Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees (open access)

Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees

The goal of this project is to develop forensic genotyping assays for select agent viruses, addressing a significant capability gap for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the Taqman signature development for South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.
Date: March 27, 2012
Creator: Gardner, S & Jaing, C
Object Type: Report
System: The UNT Digital Library
Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array (open access)

Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.
Date: March 27, 2012
Creator: Gardner, S & Jaing, C
Object Type: Report
System: The UNT Digital Library
Limit of detection of Bacillus anthracis in complex soil and air samples using next-generation sequencing (open access)

Limit of detection of Bacillus anthracis in complex soil and air samples using next-generation sequencing

None
Date: March 15, 2012
Creator: Be, Nicholas A.; Thissen, James B.; Gardner, Shea; McLoughlin, Kevin; Fofanov, Viacheslav; Koshinsky, Heather et al.
Object Type: Article
System: The UNT Digital Library
Novel Perspectives for Hadron Physics (open access)

Novel Perspectives for Hadron Physics

I discuss several novel and unexpected aspects of quantum chromodynamics. These include: (a) the nonperturbative origin of intrinsic strange, charm and bottom quarks in the nucleon at large x; the breakdown of pQCD factorization theorems due to the lensing effects of initial- and final-state interactions; (b) important corrections to pQCD scaling for inclusive reactions due to processes in which hadrons are created at high transverse momentum directly in the hard processes and their relation to the baryon anomaly in high-centrality heavy-ion collisions; and (c) the nonuniversality of quark distributions in nuclei. I also discuss some novel theoretical perspectives in QCD: (a) light-front holography - a relativistic color-confining first approximation to QCD based on the AdS/CFT correspondence principle; (b) the principle of maximum conformality - a method which determines the renormalization scale at finite order in perturbation theory yielding scheme independent results; (c) the replacement of quark and gluon vacuum condensates by 'in-hadron condensates' and how this helps to resolve the conflict between QCD vacuum and the cosmological constant.
Date: March 9, 2012
Creator: Brodsky, Stanley J.
Object Type: Article
System: The UNT Digital Library
Evaluation of Visual Impact on Cultural Resources/Historic Properties: North Atlantic, Mid-Atlantic, South Atlantic, and Florida Straits, Volume 2: Appendices (open access)

Evaluation of Visual Impact on Cultural Resources/Historic Properties: North Atlantic, Mid-Atlantic, South Atlantic, and Florida Straits, Volume 2: Appendices

A list of appendices for reference to the "Evaluation of Visual Impact on Cultural Resources/Historic Properties: North Atlantic, Mid-Atlantic, South Atlantic, and Florida Straits" study.
Date: March 2012
Creator: Klein, Joel I.; Harris, Matthew D.; Tankersley, W. Matthew; Meyer, Richard; Smith, Greg C. & Chadwick, William J.
Object Type: Text
System: The UNT Digital Library
Messiah College Biodiesel Fuel Generation Project Final Technical Report (open access)

Messiah College Biodiesel Fuel Generation Project Final Technical Report

Many obvious and significant concerns arise when considering the concept of small-scale biodiesel production. Does the fuel produced meet the stringent requirements set by the commercial biodiesel industry? Is the process safe? How are small-scale producers collecting and transporting waste vegetable oil? How is waste from the biodiesel production process handled by small-scale producers? These concerns and many others were the focus of the research preformed in the Messiah College Biodiesel Fuel Generation project over the last three years. This project was a unique research program in which undergraduate engineering students at Messiah College set out to research the feasibility of small-biodiesel production for application on a campus of approximately 3000 students. This Department of Energy (DOE) funded research program developed out of almost a decade of small-scale biodiesel research and development work performed by students at Messiah College. Over the course of the last three years the research team focused on four key areas related to small-scale biodiesel production: Quality Testing and Assurance, Process and Processor Research, Process and Processor Development, and Community Education. The objectives for the Messiah College Biodiesel Fuel Generation Project included the following: 1. Preparing a laboratory facility for the development and optimization of processors …
Date: March 30, 2012
Creator: Zummo, Michael M.; Munson, J.; Derr, A.; Zemple, T.; Bray, S.; Studer, B. et al.
Object Type: Report
System: The UNT Digital Library
Radar-cross-section reduction of wind turbines. part 1. (open access)

Radar-cross-section reduction of wind turbines. part 1.

