PNNL-13501 - Pacific Northwest National Laboratory

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Bruckner-Lea CJ, MS Stottlemyre, JW Grate, DA Holman, FJ Brockman, and DP Chandler. 2000. “Rotating rod renewable microcolumns for automated, solid-phase DNA hybridization studies.” Anal. Chem. 72:4135-4141. Chandler DP, FJ Brockman, DA Holman, JW Grate, and CJ Bruckner-Lea. 2000. “Renewable microcolumns for solid-phase nucleic acid separations and analysis from environmental samples.” Trends Anal. Chem. 19:314-321. Chandler DP, BL Schuck, FJ Brockman, and CJ Bruckner-Lea. 1999. “Automated nucleic acid isolation and purification from soil extracts using renewable affinity microcolumns in a sequential injection system.” Talanta 49:969-983. Ruzicka J. 1998. “Bioligand interaction assay by flow injection absorptiometry using a renewable biosensor system enhanced by spectral resolution.” Analyst 123:1617-1623. Ruzicka J and EH Hansen. 2000. “Flow injection: from beaker to microfluidics.” Anal. Chem. 72:212A-217A. Ruzicka J and L Scampavia. 1999. “From flow injection to bead injection.” Anal. Chem. 71:257A-263A. 44 FY 2000 Laboratory Directed Research and Development Annual Report Publications and Presentations Bruckner-Lea CJ, MS Stottlemyre, DA Holman, JW Grate, FJ Brockman, and DP Chandler. 2000. “Rotating rod renewable microcolumns for automated, solid-phase DNA hybridization studies.” Anal. Chem. 72:4135-4141. Chandler DP, DA Holman, FJ Brockman, JW Grate, and CJ Bruckner-Lea. 2000. “Renewable microcolumns for solid-phase nucleic acid separations and analysis from environmental samples.” Trends in Analytical Chemistry 19(5):314-321. Grate JW, OB Egorov, and CJ Bruckner-Lea. 1999. “Renewable surfaces for separation and sensing.” Proceedings of Photonics East, SPIE International Symposium on Environmental and Industrial Sensing 3857:70-73. Bruckner-Lea CJ, DA Holman, M Stottlemyre, P Rieke, FJ Brockman, JW Grate, and DP Chandler. October 1999. “Renewable surface biosensors.” Presented at the Biosensors and Biomolecular Electronics Session of the 196th Meeting of the Electrochemical Society, Honolulu, Hawaii. Bruckner-Lea CJ, D Chandler, L Olson, D Holman, and J Grate. May 1999. “Renewable surface biosensors.” Poster presentation, IBC’s 2nd Annual International Conference on Biosensor Technologies, San Diego, California.
Characterization of Global Gene Regulation by Tumor Necrosis Factor Alpha in Genetically Defined Mice Study Control Number: PN00019/1426 Brian D. Thrall, Kwong-Kwok Wong The scientific goal of this project is to characterize gene regulation mediated by cell signaling pathways of broad applicability to human biology and environmental health. This project will serve as a means to implement and focus the Laboratory’s capabilities in mouse genomics (cDNA arrays and informatics), provide a focus and direction for the integration of genomics and bioinformatics capabilities at the Laboratory, and build capabilities in support of our biological sciences program. Project Description The cytokine tumor necrosis factor alpha (TNFα) mediates a diverse range of cellular responses induced by environmental agents, including apoptosis, cell proliferation, and differentiation. TNFα-mediated signaling pathways are known to be stimulated by a broad range of environmental agents, including radiation, chemicals, and pathogenic microbes. The cellular responses to TNFα are tissue-specific, a reflection of cell-specific patterns of genes regulated by the signaling pathways stimulated by TNFα. This project will create a mouse-specific cDNA microarray which will then be used to globally assess these gene expression patterns regulated by TNFα in isolated cells and in the whole animal. By understanding these global patterns, tissue-specific differences in gene regulation will be identified that will help integrate the key signaling pathways that govern the cell-specific responses to TNFα, in the context of the whole animal. This information can then be extended to identify the key molecular pathways that govern cell-specific responses mediated by TNFα in response to exposure to environmental contaminants such as radiation and chemicals. Introduction Among the cytokines that contribute to immune responses, tumor necrosis factor alpha (TNFα) plays both a major and early role in the inflammatory response. In addition to a physiological role in immune function, TNFα can also mediate direct cellular effects, including apoptosis and mitogenesis, as well as promote differentiation in a cell type-specific manner. Disruption of the normal signaling pathways associated with abnormal release and/or synthesis of TNFα is hypothesized to contribute to a wide range of disease states (reviewed in Luster et al. 1999). For example, an essential role for TNFα in promotion of mouse skin tumors has been independently demonstrated by two studies (Saganuma et al. 1999; Moore et al. 1999). Although the mechanisms for this are not understood, the stimulation of clonal growth of initiated cells by TNFα (secreted by tissue macrophages) is hypothesized. This hypothesis is supported