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Analytics for Investigation of Disease Outbreaks: Web-Based Analytics Facilitating Situational Awareness in Unfolding Disease Outbreaks
Background: Information from historical infectious disease outbreaks provides real-world data about outbreaks and their impacts on affected populations. These data can be used to develop a picture of an unfolding outbreak in its early stages, when incoming information is sparse and isolated, to identify effective control measures and guide their implementation. Objective: This study aimed to develop a publicly accessible Web-based visual analytic called Analytics for the Investigation of Disease Outbreaks (AIDO) that uses historical disease outbreak information for decision support and situational awareness of an unfolding outbreak. Methods: We developed an algorithm to allow the matching of unfolding outbreak data to a representative library of historical outbreaks. This process provides epidemiological clues that facilitate a user’s understanding of an unfolding outbreak and facilitates informed decisions about mitigation actions. Disease-specific properties to build a complete picture of the unfolding event were identified through a data-driven approach. A method of analogs approach was used to develop a short-term forecasting feature in the analytic. The 4 major steps involved in developing this tool were (1) collection of historic outbreak data and preparation of the representative library, (2) development of AIDO algorithms, (3) development of user interface and associated visuals, and (4) verification and validation. Results: The tool currently includes representative historical outbreaks for 39 infectious diseases with over 600 diverse outbreaks. We identified 27 different properties categorized into 3 broad domains (population, location, and disease) that were used to evaluate outbreaks across all diseases for their effect on case count and duration of an outbreak. Statistical analyses revealed disease-specific properties from this set that were included in the disease-specific similarity algorithm. Although there were some similarities across diseases, we found that statistically important properties tend to vary, even between similar diseases. This may be because of our emphasis on including diverse representative outbreak presentations in our libraries. AIDO algorithm evaluations (similarity algorithm and short-term forecasting) were conducted using 4 case studies and we have shown details for the Q fever outbreak in Bilbao, Spain (2014), using data from the early stages of the outbreak. Using data from only the initial 2 weeks, AIDO identified historical outbreaks that were very similar in terms of their epidemiological picture (case count, duration, source of exposure, and urban setting). The short-term forecasting algorithm accurately predicted case count and duration for the unfolding outbreak. Conclusions: AIDO is a decision support tool that facilitates increased situational awareness during an unfolding outbreak and enables informed decisions on mitigation strategies. AIDO analytics are available to epidemiologists across the globe with access to internet, at no cost. In this study, we presented a new approach to applying historical outbreak data to provide actionable information during the early stages of an unfolding infectious disease outbreak.
Analytical Expression for DC Link Capacitor Current in a Cascaded H-Bridge Multi-Level Active Front-End Converter
Medium-voltage grid-tied systems often use a cascaded H-bridge multi-level active front-end. In this converter, dc link bus capacitors play an important role in stabilizing the converter and enabling both active and reactive power injections. The present work provides analytical expressions for the capacitor current, which are essential for optimizing system design (especially capacitor size vs. lifetime). Then, the expression is incorporated into the grid connected bidirectional power system model. Consequently, this work contributes to the guiding principles to choose accurate dc link capacitor ratings against grid-side power delivery requirements. The analytical results have been validated with detailed simulations and hardware results.
A Big Data Analytics Framework for HPC Log Data: Three Case Studies Using the Titan Supercomputer Log
Reliability, availability and serviceability (RAS) logs of high performance computing (HPC) resources, when closely investigated in spatial and temporal dimensions, can provide invaluable information regarding system status, performance, and resource utilization. These data are often generated from multiple logging systems and sensors that cover many components of the system. The analysis of these data for finding persistent temporal and spatial insights faces two main difficulties: the volume of RAS logs makes manual inspection difficult and the unstructured nature and unique properties of log data produced by each subsystem adds another dimension of difficulty in identifying implicit correlation among recorded events. To address these issues, we recently developed a multi-user Big Data analytics framework for HPC log data at Oak Ridge National Laboratory (ORNL). This paper introduces three in-progress data analytics projects that leverage this framework to assess system status, mine event patterns, and study correlations between user applications and system events. We describe the motivation of each project and detail their workflows using three years of log data collected from ORNL's Titan supercomputer.
