PNNL-13501 - Pacific Northwest National Laboratory

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Cort JR, A Yee, AM Edwards, CH Arrowsmith, and MA Kennedy. 2000. “Structure-based functional classification of hypothetical protein MTH538 from Mehtanobacterium thermoautotrophicum.” J. Mol. Biol., 302:189-203. Cort JR, A Yee, AM Edwards, CH Arrowsmith, and MA Kennedy. 2000. “NMR structure determination and structure-based functional characterization of a conserved, hypothetical protein MTH1175 from Methanobacterium thermoautotrophicum.” J. Structural & Functional Genomics (submitted). 90 FY 2000 <strong>Laboratory</strong> Directed Research and Development Annual Report Acknowledgments We are grateful to L. Aravind for his help in the analysis of the COGs for target selection. John R. Cort is a 1999 recipient of an American Cancer Society postdoctoral fellowship.
Plant Root Exudates and Microbial Gene Expression in the Rhizosphere Study Control Number: PN99056/1384 Mark T. Kingsley Nucleic acid arrays are widely used in the pharmaceutical industry to provide information on differentially expressed genes when screening drugs and drug candidate compounds. Nucleic acid, DNA array analyses provide an automatable, compact, discrete, reproducible format for analyzing genomic information of microbes and higher organisms. Gene chips are also being developed for the specific identification of organisms by both government and industry. This project explored the use of an array based on short oligonucleotide targets, for identifying agricultural pathogens by differential pattern development and recognition. Project Description This research involved 1) developing DNA microarray analytical methods for 16S rRNA from environmental samples to rapidly identify members of microbial communities, and 2) genotyping arrays for environmental organisms and potential food pathogens, and “fingerprinting” arrays for discriminating closely related organisms. We are developing fluorescent polymerase chain reaction analytical methods for agricultural crop pathogens (Kingsley 2000; Kingsley and Fritz 2000) that could have the potential to be employed in agricultural bioterrorism. DNA microarrays offer a unique ability to provide inexpensive, rapid, and specific identification of microbes. Since productivity of renewable energy biomass sources (crop, forest) can be drastically limited by bacterial, fungal, or viral pathogen attack, rapid methods for the specific identification of the causitive agent(s) is desirable. The high density of diagnostic probes achievable on microarrays provides for a highly robust analytical tool. The array technology can be integrated into online analytical devices currently under development. A goal of this project was to develop appropriate DNA diagnostic suites of oligonucleotides for agricultural and forest pathogens. As part of this initial proof-of-concept demonstration, we tested microarrays for analysis of bacterial pathogens in the genus Xanthomonas and fungal pathogens in the genus Fusarium. Some members of the genus Fusarium, in addition to leading to crop productivity losses, produce mycotoxins which are toxic and/or carcinogenic to humans or animals. Introduction The development and use of nucleic acid arrays in detection, genotyping, and analysis of gene expression, is increasing rapidly (Behr et al. 1999; Cockerill 1999; Tao et al. 1999; Westin et al. 2000). Currently, many groups are developing DNA arrays for microbial detection and identification. Genetic arrays, once prototyped and developed, offer extremely robust, yet relatively inexpensive means (the array itself is cheap) for identifying organisms. Arrays offer the ability to create multiplexed (combined) assays providing for the analysis of multiple targets simultaneously. Exploiting this powerful analytical tool for analysis of phytopathogens has not been reported. This project aims to explore the use of DNA microarrays for differentiating and identifying various Xanthomonas (bacterial) and Fusarium (fungal) phytopathogens. Since agricultural and forest productivity can be compromised by rhizosphere inhabiting pathogens such as the Fusarium species, and foliar pathogens such as Xanthomonas, rapid and sensitive methods for analysis of seeds, plant tissues, and soils by DNA microarrays offers the benefit of a highly accurate method of detection and pathogen identification. Often these pathogens remain undetected until the plants are symptomatic, which often is too late. Preventing crop losses due to early pathogen detection could become an important issue for DOE’s Bioenergy initiative where the goal is to triple the use of renewable crops for fuels and feedstock by the year 2010. Phytopathogen analysis, especially of orgranisms in the bacterial genus Xanthomonas and the fungal genus Fusarium would benefit greatly from the power of nucleic acid array analysis. Numerous clonally derived species and subspecies are known within both Fusarium and Xanthomonas. Historically, these organisms were classed according to their pathogenicity to particular hosts. Issues of genetic relatedness to other members of the genus that attacked different hosts were ignored. Only with the advent and power of nucleic acid analysis have a number of issues of taxonomic position and relatedness been Biosciences and Biotechnology 91
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Laboratory Directed Research and De
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Laboratory Directed Research and De
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Computational Science and Engineeri
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Policy and Management Sciences Asse
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Introduction Department of Energy O
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5. After reviews by the Technical a
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• The Technical Council peer revi
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methods applicable to combustion, s
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Summary Each national laboratory mu
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Study Control Number: PN0004/1411 A
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Table 1. Positive and negative ions
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m/z Arbitrary Units Figure 1. Mass
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introduce low-volatility compounds
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arrangement, but the charge is reta
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two liquid chromatographic gradient
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Integrated Microfabricated Devices
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Matrix Assisted Laser Desorption/Io
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Molecular Beam Synthesis and Charac
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temperature distribution of the des
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expected to result in significant a
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Study Control Number: PN99069/1397
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Seuss DT and KA Prather. 1999. “M
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Analysis of Receptor-Modulated Ion
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laboratory (Lu and Xie 1997; Lu et
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Automated DNA Fingerprinting Microa
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Comparison of 4 Xanthomonas Isolate
Page 55 and 56: Approach Hematopoietic (bone marrow
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Page 59 and 60: Anti-Human lgG Human lgG Protein G
Page 61 and 62: Characterization of Global Gene Reg
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Page 69 and 70: Coupled NMR and Confocal Microscopy
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in the Environmental Molecular Scie
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Simulation and Modeling of Electroc
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Summary and Conclusions We implemen
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Since the implementation of the gen
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asis of previous performance, perce
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Bioinformatics for High-Throughput
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Summary and Conclusions In previous
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User Cat - Supervisor (client) Anal
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The second goal was to research way
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Figure 1. A visualization technique
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and interactions. The flexibility o
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Figure 4. A filtered version of Fig
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Development of Modeling Tools for J
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Figure 2. Schematic of experimental
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Integrated Modeling and Simulation
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(a) (b) (c) (d) Figure 1. Results o
