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At least 1,171 records · Page 65

CMS readiness for multi-core workload scheduling

In the present run of the LHC, CMS data reconstruction and simulation algorithms benefit greatly from being executed as multiple threads running on several processor cores. The complexity of the Run 2 events requires parallelization of the code to reduce the memory-per- core footprint constraining serial execution programs, thus optimizing the exploitation of present multi-core processor architectures. The allocation of computing resources for multi-core tasks, however, becomes a complex problem in itself. The CMS workload submission infrastructure employs multi-slot partitionable pilots, built on HTCondor and GlideinWMS native features, to enable scheduling of single and multi-core jobs simultaneously. This provides a solution for the scheduling problem in a uniform way across grid sites running a diversity of gateways to compute resources and batch system technologies. This paper presents this strategy and the tools on which it has been implemented. The experience of managing multi-core resources at the Tier-0 and Tier-1 sites during 2015, along with the deployment phase to Tier-2 sites during early 2016 is reported. The process of performance monitoring and optimization to achieve efficient and flexible use of the resources is also described.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

WE-G-BRA-01: Patient Safety and Treatment Quality Improvement Through Incident Learning: Experience of a Non-Academic Proton Therapy Center

Purpose: Incident learning has been proven to improve patient safety and treatment quality in conventional radiation therapy. However, its application in proton therapy has not been reported yet to our knowledge. In this study, we report our experience in developing and implementation of an in-house incident learning system. Methods: An incident learning system was developed based on published principles and tailored for our clinical practice and available resource about 18 months ago. The system includes four layers of error detection and report: 1) dosimetry peer review; 2) physicist plan quality assurance (QA); 3) treatment delivery issue on call and record; and 4) other incident report. The first two layers of QA and report were mandatory for each treatment plan through easy-to-use spreadsheets that are only accessible by the dosimetry and physicist departments. The treatment delivery issues were recorded case by case by the on call physicist. All other incidents were reported through an online incident report system, which can be anonymous. The incident report includes near misses on planning and delivery, process deviation, machine issues, work flow and documentation. Periodic incident reviews were performed. Results: In total, about 116 errors were reported through dosimetry review, 137 errors through plan QA, 83 treatment issues through physics on call record, and 30 through the online incident report. Only 8 incidents (2.2%) were considered to have a clinical impact to patients, and the rest of errors were either detected before reaching patients or had negligible dosimetric impact (<5% dose variance). Personnel training & process improvements were implemented upon periodic incident review. Conclusion: An incident learning system can be helpful in personnel training, error reduction, and patient safety and treatment quality improvement. The system needs to be catered for each clinic’s practice and available resources. Incident and knowledge sharing among proton centers are encouraged.

60 APPLIED LIFE SCIENCES↗

Retrofitting Word Embeddings with the UMLS Metathesaurus for Clinical Information Extraction

Deep learning has surged in popularity and proven to be effective for various artificial intelligence applications including information extraction from cancer pathology reports. Since word representation is a core unit that enables deep learning algorithms to understand words and be able to perform NLP, this representation must include as much information as possible to help these algorithms achieve high classification performance. Therefore, in this work in addition to the distributional information of words in large sized corpora, we use UMLS vocabulary resources to enrich the vector space representation of words with the semantic relations between words. These resources provide many terminologies pertaining to cancer. The refined word embeddings are used with a convolutional neural (CNN) model to extract four data elements from cancer pathology reports; ICD-O-3 tumor topography codes, tumor laterality, behavior, and histological grade. We observed that using UMLS vocabulary resources to enrich word embeddings of CNN models consistently outperformed CNN models without pre-training word embeddings and even with pre-trained word embeddings on a domain specific corpus across all four tasks. The results show marginal improvement on the laterality task, but a significant improvement on the other tasks, especially for the macro-f score. Specifically, the improvements are 3%, 13%, and 15% for tumor site, histological grade, and behavior tasks, respectively. This approach is encouraging to enrich word embeddings with more clinical data resources to be used for information abstraction tasks from clinical pathology reports.

