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Abbreviated Pandemic Influenza Planning Template for Primary Care Offices (open access)

Abbreviated Pandemic Influenza Planning Template for Primary Care Offices

The Abbreviated Pandemic Influenza Plan Template for Primary Care Provider Offices is intended to assist primary care providers and office managers with preparing their offices for quickly putting a plan in place to handle an increase in patient calls and visits, whether during the 2009-2010 influenza season or future influenza seasons.
Date: January 1, 2010
Creator: CHE, HCTT
System: The UNT Digital Library
The ArgoNeuT experiment (open access)

The ArgoNeuT experiment

ArgoNeuT is a Liquid Argon Time Projection Chamber neutrino experiment that recently completed its physics run in the NuMI beamline at Fermilab. Along with research and design for future LArTPCs, the experiments goals include performing a number of neutrino and anti-neutrino cross section measurements. Also, ArgoNeuT hopes to further the understanding of the nuclear physics involved in neutrino scattering by characterizing the low energy protons created in such interactions.
Date: January 1, 2010
Creator: Spitz, J. & U., /Yale
System: The UNT Digital Library
B baryon production and decays and B hadron lifetimes (open access)

B baryon production and decays and B hadron lifetimes

In this paper we review the most recent results concerning B Baryons at CDF and D0, including the observation and the study of the properties of the {Omega}{sub b}{sup -}, {Xi}{sub b}{sup -} and {Sigma}{sub b}{sup {+-}(*)}, the observation of new {Lambda}{sub b}{sup 0} decay modes, and a new measurement of the lifetime of the b hadrons in decays with a J/{Psi}. The {Omega}{sub b}{sup -} baryon is observed through the decay chain {Omega}{sub b}{sup -} {yields} J/{Psi}{Omega}{sup -}, where J/{Psi} {yields} {mu}{sup +}{mu}{sup -}, {Omega}{sup -} {yields} {Lambda}K{sup -}, and {Lambda} {yields} pK{sup -}, using 4.2 fb{sup -1} of data. The {Omega}{sub b}{sup -} mass is measured to be 6054.4 {+-} 6.8(stat.) {+-} 0.9(syst.) MeV/c{sup 2}, and the lifetime 1.13{sub -0.40}{sup +0.53}(stat.) {+-} 0.02(syst.) ps. For the {Xi}{sub b}{sup -} the mass is measured 5790.9 {+-} 2.6(stat.) {+-} 0.8(syst.) MeV/c{sup 2} and the lifetime 1.56{sub -0.25}{sup +0.27}(stat.) {+-} 0.02(syst.) ps. A new accurate measurement of the properties of the resonances {Sigma}{sub b}{sup +}, {Sigma}{sub b}{sup -}, {Sigma}*{sub b}{sup +}, and {Sigma}*{sub b}{sup -} has been performed in 6 fb{sup -1} of data, and the masses have been determined, m({Sigma}{sub b}{sup +}) = 5811.2{sub -0.8}{sup +0.9}(stat.) {+-} 1.7(syst.), m({Sigma}{sub b}{sup …
Date: January 1, 2010
Creator: Donati, S.
System: The UNT Digital Library
Baryon spectroscopy results at the Tevatron (open access)

Baryon spectroscopy results at the Tevatron

The Tevatron at Fermilab continues to collect data at high luminosity resulting in datasets in excess of 6 fb{sup -1} of integrated luminosity. The high collision energies allow for the observation of new heavy quark baryon states not currently accessible at any other facility. In addition to the ground state {Lambda}{sub b}, the spectroscopy and properties of the new heavy baryon states {Omega}{sub b}, {Xi}{sub b}, and {Sigma}{sub b}{sup (*)} as measured by the CDF and D0 Collaborations are presented.
Date: January 1, 2010
Creator: Van Kooten, R.
System: The UNT Digital Library
CDF GlideinWMS usage in grid computing of high energy physics (open access)

