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All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Exascale Workload Characterization and Architecture Implications

We use a hybrid methodology based on binary instrumentation and performance counters to characterize a set of proxy applications (mini-apps and PETSc applications) representative of a broad range of scientific applications (and particularly DOE's future high performance computing workloads). From this empirical basis, we create statistical models that extrapolate application properties (instruction mix, memory size, and memory bandwidth) as a function of problem size. We validate them and project the first quantitative characterization of an exascale computing workload. Finally, the exascale workload is used to evaluate a radical new exascale architecture, stacked DRAM with processor under memory (PUM). Of the two projections, one shows major potential benefits in using PUM. However, the second, more conservative projection suggests that only a small number of exascale applications are likely to be memory-bandwidth limited, but even these are fundamentally memory-capacity limited.

Balaprakash, Prasanna↗
DOE OSTI2021

A Generalized Copula-Polynomial Chaos Expansion for Probabilistic Power Flow Considering Nonlinear Correlations of PV Injections

This paper develops a generalized Copula-polynomial chaos expansion (PCE) framework for power system probabilistic power flow that can handle both linear and nonlinear correlations of uncertain power injections, such as wind and PVs. A data-driven Copula statistical model is used to capture the correlations of uncertain power injections. This allows us to resort to the Rosenblatt transformation to transform correlated variables into independent ones while preserving the dependence structure. This paves the way of leveraging the PCE for surrogate modeling and uncertainty quantification of power flow results, i.e., achieving the probabilistic distributions of power flows. Simulations carried out on the IEEE 57-bus system show that the proposed framework can get much more accurate results than other alternatives with different linear and nonlinear power injection correlations.

copula↗
DOE OSTI2017

Optimal Pulse Processing, Pile-Up Decomposition, and Applications of Silicon Drift Detectors at LCLS

Silicon drift detectors (SDDs) revolutionized spectroscopy in fields as diverse as geology and dentistry. For a subset of experiments at ultrafast, X-ray free-electron lasers (FELs), SDDs can make substantial contributions. Often the unknown spectrum is interesting, carrying science data, or the background measurement is useful to identify unexpected signals. Many measurements involve only several discrete photon energies known a priori, allowing single-event decomposition of pile-up and spectroscopic photon counting. We designed a pulse function and demonstrated that the signal amplitude (i.e., proportional to the detected energy and obtained from fitting with the pulse function), rise time, and pulse height are interrelated, and at short peaking times, the pulse height and pulse area are not optimal estimators for detected energy; instead, the signal amplitude and rise time are obtained for each pulse by fitting, thus removing the need for pulse shaping. By avoiding pulse shaping, rise times of tens of nanoseconds resulted in reduced pulse pile-up and allowed decomposition of remaining pulse pile-up at photon separation times down to hundreds of nanoseconds while yielding time-of-arrival information with the precision of 10 ns. Waveform fitting yields simultaneously high energy resolution and high counting rates (two orders of magnitude higher than current digital pulse processors). At pulsed sources or high photon rates, photon pile-up still occurs. We showed that pile-up spectrum fitting is relatively simple and preferable to pile-up spectrum deconvolution. We then developed a photon pile-up statistical model for constant intensity sources, extended it to variable intensity sources (typical for FELs), and used it to fit a complex pileup spectrum. We subsequently developed a Bayesian pile-up decomposition method that allows decomposing pile-up of single events with up to six photons from six monochromatic lines with 99% accuracy. The usefulness of SDDs will continue into the X-ray FEL era of science. Their successors, the ePixS hybrid pixel detectors, already offer hundreds of pixels, each with a similar performance to an SDD, in a compact, robust and affordable package.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Landscape‐scale lidar analysis of aboveground biomass distribution in secondary Brazilian Atlantic Forest

