Other written product issued by the Government Accountability Office with an abstract that begins "This is Appendix 2 of GAO's 2006 Performance and Accountability Report. Section 6 of the GAO Personnel Flexibilities Act of 2000, Pub. L. No. 106-303 (2000), and section 11 of the GAO Human Capital Reform Act of 2004, Pub. L. No. 108-271 (2004), require GAO to report to the Congress regarding its use of certain of the provisions of these acts."

We discuss the recent results on open charm measurements at RHIC. The heavy flavor upgrade program for both PHENIX and STAR experiments are briefly discussed. The completion of the program will yield important information on light flavor thermalization of the partonic matter created in high-energy nuclear collisions at RHIC. A new era of RHIC is ahead of us with the progress of the upgrade program.

The long range strategic goal of the Department of Energy's Building Technologies (DOE/BT) Program is to create, by 2020, technologies and design approaches that enable the construction of net-zero energy homes at low incremental cost (DOE/BT 2005). A net zero energy home (NZEH) is a residential building with greatly reduced needs for energy through efficiency gains, with the balance of energy needs supplied by renewable technologies. While initially focused on new construction, these technologies and design approaches are intended to have application to buildings constructed before 2020 as well resulting in substantial reduction in energy use for all building types and ages. DOE/BT's Emerging Technologies (ET) team is working to support this strategic goal by identifying and developing advanced heating, ventilating, air-conditioning, and water heating (HVAC/WH) technology options applicable to NZEHs. Although the energy efficiency of heating, ventilating, and air-conditioning (HVAC) equipment has increased substantially in recent years, new approaches are needed to continue this trend. Dramatic efficiency improvements are necessary to enable progress toward the NZEH goals, and will require a radical rethinking of opportunities to improve system performance. The large reductions in HVAC energy consumption necessary to support the NZEH goals require a systems-oriented analysis approach that characterizes …

Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity--based (blast hit distribution) and two sequence composition--based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.

This note discusses the estimation of systematic uncertainties and their incorporation into upper limit calculations. Two different approaches to reducing systematics and their degrading impact on upper limits are introduced. An improved {chi}{sup 2} function is defined which is useful in comparing Poisson distributed data with models marginalized by systematic uncertainties. Also, a technique using profile likelihoods is introduced which provides a means of constraining the degrading impact of systematic uncertainties on limit calculations.

Most cosmic-ray air shower arrays have focused on detectingelectromagnetic shower particles and low energy muons. A few groups (mostnotably MACRO + EASTOP and SPASE + AMANDA) have studied the high energymuon component of showers. However, these experiments had small solidangles, and did not study muons far from the core. The IceTop + IceCubecombination, with its 1 km$^2$ muon detection area can study muons farfrom the shower core. IceCube can measure their energy loss ($dE/dx$),and hence their energy. With the energy, and the known distribution ofproduction heights, the transverse momentum ($p_T$) spectrum of high$p_T$ muons can be determined. The production of the semuons iscalculable in perturbative QCD, so the measured muon spectra can be usedto probe the composition of incident cosmic-rays.

I study the incorporation of renormalization group (RG)improved BFKL kernels in the Balitsky-Kovchegov (BK) equation whichdescribes parton saturation. The RG improvement takes into accountimportant parts of the next-to-leading and higher order logarithmiccorrections to the kernel. The traveling wave front method for analyzingthe BK equation is generalized to deal with RG-resummed kernels,restricting to the interesting case of fixed QCD coupling. The resultsshow that the higher order corrections suppress the rapid increase of thesaturation scale with increasing rapidity. I also perform a "diffusive"differential equation approximation, which illustrates that someimportant qualitative properties of the kernel change when including RGcorrections.

