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Grim GP, Archuleta TN, Aragonez RJ, Atkinson DP, Batha SH, Barrios MA, Bower DE, Bradley DK, Buckles RA, Clark DD, Clark DJ, Cradick JR, Danly C, Drury OB, Fatherley VE, Finch JP, Garcia FP, Gallegos RA, Guler N, Glenn SM, Hsu AH, Izumi N, Jaramillo SA, Kyrala GA, Pape SL, Loomis EN, Mares D, Martinson DD, Ma T, Mackinnon AJ, Merrill FE, Morgan GL, Munson C, Murphy TJ, Polk PJ, Schmidt DW, Tommasini R, Tregillis IL, Valdez AC, Volegov PL, Wang TSF, Wilde CH, Wilke MD, Wilson DC, Dzenitis JM, Felker B, Fittinghoff DN, Frank M, Liddick SN, Moran MJ, Roberson GP, Weiss P, Kauffman MI, Lutz SS, Malone RM, Traille A. Summary of the first neutron image data collected at the National Ignition Facility. EPJ Web of Conferences 2013. [DOI: 10.1051/epjconf/20135913017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Guler N, Aragonez RJ, Archuleta TN, Batha SH, Clark DD, Clark DJ, Danly CR, Day RD, Fatherley VE, Finch JP, Gallegos RA, Garcia FP, Grim G, Hsu AH, Jaramillo SA, Loomis EN, Mares D, Martinson DD, Merrill FE, Morgan GL, Munson C, Murphy TJ, Oertel JA, Polk PJ, Schmidt DW, Tregillis IL, Valdez AC, Volegov PL, Wang TSF, Wilde CH, Wilke MD, Wilson DC, Atkinson DP, Bower DE, Drury OB, Dzenitis JM, Felker B, Fittinghoff DN, Frank M, Liddick SN, Moran MJ, Roberson GP, Weiss P, Buckles RA, Cradick JR, Kaufman MI, Lutz SS, Malone RM, Traille A. First downscattered neutron images from Inertial Confinement Fusion experiments at the National Ignition Facility. EPJ Web of Conferences 2013. [DOI: 10.1051/epjconf/20135913018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Merrill FE, Bower D, Buckles R, Clark DD, Danly CR, Drury OB, Dzenitis JM, Fatherley VE, Fittinghoff DN, Gallegos R, Grim GP, Guler N, Loomis EN, Lutz S, Malone RM, Martinson DD, Mares D, Morley DJ, Morgan GL, Oertel JA, Tregillis IL, Volegov PL, Weiss PB, Wilde CH, Wilson DC. The neutron imaging diagnostic at NIF (invited). Rev Sci Instrum 2012; 83:10D317. [PMID: 23126843 DOI: 10.1063/1.4739242] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A neutron imaging diagnostic has recently been commissioned at the National Ignition Facility (NIF). This new system is an important diagnostic tool for inertial fusion studies at the NIF for measuring the size and shape of the burning DT plasma during the ignition stage of Inertial Confinement Fusion (ICF) implosions. The imaging technique utilizes a pinhole neutron aperture, placed between the neutron source and a neutron detector. The detection system measures the two dimensional distribution of neutrons passing through the pinhole. This diagnostic has been designed to collect two images at two times. The long flight path for this diagnostic, 28 m, results in a chromatic separation of the neutrons, allowing the independently timed images to measure the source distribution for two neutron energies. Typically the first image measures the distribution of the 14 MeV neutrons and the second image of the 6-12 MeV neutrons. The combination of these two images has provided data on the size and shape of the burning plasma within the compressed capsule, as well as a measure of the quantity and spatial distribution of the cold fuel surrounding this core.
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Affiliation(s)
- F E Merrill
- Los Alamos National Laboratory, Los Alamos, New Mexico 87544, USA.