Numerical simulation of the hot-tail runaway electron production mechanism using CQL3D and comparison with Smith–Verwichte analytical model
Abstract The hot-tail mechanism of runaway electron (RE) production (Harvey et al 2000 Phys. Plasmas 7 4590) is the primary source of RE in the case of rapidly cooling tokamak plasma. Quantifying this mechanism is very important as it can provide most of the post-thermal-quench (TQ) current, or a seed current for the secondary source of RE through the avalanche mechanism. An analytic model which omits pitch-angle scattering is often used in literature for estimating the hot-tail RE density (Smith and Verwichte 2008 Phys. Plasmas 15 072502). In the present study, we use the CQL3D bounce-averaged Fokker–Planck code (Harvey and McCoy 1992 Proc. IAEA Technical Committee Meeting on Advances in Simulation and Modeling of Thermonuclear Plasmas p 527) to test the limits of validity of the model. In particular, we examine the cases of Z = 1 and Z = 18 ions, for sets of different initial temperature, density, electric field and the characteristic time of temperature decay. We show that for Z = 1 plasma, the ratio of RE density computed by CQL3D to that estimated from the model is within 0.6–6.0 in studied cases. For the Z = 18 case, this factor is systematically a much smaller number, typically 0.02–0.6. We suggest a simple correction to the model that narrows down the range of this ratio to 0.3–3.8 in all of the cases, including Z = 1 and Z = 18 plasmas.
Autonomy Loops for Monitoring, Operational Data Analytics, Feedback, and Response in HPC Operations
Many High Performance Computing (HPC) facilities have developed and deployed frameworks in support of continuous monitoring and operational data analytics (MODA) to help improve efficiency and throughput. Because of the complexity and scale of systems and workflows and the need for low-latency response to address dynamic circumstances, automated feedback and response have the potential to be more effective than current human-in-the-loop approaches which are laborious and error prone. Progress has been limited, however, by factors such as the lack of infrastructure and feedback hooks, and successful deployment is often site- and case-specific. In this position paper we report on the outcomes and plans from a recent Dagstuhl Seminar, seeking to carve a path for community progress in the development of autonomous feedback loops for MODA, based on the established formalism of similar (MAPE-K) loops in autonomous computing and self-adaptive systems. By defining and developing such loops for significant cases experienced across HPC sites, we seek to extract commonalities and develop conventions that will facilitate interoperability and interchangeability with system hardware, software, and applications across different sites, and will motivate vendors and others to provide telemetry interfaces and feedback hooks to enable community development and pervasive deployment of MODA autonomy loops.
LLNL ES&H Analytical Services and Instrumentation Analytical Laboratory (ALAB) (CY2022 Management Review Report)
"An annual review shall be conducted of the analytical activities to ensure continuing suitability, adequacy, and effectiveness." (ALAB-01 Rev 6 ALQAP section 6.11.2) "The laboratory management shall review its management system at planned intervals, in order to ensure its continuing suitability, adequacy and effectiveness..."(ISO/IEC 17025:2017 Section 8.9.1) "In accordance with a predetermined schedule and procedure, the laboratory's top management shall periodically conduct a review of the laboratory's management system and testing and/or calibration activities to ensure their continuing suitability and effectiveness, and to introduce necessary changes or improvements. "(TNI Standard EL-V1M2-2016-Rev2.1:Quality Systems General Requirements)
Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures
Natural organic matter (NOM) is composed of a highly complex mixture of thousands of organic compounds which, historically, proved difficult to characterize. However, to understand the thermodynamic and kinetic controls on greenhouse gas (carbon dioxide [CO 2 ] and methane [CH 4 ]) production resulting from the decomposition of NOM, a molecular-level characterization coupled with microbial proteome analyses is necessary. Further, climate and environmental changes are expected to perturb natural ecosystems, potentially upsetting complex interactions that influence both the supply of organic matter substrates and the microorganisms performing the transformations. A detailed molecular characterization of the organic matter, microbial proteomics, and the pathways and transformations by which organic matter is decomposed will be necessary to predict the direction and magnitude of the effects of environmental changes. This article describes a methodological throughput for comprehensive metabolite characterization in a single sample by direct injection Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), gas chromatography mass spectrometry (GC-MS), nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography mass spectrometry (LC-MS), and proteomics analysis. Furthermore, this approach results in a fully-paired dataset which improves statistical confidence for inferring pathways of organic matter decomposition, the resulting CO 2 and CH 4 production rates, and their responses to environmental perturbation. Herein we present results of applying this method to NOM samples collected from peatlands; however, the protocol is applicable to any NOM sample (e.g., peat, forested soils, marine sediments, etc.).