Aggregation and integration are processes that occur in human societies throughout the globe. An informative example of population aggregation and social integration can be observed in the North American desert borderlands from A.D. 250 to 1450 in the area known as the Mogollon region. In fact, Mogollon communities oscillated from smaller social groups into larger ones and dispersed into smaller groups only to form larger ones again. For this reason, examining the groups of people living in the Mogollon region provides a magnified view of social change over a substantial period. Understanding patterns of aggregation and integration provides researchers with the promise for research into the nature of these phenomena. In general, the Mogollon region is characterized by limited water supplies and low average annual precipitation. However, pockets of the Mogollon area, including the Mimbres valley and the Gila River valley, represent oases, where permanent rivers and their associated tributaries allowed for the pursuit of agricultural endeavors and access to a wide variety of wild plant and animal resources. The areas with these kinds of potential became population centers for previously dispersed groups of people living in the region. These people exploited natural resources and practiced agriculture in areas surrounding …

The detector of the D0 experiment at the proton anti-proton collider Tevatron in Run II is discussed in detail. The performance of the collider and the experiment is presented. Standard model Higgs searches with integrated luminosities between 260 pb{sup -1} and 950 pb{sup -1} and their combination are performed. No deviation from SM background expectation has been observed. Sensitivity prospects at the Tevatron are shown.

An RFQ-based neutron generator system is described that produces pulsed neutrons for the active screening of sea-land cargo containers for the detection of shielded special nuclear materials (SNM). A microwave-driven deuteron source is coupled to an electrostatic LEBT that injects a 40 mA D+ beam into a 6 MeV, 5.1 meter-long 200 MHz RFQ. The RFQ has a unique beam dynamics design and is capable of operating at duty factors of 5 to 10% accelerating a D+ time-averaged current of up to 1.5 mA at 5% duty factor, including species and transmission loss. The beam is transported through a specially-designed thin-window into a 2.5-atmosphere deuterium gas target. A high-frequency dipole magnet is used to scan the beam over the long dimension of the 5 by 35 cm target window. The source will deliver a neutron flux of 1x10$sup 7$ n/(cm$sup 2$s) to the center of an empty cargo container. Details of the ion source, LEBT, RFQ beam dynamics and gas target design are presented.

We performed a search for Standard Model Higgs boson production in association with W boson (p{bar p} {yields} W{sup {+-}}H {yields} {ell}{nu}b{bar b}) in p{bar p} collisions at {radical}s = 1.96 TeV. The search uses the data collected between February 2002 and February 2006 at Collider Detector at Fermilab (CDF), which corresponds to an integrated luminosity of about 1 fb{sup -1}. The experimental final state of WH {yields} {ell}{nu}b{bar b} process is lepton (e{sup {+-}}/{mu}{sup {+-}}), missing transverse energy and two jets. The largest background in lepton+jets events is W+light flavor process, therefore the identification of jets as b-jets reduces this kind of background significantly. We used displaced SECondary VerTeX b-tagging (SECVTX) technique, which utilizes the signature that b-jets have secondary vertex displaced away from primary vertex because of the long life time of B-mesons. However, there is still much contamination in SECVTX b-tagged jets. Finite resolution of secondary vertex tracking measurements results in false tags, and c-jets are also identified as b-jets due to the long life time of D-mesons frequently. For the purpose of increasing the purity of the SECVTX b-tagged jets, we applied Neural Network to SECVTX tagged jets for the first time by using secondary vertex …

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This document is the third revision of the 'Monitoring Well Inspection and Maintenance Plan' for groundwater wells associated with the US Department of Energy (DOE) Y-12 National Security Complex (Y-12) in Oak Ridge, Tennessee. This plan describes the systematic approach for: (1) inspecting the physical condition of monitoring wells at Y-12; (2) identifying maintenance needs that extend the life of the well and assure well-head protection is in place, and (3) identifying wells that no longer meet acceptable monitoring-well design or well construction standards and require plugging and abandonment. The inspection and maintenance of groundwater monitoring wells is one of the primary management strategies of the Y-12 Groundwater Protection Program (GWPP) Management Plan, 'proactive stewardship of the extensive monitoring well network at Y-12' (BWXT 2004a). Effective stewardship, and a program of routine inspections of the physical condition of each monitoring well, ensures that representative water-quality monitoring and hydrologic data are able to be obtained from the well network. In accordance with the Y-12 GWPP Monitoring Optimization Plan (MOP) for Groundwater Monitoring Wells at the Y-12 National Security Complex, Oak Ridge, Tennessee (BWXT 2006b), the status designation (active or inactive) for each well determines the scope and extent of well inspections …

