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At least 919 records · Page 51

Correcting for reporting delay: an example using dengue fever data

One complication to infectious disease forecasting efforts is delay in reporting of cases, where real-time data often under-report the true disease burden. This pair of R scripts (1) provides example code demonstrating several strategies to account for the reporting delay and improve disease forecasts and (2) applies these methods using publicly-available data on dengue fever case reporting in Puerto Rico from 1990 to 2009.

Joann VanDervort, Lauren↗

Fully Bayesian Analysis With Model Inadequacy Correction For Nuclear Graphite Property Models With Hierarchical Variance Structure

Nuclear-grade graphites are extensively utilized in the core designs of various advanced nuclear reactors. Within the reactor environment, graphite is subjected to prolonged exposure to extreme conditions, including high temperatures, radiation, and potentially molten salt and oxygen. Such exposure can induce several degradation mechanisms in graphite, such as nonuniform volumetric strains caused by irradiation and thermal expansion, leading to stresses that may compromise the performance of graphite components. Assessing component integrity, forecasting component performance over the reactor's lifespan, and developing design standards necessitate robust tools for predicting fracture initiation and propagation in graphite structural components within nuclear reactors. This code enables the Bayesian calibration of properties for nuclear-grade graphites. Using a hierarchical Bayesian approach, multiple experimental data sources are combined to develop Gaussian process models for the properties. Using the Kennedy O'Hagan framework, the uncertainties due inadequacies in the model and the inherent spread in the experimental data are quantified.

Dhulipala, Som Lakshmi NarasimhaLakshmi Narasimha ↗

iBLAST: Incremental BLAST of new sequences via automated e-value correction

Search results from local alignment search tools use statistical scores that are sensitive to the size of the database to report the quality of the result. For example, NCBI BLAST reports the best matches using similarity scores and expect values (i.e., e-values) calculated against the database size. Given the astronomical growth in genomics data throughout a genomic research investigation, sequence databases grow as new sequences are continuously being added to these databases. As a consequence, the results (e.g., best hits) and associated statistics (e.g., e-values) for a specific set of queries may change over the course of a genomic investigation. Thus, to update the results of a previously conducted BLAST search to find the best matches on an updated database, scientists must currently rerun the BLAST search against the entire updated database, which translates into irrecoverable and, in turn, wasted execution time, money, and computational resources. To address this issue, we devise a novel and efficient method to redeem past BLAST searches by introducing iBLAST. iBLAST leverages previous BLAST search results to conduct the same query search but only on the incremental (i.e., newly added) part of the database, recomputes the associated critical statistics such as e-values, and combines these results to produce updated search results. Our experimental results and fidelity analyses show that iBLAST delivers search results that are identical to NCBI BLAST at a substantially reduced computational cost, i.e., iBLAST performs (1 + δ )/ δ times faster than NCBI BLAST, where δ represents the fraction of database growth. We then present three different use cases to demonstrate that iBLAST can enable efficient biological discovery at a much faster speed with a substantially reduced computational cost.

59 BASIC BIOLOGICAL SCIENCES↗

Correction: “When I talk about it, my eyes light up!” Impacts of a national laboratory internship on community college student success

The ORCID iDs are missing for the second, fourth, sixth, seventh, eighth and ninth author. Please see the authors’ respective ORCID iDs here: Author Seth Van Doren’s ORCID iD is: 0000-0003-0674-277X (https://orcid.org/0000-0003-0674-277X). Author Julio Jaramillo Salcido’s ORCID iD is: 0000-0002-4113-5345 (https://orcid.org/orcid.org/0000-0002-4113-5345) Author Gabriel Otero Munoz’s ORCID iD is: 0000-0002-1444-8020 (https://orcid.org/0000-0002-1444-8020) Author Aparna Manocha’s ORCID iD is: 0000-0001-7824-9971 (https://orcid.org/0000-0001-7824-9971) Author Colette L. Flood’s ORCID iD is: 0000-0002-8674-0872 (https://orcid.org/0000-0002-8674-0872) Author Anne M. Baranger’s ORCID iD is: 0000-0002-1973-4632 (https://orcid.org/0000-0002-1973-4632)

99 GENERAL AND MISCELLANEOUS↗

Optimizing the sextupole configuration for simultaneous correction of third order resonances at the recycler ring

For the Recycler Ring at Fermilab, space charge tune shifts of almost 0.1 will have to be dealt with under the Proton Improvement Plan (PIP-II) framework. This will lead to the excitation of third order resonances. The minimization of Resonance Driving Terms (RDTs) allows to mitigate the harmful effect of these betatron resonances. Past work has shown that previously-installed sextupoles can compensate the RDTs of individual third order resonance lines, thus reducing particle losses in these operational regimes. Nevertheless, trying to compensate multiple resonances of the same order simultaneously with these existing sextupoles is limited due to current constraints in the magnets. The following study showcases the procedure to install additional sextupoles in order to aid the compensation of multiple resonances. This includes the optimization of the new sextupoles' locations in order to cancel out multiple RDTs while minimizing the currents needed. This is followed by a verification of their effectiveness by means of the RDT response matrix.