by in vitro studies that demonstrate a promoting role of TNFα in mouse JB6 cells. Other pathological states linked to TNFα release or deregulation include pathologies involving the immune system, including autoimmune diseases, arthritis, multiple schlerosis, and inflammatory bowel disease (Kollias et al. 1999). Evidence for a causative role of TNFα in the etiology of lung fibrosis is particularly strong. For example, TNFα released by phagocytic lung macrophages may be responsible for a local induction of apoptosis after exposure to particulate matter associated with air pollution associated with energy-related facilities (Chin et al. 1998). Stimulation of collagen and fibrinogen synthesis in endothelial cells by TNFα is likely the initial signal that leads to lung fibrosis after prolonged exposure to particulate matter. Exposure to ionizing radiation also stimulates TNFα release in lung cells. For example, TNFα is a central mediator of the events leading to radiation-induced lung fibrosis. Interestingly however, low dose total body irradiation (0.2 Gy) has also been associated with beneficial effects of TNFα, such as inhibition of tumor cell metastasis (Hashimoto et al. 1999). The reasons for the pleitropic responses to TNFα are unclear, but most likely reflect differences in the signaling pathways induced and the global patterns of genes regulated by TNFα in different cell types. Thus, to understand the underlying basis for TNFα-mediated effects, we need to evaluate the gene networks regulated by TNFα in a global manner. Biosciences and Biotechnology 45
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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
Page 9 and 10: Introduction Department of Energy O
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Page 13 and 14: • The Technical Council peer revi
Page 15 and 16: methods applicable to combustion, s
Page 17 and 18: Summary Each national laboratory mu
Page 19 and 20: Study Control Number: PN0004/1411 A
Page 21 and 22: Table 1. Positive and negative ions
Page 23 and 24: m/z Arbitrary Units Figure 1. Mass
Page 25 and 26: introduce low-volatility compounds
Page 27 and 28: arrangement, but the charge is reta
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Page 31 and 32: Integrated Microfabricated Devices
Page 33 and 34: Matrix Assisted Laser Desorption/Io
Page 35 and 36: Molecular Beam Synthesis and Charac
Page 37 and 38: temperature distribution of the des
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Page 41 and 42: Study Control Number: PN99069/1397
Page 45 and 46: Seuss DT and KA Prather. 1999. “M
Page 47 and 48: Analysis of Receptor-Modulated Ion
Page 49 and 50: laboratory (Lu and Xie 1997; Lu et
Page 51 and 52: Automated DNA Fingerprinting Microa
Page 53 and 54: Comparison of 4 Xanthomonas Isolate
Page 55 and 56: Approach Hematopoietic (bone marrow
Page 59: Anti-Human lgG Human lgG Protein G
Page 63 and 64: PCR products for immobilization on
Page 65 and 66: identify novel proteins of importan
Page 67 and 68: Immunoprecipitaton of tyrosinephosp
Page 69 and 70: Coupled NMR and Confocal Microscopy
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Page 75 and 76: Figure 3. Hepa-1 cells undergoing a
Page 77 and 78: cellular processing (such as post-t
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Page 91 and 92: Summary and Conclusions We demonstr
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Study Control Number: PN00077/1484
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Summary and Conclusions • The gre
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Jones-Oliveira JB, JS Oliveira, HE
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• securely moves files to a targe
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Plenary invited lecture, “The Ele
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Figure 1. X3DGEN tetrahedral mesh o
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Figure 5a. OSO volume rendering of
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Development of Models of Cell-Signa
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SOS p 23 EGFR Professor Rodland at
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Oliveira JS, JB Jones-Oliveira, and
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Figure 2. Associating a dataset mar
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to 1) incorporate three-dimensional
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shown in Figure 1. Simulated result
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HostBuilder: A Tool for the Combina
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Invariant Discretization Methods fo
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Graphics, Inc., workstation. The co
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Mixed Hamiltonian Methods for Geoch
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guyanaite, and grimaldiite (see Fig
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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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