Alawad, Mohammed↗

Developing County-level Water Footprints of Biofuel Produced from Switchgrass and Miscanthus x Giganteus in the United States

Perennial grass has been proposed as a potential candidate for producing cellulosic biofuel because of its promising productivity and benefits to water quality, and because it is a non-food feedstock. While extensive research focuses on selecting and developing species and conversion technologies, the impact of grass-based biofuel production on water resources remains less clear. As feedstock growth requires water and the type of water consumed may vary considerably from region to region, water use must be characterized with spatial resolution and on a fuel production basis. This report summarizes a study that assesses the impact of biofuel production on water resource use and water quality at county, state, and regional scales by developing a water footprint of biofuel produced from switchgrass and Miscanthus × giganteus via biochemical conversion.

09 BIOMASS FUELS↗

Radiological Considerations Supporting the American Medical Isotope Producer Niowave

This report provides a summary of work performed by Savannah River National Laboratory (SRNL) during FY22 in support of Niowave, an American Medical Isotope Production (AMIP) facility. SRNL served in a technical support role, funded by NA-231, supporting Niowave in the beginning of non radiological functional testing of their airport facility in FY22. Through this agreement, SRNL provides Niowave access to subject matter experts (SMEs) for questions that may arise during the drafting of engineering plans, facility policies, and/or response procedures. This report summarizes discussions between SRNL and Niowave about guidance concerning issues with the floor of the hot cells, dispersible removable contamination (beta emitting fission product), hot cell operation specifically utilization of cameras or mirrors, and the process for removing contaminated waste from the hot cell. Lessons learned and other various resources provided to Niowave by SRNL during FY22 are referenced in this report. This work was funded through NNSA’s Office of Material Management and Minimization, Conversion Office (NA-231).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Geological Carbon Sequestration Storage Resource Estimates for the Ordovician St. Peter Sandstone, Illinois and Michigan Basins, USA

The Cambro-Ordovician strata of the Midwest of the United States is a primary target for potential geological storage of CO2 in deep saline formations. The objective of this project is to develop a comprehensive evaluation of the Cambro-Ordovician strata in the Illinois and Michigan Basins above the basal Mount Simon Sandstone since the Mount Simon is the subject of other investigations including a demonstration-scale injection at the Illinois Basin Decatur Project. The primary reservoir targets investigated in this study are the middle Ordovician St Peter Sandstone and the late Cambrian to early Ordovician Knox Group carbonates. The topic of this report is a regional-scale evaluation of the geologic storage resource potential of the St Peter Sandstone in both the Illinois and Michigan Basins. Multiple deterministic-based approaches were used in conjunction with the probabilistic-based storage efficiency factors published in the DOE methodology to estimate the carbon storage resource of the formation. Extensive data sets of core analyses and wireline logs were compiled to develop the necessary inputs for volumetric calculations. Results demonstrate how the range in uncertainty of storage resource estimates varies as a function of data availability and quality, and the underlying assumptions used in the different approaches. In the simplest approach, storage resource estimates were calculated from mapping the gross thickness of the formation and applying a single estimate of the effective mean porosity of the formation. Results from this approach led to storage resource estimates ranging from 3.3 to 35.1 Gt in the Michigan Basin, and 1.0 to 11.0 Gt in the Illinois Basin at the P10 and P90 probability level, respectively. The second approach involved consideration of the diagenetic history of the formation throughout the two basins and used depth-dependent functions of porosity to derive a more realistic spatially variable model of porosity rather than applying a single estimate of porosity throughout the entire potential reservoir domains. The second approach resulted in storage resource estimates of 3.0 to 31.6 Gt in the Michigan Basin, and 0.6 to 6.1 Gt in the Illinois Basin. The third approach attempted to account for the local-scale variability in reservoir quality as a function of both porosity and permeability by using core and log analyses to calculate explicitly the net effective porosity at multiple well locations, and interpolate those results throughout the two basins. This approach resulted in storage resource estimates of 10.7 to 34.7 Gt in the Michigan Basin, and 11.2 to 36.4 Gt in the Illinois Basin. A final approach used advanced reservoir characterization as the most sophisticated means to estimating storage resource by defining reservoir properties for multiple facies within the St Peter formation. This approach was limited to the Michigan Basin since the Illinois Basin data set did not have the requisite level of data quality and sampling density to support such an analysis. Results from this approach led to storage resource estimates of 15.4 Gt to 50.1 Gt for the Michigan Basin. The observed variability in results from the four different approaches is evaluated in the context of data and methodological constraints, leading to the conclusion that the storage resource estimates from the first two approaches may be conservative, whereas the net porosity based approaches may over-estimate the resource.