43 PARTICLE ACCELERATORS↗

Selection of Vadose Zone Flow and Transport Properties with Gravel Fraction Corrections for the Hanford Site Composite Analysis and Cumulative Impact Evaluation

This environmental calculation file (ECF) is a compilation of hydrologic and radiological/chemical properties to be used for the updated Hanford Site Composite Analysis (CA) and Cumulative Impact Evaluation (CIE) vadose zone (VZ) modeling. The CA will provide an all-pathways dose projection to a hypothetical future member of the public from all planned low-level radioactive waste disposal facilities and potential contributions from all other projected end-state sources of radioactive material left at the Hanford Site following site closure. Its primary purpose is to support the decision-making process of the U.S. Department of Energy (DOE) under DOE O 435.1 Chg 1, Radioactive Waste Management, related to managing low-level waste disposal facilities at the Hanford Site. The CIE evaluates the effects of cleanup decisions regarding groundwater quality in the Hanford Site Central Plateau (DOE/RL-2018-69, Cumulative Impact Evaluation Technical Approach Document). Due to the complexity and large number of waste sites in source operable units (OUs), the computational tools used for the CIE must be capable of representing a range of site conditions and source terms in the VZ while also efficiently computing the impact that cleanup decisions have on the underlying aquifer. Waste-site proximity between and within source OUs has resulted in contaminants commingling in the vadose and saturated zones in complex ways. Plume commingling requires cleanup decisions to be evaluated considering the surrounding waste sites and existing groundwater contamination, therefore demonstrating the need to evaluate cumulative impacts from the VZ to groundwater.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Stewardship Considerations for Nevada FFACO Corrective Action Units Closed through the EM NV Soils Activity based on Monitoring of Radionuclide Transport

This report summarizes the EM NV/DRI work with the intent of conveying this information to the long-term land managers who will assume responsibility as EM NV completes its environmental restoration mission. A brief description of each of the six evaluated Soils Activity sites is provided, which is followed by a discussion of the findings regarding radionuclide transport learned at the sites. The implications of these findings are examined for site management, routine monitoring, and monitoring during potentially adverse events. Possible mitigation actions are also identified. The appendices provide a more detailed examination of the conditions under which radionuclide transport occurs at these sites.

54 ENVIRONMENTAL SCIENCES↗

CY2019 Annual Closure Monitoring Report for Corrective Action Unit 98, Frenchman Flat, Underground Test Area, Nevada National Security Site, Nevada (January 2019–December 2019), Revision 1

Three types of monitoring are performed for CAU 98: water quality, water level, and institutional control. These are monitored to determine whether the URs remain protective of human health and the environment, and to ensure that the regulatory boundary objectives are being met. Monitoring data will be used in the future, once multiple years of data are available, to evaluate consistency with the groundwater flow and contaminant transport models because the contaminant boundaries calculated with the models are the primary basis of the UR boundaries. Six wells were sampled for water-quality monitoring in 2019. Contaminants of concern were detected only in the two source/plume wells already known to contain contamination as a result of a radionuclide migration experiment. Tritium concentrations in both of these wells, RNM-2S and UE-5n, remain above the Safe Drinking Water Act maximum contaminant level of 20,000 picocuries per liter but declined in 2019 as compared to measurements in 2018. All other contaminants of concern are below the minimum detection level plus analytical error. The water-level monitoring network includes 16 wells. Depth to water measured in 2019 is generally consistent with recent measurements for all wells. Many wells continue to exhibit a long-term downward trend in water level, though changes from 2018 to 2019 are minimal. The sharp 2016 decline in water level in Well ER-5-3-2 remains unexplained, with the lower level persisting through 2019. Rising water-level trends continue to be observed in Well ER-5-3 deep piezometer and former water supply Well WW-5A. Water supply Well WW-5B experienced a rise in water level as a result of an absence of pumping in the first part of the year (due to a mechanical problem), whereas water levels declined in WW-4 and WW-4A in response to greater pumping in 2019. Institutional control monitoring confirmed the URs are recorded in U.S. Department of Energy and U.S. Air Force land management systems, and that no activities within Frenchman Flat basin are occurring that could potentially affect the contaminant boundaries. Survey of groundwater resources in basins surrounding Frenchman Flat similarly identify no current or pending development that would indicate the need to increase monitoring activities or would otherwise cause concern for the closure decision. The URs continue to prevent exposure of the public, workers, and the environment to contaminants of concern by preventing use of potentially contaminated groundwater.

54 ENVIRONMENTAL SCIENCES↗

Plutonium and poetry: Where Trinity and Oppenheimer's reading habits met Literary inspirations, correcting misinterpretation of his famous quote

The Lab’s first director, J. Robert Oppenheimer, was a man of sonnets and scientific synthesis. Oppenheimer’s work at Los Alamos was defined not only by physics and administrative skill, but also by a life philosophy inspired, in part, by literature. The Trinity test, which took place 76 years ago on July 16th in the New Mexico desert, epitomizes this. Known as one of the greatest scientific achievements ever, the successful detonation of the world’s first nuclear weapon marked the dawn of the Atomic Age. Created in just 27, albeit harrowing, months, Oppenheimer and his team at the Los Alamos Lab worked nonstop on this clandestine effort to help end World War II. As he had done throughout his life, Oppenheimer continued to foster his love of literature during the Manhattan Project. Two of his influences were John Donne and the Hindu scripture Bhagavad-Gita. Oppenheimer recalled both during the Trinity test.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