CDF GlideinWMS usage in grid computing of high energy physics

Many members of large science collaborations already have specialized grids available to advance their research in the need of getting more computing resources for data analysis. This has forced the Collider Detector at Fermilab (CDF) collaboration to move beyond the usage of dedicated resources and start exploiting Grid resources. Nowadays, CDF experiment is increasingly relying on glidein-based computing pools for data reconstruction. Especially, Monte Carlo production and user data analysis, serving over 400 users by central analysis farm middleware (CAF) on the top of Condor batch system and CDF Grid infrastructure. Condor is designed as distributed architecture and its glidein mechanism of pilot jobs is ideal for abstracting the Grid computing by making a virtual private computing pool. We would like to present the first production use of the generic pilot-based Workload Management System (glideinWMS), which is an implementation of the pilot mechanism based on the Condor distributed infrastructure. CDF Grid computing uses glideinWMS for its data reconstruction on the FNAL campus Grid, user analysis and Monte Carlo production across Open Science Grid (OSG). We review this computing model and setup used including CDF specific configuration within the glideinWMS system which provides powerful scalability and makes Grid computing working like …
Date: January 1, 2010
Creator: Zvada, Marian; /Fermilab /Kosice, IEF; Benjamin, Doug; U., /Duke; Sfiligoi, Igor & /Fermilab
System: The UNT Digital Library
CDF software distribution on the grid using Parrot (open access)

CDF software distribution on the grid using Parrot

Large international collaborations that use decentralized computing models are becoming a custom rather than an exception in High Energy Physics. A good computing model for such big collaborations has to deal with the distribution of the experiment-specific software around the world. When the CDF experiment developed its software infrastructure, most computing was done on dedicated clusters. As a result, libraries, configuration files and large executables were deployed over a shared file system. In order to adapt its computing model to the Grid, CDF decided to distribute its software to all European Grid sites using Parrot, a user-level application capable of attaching existing programs to remote I/O systems through the filesystem interface. This choice allows CDF to use just one centralized source of code and a scalable set of caches all around Europe to efficiently distribute its code and requires almost no interaction with the existing Grid middleware or with local system administrators. This system has been in production at CDF in Europe since almost two years. Here, we present CDF implementation of Parrot and some comments on its performances.
Date: January 1, 2010
Creator: Compostella, G.; /INFN, CNAF; Pagan Griso, S.; U., /Padua; Lucchesi, D.; U., /Padua et al.
System: The UNT Digital Library
CMS centres worldwide: A new collaborative infrastructure (open access)

CMS centres worldwide: A new collaborative infrastructure

The CMS Experiment at the LHC is establishing a global network of inter-connected 'CMS Centres' for controls, operations and monitoring. These support: (1) CMS data quality monitoring, detector calibrations, and analysis; and (2) computing operations for the processing, storage and distribution of CMS data. We describe the infrastructure, computing, software, and communications systems required to create an effective and affordable CMS Centre. We present our highly successful operations experiences with the major CMS Centres at CERN, Fermilab, and DESY during the LHC first beam data-taking and cosmic ray commissioning work. The status of the various centres already operating or under construction in Asia, Europe, Russia, South America, and the USA is also described. We emphasise the collaborative communications aspects. For example, virtual co-location of experts in CMS Centres Worldwide is achieved using high-quality permanently-running 'telepresence' video links. Generic Web-based tools have been developed and deployed for monitoring, control, display management and outreach.
Date: January 1, 2010
Creator: Taylor, Lucas & Gottschalk, Erik
System: The UNT Digital Library
A collaborative network middleware project by Lambda Station, TeraPaths, and Phoebus (open access)

A collaborative network middleware project by Lambda Station, TeraPaths, and Phoebus

The TeraPaths, Lambda Station, and Phoebus projects, funded by the US Department of Energy, have successfully developed network middleware services that establish on-demand and manage true end-to-end, Quality-of-Service (QoS) aware, virtual network paths across multiple administrative network domains, select network paths and gracefully reroute traffic over these dynamic paths, and streamline traffic between packet and circuit networks using transparent gateways. These services improve network QoS and performance for applications, playing a critical role in the effective use of emerging dynamic circuit network services. They provide interfaces to applications, such as dCache SRM, translate network service requests into network device configurations, and coordinate with each other to setup up end-to-end network paths. The End Site Control Plane Subsystem (ESCPS) builds upon the success of the three projects by combining their individual capabilities into the next generation of network middleware. ESCPS addresses challenges such as cross-domain control plane signalling and interoperability, authentication and authorization in a Grid environment, topology discovery, and dynamic status tracking. The new network middleware will take full advantage of the perfSONAR monitoring infrastructure and the Inter-Domain Control plane efforts and will be deployed and fully vetted in the Large Hadron Collider data movement environment.
Date: January 1, 2010
Creator: Bobyshev, A.; /Fermilab; Bradley, S.; /Brookhaven; Crawford, M.; /Fermilab et al.
System: The UNT Digital Library
Commissioning of the Cryogenics of the LHC Long Straight Sections (open access)

