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At least 19 records

Edge Bioinformatics

Edge Bioinformatics is a developmental bioinformatics and data management platform which seeks to supply laboratories with bioinformatics pipelines for analyzing data associated with common samples case goals. Edge Bioinformatics enables sequencing as a solution and forward-deployed situations where human-resources, space, bandwidth, and time are limited. The Edge bioinformatics pipeline was designed based on following USE CASES and specific to illumina sequencing reads. 1. Assay performance adjudication (PCR): Analysis of an existing PCR assay in a genomic context, and automated design of a new assay to resolve conflicting results; 2. Clinical presentation with extreme symptoms: Characterization of a known pathogen or co-infection with a. Novel emerging disease outbreak or b. Environmental surveillance

Lo, Chien-Chi↗

Novel covariance-based neutrality test of time-series data reveals asymmetries in ecological and economic systems

Systems as diverse as the interacting species in a community, alleles at a genetic locus, and companies in a market are characterized by competition (over resources, space, capital, etc) and adaptation. Neutral theory, built around the hypothesis that individual performance is independent of group membership, has found utility across the disciplines of ecology, population genetics, and economics, both because of the success of the neutral hypothesis in predicting system properties and because deviations from these predictions provide information about the underlying dynamics. However, most tests of neutrality are weak, based on static system properties such as species-abundance distributions or the number of singletons in a sample. Time-series data provide a window onto a system’s dynamics, and should furnish tests of the neutral hypothesis that are more powerful to detect deviations from neutrality and more informative about to the type of competitive asymmetry that drives the deviation. Here, we present a neutrality test for time-series data. We apply this test to several microbial time-series and financial time-series and find that most of these systems are not neutral. Our test isolates the covariance structure of neutral competition, thus facilitating further exploration of the nature of asymmetry in the covariance structure of competitive systems. Much like neutrality tests from population genetics that use relative abundance distributions have enabled researchers to scan entire genomes for genes under selection, we anticipate our time-series test will be useful for quick significance tests of neutrality across a range of ecological, economic, and sociological systems for which time-series data are available. Here, future work can use our test to categorize and compare the dynamic fingerprints of particular competitive asymmetries (frequency dependence, volatility smiles, etc) to improve forecasting and management of complex adaptive systems.

59 BASIC BIOLOGICAL SCIENCES↗

Edge Bioinformatics

Edge Bioinformatics is a developmental bioinformatics and data management platform which seeks to supply laboratories with bioinformatics pipelines for analyzing data associated with common samples case goals. Edge Bioinformatics enables sequencing as a solution and forward-deployed situations where human-resources, space, bandwidth, and time are limited. The Edge bioinformatics pipeline was designed based on following USE CASES and specific to illumina sequencing reads. 1. Assay performance adjudication (PCR): Analysis of an existing PCR assay in a genomic context, and automated design of a new assay to resolve conflicting results; 2. Clinical presentation with extreme symptoms: Characterization of a known pathogen or co-infection with a. Novel emerging disease outbreak or b. Environmental surveillance

Lo, Chien-Chi↗

Towards synthetic biological approaches to resource utilization on space missions

This paper demonstrates the significant utility of deploying non-traditional biological techniques to harness available volatiles and waste resources on manned missions to explore the Moon and Mars. Compared with anticipated non-biological approaches, it is determined that for 916 day Martian missions: 205 days of high-quality methane and oxygen Mars bioproduction with Methanobacterium thermoautotrophicum can reduce the mass of a Martian fuel-manufacture plant by 56%; 496 days of biomass generation with Arthrospira platensis and Arthrospira maxima on Mars can decrease the shipped wet-food mixed-menu mass for a Mars stay and a one-way voyage by 38%; 202 days of Mars polyhydroxybutyrate synthesis with Cupriavidus necator can lower the shipped mass to three-dimensional print a 120 m3 six-person habitat by 85% and a few days of acetaminophen production with engineered Synechocystis sp. PCC 6803 can completely replenish expired or irradiated stocks of the pharmaceutical, thereby providing independence from unmanned resupply spacecraft that take up to 210 days to arrive. Analogous outcomes are included for lunar missions. Because of the benign assumptions involved, the results provide a glimpse of the intriguing potential of ‘space synthetic biology’, and help focus related efforts for immediate, near-term impact.

