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At least 127 records · Page 7

A DESI ‘Petal’ in Bloom: Time-Lapse Video

This time-lapse video sequence shows how how components are assembled for a single wedge-shaped petal that is part of the Dark Energy Spectroscopic Instrument’s focal plane. This video condenses the work on this petal – which took several weeks – down to about 5 minutes. In all, the focal plane will be composed of 10 petals, each holding 500 robotic positioners. Each of these positioners carries a fiber-optic cable, and the cables will be individually pointed at preset sequences of distant galaxies to gather their light. The light signatures from these galaxies will form the basis for the largest 3-D map of the universe. Each positioner is outfitted with a 3-meter length of fiber-optic cable that will be precisely fused with a 50-meter cable. The focal plane will sit high atop the Mayall Telescope at Kitt Peak National Observatory near Tucson, Arizona. (Credit: Berkeley Lab)

47 OTHER INSTRUMENTATION↗

DESI Focal Plane Assembly: Time-Lapse Video

This 56-second time-lapse video shows three different camera views of assembly work for the Dark Energy Spectroscopic Instrument’s Focal Plane. First, it shows the process of joining separate lengths of fiber-optic cables, known as fusion splicing. More than 5,000 fiber-optic cables, each measuring over 50 meters, will extend from near the top of the Mayall Telescope down to devices known as spectrographs that will be used to measure the properties of light from millions of distant galaxies. The Mayall Telescope is at Kitt Peak National Observatory near Tucson, Arizona. The middle portion of the video shows another view of the focal plane assembly area, and the final camera view shows the installation of robotic positioners into a wedge-shaped “petal.” The focal plan will be composed of 10 of these petals, each carrying 500 robotic positioners. (Credit: Berkeley Lab)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Time-Lapse Monitoring of DNA Damage Colocalized With Particle Tracks in Single Living Cells

Purpose: Understanding the DNA damage and repair induced by hadron therapy (HT) beams is crucial for developing novel strategies to maximize the use of HT beams to treat cancer patients. However, spatiotemporal studies of DNA damage and repair for beam energies relevant to HT have been challenging. We report a technique that enables spatiotemporal measurement of radiation-induced damage in live cells and colocalization of this damage with charged particle tracks over a broad range of clinically relevant beam energies. The technique uses novel fluorescence nuclear track detectors with fluorescence confocal laser scanning microscopy in the beam line to visualize particle track traversals within the subcellular compartments of live cells within seconds after injury. Methods and Materials: We designed and built a portable fluorescence confocal laser scanning microscope for use in the beam path, coated fluorescence nuclear track detectors with fluorescent-tagged live cells (HT1080 expressing enhanced green fluorescent protein tagged to XRCC1, a single-strand break repair protein), placed the entire assembly into a proton therapy beam line, and irradiated the cells with a fluence of ∼1 × 10{sup 6} protons/cm{sup 2}. Results: We successfully obtained confocal images of proton tracks and foci of DNA single-strand breaks immediately after irradiation. Conclusions: This technique represents an innovative method for analyzing biological responses in any HT beam line at energies and dose rates relevant to therapy. It allows precise determination of the number of tracks traversing a subcellular compartment and monitoring the cellular damage therein, and has the potential to measure the linear energy transfer of each track from therapeutic beams.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Measurement of moisture-dependent ion diffusion constants in wood cell wall layers using time-lapse micro X-ray fluorescence microscopy

Our future bioeconomy depends on increased utilization of renewable lignocellulosic biomass. Controlling the diffusion of chemicals, such as inorganic ions, within secondary plant cell walls is central to many biomass applications. However, insufficient understanding of intra-cell-wall diffusion within secondary plant cell walls is hindering the advancement of many lignocellulosic biomass applications. In this work, X-ray fluorescence microscopy was used to measure diffusion constants of K + , Cu 2+ , and Cl - diffusing through loblolly pine (Pinus taeda) cell wall layers under 70%, 75%, or 80% relative humidity (RH). Results revealed that diffusion constants increased with RH, the larger Cu 2+ diffused more slowly than the K + , and the Cl - diffusion constant was the same as that for the counter cation, indicating cations and anions diffused together to maintain charge neutrality. Comparison with electrical conductivity measurements showed that conductivity is being controlled by ion mobility over these RH. The results further support that intra-cell-wall diffusion of inorganic ions is a Fickian diffusion process occurring through rubbery amorphous polysaccharides, which contradicts previous assertions that intra-cell-wall diffusion is an aqueous process occurring through water pathways. Researchers can now utilize polymer science approaches to engineer the molecular architecture of lignocellulosic biomass to optimize properties for specific end uses.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing the DNA damage response by cell tracking algorithms and cell features classification using high-content time-lapse analysis

Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm 2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too many DSB occur at once. High doses of ionizing radiation lead to RIF merging into repair domains which in turn increases DSB proximity and misrepair. Furthermore, such finding may therefore be critical to explain the supralinear dose dependence for chromosomal rearrangement and cell death measured after exposure to ionizing radiation.