Commissioning of the Cryogenics of the LHC Long Straight Sections

The LHC is made of eight circular arcs interspaced with eight Long Straight Sections (LSS). Most powering interfaces to the LHC are located in these sections where the particle beams are focused and shaped for collision, cleaning and acceleration. The LSSs are constituted of several unique cryogenic devices and systems like electrical feed-boxes, standalone superconducting magnets, superconducting links, RF cavities and final focusing superconducting magnets. This paper presents the cryogenic commissioning and the main results obtained during the first operation of the LHC Long Straight Sections.
Date: January 1, 2010
Creator: Perin, A.; Casas-Cubillos, J.; Claudet, S.; Darve, C.; Ferlin, G.; Millet, F. et al.
System: The UNT Digital Library
Comparison Between Nb3Al and Nb3Sn Strands and Cables for High Field Accelerator Magnets (open access)

Comparison Between Nb3Al and Nb3Sn Strands and Cables for High Field Accelerator Magnets

The Nb{sub 3}Al small racetrack magnet, SR07, has been successfully built and tested to its short sample limit beyond 10 Tesla without any training. Thus the practical application of Nb{sub 3}Al strands for high field accelerator magnets is established. The characteristics of the representative F4 strand and cable, are compared with the typical Nb{sub 3}Sn strand and cable. It is represented by the OST high current RRP Nb{sub 3}Sn strand with 108/127 configuration. The effects of Rutherford cabling to both type strands are explained and the inherent problem of the Nb{sub 3}Sn strand is discussed. Also the test results of two representative small racetrack magnets are compared from the stand point of Ic values, and training. The maximum current density of the Nb{sub 3}Al strands is still smaller than that of the Nb{sub 3}Sn strands, but if we take into account of the stress-strain characteristics, Nb{sub 3}Al strands become somewhat favorable in some applications.
Date: January 1, 2010
Creator: Yamada, R.; Kikuchi, A.; Barzi, E.; Chlachidze, G.; Rusy, A.; Takeuchi, T. et al.
System: The UNT Digital Library
Comparison of Direct Normal Irradiance Derived from Silicon and Thermopile Global Hemispherical Radiation Detectors: Preprint (open access)

Comparison of Direct Normal Irradiance Derived from Silicon and Thermopile Global Hemispherical Radiation Detectors: Preprint

Concentrating solar applications utilize direct normal irradiance (DNI) radiation, a measurement rarely available. The solar concentrator industry has begun to deploy numerous measurement stations to prospect for suitable system deployment sites. Rotating shadowband radiometers (RSR) using silicon photodiodes as detectors are typically deployed. This paper compares direct beam estimates from RSR to a total hemispherical measuring radiometer (SPN1) multiple fast thermopiles. These detectors simultaneously measure total and diffuse radiation from which DNI can be computed. Both the SPN1 and RSR-derived DNI are compared to DNI measured with thermopile pyrheliometers. Our comparison shows that the SPN1 radiometer DNI estimated uncertainty is somewhat greater than, and on the same order as, the RSR DNI estimates for DNI magnitudes useful to concentrator technologies.
Date: January 1, 2010
Creator: Myers, D. R.
System: The UNT Digital Library
Computational Investigation of FeS2 Surfaces and Prediction of Effects of Sulfur Environment on Stabilities (open access)

Computational Investigation of FeS2 Surfaces and Prediction of Effects of Sulfur Environment on Stabilities

Density functional theory calculations were employed to investigate the (001), (210), (III), and (110) surfaces of, F~S2' The surface free ene:gies were calculated in equilibrium with a sulfur environment using firstpnnclples based thermodynamics approach. Surfaces that feature metal atoms in their outermost layer are predicted to be higher m energy. Wlthm the studied subset of (I x I) terminations, the stoichiometric (001) surface termmated by a layer of sulfur atoms is the most stable for sulfur-lean condition. For increasingly sulfur-nch enVIronment, two structures were found to have notably lower surface energies compared to others. They have (210) and (Ill) orientation, both terminated by layers of sulfur. Interestingly, these surfaces are nonstoichiometric exhibiting an excess of sulfur atoms.
Date: January 1, 2010
Creator: Alfonso, D. R.
System: The UNT Digital Library
Coordinating Pediatric Medical Care during an Influenza Pandemic - Hospital Workbook (open access)