Barnes, David↗

Predicting Kyasanur forest disease in resource-limited settings using event-based surveillance and transfer learning

In recent years, the reports of Kyasanur forest disease (KFD) breaking endemic barriers by spreading to new regions and crossing state boundaries is alarming. Effective disease surveillance and reporting systems are lacking for this emerging zoonosis, hence hindering control and prevention efforts. We compared time-series models using weather data with and without Event-Based Surveillance (EBS) information, i.e., news media reports and internet search trends, to predict monthly KFD cases in humans. We fitted Extreme Gradient Boosting (XGB) and Long Short-Term Memory models at the national and regional levels. We utilized the rich epidemiological data from endemic regions by applying Transfer Learning (TL) techniques to predict KFD cases in new outbreak regions where disease surveillance information was scarce. Overall, the inclusion of EBS data, in addition to the weather data, substantially increased the prediction performance across all models. The XGB method produced the best predictions at the national and regional levels. The TL techniques outperformed baseline models in predicting KFD in new outbreak regions. Novel sources of data and advanced machine-learning approaches, e.g., EBS and TL, show great potential towards increasing disease prediction capabilities in data-scarce scenarios and/or resource-limited settings, for better-informed decisions in the face of emerging zoonotic threats.

60 APPLIED LIFE SCIENCES↗

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

Broad-scale protein–protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions. By performing ten independent screens testing a total of 36 million binary interaction combinations, and uncovering a network of 8,577 interactions among 1,453 transcription factors, we demonstrate CrY2H-seq's improved screening capacity, efficiency, and sensitivity over those of existing technologies. The deep-coverage network resource we call AtTFIN-1 recapitulates one-third of previously reported interactions derived from diverse methods, expands the number of known plant transcription factor interactions by three-fold, and reveals previously unknown family-specific interaction module associations with plant reproductive development, root architecture, and circadian coordination.

59 BASIC BIOLOGICAL SCIENCES↗

Technology Transfer Annual Report - Fiscal Year 2017

TECHNOLOGY TRANSFER Idaho National Laboratory (INL) is a U.S. Department of Energy (DOE) multiprogram national laboratory that conducts research and development in all DOE mission areas. Like all other national laboratories, INL has a statutory, technology transfer mission to make its capabilities and technologies available to federal agencies, state and local governments, universities and industry. To fulfill this mission, INL encourages its scientific, engineering and technical staff to disclose new inventions and creations to ensure the resulting intellectual property is captured, protected and made available to others who might benefit from it. As part of the mission, intellectual property is licensed to industrial partners for commercialization, job creation and delivering the benefits of federally funded technology to consumers. In some cases, unique capabilities are made available to other federal agencies, international organizations, domestic and foreign commercial entities or small businesses to solve specific technical challenges. INL employees work cooperatively with researchers and technical staff from the university and industrial sectors to further develop emerging technologies. In this global economy, INL is contributing to the development of the next generation of engineers and scientists by licensing software to educational institutions throughout the world. Abstract This report is a catalog of select INL technology transfer activities, including commercialization transactions and research agreements, executed during this past year. The size and diversity of INL technical resources, coupled with the large number of relationships with other organizations, virtually ensures that a report of this nature will fail to capture all interactions. Recognizing this limitation, this report focuses on transactions that are specifically authorized by technology transfer legislation (and corresponding contractual provisions) or involve the transfer of legal rights to technology to other parties. This report was compiled from primary records that were readily available to the INL’s Technology Deployment and Contracts Management offices. Accomplishments cataloged in the report reflect the achievements and creativity of the researchers, technicians, support staff and operators of the INL workforce. Prepared for the U.S. Department of Energy Under DOE Idaho Operations Office Contract DE-AC07-05ID14517