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Thurman DA. August 2000. Collaborat
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MARC Input initial m esh and result
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(Johnson 1999; Colligan 1999; Gould
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Modeling of High-Velocity Forming f
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Global divergence error 1 10 -14 0
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that users were unlikely to appreci
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Earth System Science
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the lateral extent of the plume so
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Biogeochemical Processes and Microb
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Analyses of populations of viable a
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The first task was to establish fiv
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purged for 2 minutes. The gas sampl
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developing code architecture to min
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Berkowitz, CM. June 2000. “Atmosp
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environmental monitoring, 2) portab
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corresponded to a current density o
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Enhancing Emissions Pre-Processing
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Environmental Fate and Effects of D
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nitrogen and unpredictable eutrophi
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Figure 1. Ordinary kriging of 2 m d
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precipitation of calcite occurred i
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Interrelationships Between Processe
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phenanthrene resistant fraction con
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injection of an immiscible gas phas
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still some key kinetic issues that
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Application of a Crop Model The res
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The Nature, Occurrence, and Origin
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Particle number concentration, 1/cm
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geometry optimized AlOOH and FeOOH
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allowable parameters using thermody
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TCE + 3H + + 3Fe 2+ Fe)=> acetylene
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Use of Shear-Thinning Fluids for In
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concentration of 0.5% AMX was the m
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Roberts AL, LA Totten, WA Arnold, D
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tetra-scale computing, envisioned a
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Energy Technology and Management
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Figure 2. Setup for the second expe
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phase. The algorithms will be teste
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[Pb-212]/[Pb-212] final 100 10 1 0.
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Plasma Particle Dielectric Fiber El
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(species, sub-species, and sex), sp
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Figure 3. Relative risk of bone and
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Development of a Preliminary Physio
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Development of a Virtual Respirator
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Figure 3. Use of the chest cavity a
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Examination of the Use of Diazolumi
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Indoor Air Pathways to Nuclear, Che
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Source Building Release Observed re
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To illustrate the potential impact
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Non-Invasive Biological Monitoring
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Materials Science and Technology
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Figure 1. (a) - (c) Successive magn
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Component Fabrication and Assembly
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Development of a Low-Cost Photoelec
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elaxations, indicating the adequacy
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Promising chemical durability, as m
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Study Control Number : PN98028/1274
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High Power Density Solid Oxide Fuel
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Hybrid Plasma Process for Vacuum De
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Matson DW, PM Martin, WD Bennett, J
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We showed the proof-of-principle ap
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Bandgap Energy (eV) 2.9 2.85 2.8 2.
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Ultrathin Electrolyte Test Results
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Detailed Investigations on Hydrogen
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identified low energy step structur
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Development of Novel Photo-Catalyst
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-2 -1 Energy (eV) 0 1 2 Cu2O SrTiO3
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Here, we perform adsorption and des
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exceed those in the all-metal devic
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Intensity (a.u.) 0 100 200 300 400
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integrated voltage (V) 0.10 0.08 0.
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The first step was to implement thi
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Spontaneous Formation of Cu2O Nano-
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Actinide Chemistry at the Aqueous-M
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Figure 5. Close-up atomic force mic
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to 300°C and 400°C. Unfortunately
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Summary and Conclusions Transmutati
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Advanced Calibration/Registration T
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Figure 1a. Violet filter Figure 1b.
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Autonomous Ultrasonic Probe for Pro
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containing nitrous oxide, an optica
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Chemical Detection Using Cavity Enh
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Figure 3 is a color rendered simula
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appropriate study has been performe
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Exploitation of Conventional Chemic
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Figures 3 and 4 illustrate the impa
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enefits of using a modified spread-
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Single Channel Signal 0.0025 0.0020
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Therefore, in order to extract the
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A next-generation technology is nee
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Wind Dir. Figure 2. Negative ion co
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Volumetric Imaging of Materials by
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amplitude and peak frequency change
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Figure 3. 13 C NMR spectrum of corn
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Approach Two flow loops, one that o
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Modification of Ion Exchange Resins
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Permanganate Treatment for the Deco
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minimized by medium exchange. After
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Figure 1. Thermogravimetric analysi
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Validation and Scale-Up of Monosacc
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Concentration (g/100g solution) Con
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Analysis of High-Volume, Hyper-Dime
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ecent figure of merit values. Shoul
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Probabilistic Methods Development f
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a) Traditional PCA-based process co
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Acronyms and Abbreviations 2-D two-
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