In recent years, increasing deployment of large wind-turbine farms has become an issue of growing concern for the radar community. The large radar cross section (RCS) presented by wind turbines interferes with radar operation, and the Doppler shift caused by blade rotation causes problems identifying and tracking moving targets. Each new wind-turbine farm installation must be carefully evaluated for potential disruption of radar operation for air defense, air traffic control, weather sensing, and other applications. Several approaches currently exist to minimize conflict between wind-turbine farms and radar installations, including procedural adjustments, radar upgrades, and proper choice of low-impact wind-farm sites, but each has problems with limited effectiveness or prohibitive cost. An alternative approach, heretofore not technically feasible, is to reduce the RCS of wind turbines to the extent that they can be installed near existing radar installations. This report summarizes efforts to reduce wind-turbine RCS, with a particular emphasis on the blades. The report begins with a survey of the wind-turbine RCS-reduction literature to establish a baseline for comparison. The following topics are then addressed: electromagnetic model development and validation, novel material development, integration into wind-turbine fabrication processes, integrated-absorber design, and wind-turbine RCS modeling. Related topics of interest, including alternative …
Date: March 5, 2012
Creator: Brock, Billy C.; Loui, Hung; McDonald, Jacob J.; Paquette, Joshua A.; Calkins, David A.; Miller, William K. et al.
Object Type: Report
System: The UNT Digital Library
Integrated Detection of Pathogens and Host Biomarkers for Wounds (open access)

Integrated Detection of Pathogens and Host Biomarkers for Wounds

The increasing incidence and complications arising from combat wounds has necessitated a reassessment of methods for effective treatment. Infection, excessive inflammation, and incidence of drug-resistant organisms all contribute toward negative outcomes for afflicted individuals. The organisms and host processes involved in wound progression, however, are incompletely understood. We therefore set out, using our unique technical resources, to construct a profile of combat wounds which did or did not successfully resolve. We employed the Lawrence Livermore Microbial Detection Array and identified a number of nosocomial pathogens present in wound samples. Some of these identities corresponded with bacterial isolates previously cultured, while others were not obtained via standard microbiology. Further, we optimized proteomics protocols for the identification of host biomarkers indicative of various stages in wound progression. In combination with our pathogen data, our biomarker discovery efforts will provide a profile corresponding to wound complications, and will assist significantly in treatment of these complex cases.
Date: March 19, 2012
Creator: Jaing, C
Object Type: Report
System: The UNT Digital Library
Aleutian Pribilof Islands Wind Energy Feasibility Study (open access)

Aleutian Pribilof Islands Wind Energy Feasibility Study

Under this project, the Aleutian Pribilof Islands Association (APIA) conducted wind feasibility studies for Adak, False Pass, Nikolski, Sand Point and St. George. The DOE funds were also be used to continue APIA's role as project coordinator, to expand the communication network quality between all participants and with other wind interest groups in the state and to provide continued education and training opportunities for regional participants. This DOE project began 09/01/2005. We completed the economic and technical feasibility studies for Adak. These were funded by the Alaska Energy Authority. Both wind and hydro appear to be viable renewable energy options for Adak. In False Pass the wind resource is generally good but the site has high turbulence. This would require special care with turbine selection and operations. False Pass may be more suitable for a tidal project. APIA is funded to complete a False Pass tidal feasibility study in 2012. Nikolski has superb potential for wind power development with Class 7 wind power density, moderate wind shear, bi-directional winds and low turbulence. APIA secured nearly $1M from the United States Department of Agriculture Rural Utilities Service Assistance to Rural Communities with Extremely High Energy Costs to install a 65kW wind …
Date: March 27, 2012
Creator: Wright, Bruce A.
Object Type: Report
System: The UNT Digital Library
APPLICATION OF COLUMN EXTRACTION METHOD FOR IMPURITIES ANALYSIS ON HB-LINE PLUTONIUM OXIDE IN SUPPORT OF MOX FEED PRODUCT SPECIFICATIONS (open access)

APPLICATION OF COLUMN EXTRACTION METHOD FOR IMPURITIES ANALYSIS ON HB-LINE PLUTONIUM OXIDE IN SUPPORT OF MOX FEED PRODUCT SPECIFICATIONS

The current mission at H-Canyon involves the dissolution of an Alternate Feedstocks 2 (AFS-2) inventory that contains plutonium metal. Once dissolved, HB-Line is tasked with purifying the plutonium solution via anion exchange, precipitating the Pu as oxalate, and calcining to form plutonium oxide (PuO{sub 2}). The PuO{sub 2} will provide feed product for the Mixed Oxide (MOX) Fuel Fabrication Facility, and the anion exchange raffinate will be transferred to H-Canyon. The results presented in this report document the potential success of the RE resin column extraction application on highly concentrated Pu samples to meet MOX feed product specifications. The original 'Hearts Cut' sample required a 10000x dilution to limit instrument drift on the ICP-MS method. The instrument dilution factors improved to 125x and 250x for the sample raffinate and sample eluent, respectively. As noted in the introduction, the significantly lower dilutions help to drop the total MRL for the analyte. Although the spike recoveries were half of expected in the eluent for several key elements, they were between 94-98% after Nd tracer correction. It is seen that the lower ICD limit requirements for the rare earths are attainable because of less dilution. Especially important is the extremely low Ga limit …
Date: March 20, 2012
Creator: Jones, M.; Diprete, D. & Wiedenman, B.
Object Type: Report
System: The UNT Digital Library
Cybersecurity: Selected Legal Issues (open access)

