network Traffic /
Over the laqt decade, network practitioners have focused on monitoring, measuring, and characterizing traffic in the network to gain insight into building critical network components (from the protocol stack to routers and switches to network interface cards). Recent research shows that additional insight can be obtained by monitoring traffic at the application level (Le,, before application-sent traffic is modulated by the protocol stack) rather than in the network (i-e., after it is modulated by the protocol stack). Consequently, this paper describes a Monitor for Application-Generated Network Traffic (MAGNeT) that captures traffic generated by the application rather than traffic in the network. MAGNeT consists of application programs as well as modifications to the standard Linux kernel. Together, these tools provide the capability of monitoring an application's network behavior and protocol state information in production systems. The use of MAGNeT will enable the research community to construct a library of real traces of application-generated traffic from which researchers can more realistically test network protocol designs and theory. MAGNeT can also be used to verify the correct operation of protocol enhancements and to troubleshoot and tune protocol implementations.
Date:
January 1, 2001
Creator:
Feng, W. C. (Wu-Chun); Hay, J. R. (Jeffrey R.) & Gardner, M. K. (Mark K.)
Object Type:
Article
System:
The UNT Digital Library
MAGNET TOOLKIT: DESIGN, IMPLEMENTATION, AND EVALUATION.
The current trend in constructing high-performance computing systems is to connect a large number of machines via a fast interconnect or a large-scale network such as the Internet, This approach relies on the performance of the interconnect (or Internet) to enable Past, large-scale distributed computing. A detailed understanding of the communication traffic is required in order to optimize the operation of entire system. Network researchers traditionally monitor traffic in the network to gain the insight necessary to optimize network operations. Recent work suggests additional insight can be obtained by also monitoring trafflc at the application level. The Monitor for Application-Generated Network Traffic toolkit (MAGNeT) we describe here monitors application trallic patterns In production systems, thus enabling more highly optimized networks and interconnects for the next generation of high performance computing system. Keywords- monitor, measurement, network protocol, traffic characterization, TCP, MAGNet, traces, application-generated traffic, virtual supercomputing, network-aware applications, computational giids, high-perfomiance computing.
Date:
January 1, 2001
Creator:
Hay, J. R. (Jeffrey R.); Feng, W. C. (Wu-Chun) & Gardner, M. K. (Mark K.)
Object Type:
Article
System:
The UNT Digital Library
Draft versus finished sequence data for DNA and protein diagnostic signature development
Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors, or NNs) to sequence. We use SAP to assess whether draft data is sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high quality draft with error rates of 10{sup -3}-10{sup -5} ({approx} 8x coverage) of target organisms is suitable for DNA signature prediction. Low quality draft with error rates of {approx} 1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high quality draft of target and low quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation …
Date:
October 29, 2004
Creator:
Gardner, S N; Lam, M W; Smith, J R; Torres, C L & Slezak, T R
Object Type:
Article
System:
The UNT Digital Library
Recess Appointments Made by President George W. Bush, January 20, 2001- October 31, 2008
This report identifies recess appointments made by President George W. Bush from the time he took office on January 20, 2001, through October 31, 2008. Basic descriptive statistics regarding these appointments are also provided.
Date:
November 3, 2008
Creator:
Hogue, Henry B. & Bearden, Maureen
Object Type:
Report
System:
The UNT Digital Library
SUPPORTING SAFE STORAGE OF PLUTONIUM-BEARING MATERIALS THROUGH SCIENCE, ENGINEERING AND SURVEILLANCE
Reductions in the size of the U. S. nuclear weapons arsenal resulted in the need to store large quantities of plutonium-bearing metals and oxides for prolonged periods of time. To assure that the excess plutonium from the U. S. Department of Energy (DOE) sites was stored in a safe and environmentally friendly manner the plutonium-bearing materials are stabilized and packaged according to well developed criteria published as a DOE Standard. The packaged materials are stored in secure facilities and regular surveillance activities are conducted to assure continuing package integrity. The stabilization, packaging, storage and surveillance requirements were developed through extensive science and engineering activities including those related to: plutonium-environment interactions and container pressurization, corrosion and stress corrosion cracking, plutonium-container material interactions, loss of sealing capability and changes in heat transfer characteristics. This paper summarizes some of those activities and outlines ongoing science and engineering programs that assure continued safe and secure storage of the plutonium-bearing metals and oxides.
