The polymerase chain reaction (PCR) is an enzyme-based chemical reaction that manufactures copies of one or more identifying regions of double-stranded DNA sequences (target sequences). These copies of target DNA are known as ''amplicons''. By creating millions of these copies of the identifying sequences (when they are present!), PCR allows researchers to detect by them, and hence the presence of the relevant organism, with techniques such as electrophoresis, flow cytometry, or spectrometry. Although there are numerous commercial PCR instruments that are designed for bench-top use in a laboratory, the challenges of building a battery-powered instrument that could perform such assays in the field.

Optical design capabilities continue to play the same strong role at Lawrence Livermore National Laboratory (LLNL) that they have played in the past. From defense applications to the solid-state laser programs to the Atomic Vapor Laser Isotope Separation (AVLIS), members of the optical design group played critical roles in producing effective system designs and are actively continuing this tradition. This talk will explain the role optical design plays at LLNL, outline current capabilities and summarize a few activities in which the optical design team has been recently participating.

Geological, geophysical, and engineering-geological research conducted at the 'Yeniseisky' site obtained data on climatic, geomorphologic, geological conditions, structure and properties of composing rock, and conditions of underground water recharge and discharge. These results provide sufficient information to make an estimate of the suitability of locating a radioactive waste (R W) underground isolation facility at the Nizhnekansky granitoid massif

We have developed a Nd:doped cladding pumped fiber amplifier, which operates at 938nm with greater than 2W of output power. The core co-dopants were specifically chosen to enhance emission at 938nm. The fiber was liquid nitrogen cooled in order to achieve four-level laser operation on a laser transition that is normally three level at room temperature, thus permitting efficient cladding pumping of the amplifier. Wavelength selective attenuation was induced by bending the fiber around a mandrel, which permitted near complete suppression of amplified spontaneous emission at 1088nm. We are presently seeking to scale the output of this laser to 10W. We will discuss the fiber and laser design issues involved in scaling the laser to the 10W power level and present our most recent results.

The BTeV collaboration will record approximately 2 petabytes of raw data per year. It plans to analyze this data using the distributed resources of the collaboration as well as dedicated resources, primarily residing in the very large BTeV trigger farm, and resources accessible through the developing world-wide data grid. The data analysis system is being designed from the very start with this approach in mind. In particular, we plan a fully disk-based data storage system with multiple copies of the data distributed across the collaboration to provide redundancy and to optimize access. We will also position ourself to take maximum advantage of shared systems, as well as dedicated systems, at our collaborating institutions.

We discuss the possible signatures in the electroweak symmetry breaking sector by new strong dynamics at future hadron colliders such as the Tevatron upgrade, the LHC and VLHC, and e{sup +}e{sup -} linear colliders. Examples include a heavy Higgs-like scalar resonance, a heavy Technicolor-like vector resonance and pseudo-Goldstone states, non-resonance signatures via enhanced gauge-boson scattering and fermion compositeness.

Recent revolutions in computer hardware and software technologies have paved the way for the large-scale deployment of clusters of commodity computers to address problems heretofore the domain of tightly coupled SMP processors. Near term projects within High Energy Physics and other computing communities will deploy clusters of scale 1000s of processors and be used by 100s to 1000s of independent users. This will expand the reach in both dimensions by an order of magnitude from the current successful production facilities. The goals of this workshop were: (1) to determine what tools exist which can scale up to the cluster sizes foreseen for the next generation of HENP experiments (several thousand nodes) and by implication to identify areas where some investment of money or effort is likely to be needed. (2) To compare and record experimences gained with such tools. (3) To produce a practical guide to all stages of planning, installing, building and operating a large computing cluster in HENP. (4) To identify and connect groups with similar interest within HENP and the larger clustering community.

Since their early application to elliptic partial differential equations, multigrid methods have been applied successfully to a large and growing class of problems, from elasticity and computational fluid dynamics to geodetics and molecular structures. Classical multigrid begins with a two-grid process. First, iterative relaxation is applied, whose effect is to smooth the error. Then a coarse-grid correction is applied, in which the smooth error is determined on a coarser grid. This error is interpolated to the fine grid and used to correct the fine-grid approximation. Applying this method recursively to solve the coarse-grid problem leads to multigrid. The coarse-grid correction works because the residual equation is linear. But this is not the case for nonlinear problems, and different strategies must be employed. In this presentation we describe how to apply multigrid to nonlinear problems. There are two basic approaches. The first is to apply a linearization scheme, such as the Newton's method, and to employ multigrid for the solution of the Jacobian system in each iteration. The second is to apply multigrid directly to the nonlinear problem by employing the so-called Full Approximation Scheme (FAS). In FAS a nonlinear iteration is applied to smooth the error. The full equation is …