Science & Technology - Other Topics↗

Sensitivity of Regulated Flow Regimes to Climate Change in the Western United States

Water management activities or flow regulations modify water fluxes at the land surface and affect water resources in space and time. We hypothesize that flow regulations change the sensitivity of river flow to climate change with respect to unmanaged water resources. Quantifying these changes in sensitivity could help elucidate the impacts of water management at different spatiotemporal scales and inform climate adaptation decisions. In this study, we compared the emergence of significant changes in natural and regulated river flow regimes across the Western United States from simulations driven by multiple climate models and scenarios. We find that significant climate change-induced alterations in natural flow do not cascade linearly through water management activities. At the annual time scale, 50% of the Hydrologic Unit Code 4 (HUC4) sub-basins over the Western U.S. regions tend to have regulated flow regime more sensitive to the climate change than natural flow regime. Seasonality analyses show that the sensitivity varies remarkably across the seasons. We also find that the sensitivity is related to the level of water management. For 35% of the HUC4 sub-basins with the highest level of water management, the summer and winter flows tend to show a heightened sensitivity to climate change due to the complexity of joint reservoir operations. We further demonstrate that the impacts of considering water management in models are comparable to those that arises from uncertainties across climate models and emission scenarios. This prompts further climate adaptation studies research about nonlinearity effects of climate change through water management activities.

Zhou, Tian↗

Energy Efficiency in Small Server Rooms: Field Surveys and Findings

Fifty-seven percent of US servers are housed in server closets, server rooms, and localized data centers, in what are commonly referred to as small server rooms, which comprise 99percent of all server spaces in the US. While many mid-tier and enterprise-class data centers are owned by large corporations that consider energy efficiency a goal to minimize business operating costs, small server rooms typically are not similarly motivated. They are characterized by decentralized ownership and management and come in many configurations, which creates a unique set of efficiency challenges. To develop energy efficiency strategies for these spaces, we surveyed 30 small server rooms across eight institutions, and selected four of them for detailed assessments. The four rooms had Power Usage Effectiveness (PUE) values ranging from 1.5 to 2.1. Energy saving opportunities ranged from no- to low-cost measures such as raising cooling set points and better airflow management, to more involved but cost-effective measures including server consolidation and virtualization, and dedicated cooling with economizers. We found that inefficiencies mainly resulted from organizational rather than technical issues. Because of the inherent space and resource limitations, the most effective measure is to operate servers through energy-efficient cloud-based services or well-managed larger data centers, rather than server rooms. Backup power requirement, and IT and cooling efficiency should be evaluated to minimize energy waste in the server space. Utility programs are instrumental in raising awareness and spreading technical knowledge on server operation, and the implementation of energy efficiency measures in small server rooms.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The agile alert system for gamma-ray transients

In recent years, a new generation of space missions has offered great opportunities for discovery in high-energy astrophysics. In this article we focus on the scientific operations of the Gamma-Ray Imaging Detector (GRID) on board the AGILE space mission. AGILE-GRID, sensitive in the energy range of 30 MeV-30 GeV, has detected many γ-ray transients of both galactic and extragalactic origin. This work presents the AGILE innovative approach to fast γ-ray transient detection, which is a challenging task and a crucial part of the AGILE scientific program. The goals are to describe (1) the AGILE Gamma-Ray Alert System, (2) a new algorithm for blind search identification of transients within a short processing time, (3) the AGILE procedure for γ-ray transient alert management, and (4) the likelihood of ratio tests that are necessary to evaluate the post-trial statistical significance of the results. Special algorithms and an optimized sequence of tasks are necessary to reach our goal. Data are automatically analyzed at every orbital downlink by an alert pipeline operating on different timescales. As proper flux thresholds are exceeded, alerts are automatically generated and sent as SMS messages to cellular telephones, via e-mail, and via push notifications from an application for smartphones and tablets. These alerts are crosschecked with the results of two pipelines, and a manual analysis is performed. Being a small scientific-class mission, AGILE is characterized by optimization of both scientific analysis and ground-segment resources. The system is capable of generating alerts within two to three hours of a data downlink, an unprecedented reaction time in γ-ray astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗

On an improved sub-regional water resources management representation for integration into earth system models

Human influence on the hydrologic cycle includes regulation and storage, consumptive use and overall redistribution of water resources in space and time. Representing these processes is essential for applications of earth system models in hydrologic and climate predictions, as well as impact studies at regional to global scales. Emerging large-scale research reservoir models use generic operating rules that are flexible for coupling with earth system models. Those generic operating rules have been successful in reproducing the overall regulated flow at large basin scales. This study investigates the uncertainties of the reservoir models from different implementations of the generic operating rules using the complex multi-objective Columbia River Regulation System in northwestern United States as an example to understand their effects on not only regulated flow but also reservoir storage and fraction of the demand that is met. Numerical experiments are designed to test new generic operating rules that combine storage and releases targets for multi-purpose reservoirs and to compare the use of reservoir usage priorities, withdrawals vs. consumptive demand, as well as natural vs. regulated mean flow for calibrating operating rules. Overall the best performing implementation is the use of the combined priorities (flood control storage targets and irrigation release targets) operating rules calibrated with mean annual natural flow and mean monthly withdrawals. The challenge of not accounting for groundwater withdrawals, or on the contrary, assuming that all remaining demand is met through groundwater extractions, is discussed.

Columbia↗

Aviation security screening optimizer for risk and throughput (ASSORT)

The increasing number of air travelers each year presents a challenge as many airports are near their capacity in terms of resources and space for passenger screening. Fortunately, advancements in technologies like next-generation millimeter wave scanning offer solutions to ease this strain. The focus remains on managing risk while enhancing the passenger experience for the traveling public. The risk model presented in this paper known as the Aviation Security Screening Optimizer for Risk and Throughput (ASSORT) is designed to assess risk-based approaches for passenger screening and checkpoint operations. Additionally, ASSORT is exploring various traveler categories — general, trusted, and trusted-plus — along with different checkpoint screening Concept of Operations tailored to each traveler type. For instance, travelers with a higher trust level may experience fewer screening technologies, resulting in quicker processing times at the checkpoint. The output of ASSORT provides a risk score for predefined threat scenarios, as well as the overall risk to the checkpoint, aircraft, and airport by traveler type. In conclusion, benefits of using this tool include assessing the trade-offs between the overall risk associated with checkpoints and the throughput rate of passengers screened. We show for example the impact that different passenger volumes at the checkpoint can have on risk.

99 GENERAL AND MISCELLANEOUS↗

Recyclable Materials for Resource Constrained Environments

In-space manufacturing exhibits severe limitations in resources as astronauts are only afforded with the materials that are brought on-board the space craft. Consequently, the use of recyclable and re-usable materials is paramount. Researchers at NLR leverage their expertise in polymer and recycling chemistry to develop material systems capable of high performance applications with intentional consideration on multi-life use through chemical recycling, mechanical recycling, bio-degradation, and thermoforming. Disclosed within this poster presentation are highlighted projects that illustrate several recyclable by design material systems that have been developed.