Abstract Secondary forests account for more than half of tropical forests and represent a growing carbon sink, but rates of biomass accumulation vary by a factor of two or more even among plots in the same landscape. To better understand the drivers of this variability, we used airborne lidar to measure forest canopy height and estimate biomass over 4529 ha at Serra do Conduru Park in Southern Bahia, Brazil. We measured trees in 30 georeferenced field plots (0.25‐ha each) to estimate biomass using allometry. Then we estimated aboveground biomass density ( ABD ) across the lidar study area using a statistical model developed from our field plots. This model related the 95th percentile of the distribution of lidar return heights to ABD . We overlaid this map of ABD on a Landsat‐derived forest age map to determine rates of biomass accumulation. We found rapid initial biomass regeneration (~6 Mg/ha yr), which slowed as forests aged. We also observed high variability in both height and biomass across the landscape within forests of similar age. Nevertheless, a regression model that accounted for spatial autocorrelation and included forest age, slope, and distance to roads or open areas explained 62 and 77 percent of the landscape variation in ABD and canopy height, respectively. Thus, while there is high spatial heterogeneity in forest recovery, and the drivers of this heterogeneity warrant further investigation, we suggest that a relatively simple set of predictor variables is sufficient to explain the majority of variance in both height and ABD in this landscape.

Becknell, Justin M.↗
DOE OSTI2015

The importance of retaining a phylogenetic perspective in traits-based community analyses

1) Many environmental stressors manifest their effects via physiological processes (traits) that can differ significantly among species and species groups. We compiled available data for three traits related to the bioconcentration of the toxic metal cadmium (Cd) from 42 aquatic insect species representing orders Ephemeroptera (mayfly), Plecoptera (stonefly), and Trichoptera (caddisfly). These traits included the propensity to take up Cd from water (uptake rate constant, ku), the ability to excrete Cd (efflux rate constant, ke), and the net result of these two processes (bioconcentration factor, BCF). 2) Ranges in these Cd bioaccumulation traits varied in magnitude across lineages (some lineages had a greater tendency to bioaccumulate Cd than others). Overlap in the ranges of trait values among different lineages was common and highlights situations where species from different lineages can share a similar trait state, but represent the high end of possible physiological values for one lineage and the low end for another. 3) Variance around the mean trait state differed widely across clades, suggesting that some groups (e.g., Ephemerellidae) are inherently more variable than others (e.g., Perlidae). Thus, trait variability/lability is at least partially a function of lineage. 4) Akaike information criterion (AIC) comparisons of statistical models were more often driven by clade than by other potential biological or ecological explanation tested. Clade-driven models generally improved with increasing taxonomic resolution. 5) Altogether, these findings suggest that lineage provides context for the analysis of species traits, and that failure to consider lineage in community-based analysis of traits may obscure important patterns of species responses to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Thermokarst rates intensify due to climate change and forest fragmentation in an Alaskan boreal forest lowland

Abstract Lowland boreal forest ecosystems in Alaska are dominated by wetlands comprised of a complex mosaic of fens, collapse‐scar bogs, low shrub/scrub, and forests growing on elevated ice‐rich permafrost soils. Thermokarst has affected the lowlands of the Tanana Flats in central Alaska for centuries, as thawing permafrost collapses forests that transition to wetlands. Located within the discontinuous permafrost zone, this region has significantly warmed over the past half‐century, and much of these carbon‐rich permafrost soils are now within ~0.5 °C of thawing. Increased permafrost thaw in lowland boreal forests in response to warming may have consequences for the climate system. This study evaluates the trajectories and potential drivers of 60 years of forest change in a landscape subjected to permafrost thaw in unburned dominant forest types (paper birch and black spruce) associated with location on elevated permafrost plateau and across multiple time periods (1949, 1978, 1986, 1998, and 2009) using historical and contemporary aerial and satellite images for change detection. We developed (i) a deterministic statistical model to evaluate the potential climatic controls on forest change using gradient boosting and regression tree analysis, and (ii) a 30 × 30 m land cover map of the Tanana Flats to estimate the potential landscape‐level losses of forest area due to thermokarst from 1949 to 2009. Over the 60‐year period, we observed a nonlinear loss of birch forests and a relatively continuous gain of spruce forest associated with thermokarst and forest succession, while gradient boosting/regression tree models identify precipitation and forest fragmentation as the primary factors controlling birch and spruce forest change, respectively. Between 1950 and 2009, landscape‐level analysis estimates a transition of ~15 km² or ~7% of birch forests to wetlands, where the greatest change followed warm periods. This work highlights that the vulnerability and resilience of lowland ice‐rich permafrost ecosystems to climate changes depend on forest type.