2017↗

Resource-efficient generation of linear cluster states by linear optics with postselection

Here we report on theoretical research in photonic cluster-state computing. Finding optimal schemes of generating non-classical photonic states is of critical importance for this field as physically implementable photon-photon entangling operations are currently limited to measurement-assisted stochastic transformations. A critical parameter for assessing the efficiency of such transformations is the success probability of a desired measurement outcome. At present there are several experimental groups that are capable of generating multi-photon cluster states carrying more than eight qubits. Separate photonic qubits or small clusters can be fused into a single cluster state by a probabilistic optical CZ gate conditioned on simultaneous detection of all photons with 1/9 success probability for each gate. This design mechanically follows the original theoretical scheme of cluster state generation proposed more than a decade ago by Raussendorf, Browne, and Briegel. The optimality of the destructive CZ gate in application to linear optical cluster state generation has not been analyzed previously. Our results reveal that this method is far from the optimal one. Employing numerical optimization we have identified that the maximal success probability of fusing n unentangled dual-rail optical qubits into a linear cluster state is equal to 1/2 n-1 ; an m-tuple of photonic Bell pair states, commonly generated via spontaneous parametric down-conversion, can be fused into a single cluster with the maximal success probability of 1/4 m-1 .

97 MATHEMATICS AND COMPUTING↗

Hiilangaay Hydroelectric Project – Final Report

The Hiilangaay Hydroelectric Project (“Hiilangaay” or the “Project”) is a 5-megawatt hydroelectric resource currently under construction on Prince of Wales Island (POW), Alaska, approximately ten miles east of Hydaburg. The objective of the Project is to interconnect with the existing transmission grid on Prince of Wales Island, increasing the hydroelectric generation capability by 5 MW, eliminating the need for diesel generation, increasing the reliability of the electrical system, and allowing the interconnected portion of the island to have 100 percent renewable energy generation. Pre-construction activities including construction planning, permit coordination and compliance, and final design have made it possible to move forward with construction of the Hiilangaay Project. Despite repeated delays to the schedule, persistence and long-term planning will culminate in the construction of the Project, and make Prince of Wales Island independent of diesel-fueled energy

13 HYDRO ENERGY↗

Agile Electro-Mechanical Product Accelerator - Final Research Performance Progress Report

NCDMM recognized the need to focus on the most efficient use of limited resources while ensuring compliance with regulations and minimizing the energy intensity and environmental impact of manufactured components. This was accomplished through the evaluation of current machining and processing practices, and their efficiencies, to further the sustainability of manufacturing as a whole. Additionally, the activities also identified, and furthered the implementation of new “best practices” within the southwestern Pennsylvania manufacturing sector.

42 ENGINEERING↗

Database of Renewable Energy and Energy Efficiency Incentives and Policies Final Technical Report

The Database of State Incentives for Renewables and Efficiency (DSIRE) is an online resource that provides summaries of all financial incentives and regulatory policies that support the use of renewable energy and energy efficiency across all 50 states. This project involved making enhancements to the database and website, and the ongoing research and maintenance of the policy and incentive summaries.

99 GENERAL AND MISCELLANEOUS↗

Automatic cartography techniques for earth resources research

Progress in developing instrumentation and software for the EROS user facilities is reported. Significant progress has been made in developing the USGS binary-mode scanning digitizer which is described in detail. Other instrumentation and processes discussed include profile-generating techniques, a manual digitizer, image correlation systems, and some new photomechanical data processing techniques.

Edson, D. T.↗