Date:
November 10, 2009
Creator:
Dunn, K.; Chandler, G.; Gardner, C.; Louthan, M. & Mcclard, J.
Object Type:
Article
System:
The UNT Digital Library
Uniform Beam Distributions at the Target of the NSRL Beam Transfer Line
Uniform irradiation of biological or material samples with charged particle beams is desired by experimenters because it reduces radiation dose errors. In this paper we present results of uniform beams produced in the NASA SPACE RADIATION LABORATORY (NSRL) at the Brookhaven National Laboratory (BNL) by a method which was developed theoretically and was proven experimentally at BNL. A similar method which requires collimation of the beam, and also lacks the flexibility of the present method to produce beam various beam sizes at the target, was patented in the year 1988. The present method of producing uniform beam distributions on a plane transverse to the direction of the beam, is based on purely magnetic focusing of the beam and requires no collimation of the beam or any other type of beam interaction with materials. It can also generate uniform beam distributions of various sizes. The method is favorably compared with alternative methods of producing uniform beam distributions and can be applied to the whole energy spectrum of the charged particle beams that are delivered by the BNL Booster synchrotron.
Date:
June 25, 2007
Creator:
Tsoupas, N.; Ahrens, L.; Brown, K. Chiang, I-Hung, Gardner, C. J.; MacKay, W. W.; Pile, P. & Rusek, A.
Object Type:
Article
System:
The UNT Digital Library
Characterization of Vadose Zone Sediments Below the TX Tank Farm: Probe Holes C3830, C3831, C3832 and 299-W10-27
Pacific Northwest National Laboratory performed detailed analyses on vadose zone sediments from within Waste Management Area T-TX-TY. This report contains all the geologic, geochemical, and selected physical characterization data collected on vadose zone sediment recovered from three probe holes (C3830, C3831, and C3832) in the TX Tank Farm, and from borehole 299-W-10-27. Sediments from borehole 299-W-10-27 are considered to be uncontaminated sediments that can be compared with contaminated sediments. This report also presents our interpretation of the sediment lithologies, the vertical extent of contamination, the migration potential of the contaminants, and the likely source of the contamination in the vadose zone and groundwater below the TX Tank Farm. Sediment from the probe holes was analyzed for: moisture, radionuclide and carbon contents;, one-to-one water extracts (soil pH, electrical conductivity, cation, trace metal, and anion data), and 8 M nitric acid extracts. Overall, our analyses showed that common ion exchange is a key mechanism that influences the distribution of contaminants within that portion of the vadose zone affected by tank liquor. We did not observe significant indications of caustic alteration of the sediment mineralogy or porosity, or significant zones of slightly elevated pH values in the probe holes. The sediments do show …
Date:
April 1, 2004
Creator:
Serne, R JEFFREY.; Bjornstad, Bruce N.; Horton, Duane G.; Lanigan, David C.; Lindenmeier, Clark W.; Lindberg, Michael J. et al.
Object Type:
Report
System:
The UNT Digital Library
TMTI Task 1.6 Genetic Engineering Methods and Detection
A large number of GE techniques can be adapted from other microorganisms to biothreat bacteria and viruses. Detection of GE in a microorganism increases in difficulty as the size of the genetic change decreases. In addition to the size of the engineered change, the consensus genomic sequence of the microorganism can impact the difficulty of detecting an engineered change in genomes that are highly variable from strain to strain. This problem will require comprehensive databases of whole genome sequences for more genetically variable biothreat bacteria and viruses. Preliminary work with microarrays for detecting synthetic elements or virulence genes and analytic bioinformatic approaches for whole genome sequence comparison to detect genetic engineering show promise for attacking this difficult problem but a large amount of future work remains.