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Mackinnon AJ, Kline JL, Dixit SN, Glenzer SH, Edwards MJ, Callahan DA, Meezan NB, Haan SW, Kilkenny JD, Döppner T, Farley DR, Moody JD, Ralph JE, MacGowan BJ, Landen OL, Robey HF, Boehly TR, Celliers PM, Eggert JH, Krauter K, Frieders G, Ross GF, Hicks DG, Olson RE, Weber SV, Spears BK, Salmonsen JD, Michel P, Divol L, Hammel B, Thomas CA, Clark DS, Jones OS, Springer PT, Cerjan CJ, Collins GW, Glebov VY, Knauer JP, Sangster C, Stoeckl C, McKenty P, McNaney JM, Leeper RJ, Ruiz CL, Cooper GW, Nelson AG, Chandler GGA, Hahn KD, Moran MJ, Schneider MB, Palmer NE, Bionta RM, Hartouni EP, LePape S, Patel PK, Izumi N, Tommasini R, Bond EJ, Caggiano JA, Hatarik R, Grim GP, Merrill FE, Fittinghoff DN, Guler N, Drury O, Wilson DC, Herrmann HW, Stoeffl W, Casey DT, Johnson MG, Frenje JA, Petrasso RD, Zylestra A, Rinderknecht H, Kalantar DH, Dzenitis JM, Di Nicola P, Eder DC, Courdin WH, Gururangan G, Burkhart SC, Friedrich S, Blueuel DL, Bernstein LA, Eckart MJ, Munro DH, Hatchett SP, Macphee AG, Edgell DH, Bradley DK, Bell PM, Glenn SM, Simanovskaia N, Barrios MA, Benedetti R, Kyrala GA, Town RPJ, Dewald EL, Milovich JL, Widmann K, Moore AS, LaCaille G, Regan SP, Suter LJ, Felker B, Ashabranner RC, Jackson MC, Prasad R, Richardson MJ, Kohut TR, Datte PS, Krauter GW, Klingman JJ, Burr RF, Land TA, Hermann MR, Latray DA, Saunders RL, Weaver S, Cohen SJ, Berzins L, Brass SG, Palma ES, Lowe-Webb RR, McHalle GN, Arnold PA, Lagin LJ, Marshall CD, Brunton GK, Mathisen DG, Wood RD, Cox JR, Ehrlich RB, Knittel KM, Bowers MW, Zacharias RA, Young BK, Holder JP, Kimbrough JR, Ma T, La Fortune KN, Widmayer CC, Shaw MJ, Erbert GV, Jancaitis KS, DiNicola JM, Orth C, Heestand G, Kirkwood R, Haynam C, Wegner PJ, Whitman PK, Hamza A, Dzenitis EG, Wallace RJ, Bhandarkar SD, Parham TG, Dylla-Spears R, Mapoles ER, Kozioziemski BJ, Sater JD, Walters CF, Haid BJ, Fair J, Nikroo A, Giraldez E, Moreno K, Vanwonterghem B, Kauffman RL, Batha S, Larson DW, Fortner RJ, Schneider DH, Lindl JD, Patterson RW, Atherton LJ, Moses EI. Assembly of high-areal-density deuterium-tritium fuel from indirectly driven cryogenic implosions. Phys Rev Lett 2012; 108:215005. [PMID: 23003274 DOI: 10.1103/physrevlett.108.215005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Indexed: 06/01/2023]
Abstract
The National Ignition Facility has been used to compress deuterium-tritium to an average areal density of ~1.0±0.1 g cm(-2), which is 67% of the ignition requirement. These conditions were obtained using 192 laser beams with total energy of 1-1.6 MJ and peak power up to 420 TW to create a hohlraum drive with a shaped power profile, peaking at a soft x-ray radiation temperature of 275-300 eV. This pulse delivered a series of shocks that compressed a capsule containing cryogenic deuterium-tritium to a radius of 25-35 μm. Neutron images of the implosion were used to estimate a fuel density of 500-800 g cm(-3).
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Affiliation(s)
- A J Mackinnon
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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Preston CM, Harris A, Ryan JP, Roman B, Marin R, Jensen S, Everlove C, Birch J, Dzenitis JM, Pargett D, Adachi M, Turk K, Zehr JP, Scholin CA. Underwater application of quantitative PCR on an ocean mooring. PLoS One 2011; 6:e22522. [PMID: 21829630 PMCID: PMC3148215 DOI: 10.1371/journal.pone.0022522] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 06/22/2011] [Indexed: 11/21/2022] Open
Abstract
The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.
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Affiliation(s)
- Christina M Preston
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.
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Torres C, Vitalis EA, Baker BR, Gardner SN, Torres MW, Dzenitis JM. LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures. BMC Bioinformatics 2011; 12:240. [PMID: 21679460 PMCID: PMC3213686 DOI: 10.1186/1471-2105-12-240] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 06/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs. RESULTS LAVA identifies combinations of six primer regions for basic LAMP signatures, or combinations of eight primer regions for LAMP signatures with loop primers, which can be used as LAMP signatures. The identified primers are conserved among target organism sequences. Primer combinations are optimized based on lengths, melting temperatures, and spacing among primer sites. We compare LAMP signature candidates for Staphylococcus aureus created both by LAVA and by PrimerExplorer. We also include signatures from a sample run targeting all strains of Mycobacterium tuberculosis. CONCLUSIONS We have designed and demonstrated new software for identifying signature candidates appropriate for LAMP assays. The software is available for download at http://lava-dna.googlecode.com/.
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Affiliation(s)
- Clinton Torres
- Lawrence Livermore National Laboratory, Livermore, California, USA.