Determination of Biogenic Content by 14 C in fuels using Liquid Scintillation Analysis Laboratory Analytical Procedure (Laboratory Analytical Procedure)
This procedure covers the determination of the percent 14 C in biogenic gasoline, jet fuel, and diesel range hydrocarbons prepared from distillation of hydrotreated pyrolysis oils and blended with fossil derived hydrocarbons (e.g. fossil diesel, gasoline, jet, or toluene). Either an internal 14C standard or a color quench curve is used to correct for potential signal quenching effects. Recent publications provide some background of direct LSC methods used for determination of biogenic fuel content.
Analytical Determination of Radioactive Strontium and Cesium by Thermal Ionization Mass Spectrometry
Thermal ionization mass spectrometry (TIMS) has been evaluated for the detection of the radioactive isotopes of strontium and cesium. The instrument was investigated for the analysis of isotopic ratios of 89Sr to 90Sr and 135Cs to 137Cs in the presence of atomic isobars (Y and Zr for Sr analysis and Ba for Cs analysis). Signicant discrimination using TIMS was found for both Sr and Cs through evaluation using stable isotopes. Fusion procedures with different flux were evaluated for preparation of sample matrices. Chemical separations were developed and used after fusion to isolate the Sr and Cs from a prepared background matrix (i.e., Montana Soil). A graded approach, increasing in stable background isotopes, was performed to monitor the chemistry and instrument response. A thermal neutron irradiation was performed to produce a sample that contained the radioisotopes of Sr and Cs. Even though the irradiated sample was not a certified standard it does provide accurate expectation values via published, well understood cumulative fission yield data. The results presented in this work correlate extremely well with the published data. Furthermore, a significant decrease in uncertainty (by a factor of 5 { 10) was found for the isotopic ratios measured with TIMS compared to the published values.
The Area Localized Coupled Model for Analytical Mean Flow Prediction in Arbitrary Wind Farm Geometries
This work introduces the area localized coupled (ALC) model, which extends the applicability of approaches that couple classical wake superposition models and atmospheric boundary layer models to wind farms with arbitrary layouts. Coupling wake and top–down boundary layer models is particularly challenging since the latter requires averaging over planform areas associated with turbine-specific regions of the flow that need to be specified. The ALC model uses Voronoi tessellation to define this local area around each turbine. A top–down description of a developing internal boundary layer is then applied over Voronoi cells upstream of each turbine to estimate the local mean velocity profile. Coupling between the velocity at hub-height based on this localized top–down model and a wake model is achieved by enforcing a minimum least-square-error in mean velocity in each cell. The wake model in the present implementation takes into account variations in wind farm inflow velocity and represents the wake profile behind each turbine as a super-Gaussian function that smoothly transitions between a top-hat shape in the region immediately following the turbine to a Gaussian profile downstream. Detailed comparisons to large-eddy simulation (LES) data from two different wind farms demonstrate the efficacy of the model in accurately predicting both wind farm power output and local turbine hub-height velocity for different wind farm geometries. These validations using data generated from two different LES codes demonstrate the model's versatility with respect to capturing results from different simulation setups and wind farm configurations.