Date:
December 4, 2009
Creator:
Slezak, T.; Lenhoff, R.; Allen, J.; Borucki, M.; Vitalis, E. & Gardner, S.
Object Type:
Report
System:
The UNT Digital Library
Dark Matter Constraints from a Cosmic Index of Refraction
The dark-matter candidates of particle physics invariably possess electromagnetic interactions, if only via quantum fluctuations. Taken en masse, dark matter can thus engender an index of refraction which deviates from its vacuum value. Its presence is signaled through frequency-dependent effects: the real part yields dispersive effects in propagation, and the imaginary part yields such in attenuation. We discuss theoretical constraints on the expansion of the index of refraction with frequency, the physical interpretation of the terms, and the particular observations needed to isolate its coefficients. This, with the advent of new opportunities to view gamma-ray bursts at cosmological distance scales, gives us a new probe of dark matter. As a first application we use the time delay determined from radio afterglow observations of gamma-ray bursts to limit the charge-to-mass ratio of dark matter to |{var_epsilon}|/M < 1.8 x 10{sup -5} eV{sup -1} at 95% CL.
Date:
April 1, 2009
Creator:
Gardner, Susan & Latimer, David C.
Object Type:
Article
System:
The UNT Digital Library
R_transport_matrices
N/A
Date:
January 1, 2008
Creator:
N., Tsoupas; MacKay, W. W.; Satogata, T.; Glenn, W.; Ahrens, L.; Brown, K. et al.
Object Type:
Report
System:
The UNT Digital Library
Characterization of Vadose Zone Sediments Below the TX Tank Farm: Boreholes C3830, C3831, C3832 and RCRA Borehole 299-W10-27
This report was revised in September 2008 to remove acid-extractable sodium data from Tables 4.8, 4.28,4.43, and 4.59. The sodium data was removed due to potential contamination introduced during the acid extraction process. The rest of the text remains unchanged from the original report issued in April 2004. The overall goal of the Tank Farm Vadose Zone Project, led by CH2M HILL Hanford Group, Inc., is to define risks from past and future single-shell tank farm activities at Hanford. To meet this goal, CH2M HILL Hanford Group, Inc. tasked scientists from Pacific Northwest National Laboratory to perform detailed analyses on vadose zone sediments from within Waste Management Area (WMA) T-TX-TY. This report is the first of two reports written to present the results of these analyses. Specifically, this report contains all the geologic, geochemical, and selected physical characterization data collected on vadose zone sediment recovered from boreholes C3830, C3831, and C3832 in the TX Tank Farm, and from borehole 299-W-10-27 installed northeast of the TY Tank Farm.
Date:
September 11, 2008
Creator:
Serne, R. Jeffrey; Bjornstad, Bruce N.; Horton, Duane G.; Lanigan, David C.; Lindenmeier, Clark W.; Lindberg, Michael J. et al.
Object Type:
Report
System:
The UNT Digital Library
Direct measurement of the W boson decay width in proton-antiproton collisions at s**(1/2) = 1.96-TeV
This dissertation describes a direct measurement of the W boson total decay width, {Lambda}{sub W}, using the D0 detector at the Fermilab Tevatron Collider. The measurement uses an integrated luminosity of 177.3 pb{sup -1} data, collected during the 2002-2003 run. The width is determined from the shape of the transverse mass distribution, M{sub T}, by fitting the data in the tail region 100 < M{sub T} < 200 GeV. The result if {Lambda}{sub W} = 2.011 {+-} 0.093(stat) {+-} 0.107(syst) GeV.
Date:
October 1, 2004
Creator:
Zhu, Jun-jie
Object Type:
Thesis or Dissertation
System:
The UNT Digital Library