59 BASIC BIOLOGICAL SCIENCES↗

Data and scripts associated with the manuscript "Estimating soil moisture and salinity response to simulated coastal flooding using time-lapse electrical resistivity and induced polarization monitoring”

This package contains geophysics datasets generated during the simulated ecosystem-flooding experiment – TEMPEST (Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatment). These geophysics data consist of Electrical Resistivity Imaging (ERI) and Induced Polarization (IP) datasets collected to estimate the soil moisture and salinity response to the simulated coastal flooding experiment. In addition to using geophysics datasets to estimate soil moisture and salinity response, petrophysical relationship between the measured resistivity and moisture content and salinity using the multisalinity. This package consists of two folders: “MultiSalinity Experiment” folder and “TEMPEST Experiment and petrophysical conversion” folders. The “MultiSalinity Experiment” folder contains the datasets generated from the multisalinity experiment used to develop the petrophysical reslationship. The “TEMPEST Experiment and petrophysical conversion” folder contains ERI, IP, Ground Penetrating Radar (GPR) and Electromagnetic Induction (EMI) datasets collected during the TEMPEST experiment. This study shows the ability to used geophysical datasets in estimating moisture content and salinity at scale will be useful in calibrating Earth System Models.

54 ENVIRONMENTAL SCIENCES↗

Progress Report, December 2010: Improved Site Characterization And Storage Prediction Through Stochastic Inversion Of Time-Lapse Geophysical And Geochemical Data

Over the last project six months, our project activities have concentrated on three areas: (1) performing a stochastic inversion of pattern 16 seismic data to deduce reservoir permeability, (2) development of the geochemical inversion strategy and implementation of associated software, and (3) completing the software implementation of TProGS and the geostatistical analysis that provides the information needed when using the software to produce realizations of the Midale reservoir. The report partially the following deliverables: D2: Model development: MCMC tool (synthetic fluid chemistry data); deliverable completed. D4: Model development/verification: MCMC tool (TProGS, field seismic/chemistry data) work product; deliverable requirements partially fulfilled. D5: Field-based single-pattern simulations work product; deliverable requirements partially fulfilled. When completed, our completed stochastic inversion tool will explicitly integrate reactive transport modeling, facies-based geostatistical methods, and a novel stochastic inversion technique to optimize agreement between observed and predicted storage performance. Such optimization will be accomplished through stepwise refinement of: (1) the reservoir model - principally its permeability magnitude and heterogeneity - and (2) geochemical parameters - primarily key mineral volume fractions and kinetic data. We anticipate that these refinements will facilitate significantly improved history matching and forward modeling of CO{sub 2} storage. Our tool uses the Markov Chain Monte Carlo (MCMC) methodology. Deliverable D1, previously submitted as a report titled ''Development of a Stochastic Inversion Tool To Optimize Agreement Between The Observed And Predicted Seismic Response To CO{sub 2} Injection/Migration in the Weyburn-Midale Project'' (Ramirez et al., 2009), described the stochastic inversion approach that will identify reservoir models that optimize agreement between the observed and predicted seismic response. The software that implements this approach has been completed, tested, and used to process seismic data from pattern 16. A previously submitted report titled ''Model verification: synthetic single pattern simulations using seismic reflection data'', Ramirez et al. 2010, partially fulfilled deliverable D3 by summarizing verification activities that evaluate the performance of the seismic software and its ability to recover reservoir model permeabilities using synthetic seismic reflection data. A future progress report will similarly describe summarizing verification activities of the geochemical inversion software, thereby completing deliverable D3. This document includes a chapter that shows and discusses permeability models produced by seismic inversion that used seismic data from pattern 16 in Phase 1A. It partially fulfills deliverable D5: Field-based single-pattern simulations work product. The D5 work product is supposed to summarize the results of applying NUFT/MCMC to refine the reservoir model and geochemical parameters by optimizing observation/prediction agreement for the seismic/geochemical response to CO{sub 2} injection/migration within a single pattern of Phase 1A/1B. A future progress report will show inversion results for the same pattern using geochemical data, thereby completing deliverable D5. This document also contains a chapter that fulfills deliverable D2: Model development: MCMC tool (synthetic fluid chemistry data). The chapter will summarize model development activities required to facilitate application of NUFT/MCMC to optimize agreement between the observed and predicted geochemical response to CO{sub 2} injection/migration. Lastly, this document also contains a chapter that partially fulfills deliverable D4: Model development/verification: MCMC tool (TProGS, field seismic/chemistry data) work product. This work product is supposed to summarize model development activities required for (1) application of TProGS to Weyburn, (2) use of TProGS within the MCMC tool, and (3) application of the MCMC tool to address field seismic and geochemical data. The chapter included here fulfills requirements 1 and 2. Requirement 3 will be addressed in a future progress report.

58 GEOSCIENCES↗

Final Report: Improved Site Characterization And Storage Prediction Through Stochastic Inversion Of Time-Lapse Geophysical And Geochemical Data

During the last months of this project, our project activities have concentrated on four areas: (1) performing a stochastic inversion of pattern 16 seismic data to deduce reservoir bulk/shear moduli and density; the need for this inversion was not anticipated in the original scope of work, (2) performing a stochastic inversion of pattern 16 seismic data to deduce reservoir porosity and permeability, (3) complete the software needed to perform geochemical inversions and (4) use the software to perform stochastic inversion of aqueous chemistry data to deduce mineral volume fractions. This report builds on work described in progress reports previously submitted (Ramirez et al., 2009, 2010, 2011 - reports fulfilled the requirements of deliverables D1-D4) and fulfills deliverable D5: Field-based single-pattern simulations work product. The main challenge with our stochastic inversion approach is its large computational expense, even for single reservoir patterns. We dedicated a significant level of effort to improve computational efficiency but inversions involving multiple patterns were still intractable by project's end. As a result, we were unable to fulfill Deliverable D6: Field-based multi-pattern simulations work product.

58 GEOSCIENCES↗