Coordinating Pediatric Medical Care during an Influenza Pandemic - Hospital Workbook

This workbook is intended to assist hospitals with coordinating medical care for pediatric influenza-like illness across their community.
Date: January 1, 2010
Creator: CHE, HCTT
System: The UNT Digital Library
Current Lead Design for the Accelerator Project for Upgrade of LHC (open access)

Current Lead Design for the Accelerator Project for Upgrade of LHC

The Accelerator Project for Upgrade of LHC (APUL) is a U.S. project participating in and contributing to CERN's Large Hadron Collider (LHC) upgrade program. In collaboration with Brookhaven National Laboratory, Fermilab is developing sub-systems for an upgrade of the LHC final focus magnet systems. A concept of main and auxiliary helium flow was developed that allows the superconductor to remain cold while the lead body warms up to prevent upper section frosting. The auxiliary flow will subsequently cool the thermal shields of the feed box and the transmission line cryostats. A thermal analysis of the current lead central heat exchange section was performed using analytic and FEA techniques. A method of remote soldering was developed that allows the current leads to be field replaceable. The remote solder joint was designed to be made without flux or additional solder, and able to be remade up to ten full cycles. A method of upper section attachment was developed that allows high pressure sealing of the helium volume. Test fixtures for both remote soldering and upper section attachment for the 13 kA lead were produced. The cooling concept, thermal analyses, and test results from both remote soldering and upper section attachment fixtures are …
Date: January 1, 2010
Creator: Brandt, Jeffrey S.; Cheban, Sergey; Feher, Sandor; Kaducak, Marc; Nobrega, Fred & Peterson, Tom
System: The UNT Digital Library
D0 Measurement of the elastic p anti-p differential cross section for 0.25<|t|<1.2-GeV**2 at s**(1/2) = 1.96-TeV (open access)

D0 Measurement of the elastic p anti-p differential cross section for 0.25<|t|<1.2-GeV**2 at s**(1/2) = 1.96-TeV

A measurement of the p{bar p} elastic differential cross section, d{sigma}/d|t|, is presented as a function of the four-momentum transfer squared, |t|. The results are obtained from L {approx} 30 nb{sup -1} of data collected by the D0 experiment at {radical}s = 1.96 TeV at the Fermilab Tevatron during a two-day period optimized for low |t| acceptance. In the range 0.25 &lt; |t| &lt; 0.6 GeV{sup 2} the differential cross section is observed to decay more rapidly than in the range 0.6 &lt; |t| &lt; 1.2 GeV2, where a much more gradual decay is observed. A fit of the form d{sigma}/d|t| = C exp-b|t|, performed in the range 0.25 &lt; |t| &lt; 0.6 GeV{sup 2}, yields an exponential slope parameter of b = 16.54 {+-} 0.10(stat) {+-} 0.80(syst) GeV{sup -2}.
Date: January 1, 2010
Creator: Brandt, Andrew & /Texas U., Arlington
System: The UNT Digital Library
D0 results on diphoton direct production and double parton interactions in photon + 3 jet events (open access)

D0 results on diphoton direct production and double parton interactions in photon + 3 jet events

We report the measurement of differential diphoton direct production cross sections and a study of photon + 3-jet events with double parton (DP) interactions, based on data taken with the D0 experiment at the Fermilab Tevatron proton-antiproton collider. We measure single differential cross sections as a function of the diphoton mass, the transverse momentum of the diphoton system, the azimuthal angle between the photons, and the polar scattering angle of the photons. In addition, we measure double differential cross sections considering the last three kinematic variables in three diphoton mass bins. The results are compared with different perturbative QCD predictions and event generators. We have used a sample of photon + 3-jet events collected by the D0 experiment with an integrated luminosity of about 1 fb{sup -1} to determine the fraction of events with double parton scattering (f{sub DP}) in a single p{bar p} collision at {radical}s = 1.96 TeV. The DP fraction and effective cross section ({sigma}{sub eff}), a process-independent scale parameter related to the parton density inside the nucleon, are measured in three intervals of the second (ordered in p{sub T}) jet transverse momentum p{sub T}{sup jet2} within the range 15 &lt; p{sub T}{sup jet} &lt; 30 GeV. …
Date: January 1, 2010
Creator: Sawyer, Lee & U., /Louisiana Tech.
System: The UNT Digital Library
D0 results on three-jet production, multijet cross-section ratios, and minimum bias angular correlations (open access)