Just as automobiles need fuel to operate, so do nuclear reactors. When fossil fuels such as gasoline are burned to power an automobile, they are consumed immediately and nearly completely in the process. When the fuel is gone, energy production stops. Nuclear reactors are incapable of achieving this near complete burn-up because as the fuel (uranium) that powers them is burned through the process of nuclear fission, a variety of other elements are also created and become intimately associated with the uranium. Because they absorb neutrons, which energize the fission process, these accumulating fission products eventually poison the fuel by stopping the production of energy from it. The fission products may also damage the structural integrity of the fuel elements. Even though the uranium fuel is still present, sometimes in significant quantities, it is unburnable and will not power a reactor unless it is separated from the neutron-absorbing fission products by a method called fuel reprocessing. Construction of the Fuel Reprocessing Complex at the Chem Plant started in 1950 with the Bechtel Corporation serving as construction contractor and American Cyanamid Company as operating contractor. Although the Foster Wheeler Corporation assumed responsibility for the detailed working design of the overall plant, …

The alignment system for the CMS Muon Endcap detector employs several hundred sensors such as optical 1-D CCD sensors illuminated by lasers and analog distance- and tilt-sensors to monitor the positions of one sixth of 468 large Cathode Strip Chambers. The chambers mounted on the endcap yoke disks undergo substantial deformation on the order of centimeters when the 4T field is switched on and off. The Muon Endcap alignment system is required to monitor chamber positions with 75-200 {micro}m accuracy in the R? plane, {approx}400 {micro}m in the radial direction, and {approx}1 mm in the z-direction along the beam axis. The complete alignment hardware for one of the two endcaps has been installed at CERN. A major system test was performed when the 4T solenoid magnet was ramped up to full field for the first time in August 2006. We present the overall system design and first results on disk deformations, which indicate that the measurements agree with expectations.

This report estimate the energy savings, economic impacts, and pollution reduction from adopting the 2003 International Code Council’s 2003 International Energy Conservation Code (as the mandatory residential energy efficiency code in the state of West Virginia. The state currently allows a less stringent replacement option. This report addresses the impacts for low-rise residential buildings only.

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NbTi accelerator dipoles are limited to magnetic fields (H)of about 10 T, due to an intrinsic upper critical field(Hc2) limitationof 14 T. To surpass this restriction, prototype Nb3Sn magnets are beingdeveloped which have reached 16 T. We show that Nb3Sn dipole technologyis practically limited to 17 to 18 T due to insufficient high fieldpinning, and intrinsically to 20 to 22 T due to Hc2 limitations.Therefore, to obtain magnetic fields approaching 20 T and higher, amaterial is required with a higher Hc2 and sufficient high field pinningcapacity. A realistic candidate for this purpose is Bi-2212, which isavailable in roundwires and sufficient lengths for the fabrication ofcoils based on Rutherford-type cables. We initiated a program to developthe required technology to construct accelerator magnets from'windand-react' (W&R) Bi-2212 coils. We outline the complicationsthat arise through the use of Bi-2212, describe the development paths toaddress these issues, and conclude with the design of W&R Bi-2212sub-scale magnets.

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

Quantum mechanical ab initio calculation constitutes the biggest portion of the computer time in material science and chemical science simulations. As a computer center like NERSC, to better serve these communities, it will be very useful to have a prediction for the future trends of ab initio calculations in these areas. Such prediction can help us to decide what future computer architecture can be most useful for these communities, and what should be emphasized on in future supercomputer procurement. As the size of the computer and the size of the simulated physical systems increase, there is a renewed interest in using the real space grid method in electronic structure calculations. This is fueled by two factors. First, it is generally assumed that the real space grid method is more suitable for parallel computation for its limited communication requirement, compared with spectrum method where a global FFT is required. Second, as the size N of the calculated system increases together with the computer power, O(N) scaling approaches become more favorable than the traditional direct O(N{sup 3}) scaling methods. These O(N) methods are usually based on localized orbital in real space, which can be described more naturally by the real space basis. …