Generalized boundary detection using compression-based analytics.
Abstract not provided.
Analytics for Stream-Processing Architecture for Real-time Cyber-physical Security (Analytic-SPARCS) v0.9
This code is a set of modules designed to detect certain classes of cyber attacks against equipment in power distribution grid substations, including attacks against transformer tap changers and capacitor bank switches, as well as "reconnaissance" attacks against equipment in power grid substations.
Software Engineering Analytics Toolkit (SEAT): A Resource for Dependency Analytics and Management and Web-based Interactive Visualization.
Abstract not provided.
Characterization techniques for TRU waste from the Analytical Laboratory Hot Cells at Idaho National Laboratory
Characterization techniques for TRU waste from the Analytical Laboratory Hot Cells at Idaho National Laboratory Since the first reactor went hot in 1942, there has been a never ending desire to improve the nuclear reactor and the fuel that it burns. The Idaho National Laboratory has been a key player in reactor and fuel development. As more research projects begin, the spectrum of waste parameters grows. Over the years, the Analytical Laboratory (AL) at the Materials and Fuels Complex (MFC) at Idaho National Laboratory (INL) has supported a large range of various research projects. Each project brings its own challenge and analytical technique that, in turn, yields its own unique waste parameters. The AL Hot Cells at INL consist of 6 small cells that can support around 12 different fuel research projects at a time along with infrastructure and environmental samples. Each different project yields different levels of transuranic (TRU) material, RCRA constituents, dose, and contamination levels. The waste parameters from each project dictate a path forward for the waste Low-Level Waste (LLW), Contact Handled TRU (CH-TRU), Mixed Contact Handled TRU (M-CH-TRU), Remote Handled TRU (RH-TRU), or Mixed Remote Handled TRU (M-RH-TRU). With visual examination techniques and process knowledge as an aid, there have been waste handling methods developed that allow debris and sample material to be segregated. Unique characterization mechanisms have been applied for each debris and sample material that are generally more accurate than smear and surface contamination data. For debris found in the Hot Cells, analytical data is gathered and conservatively summarized for each fuel type and research method. This consists of data from Quadrupole Inductively Coupled Plasma Mass Spectrometry (Q-ICP-MS), Gamma Spectroscopy, and some data verification through Thermal Ionization Mass Spectrometry (TIMS) and Multi-Collector Inductively Coupled Plasma Mass Spectrometry (MC-ICP-MS). This data gives a range of TRU isotope concentrations. Fuel age is taken into account to determine the dominant TRU activity isotopes. Cesium concentrations are also gathered. Each parameter/fuel type then ties a measured Cesium number to TRU content based on historical analytical data. Debris in the hot cells is segregated by project and packaged in individual 2 gallon metal paint cans. Each can is counted by gamma spectroscopy in a calculated and measured geometry. Using process knowledge to determine the fuel or project type, newly counted cesium numbers can be applied to the historic analytical data and TRU content can be estimated. The TRU content allows waste debris to be segregated between CH-TRU and RH-TRU. Packaging techniques can allow for the minimization if RH-TRU waste. Sample material received into the AL must be dissolved into a liquid matrix in order to be analyzed in most cases. When analysis is complete, these liquids go through a consolidation, complexation, neutralization, and solidification process where real time analytical data can be used to calculate TRU content and RCRA constitutes. These calculations allow for no further analytical data to be gathered. The waste matrix is considered stable and acceptable by all AK [define AK] documents. The unique techniques used in characterizing and handling the Analytical Laboratories Hot Cell waste can be applied to various situations and various laboratories. They allow for more accurate data for waste constituents and also for the minimization of RH-TRU waste.