D0 results on three-jet production, multijet cross-section ratios, and minimum bias angular correlations

We report the measurement of the cross-section for three-jet production and the ratio of inclusive three-jet to two-jet cross-sections, as well as a study of angular correlations in minimum bias events, based on data taken with the D0 experiment at the Fermilab Tevatron proton-antiproton collider. The differential inclusive three-jet cross section as a function of the invariant three-jetmass (M{sub 3jet}) is measured in p{bar p} collisions at {radical}s = 1.96 TeV using a data set corresponding to an integrated luminosity of 0.7 fb{sup -1}. The measurement is performed in three rapidity regions (|y| &lt; 0.8, |y| &lt; 1.6 and |y| &lt; 2.4) and in three regions of the third (ordered in p{sub T}) jet transverse momenta (p{sub T3} &gt; 40 GeV, p{sub T3} &gt; 70 GeV, p{sub T3} &gt; 100 GeV) for events with leading jet transverse momentum larger than 150 GeV and well separated jets. NLO QCD calculations are found to be in a reasonable agreement with the measured cross sections. Based on the same data set, we present the first measurement of ratios of multi-jet cross sections in p{bar p} collisions at {radical}s = 1.96 TeV at the Fermilab Tevatron Collider. The ratio of inclusive trijet and dijet …
Date: January 1, 2010
Creator: Sawyer, Lee & U., /Louisiana Tech.
System: The UNT Digital Library
Dependence of the $t\bar{t}$ production cross section on the transverse momentum of the top quark (open access)

Dependence of the $t\bar{t}$ production cross section on the transverse momentum of the top quark

None
Date: January 1, 2010
Creator: Abazov, V. M.; Abbott, B.; Abolins, M.; Acharya, B. S.; Adams, M.; Adams, T. et al.
System: The UNT Digital Library
Design, Simulation, Fabrication, and Preliminary Tests of 3D CMS Pixel Detectors for the Super-LHC (open access)

Design, Simulation, Fabrication, and Preliminary Tests of 3D CMS Pixel Detectors for the Super-LHC

The Super-LHC upgrade puts strong demands on the radiation hardness of the innermost tracking detectors of the CMS, which cannot be fulfilled with any conventional planar detector design. The so-called 3D detector architectures, which feature columnar electrodes passing through the substrate thickness, are under investigation as a potential solution for the closest operation points to the beams, where the radiation fluence is estimated to reach 10{sup 16} n{sub eq}/cm{sup 2}. Two different 3D detector designs with CMS pixel readout electronics are being developed and evaluated for their advantages and drawbacks. The fabrication of full-3D active edge CMS pixel devices with p-type substrate has been successfully completed at SINTEF. In this paper, we study the expected post-irradiation behaviors of these devices with simulations and, after a brief description of their fabrication, we report the first leakage current measurement results as performed on wafer.
Date: January 1, 2010
Creator: Koybasi, Ozhan; Bortoletto, Daniela; Hansen, Thor-Erik; Kok, Angela; Hansen, Trond Andreas; Lietaer, Nicolas et al.
System: The UNT Digital Library
Direct, Dynamic Measurement of Interfacial Area within Porous Media (open access)

Direct, Dynamic Measurement of Interfacial Area within Porous Media

Standard models of two-phase flow in porous media have been shown to exhibit several shortcomings that might be partially overcome with a recently developed model based on thermodynamic principles (Hassanizadeh and Gray, 1990). This alternative two-phase flow model contains a set of new and non-standard parameters, including specific interfacial area. By incorporating interfacial area production, destruction, and propagation into functional relationships that describe the capillary pressure and saturation, a more physical model has been developed. Niessner and Hassanizadeh (2008) have examined this model numerically and have shown that the model captures saturation hysteresis with drainage/imbibition cycles. Several static experimental studies have been performed to examine the validity of this new thermodynamically based approach; these allow the determination of static parameters of the model. To date, no experimental studies have obtained information about the dynamic parameters required for the model. A new experimental porous flow cell has been constructed using stereolithography to study two-phase flow phenomena (Crandall et al. 2008). A novel image analysis tool was developed for an examination of the evolution of flow patterns during displacement experiments (Crandall et al. 2009). This analysis tool enables the direct quantification of interfacial area between fluids by matching known geometrical properties of …
Date: January 1, 2010
Creator: Crandall, Dustin; Ahmadi, Goodarz; Smith, Duane H. & Bromhal, Grant
System: The UNT Digital Library
Distributed Monte Carlo production for D0 (open access)