We discuss the physics opportunities and detector challenges at future hadron colliders. As guidelines for energies and luminosities we use the proposed luminosity and/or energy upgrade of the LHC (SLHC), and the Fermilab design of a Very Large Hadron Collider (VLHC). We illustrate the physics capabilities of future hadron colliders for a variety of new physics scenarios (supersymmetry, strong electroweak symmetry breaking, new gauge bosons, compositeness and extra dimensions). We also investigate the prospects of doing precision Higgs physics studies at such a machine, and list selected Standard Model physics rates.

We report on the status and plans of experiments now running or proposed for electron-positron colliders at energies between the {phi} and the Z. The e{sup +}e{sup -}B and charm factories we considered were PEP-II/BABAR, KEKB/Belle, superKEK, SuperBABAR, and CESR-c/CLEO-c. We reviewed the programs at the {phi} factory at Frascati and the proposed PEP-N facility at Stanford Linear Accelerator Center. We studied the prospects for B physics with a dedicated linear collider Z factory, associated with the TESLA high energy linear collider. In all cases, we compared the physics reach of these facilities with that of alternative experiments at hadron colliders or fixed target facilities.

We have examined how a Linear Collider program of 1000 fb{sup -1} could be constructed in the case that a very rich program of new physics is accessible at {radical}s {le} 500 GeV. We have examined possible run plans that would allow the measurement of the parameters of a 120 GeV Higgs boson, the top quark, and could give information on the sparticle masses in SUSY scenarios in which many states are accessible. We find that the construction of the run plan (the specific energies for collider operation, the mix of initial state electron polarization states, and the use of special e{sup -}e{sup -} runs) will depend quite sensitively on the specifics of the supersymmetry model, as the decay channels open to particular sparticles vary drastically and discontinuously as the underlying SUSY model parameters are varied. We have explored this dependence somewhat by considering two rather closely related SUSY model points. We have called for operation at a high energy to study kinematic end points, followed by runs in the vicinity of several two body production thresholds once their location is determined by the end point studies. For our benchmarks, the end point runs are capable of disentangling most sparticle …

In this summary of the considerations of the QCD working group at Snowmass 2001, the roles of quantum chromodynamics in the Standard Model and in the search for new physics are reviewed, with empahsis on frontier areas in the field. We discuss the importance of, and prospects for, precision QCD in perturbative and lattice calculations. We describe new ideas in the analysis of parton distribution functions and jet structure, and review progress in small-x and in polarization experiments.

We present a summary of our experimental understanding of the top quark and discuss the significant improvements expected in Run II at the Fermilab Tevatron Collider. We also discuss prospects for a Higgs boson discovery at the Tevatron.

The properties of radio galaxies and quasars with and without optical or X-ray jets are compared. The majority of jets from which high-frequency emission has been detected so far (13 with optical emission, 11 with X-rays, 13 with both) are associated with the most powerful radio sources at any given redshift. It is found that optical/X-ray jet sources are more strongly beamed than the average population of extragalactic radio sources. This suggests that the detection or non-detection of optical emission from jets has so far been dominated by surface brightness selection effects, not by jet physics. It implies that optical jets are much more common than is currently appreciated.

Context and Objective: Vigorous exercise, alcohol and weight loss are all known to increase HDL-cholesterol, however, it is not known whether these interventions raise low HDL as effectively as has been demonstrated for normal HDL. Design: Physician-supplied medical data from 7,288 male and 2,359 female runners were divided into five strata according to their self-reported usual running distance, reported alcohol intake, body mass index (BMI) or waist circumference. Within each stratum, the 5th, 10th, 25th, 50th, 75th, 90th, and 95th percentiles for HDL-cholesterol were then determined. Bootstrap resampling of least-squares regression was applied to determine the cross-sectional relationships between these factors and each percentile of the HDL-cholesterol distribution. Results: In both sexes, the rise in HDL-cholesterol per unit of vigorous exercise or alcohol intake was at least twice as great at the 95th percentile as at the 5th percentile of the HDL-distribution. There was also a significant graded increase in the slopes relating exercise (km run) and alcohol intake to HDL between the 5th and the 95th percentile. Men's HDL-cholesterol decreased in association with fatness (BMI and waist circumference) more sharply at the 95th than at the 5th percentile of the HDL-distribution. Conclusions: Although exercise, alcohol and adiposity were all …