09 BIOMASS FUELS↗

Competition for light and water in a coupled soil-plant system

Here, it is generally accepted that resource availability shapes the structure and function of many ecosystems. Within the soil-plant-atmosphere (SPA) system, resource availability fluctuates in space and time whereas access to resources by individuals is further impacted by plant-to-plant competition. Likewise, transport and transformation of resources within an individual plant is governed by numerous interacting biotic and abiotic processes. The work here explores the co-limitations on water losses and carbon uptake within the SPA arising from fluctuating resource availability and competition. In particular, the goal is to unfold the interplay between plant access and competition for water and light, as well as the impact of transport/redistribution processes on leaf-level carbon assimilation and water fluxes within forest stands. A framework is proposed that couples a three-dimensional representation of soil-root exchanges with a one-dimensional description of stem water flow and storage, canopy photosynthesis, and transpiration. The model links soil moisture redistribution, root water uptake, xylem water flow and storage, leaf potential and stomatal conductance as driven by supply and demand for water and carbon. The model is then used to investigate plant drought resilience of overstory-understory trees simultaneously competing for water and light. Simulation results reveal that understory-overstory interactions increase ecosystem resilience to drought (i.e. stand-level carbon assimilation rates and water fluxes can be sustained at lower root-zone soil water potentials). This resilience enhancement originates from reduced transpiration (due to shading) and hydraulic redistribution in soil supporting photosynthesis over prolonged periods of drought. In particular, the presence of different rooting systems generates localized hydraulic redistribution fluxes that sustain understory transpiration through overstory-understory interactions. Such complex SPA dynamics cannot be properly summarized by equivalent ecosystem-scale Resistor-Capacitor (RC) rep- resentation. However our results show that, with proper averaging across water flow paths, RC models can provide reasonable estimates of stand-level water and carbon fluxes during inter-storm periods.

54 ENVIRONMENTAL SCIENCES↗

Efficient Execution of Recursive Programs on Commodity Vector Hardware

The pursuit of computational efficiency has led to the proliferation of throughput-oriented hardware, from GPUs to increasingly-wide vector units on commodity processors and accelerators. This hardware is designed to efficiently execute data-parallel computations in a vectorized manner. However, many algorithms are more naturally expressed as divide-and-conquer, recursive, task-parallel computations; in the absence of data parallelism, it seems that such algorithms are not well-suited to throughput-oriented architectures. This paper presents a set of novel code transformations that expose the data-parallelism latent in recursive, task-parallel programs. These transformations facilitate straightforward vectorization of task-parallel programs on commodity hardware. We also present scheduling policies that maintain high utilization of vector resources while limiting space usage. Across several task-parallel benchmarks, we demonstrate both efficient vector resource utilization and substantial speedup on chips using Intel's SSE4.2 vector units as well as accelerators using Intel's AVX512 units.

resursion↗

Extracting SIMD Parallelism from Recursive Task-Parallel Programs

The pursuit of computational efficiency has led to the proliferation of throughput-oriented hardware, from GPUs to increasingly wide vector units on commodity processors and accelerators. This hardware is designed to efficiently execute data-parallel computations in a vectorized manner. However, many algorithms are more naturally expressed as divide-and-conquer, recursive, task-parallel computations. In the absence of data parallelism, it seems that such algorithms are not well suited to throughput-oriented architectures. This paper presents a set of novel code transformations that expose the data parallelism latent in recursive, task- parallel programs. These transformations facilitate straightforward vectorization of task-parallel programs on commodity hardware. We also present scheduling policies that maintain high utilization of vector resources while limiting space usage. Across several task-parallel benchmarks, we demonstrate both efficient vector resource utilization and substantial speedup on chips using Intel’s SSE4.2 vector units, as well as accelerators using Intel’s AVX512 units. We then show through rigorous sampling that, in practice, our vectorization techniques are effective for a much larger class of programs.