Cybersecurity: Selected Legal Issues

This report discusses selected legal issues that frequently arise in the context of recent legislation to address vulnerabilities of critical infrastructure to cyber threats, efforts to protect government networks from cyber threats, and proposals to facilitate and encourage sharing of cyber threat information amongst private sector and government entities. This report also discusses the degree to which federal law may preempt state law.
Date: March 14, 2012
Creator: Liu, Edward C.; Stevens, Gina; Ruane, Kathleen Ann; Dolan, Alissa M. & Thompson, Richard M., II
Object Type: Report
System: The UNT Digital Library
Characterization of failure modes in deep UV and deep green LEDs utilizing advanced semiconductor localization techniques. (open access)

Characterization of failure modes in deep UV and deep green LEDs utilizing advanced semiconductor localization techniques.

We present the results of a two-year early career LDRD that focused on defect localization in deep green and deep ultraviolet (UV) light-emitting diodes (LEDs). We describe the laser-based techniques (TIVA/LIVA) used to localize the defects and interpret data acquired. We also describe a defect screening method based on a quick electrical measurement to determine whether defects should be present in the LEDs. We then describe the stress conditions that caused the devices to fail and how the TIVA/LIVA techniques were used to monitor the defect signals as the devices degraded and failed. We also describe the correlation between the initial defects and final degraded or failed state of the devices. Finally we show characterization results of the devices in the failed conditions and present preliminary theories as to why the devices failed for both the InGaN (green) and AlGaN (UV) LEDs.
Date: March 1, 2012
Creator: Tangyunyong, Paiboon; Miller, Mary A. & Cole, Edward Isaac, Jr.
Object Type: Report
System: The UNT Digital Library
Gas Hydrate Characterization in the GoM using Marine EM Methods (open access)

Gas Hydrate Characterization in the GoM using Marine EM Methods

In spite of the importance of gas hydrate as a low-carbon fuel, a possible contributor to rapid climate change, and a significant natural hazard, our current understanding about the amount and distribution of submarine gas hydrate is somewhat poor; estimates of total volume vary by at least an order of magnitude, and commercially useful concentrations of hydrate have remained an elusive target. This is largely because conventional geophysical tools have intrinsic limitations in their ability to quantitatively image hydrate. It has long been known from well logs that gas hydrate is resistive compared to the host sediments, and electrical and electromagnetic methods have been proposed and occasionally used to image hydrates. This project seeks to expand our capabilities to use electromagnetic methods to explore for gas hydrate in the marine environment. An important basic science aspect of our work was to quantify the resistivity of pure gas hydrate as a function of temperature at seafloor pressures. We designed, constructed, and tested a highpressure cell in which hydrate could be synthesized and then subjected to electrical conductivity measurements. Impedance spectroscopy at frequencies between 20 Hz and 2 MHz was used to separate the effect of the blocking electrodes from the intrinsic …
Date: March 31, 2012
Creator: Constable, Steven
Object Type: Report
System: The UNT Digital Library
TMB Bulletin, March 2012 (open access)

TMB Bulletin, March 2012

Newsletter of the Texas Medical Board describing news and events as well as updates about medical licenses, disciplinary actions, and other regulatory information.
Date: March 2012
Creator: Texas Medical Board
Object Type: Journal/Magazine/Newsletter
System: The Portal to Texas History
Child Labor in America: History, Policy, and Legislative Issues (open access)

Child Labor in America: History, Policy, and Legislative Issues

The history of child labor in America is long and unsavory. It dates back to the founding of the United States. Traditionally, most children, except for the privileged few, has always worked - either for their parents or for an outside employer. Through the years, however, child labor practices have changed. This report details the history of child labor in American, the Child Labor Under the Fair Labor Standards Act, the re-emergence of the child labor issue in the late 20th century, and child labor initiatives in the 108th-112th Congresses.
Date: March 26, 2012
Creator: Mayer, Gerald
Object Type: Report
System: The UNT Digital Library
Export Controls: Proposed Reforms Create Opportunities to Address Enforcement Challenges (open access)

Export Controls: Proposed Reforms Create Opportunities to Address Enforcement Challenges