Distributed Monte Carlo production for D0

The D0 collaboration uses a variety of resources on four continents to pursue a strategy of flexibility and automation in the generation of simulation data. This strategy provides a resilient and opportunistic system which ensures an adequate and timely supply of simulation data to support D0's physics analyses. A mixture of facilities, dedicated and opportunistic, specialized and generic, large and small, grid job enabled and not, are used to provide a production system that has adapted to newly developing technologies. This strategy has increased the event production rate by a factor of seven and the data production rate by a factor of ten in the last three years despite diminishing manpower. Common to all production facilities is the SAM (Sequential Access to Metadata) data-grid. Job submission to the grid uses SAMGrid middleware which may forward jobs to the OSG, the WLCG, or native SAMGrid sites. The distributed computing and data handling system used by D0 will be described and the results of MC production since the deployment of grid technologies will be presented.
Date: January 1, 2010
Creator: Snow, Joel & U., /Langston
System: The UNT Digital Library
Early evolution of the LIM homeobox gene family (open access)

Early evolution of the LIM homeobox gene family

LIM homeobox (Lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons) indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three …
Date: January 1, 2010
Creator: Srivastava, Mansi; Larroux, Claire; Lu, Daniel R; Mohanty, Kareshma; Chapman, Jarrod; Degnan, Bernard M et al.
System: The UNT Digital Library
Erythroneura lawsoni abundance and feeding injury levels are influenced by foliar nutrient status in intensively managed American sycamore. (open access)

Erythroneura lawsoni abundance and feeding injury levels are influenced by foliar nutrient status in intensively managed American sycamore.

Abstract 1 Abundance and feeding injury of the leafhopper Erythroneura lawsoni Robinson was measured in an intensively-managed American sycamore Platanus occidentalis L. plantation. Trees were planted in spring 2000 in a randomized complete block design, and received one of three annual treatments: (i) fertilization (120 kg N/ha/year); (ii) irrigation (3.0 cm/week); (iii) fertilization + irrigation; or (iv) control (no treatment). 2 Foliar nutrient concentrations were significantly influenced by the treatments because only sulphur and manganese levels were not statistically greater in trees receiving fertilization. 3 Over 116 000 E. lawsoni were captured on sticky traps during the study. Leafhopper abundance was highest on nonfertilized trees for the majority of the season, and was positively correlated with foliar nutrient concentrations. Significant temporal variation in E. lawsoni abundance occurred, suggesting five discrete generations in South Carolina. 4 Significant temporal variation occurred in E. lawsoni foliar injury levels, with the highest injury ratings occurring in late June and August. Foliar injury was negatively correlated with foliar nutrient content, and higher levels of injury occurred more frequently on nonfertilized trees. 5 The results obtained in the present study indicated that increased E. lawsoni abundance occurred on trees that did not receive fertilization. Nonfertilized trees …
Date: January 1, 2010
Creator: Coyle, David, Robert: Aubrey, Doug, Patric & Bentz, Jo-Ann
System: The UNT Digital Library
Estimating DNA coverage and abundance in metagenomes using a gamma approximation (open access)

Estimating DNA coverage and abundance in metagenomes using a gamma approximation

Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that would be most efficacious. In this work, we regard a metagenome as a population of DNA fragments (bins), each of which may be covered by one or more reads. We employ a gamma distribution to model this bin population due to its flexibility and ease of use. When a gamma approximation can be found that adequately fits the data, we may estimate the number of bins that were not sequenced and that could potentially be revealed by additional sequencing. …
Date: January 1, 2010
Creator: Hooper, Sean D; Dalevi, Daniel; Pati, Amrita; Mavromatis, Konstantinos; Ivanova, Natalia N & Kyrpides, Nikos C
System: The UNT Digital Library