Lara, Mark J.↗
DOE OSTI2016

Partitioning controls on Amazon forest photosynthesis between environmental and biotic factors at hourly to interannual timescales

Gross ecosystem productivity (GEP) in tropical forests varies both with the environment and with biotic changes in photosynthetic infrastructure, but our understanding of the relative effects of these factors across timescales is limited. Here, we used a statistical model to partition the variability of seven years of eddy covariance-derived GEP in a central Amazon evergreen forest into two main causes: variation in environmental drivers (solar radiation, diffuse light fraction, and vapor pressure deficit) that interact with model parameters that govern photosynthesis and biotic variation in canopy photosynthetic light-use efficiency associated with changes in the parameters themselves. Our fitted model was able to explain most of the variability in GEP at hourly (R 2 = 0.77) to interannual (R 2 = 0.80) timescales. At hourly timescales, we found that 75% of observed GEP variability could be attributed to environmental variability. When aggregating GEP to the longer timescales (daily, monthly, and yearly), however, environmental variation explained progressively less GEP variability: At monthly timescales, it explained only 3%, much less than biotic variation in canopy photosynthetic light-use efficiency, which accounted for 63%. These results challenge modeling approaches that assume GEP is primarily controlled by the environment at both short and long timescales. Our approach distinguishing biotic from environmental variability can help to resolve debates about environmental limitations to tropical forest photosynthesis. For example, we found that biotically regulated canopy photosynthetic light-use efficiency (associated with leaf phenology) increased with sunlight during dry seasons (consistent with light but not water limitation of canopy development) but that realized GEP was nonetheless lower relative to its potential efficiency during dry than wet seasons (consistent with water limitation of photosynthesis in given assemblages of leaves). Lastly, this work highlights the importance of accounting for differential regulation of GEP at different timescales and of identifying the underlying feedbacks and adaptive mechanisms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Call Center Arrivals: When to Jointly Forecast Multiple Streams?

We consider call centers that have multiple (potentially inter‐dependent) demand arrival streams. Workforce management of such labor intensive service systems starts with forecasting future arrival demand. We investigate the question of whether and when to jointly forecast future arrivals of the multiple streams. We first develop a general statistical model to simultaneously forecast multi‐stream arrival rates. The model takes into account three types of inter‐stream dependence. We then show with analytical and simulation studies how the forecasting benefits of the multi‐stream forecasting model vary by the type, direction, and strength of inter‐stream dependence. In particular, we find that it is beneficial to simultaneously forecast multi‐stream arrivals (instead of separately forecasting each stream), when there exists inter‐stream lag dependence among daily arrival rates. Empirical studies, using two real call center datasets further demonstrate our findings, and provide operational insights into how one chooses forecasting models for multi‐stream arrivals.

Ye, Han↗
DOE OSTI2016

The effect of a dominant initial single mode on the Kelvin–Helmholtz instability evolution: New insights on previous experimental results

This paper brings new insights on an experiment, measuring the Kelvin–Helmholtz (KH) instability evolution, performed on the OMEGA-60 laser facility. Experimental radiographs show that the initial seed perturbations in the experiment are of multimode spectrum with a dominant single-mode of 16 μm wavelength. In single-mode-dominated KH instability flows, the mixing zone (MZ) width saturates to a constant value comparable to the wavelength. However, the experimental MZ width at late times has exceeded 100 μm, an order of magnitude larger. In this work, we use numerical simulations and a statistical model in order to investigate the vortex dynamics of the KH instability for the experimental initial spectrum. Here, we conclude that the KH instability evolution in the experiment is dominated by multimode, vortex-merger dynamics, overcoming the dominant initial mode.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Stochastic analysis of surface metrology