Recursive Programs, task parallelism, vectorizatio↗

Neptunium mononitride as a target material for Pu-238 production

Deep space exploration requires specialized sources for both thermal and power applications. Radioactive decay heat of plutonium-238 (238Pu) provides these sources in the form of radioisotope thermoelectric generators (RTGs). The 238 Pu is produced via neutron capture reaction involving neptunium-237 ( 237 Np) target material. Continual optimization of 237 Np target materials and evaluation of potential alternative targets for production of 238 Pu RTGs are advantageous for meeting ongoing space power system resource requirements. Current production of 238 Pu for RTGs for the United States space program utilizes neptunium dioxide ( 237 NpO 2 ) targets; however, the use of neptunium mononitride ( 237 NpN) presents an opportunity to increase the mass of 237 Np per target compared to the dioxide form, as well as increase the thermal conductivity of the target. To assess the viability of a 237 NpN target material, the material chemistry must be thoroughly evaluated, including synthesis methods and dissolution and reprocessing schemes. This review presents a summary of synthesis pathways for 237 NpN based on published literature on actinide mononitrides. Specific literature on 237 NpN is limited, necessitating evaluation of other actinide systems to gather parallels. This suggests a need for additional experimental studies on 237 NpN. A particular limitation in the existing literature is a lack of information on the differences in material characteristics, such as morphology, particle size, and trace chemical impurities, as a function of synthesis method. These parameters may affect subsequent reactor performance or dissolution of irradiated targets. The evaluation of existing literature is presented with a focus on the efficacy of 237 NpN targets for 238 Pu production.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

A Four-Layer Cyber-Physical Security Model for Electric Machine Drives Considering Control Information Flow

Despite the IEEE Power Electronics Society (PELS) establishing Technical Committee 10 on Design Methodologies with a focus on the cyber-physical security of power electronics systems, a holistic design methodology for addressing security vulnerabilities remains underdeveloped. This gap largely stems from the limited integration of computer science and power/control engineering studies in this interdisciplinary field. Addressing the inadequacy of unilateral cyber or control perspectives, this article presents a novel four-layer cyber-physical security model specifically designed for electric machine drives. Central to this model is the innovative control information flow (CIF) model, residing within the control layer, which serves as a pivotal link between the cyber layer's vulnerable resources and the physical layer's state-space models. By mapping vulnerable resources to control variable space and tracing attack propagation, the CIF model facilitates accurate impact predictions based on tainted control laws. The effectiveness and validity of this proposed model are demonstrated through hardware experiments involving two typical cyber-attack scenarios, underscoring its potential as a comprehensive framework for multidisciplinary security strategies.

97 MATHEMATICS AND COMPUTING↗

Building the Next Generation of Regional Geothermal Potential Maps: Examples from the Great Basin Region, Western USA

Over the past decade research has greatly advanced our understanding of structurally controlled geothermal systems and the potential for “deep stratigraphic reservoirs” in the Great Basin region, western USA. For example, studies have shown that structurally controlled geothermal systems are associated with specific structural settings, such as terminations of major normal faults, accommodation zones, pull-aparts in strike-slip faults, displacement transfer zones, or step-overs in range-front faults. However, we know that not every structure (e.g., termination of a major normal fault or step-over in a range-front fault) hosts an active geothermal system. Recent research has also shown that regional strain rate model as determined from GPS geodesy, the composition of that strain (extensional versus shear or compressive strain), recency of Quaternary faulting, and slip and dilation tendency of faults correlate positively with the distribution of both high and low-temperature, structurally controlled geothermal systems within the Great Basin. Combining these strain data and fault slip history data sets with existing temperature gradient data, heat flow data, spring temperatures, fluid geothermometry, and geophysical data provides an effective platform for evaluating the geothermal potential of respective structural plays. Recent studies focused on deep stratigraphic reservoirs indicate the best conditions for economically viable development are associated with thick sedimentary basins with low-thermal-conductivity sedimentary cap rocks overlying permeable host rocks (e.g. carbonates) and co-located with areas of high heat flow. Some of the factors that contribute to the potential for deep stratigraphic reservoirs and conventional structurally controlled geothermal systems apply to both types of resources, and in some places the potential for these two types of resources overlap in space, suggesting the potential for hybrid reservoirs (structurally controlled deep stratigraphic reservoirs). Effective and complete evaluation of geothermal potential in the Great Basin should include parameters that cover both types of resources. In this study, two areas with a combined area of 26,000 km 2 were evaluated for geothermal resource potential, equating to <4% of the total 680,000 km 2 size of the Great Basin region. Within these two study areas, 73 potential structural targets and 8 potential deep sedimentary target areas were identified. Four of the 73 potential structural target areas are associated with known thermal anomalies. All 73 structural target areas were ranked according to multiple data sets.

15 GEOTHERMAL ENERGY↗

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↗