In the event of a short-term, large-scale toxic chemical release to the atmosphere, shelter-in-place (SIP) may be used as an emergency response to protect public health. We modeled hypothetical releases using realistic, empirical parameters to explore how key factors influence SIP effectiveness for single-family dwellings in a residential district. Four classes of factors were evaluated in this case-study: (a) time scales associated with release duration, SIP implementation delay, and SIP termination; (b) building air-exchange rates, including air infiltration and ventilation; (c) the degree of sorption of toxic chemicals to indoor surfaces; and (d) the shape of the dose-response relationship for acute adverse health effects. Houses with lower air leakage are more effective shelters, and thus variability in the air leakage of dwellings is associated with varying degrees of SIP protection in a community. Sorption on indoor surfaces improves SIP effectiveness by lowering the peak indoor concentrations and reducing the amount of contamination in the indoor air. Nonlinear dose-response relationships imply substantial reduction in adverse health effects from lowering the peak exposure concentration. However, if the scenario is unfavorable for sheltering (e.g. sheltering in leaky houses for protection against a nonsorbing chemical with a linear dose-response), the community must implement SIP …

Biclustering has many applications in text mining, web clickstream mining, and bioinformatics. When data entries are binary, the tightest biclusters become bicliques. We propose a flexible and highly efficient algorithm to compute bicliques. We first generalize the Motzkin-Straus formalism for computing the maximal clique from L{sub 1} constraint to L{sub p} constraint, which enables us to provide a generalized Motzkin-Straus formalism for computing maximal-edge bicliques. By adjusting parameters, the algorithm can favor biclusters with more rows less columns, or vice verse, thus increasing the flexibility of the targeted biclusters. We then propose an algorithm to solve the generalized Motzkin-Straus optimization problem. The algorithm is provably convergent and has a computational complexity of O(|E|) where |E| is the number of edges. It relies on a matrix vector multiplication and runs efficiently on most current computer architectures. Using this algorithm, we bicluster the yeast protein complex interaction network. We find that biclustering protein complexes at the protein level does not clearly reflect the functional linkage among protein complexes in many cases, while biclustering at protein domain level can reveal many underlying linkages. We show several new biologically significant results.

Demand response is the most underutilized power system reliability resource in North America. Technological advances now make it possible to tap this resource to both reduce costs and improve. Misconceptions concerning response capabilities tend to force loads to provide responses that they are less able to provide and often prohibit them from providing the most valuable reliability services. Fortunately this is beginning to change with some ISOs making more extensive use of load response. This report is structured as a series of short questions and answers that address load response capabilities and power system reliability needs. Its objective is to further the use of responsive load as a bulk power system reliability resource in providing the fastest and most valuable ancillary services.

The Remote-Handled Transuranic (RH-TRU) Content Codes (RH-TRUCON) document describes the inventory of RH-TRU waste within the transportation parameters specified by the Remote-Handled Transuranic Waste Authorized Methods for Payload Control (RH-TRAMPAC).1 The RH-TRAMPAC defines the allowable payload for the RH-TRU 72-B. This document is a catalog of RH-TRU 72-B authorized contents by site. A content code is defined by the following components: • A two-letter site abbreviation that designates the physical location of the generated/stored waste (e.g., ID for Idaho National Laboratory [INL]). The site-specific letter designations for each of the sites are provided in Table 1. • A three-digit code that designates the physical and chemical form of the waste (e.g., content code 317 denotes TRU Metal Waste). For RH-TRU waste to be transported in the RH-TRU 72-B, the first number of this three-digit code is “3.” The second and third numbers of the three-digit code describe the physical and chemical form of the waste. Table 2 provides a brief description of each generic code. Content codes are further defined as subcodes by an alpha trailer after the three-digit code to allow segregation of wastes that differ in one or more parameter(s). For example, the alpha trailers of the subcodes …