The design and evaluation of the expected performance of optical systems require sophisticated and reliable information about the surface topography for planned optical elements before they are fabricated. Modern x-ray source facilities are reliant upon the availability of optics with unprecedented quality (surface slope accuracy <0.1 μrad). The problem is especially complex in the case of x-ray optics, particularly for the X-ray Surveyor under development and other missions. The high angular resolution and throughput of future x-ray space observatories requires hundreds of square meters of high-quality optics. The uniqueness of the optics and limited number of proficient vendors makes the fabrication extremely time consuming and expensive, mostly due to the limitations in accuracy and measurement rate of metrology used in fabrication. Here, we discuss improvements in metrology efficacy via comprehensive statistical analysis of a compact volume of metrology data. The data are considered stochastic, and a statistical model called invertible time-invariant linear filter (InTILF) is developed now for two-dimensional (2-D) surface profiles to provide compact description of the 2-D data in addition to one-dimensional data treated so far. The InTILF model captures stochastic patterns in the data and can be used as a quality metric and feedback to polishing processes, avoiding high-resolution metrology measurements over the entire optical surface. The modeling, implemented in our BeatMark™ software, allows simulating metrology data for optics made by the same vendor and technology. The data are vital for reliable specification for optical fabrication, to be exactly adequate for the required system performance.

42 ENGINEERING↗
DOE OSTI2018

Raman spectroscopy of oxygen carrier particles in harsh environments

Fossil fuel combustion processes generate CO2, a greenhouse gas of considerable concern. To reduce this emission, the National Energy Technology Laboratory (NETL) is evaluating alternative combustion approaches, including chemical looping combustion (CLC). This technique generates relatively pure CO2, suitable for subsequent capture and storage. CLC uses oxygen-carrier particles (OCPs) such as iron oxides, copper oxides, calcium sulfates, etc. to provide oxygen for the combustion process. Optimization of the overall combustion process requires knowledge of the oxidation state (e.g., content of Fe2O3 vs. Fe3O4) of the OCPs during the different stages of the CLC process. Unfortunately, the ability to make on-line measurements of the oxidation state of OCPs in harsh environments is lacking and new sensors need to be developed. We are evaluating non-contact, stand-off Raman spectroscopy to determine the relative concentrations of the oxidized and reduced forms of OCPs at temperatures between 800 °C and 1000 °C, and pressures of about 10 atm. Using cw and pulsed Raman spectroscopy, in combination with a pressurized high-temperature sample chamber, we have optimized the operating parameters such as laser wavelength, laser intensity, collection optic design, focal spot size, etc. and measured Raman spectra of various OCP materials at high temperatures. To extract from the Raman spectra relevant information such as the concentration ratio of a material in different oxidation states, the measured data needs to be processed, and statistical modeling and multivariate calibration need to be performed.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2013

Strategies for automatic online treatment plan reoptimization using clinical treatment planning system: A planning parameters study

Purpose: Adaptive radiation therapy for prostate cancer using online reoptimization provides an improved control of interfractional anatomy variations. However, the clinical implementation of online reoptimization is currently limited by the low efficiency of current strategies and the difficulties associated with integration into the current treatment planning system. This study investigates the strategies for performing fast (∼2 min) automatic online reoptimization with a clinical fluence-map-based treatment planning system; and explores the performance with different input parameters settings: dose-volume histogram (DVH) objective settings, starting stage, and iteration number (in the context of real time planning).Methods: Simulated treatments of 10 patients were reoptimized daily for the first week of treatment (5 fractions) using 12 different combinations of optimization strategies. Options for objective settings included guideline-based RTOG objectives, patient-specific objectives based on anatomy on the planning CT, and daily-CBCT anatomy-based objectives adapted from planning CT objectives. Options for starting stages involved starting reoptimization with and without the original plan's fluence map. Options for iteration numbers were 50 and 100. The adapted plans were then analyzed by statistical modeling, and compared both in terms of dosimetry and delivery efficiency.Results: All online reoptimized plans were finished within ∼2 min with excellent coverage and conformity to the daily target. The three input parameters, i.e., DVH objectives, starting stage, and iteration number, contributed to the outcome of optimization nearly independently. Patient-specific objectives generally provided better OAR sparing compared to guideline-based objectives. The benefit in high-dose sparing from incorporating daily anatomy into objective settings was positively correlated with the relative change in OAR volumes from planning CT to daily CBCT. The use of the original plan fluence map as the starting stage reduced OAR dose at the mid-dose region, but increased the monitor units by 17%. Differences of only 2cc or less in OAR V50%/V70Gy/V76Gy were observed between 100 and 50 iterations.Conclusions: It is feasible to perform automatic online reoptimization in ∼2 min using a clinical treatment planning system. Selecting optimal sets of input parameters is the key to achieving high quality reoptimized plans, and should be based on the individual patient's daily anatomy, delivery efficiency, and time allowed for plan adaptation.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2014