A letter report issued by the Government Accountability Office with an abstract that begins "Agencies use a risk-based approach, including workload and threat assessment data, to allocate resources, but most do not fully track those used for export control enforcement activities. As their missions are broader than export controls, agencies can use staff resources for other activities based on need, making tracking resources used solely for export control enforcement difficult. Only Commerce’s Office of Export Enforcement allocates its resources exclusively to export control enforcement as that is its primary mission. Other agencies, such as State and the Treasury, have relatively few export control enforcement staff to track. While several agencies acknowledge the need to better track export enforcement resources and have taken steps to do so, they do not know the full extent of their use of these resources and do not use this information in resource allocation decisions. In some cities, agencies are informally leveraging export enforcement resources through voluntarily created local task forces that bring together enforcement resources to work collectively on export control cases."
Date: March 27, 2012
Creator: United States. Government Accountability Office.
Object Type: Report
System: The UNT Digital Library
Cybercrime: An Overview of the Federal Computer Fraud and Abuse Statute and Related Federal Criminal Laws (open access)

Cybercrime: An Overview of the Federal Computer Fraud and Abuse Statute and Related Federal Criminal Laws

This report discusses the Computer Fraud and Abuse Act (CFAA), 18 U.S.C. 1030, outlaws conduct that victiizes computer system.
Date: March 21, 2012
Creator: Doyle, Charles
Object Type: Report
System: The UNT Digital Library
Laboratory Directed Research and Development LDRD-FY-2011 (open access)

Laboratory Directed Research and Development LDRD-FY-2011

This report provides a summary of the research conducted at the Idaho National Laboratory (INL) during Fiscal Year (FY) 2011. This report demonstrates the types of cutting edge research the INL is performing to help ensure the nation's energy security. The research conducted under this program is aligned with our strategic direction, benefits the Department of Energy (DOE) and is in compliance with DOE order 413.2B. This report summarizes the diverse research and development portfolio with emphasis on the DOE Office of Nuclear Energy (DOE-NE) mission, encompassing both advanced nuclear science and technology and underlying technologies.
Date: March 1, 2012
Creator: Tomchak, Dena
Object Type: Report
System: The UNT Digital Library
A Preliminary Analysis of Dose Rates Associated with ITER CVCS Equipment/Area Location (open access)

A Preliminary Analysis of Dose Rates Associated with ITER CVCS Equipment/Area Location

A preliminary analysis of the ITER Chemical and Volume Control System (CVCS) Area was performed to assess dose rates outside the walls and ceiling of the facility after 1.5 years of operation at shutdown, 2 days, and 10 days after shutdown. For this purpose a simplified Monte Carlo computer model was developed using the MCNP (MCNP5 Ver. 1.51) code. Two components are included: the smaller filter tank and the larger ion exchanger. These pieces of equipment are associated with the Integrated Blanket ELM Divertor Primary Heat Transfer System, which will have the largest dose rates associated with activated corrosion products during operation in comparison with other systems. The ion exchanger contained two source regions, a 1.2-m-thick resin bed above a 0.55 m-thick skirt, and a 0.8-m-thick water region. The filter constituted an additional source. Thus the model consisted of three sources (filter, resin, water), homogeneously distributed within the appropriate source regions. However, much of the results (that address individual isotopes) are presented with the two sources in the ion exchanger combined. In these cases the sources are referred to as the 'ion exchanger source' and the 'filter source.' Dimensions for the facility and components, as well as source isotopes and …
Date: March 1, 2012
Creator: Blakeman, Edward D; Ilas, Dan & Petrov, Andrei Y
Object Type: Report
System: The UNT Digital Library
Defense Acquisitions: Assessments of Selected Weapon Programs (open access)

Defense Acquisitions: Assessments of Selected Weapon Programs

A letter report issued by the Government Accountability Office with an abstract that begins "The total estimated cost of the Department of Defense’s (DOD) 2011 portfolio of 96 major defense acquisition programs stands at $1.58 trillion. In the past year, the total acquisition cost of these programs has grown by over $74.4 billion or 5 percent, of which about $31.1 billion can be attributed to factors such as inefficiencies in production, $29.6 billion to quantity changes, and $13.7 billion to research and development cost growth. DOD’s portfolio is dominated by a small number of programs, with the Joint Strike Fighter accounting for the most cost growth in the last year, and the largest projected future funding needs. The majority of the programs in the portfolio have lost buying power in the last year as their program acquisition unit costs have increased. The number of programs in the portfolio has decreased from 98 to 96 in the past year and, looking forward, is projected to decrease again next fiscal year to its lowest level since 2004."
Date: March 29, 2012
Creator: United States. Government Accountability Office.
Object Type: Report
System: The UNT Digital Library