We present a clear and general method for constructing hierarchical vector bases of arbitrary polynomial degree for use in the finite element solution of Maxwell's equations. Hierarchical bases enable p-refinement methods, where elements in a mesh can have different degrees of approximation, to be easily implemented. This can prove to be quite useful as sections of a computational domain can be selectively refined in order to achieve a greater error tolerance without the cost of refining the entire domain. While there are hierarchical formulations of vector finite elements in publication (e.g. [1]), they are defined for tetrahedral elements only, and are not generalized for arbitrary polynomial degree. Recently, Hiptmair, motivated by the theory of exterior algebra and differential forms presented a unified mathematical framework for the construction of conforming finite element spaces [2]. In [2], both 1-form (also called H(curl)) and 2-form (also called H(div)) conforming finite element spaces and the definition of their degrees of freedom are presented. These degrees of freedom are weighted integrals where the weighting function determines the character of the bases, i.e. interpolatory, hierarchical, etc.

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High pT hadrons produced in ultra-relativistic heavy-ion collisions at RHIC probe nuclear matter at extreme conditions of high energy density. Experimental measurements in Au+Au collisions at sqrt sNN=130, 200 GeV establish the existence of strong medium effects on hadron production well into the perturbative regime.

Image segmentation transforms pixel-level information from raw images to a higher level of abstraction in which related pixels are grouped into disjoint spatial regions. Such regions typically correspond to natural or man-made objects or structures, natural variations in land cover, etc. For many image interpretation tasks (such as land use assessment, automatic target cueing, defining relationships between objects, etc.), segmentation can be an important early step. Remotely sensed images (e.g., multi-spectral and hyperspectral images) often contain many spectral bands (i.e., multiple layers of 2D images). Multi-band images are important because they contain more information than single-band images. Objects or natural variations that are readily apparent in certain spectral bands may be invisible in 2D broadband images. In this paper, the classical region growing approach to image segmentation is generalized from single to multi-band images. While it is widely recognized that the quality of image segmentation is affected by which segmentation algorithm is used, this paper shows that algorithm parameter values can have an even more profound effect. A novel self-calibration framework is developed for automatically selecting parameter values that produce segmentations that most closely resemble a calibration edge map (derived separately using a simple edge detector). Although the framework is …

The structure of the low-density lipoprotein receptor extracellular portion has been determined. The document proposes a mechanism for the release of lipoprotein in the endosome. Without this release, the mechanism of receptor recycling cannot function.

A materials test program was developed to measure mechanical properties of A285 carbon steel under conditions relevant to waste storage tanks at the Savannah River Site.

The status of ''flavor physics'' in our pursuit of knowledge in elementary particle physics is discussed. Then, the BTeV experiment, planned for the Fermilab Tevatron collider, is described briefly and its physics reach is discussed. Comparisons are made to the current B physics experiments at e{sup +}e{sup -} facilities and to the LHCb experiment, planned for the Large Hadron Collider at CERN.

It is well known that vertical head gradients exist in natural aquifer systems, and borehole flowmeter data have shown that such gradients commonly set up spontaneous vertical flows in monitoring wells, often called ambient flows. What has not been fully appreciated until recently is the serious detrimental effects such flows can have on solute concentration and hydraulic head measurements in monitoring wells. This communication explores the possibilities of diminishing ambient flows by increasing the hydraulic resistance to vertical flow within monitoring wells and limiting the penetration of such wells. Analyzed also are the surprising effects that vertical gradients may have on the equilibrium water level in a monitoring well. Results are based on collected data, numerical flow simulations, and hydraulic analysis in the near-well vicinity.

We present the construction status of the LBNL Positron Emission Mammography (PEM) camera, which utilizes a PET detector module with depth of interaction measurement consisting of 64 LSO crystals (3x3x30 mm3) coupled on one end to a single photomultiplier tube (PMT) and on the opposite end to a 64 pixel array of silicon photodiodes (PDs). The PMT provides an accurate timing pulse, the PDs identify the crystal of interaction, the sum provides a total energy signal, and the PD/(PD+PMT) ratio determines the depth of interaction. We have completed construction of all 42 PEM detector modules. All data acquisition electronics have been completed, fully tested and loaded onto the gantry. We have demonstrated that all functions of the custom IC work using the production rigid-flex boards and data acquisition system. Preliminary detector module characterization and coincidence data have been taken using the production system, including initial images.