SU-E-T-527: Prior Knowledge Guided TomoTherapy Treatment Planning

Purpose: The quality and efficiency of radiotherapy treatment planning are highly planer dependent. Previously we have developed a statistical model to correlate anatomical features with dosimetry features of head and neck Tomotherapy treatment. The model enables us to predict the best achievable dosimetry for individual patient prior to treatment planning. The purpose of this work is to study if the prediction model can facilitate the treatment planning in both the efficiency and dosimetric quality. Methods: The anatomy-dosimetry correlation model was used to calculate the expected DVH for nine patients formerly treated. In Group A (3 patients), the model prediction agreed with the clinic plan; in Group B (3 patients), the model predicted lower larynx mean dose than the clinic plan; in Group C (3 patients), the model suggested the brainstem could be further spared. Guided by the prior knowledge, we re-planned all 9 cases. The number of interactions during the optimization process and dosimetric endpoints between the original clinical plan and model-guided re-plan were compared. Results: For Group A, the difference of target coverage and organs-at-risk sparing is insignificant (p>0.05) between the replan and the clinical plan. For Group B, the clinical plan larynx median dose is 49.4±4.7 Gy, while the prediction suggesting 40.0±6.2 Gy (p<0.05). The re-plan achieved 41.5±6.6 Gy, with similar dose on other structures as clinical plan. For Group C, the clinical plan brainstem maximum dose is 44.7±5.5 Gy. The model predicted lower value 32.2±3.8 Gy (p<0.05). The re-plans reduced brainstem maximum dose to 31.8±4.1 Gy without affecting the dosimetry of other structures. In the replanning of the 9 cases, the times operator interacted with TPS are reduced on average about 50% compared to the clinical plan. Conclusion: We have demonstrated that the prior expert knowledge embedded model improved the efficiency and quality of Tomotherapy treatment planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