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Regan JF, Makarewicz AJ, Hindson BJ, Metz TR, Gutierrez DM, Corzett TH, Hadley DR, Mahnke RC, Henderer BD, Breneman IV JW, Weisgraber TH, Dzenitis JM. Environmental Monitoring for Biological Threat Agents Using the Autonomous Pathogen Detection System with Multiplexed Polymerase Chain Reaction. Anal Chem 2008; 80:7422-9. [DOI: 10.1021/ac801125x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John F. Regan
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Anthony J. Makarewicz
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Benjamin J. Hindson
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Thomas R. Metz
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Dora M. Gutierrez
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Todd H. Corzett
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Dean R. Hadley
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Ryan C. Mahnke
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Bruce D. Henderer
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - John W. Breneman IV
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - Todd H. Weisgraber
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
| | - John M. Dzenitis
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550
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Hindson BJ, Gutierrez DM, Ness KD, Makarewicz AJ, Metz TR, Setlur US, Benett WB, Loge JM, Colston, Jr. BW, Francis PS, Barnett NW, Dzenitis JM. Development of an automated DNA purification module using a micro-fabricated pillar chip. Analyst 2008; 133:248-55. [DOI: 10.1039/b713332d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hindson BJ, Makarewicz AJ, Setlur US, Henderer BD, McBride MT, Dzenitis JM. APDS: the autonomous pathogen detection system. Biosens Bioelectron 2005; 20:1925-31. [PMID: 15741059 DOI: 10.1016/j.bios.2004.09.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 09/27/2004] [Accepted: 09/29/2004] [Indexed: 11/24/2022]
Abstract
We have developed and tested a fully autonomous pathogen detection system (APDS) capable of continuously monitoring the environment for airborne biological threat agents. The system was developed to provide early warning to civilians in the event of a bioterrorism incident and can be used at high profile events for short-term, intensive monitoring or in major public buildings or transportation nodes for long-term monitoring. The APDS is completely automated, offering continuous aerosol sampling, in-line sample preparation fluidics, multiplexed detection and identification immunoassays, and nucleic acid-based polymerase chain reaction (PCR) amplification and detection. Highly multiplexed antibody-based and duplex nucleic acid-based assays are combined to reduce false positives to a very low level, lower reagent costs, and significantly expand the detection capabilities of this biosensor. This article provides an overview of the current design and operation of the APDS. Certain sub-components of the ADPS are described in detail, including the aerosol collector, the automated sample preparation module that performs multiplexed immunoassays with confirmatory PCR, and the data monitoring and communications system. Data obtained from an APDS that operated continuously for 7 days in a major U.S. transportation hub is reported.
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Affiliation(s)
- Benjamin J Hindson
- Lawrence Livermore National Laboratory, L-174, P.O. Box 808, 7000 East Avenue, Livermore, CA 94550, USA
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Hindson BJ, McBride MT, Makarewicz AJ, Henderer BD, Setlur US, Smith SM, Gutierrez DM, Metz TR, Nasarabadi SL, Venkateswaran KS, Farrow SW, Colston BW, Dzenitis JM. Autonomous Detection of Aerosolized Biological Agents by Multiplexed Immunoassay with Polymerase Chain Reaction Confirmation. Anal Chem 2004; 77:284-9. [PMID: 15623307 DOI: 10.1021/ac0489014] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The autonomous pathogen detection system (APDS) is an automated, podium-sized instrument that continuously monitors the air for biological threat agents (bacteria, viruses, and toxins). The system has been developed to warn of a biological attack in critical or high-traffic facilities and at special events. The APDS performs continuous aerosol collection, sample preparation, and detection using multiplexed immunoassay followed by confirmatory PCR using real-time TaqMan assays. We have integrated completely reusable flow-through devices that perform DNA extraction and PCR amplification. The fully integrated system was challenged with aerosolized Bacillus anthracis, Yersinia pestis, Bacillus globigii, and botulinum toxoid. By coupling highly selective antibody- and DNA-based assays, the probability of an APDS reporting a false positive is extremely low.
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Affiliation(s)
- Benjamin J Hindson
- Lawrence Livermore National Laboratory, 7000 East Avenue, P.O. Box 808, Livermore, CA 94550, USA
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Hindson BJ, Brown SB, Marshall GD, McBride MT, Makarewicz AJ, Gutierrez DM, Wolcott DK, Metz TR, Madabhushi RS, Dzenitis JM, Colston BW. Development of an Automated Sample Preparation Module for Environmental Monitoring of Biowarfare Agents. Anal Chem 2004; 76:3492-7. [PMID: 15228315 DOI: 10.1021/ac035365r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An automated sample preparation module, based upon sequential injection analysis (SIA), has been developed for use within an autonomous pathogen detection system. The SIA system interfaced aerosol sampling with multiplexed microsphere immunoassay-flow cytometric detection. Metering and sequestering of microspheres using SIA was found to be reproducible and reliable, over 24-h periods of autonomous operation. Four inbuilt immunoassay controls showed excellent immunoassay and system stability over five days of unattended continuous operation. Titration curves for two biological warfare agents, Bacillus anthracis and Yersinia pestis, obtained using the automated SIA procedure were shown to be similar to those generated using a manual microtiter plate procedure.
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Affiliation(s)
- Benjamin J Hindson
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94551, USA
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