MO-PIS-Exhibit Hall-01: Imaging: CT Dose Optimization Technologies I

Partners in Solutions is an exciting new program in which AAPM partners with our vendors to present practical “hands-on” information about the equipment and software systems that we use in our clinics. The imaging topic this year is CT scanner dose optimization capabilities. Note that the sessions are being held in a special purpose room built on the Exhibit Hall Floor, to encourage further interaction with the vendors. Dose Optimization Capabilities of GE Computed Tomography Scanners Presentation Time: 11:15 – 11:45 AM GE Healthcare is dedicated to the delivery of high quality clinical images through the development of technologies, which optimize the application of ionizing radiation. In computed tomography, dose management solutions fall into four categories: employs projection data and statistical modeling to decrease noise in the reconstructed image - creating an opportunity for mA reduction in the acquisition of diagnostic images. Veo represents true Model Based Iterative Reconstruction (MBiR). Using high-level algorithms in tandem with advanced computing power, Veo enables lower pixel noise standard deviation and improved spatial resolution within a single image. Advanced Adaptive Image Filters allow for maintenance of spatial resolution while reducing image noise. Examples of adaptive image space filters include Neuro 3-D filters and Cardiac Noise Reduction Filters. AutomA adjusts mA along the z-axis and is the CT equivalent of auto exposure control in conventional x-ray systems. Dynamic Z-axis Tracking offers an additional opportunity for dose reduction in helical acquisitions while SmartTrack Z-axis Tracking serves to ensure beam, collimator and detector alignment during tube rotation. SmartmA provides angular mA modulation. ECG Helical Modulation reduces mA during the systolic phase of the heart cycle. SmartBeam optimization uses bowtie beam-shaping hardware and software to filter off-axis x-rays - minimizing dose and reducing x-ray scatter. The DICOM Radiation Dose Structured Report (RDSR) generates a dose report at the conclusion of every examination. Dose Check preemptively notifies CT operators when scan parameters exceed user-defined dose thresholds. DoseWatch is an information technology application providing vendor-agnostic dose tracking and analysis for CT (and all other diagnostic x-ray modalities) SnapShot Pulse improves coronary CTA dose management. VolumeShuttle uses two acquisitions to increase coverage, decrease dose, and conserve on contrast administration. Color-Coding for Kids applies the Broselow-Luten Pediatric System to facilitate pediatric emergency care and reduce medical errors. FeatherLight achieves dose optimization through pediatric procedure-based protocols. Adventure Series scanners provide a child-friendly imaging environment promoting patient cooperation with resultant reduction in retakes and patient motion. Philips CT Dose Optimization Tools and Advanced Reconstruction Presentation Time: 11:45 ‘ 12:15 PM The first part of the talk will cover “Dose Reduction and Dose Optimization Technologies” present in Philips CT Scanners. The main Technologies to be presented include: DoseRight and tube current modulation (DoseRight, Z-DOM, 3D-DOM, DoseRight Cardiac) Special acquisition modes Beam filtration and beam shapers Eclipse collimator and ClearRay collimator NanoPanel detector DoseRight will cover automatic tube current selection that automatically adjusts the dose for the individual patient. The presentation will explore the modulation techniques currently employed in Philips CT scanners and will include the algorithmic concepts as well as illustrative examples. Modulation and current selection technologies to be covered include the Automatic Current Selection component of DoseRight, ZDOM longitudinal dose modulation, 3D-DOM (combination of longitudinal and rotational dose modulation), Cardiac Dose right (an ECG based dose modulation scheme), and the DoseRight Index (DRI) IQ index. The special acquisition modes covers acquisition techniques such as prospective gating that is designed to reduce exposure to the patient through the Cardiac Step and Shoot scan mode. This mode can substitute the much higher dose retrospective scan modes for certain types of cardiac imaging. The beam filtration and beam shaper portion will discuss the variety of filtration and beam shaping configurations available on Philips scanners. This topic includes the x-ray beam characteristics, tube filtration as well as dose compensator characteristics. The Eclipse collimator, ClearRay collimator and the NanoPanel detector portion will discuss additional technologies specific to wide coverage CT that address some of the unique challenges encountered and techniques employed to optimize image quality and optimize dose utilization. The Eclipse collimator reduces extraneous exposure by actively blocking the radiation tails at either end of helical scans that do not contribute to the image generation. The ClearRay collimator and the NanoPanel detector optimize the quality of the signal that reaches the detectors by addressing the increased scattered radiation present in wide coverage and the NanoPanel detector adds superior electronic noise characteristics valuable when imaging at a low dose level. The second part of the talk will present “Advanced Reconstruction Technologies” currently available on Philips CT Scanners. The talk will cover filtered back projection (FBP), iDose4 and Iterative Model Reconstruction (IMR). Each reconstruction method will include a discussion of the algorithm as well as similarities and differences between the algorithms. Examples illustrating the merits of each algorithm will be presented, and techniques and metrics to characterize the performance of each type of algorithm will be presented. The Filtered Back projection portion will discuss and provide a brief summary of relevant standard image reconstruction techniques in common use, and discuss the common tradeoffs when using the FBP algorithm. The iDose4 portion will present the algorithms used for iDose4 as well the different levels. The meaning of different levels of iDose4 available will be presented and quantified. Guidelines for selection iDose4 parameters based on the imaging need will be explained. The different image quality goals available with iDose4 and specifically how iDose4 enables noise reduction, spatial resolution improvement or both will be explained. The approaches to leveraging the benefits of iDose4 such as improved spatial resolution, decreased noise, and artifact prevention will be described and quantified; and measurements and metrics behind the improvements will be presented. The image quality benefits in specific imaging situations as well as how to best combine the technology with other dose reduction strategies to ensure the best image quality at a given dose level will be presented. Insight into the IMR algorithm as well as contrast to the iDose4 techniques and performance characteristics will be discussed. Metrics and techniques for characterizing this class of algorithm and IQ performance will be presented. The image quality benefits and the dose reduction capabilities of IMR will be explored. Illustrative examples of the noise reduction, spatial resolution improvement, and low contrast detectability improvements of the reconstruction method will be presented: clinical cases and phantom measurements demonstrating the benefits of IMR in the areas of low dose imaging, spatial resolution and low contrast resolution are discussed and the technical details behind the measurements will be presented compared to both iDose4 and traditional filtered back projection (FBP)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Sensitivity estimation in time-of-flight list-mode positron emission tomography

Purpose: An accurate quantification of the images in positron emission tomography (PET) requires knowing the actual sensitivity at each voxel, which represents the probability that a positron emitted in that voxel is finally detected as a coincidence of two gamma rays in a pair of detectors in the PET scanner. This sensitivity depends on the characteristics of the acquisition, as it is affected by the attenuation of the annihilation gamma rays in the body, and possible variations of the sensitivity of the scanner detectors. In this work, the authors propose a new approach to handle time-of-flight (TOF) list-mode PET data, which allows performing either or both, a self-attenuation correction, and self-normalization correction based on emission data only. Methods: The authors derive the theory using a fully Bayesian statistical model of complete data. The authors perform an initial evaluation of algorithms derived from that theory and proposed in this work using numerical 2D list-mode simulations with different TOF resolutions and total number of detected coincidences. Effects of randoms and scatter are not simulated. Results: The authors found that proposed algorithms successfully correct for unknown attenuation and scanner normalization for simulated 2D list-mode TOF-PET data. Conclusions: A new method is presented that can be used for corrections for attenuation and normalization (sensitivity) using TOF list-mode data.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Genome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002

ABSTRACT RNA degradation is an important process that influences the ultimate concentration of individual proteins inside cells. While the main enzymes that facilitate this process have been identified, global maps of RNA turnover are available for only a few species. Even in these cases, there are few sequence elements that are known to enhance or destabilize a native transcript; even fewer confer the same effect when added to a heterologous transcript. To address this knowledge gap, we assayed genome-wide RNA degradation in the cyanobacterium Synechococcus sp. strain PCC 7002 by collecting total RNA samples after stopping nascent transcription with rifampin. We quantified the abundance of each position in the transcriptome as a function of time using RNA-sequencing data and later analyzed the global mRNA decay map using machine learning principles. Half-lives, calculated on a per-ORF (open reading frame) basis, were extremely short, with a median half-life of only 0.97 min. Despite extremely rapid turnover of most mRNA, transcripts encoding proteins involved in photosynthesis were both highly expressed and highly stable. Upon inspection of these stable transcripts, we identified an enriched motif in the 3′ untranslated region (UTR) that had similarity to Rho-independent terminators. We built statistical models for half-life prediction and used them to systematically identify sequence motifs in both 5′ and 3′ UTRs that correlate with stabilized transcripts. We found that transcripts linked to a terminator containing a poly(U) tract had a longer half-life than both those without a poly(U) tract and those without a terminator. IMPORTANCE RNA degradation is an important process that affects the final concentration of individual mRNAs, affecting protein expression and cellular physiology. Studies of how RNA is degraded increase our knowledge of this fundamental process as well as enable the creation of genetic tools to manipulate RNA stability. By studying global transcript turnover, we searched for sequence elements that correlated with transcript (in)stability and used these sequences to guide tool design. This study probes global RNA turnover in a cyanobacterium, Synechococcus sp. strain PCC 7002, that both has a unique array of RNases that facilitate RNA degradation and is an industrially relevant strain that could be used to convert CO 2 and sunlight into useful products.

59 BASIC BIOLOGICAL SCIENCES↗