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Archive: July, 2021
  • A Quantitative Risk Assessment Method for Synthetic Biology Products in the Environment

    Abstract: The need to prevent possible adverse environmental health impacts resulting from synthetic biology (SynBio) products is widely acknowledged in both the SynBio risk literature and the global regulatory community. However, discussions of potential risks of SynBio products have been largely speculative, and the attempts to characterize the risks of SynBio products have been non-uniform and entirely qualitative. As the discipline continues to accelerate, a standardized risk assessment framework will become critical for ensuring that the environmental risks of these products are characterized in a consistent, reliable, and objective manner that incorporates all SynBio-unique risk factors. Current established risk assessment frameworks fall short of the features required of this standard framework. To address this, we propose the Quantitative Risk Assessment Method for Synthetic Biology Products (QRA-SynBio) – an incremental build on established risk assessment methodologies that supplements traditional paradigms with the SynBio risk factors that are currently absent and necessitates quantitative analysis for more transparent and objective risk characterizations. The proposed framework facilitates defensible quantification of the environmental risks of SynBio products in both foreseeable and hypothetical use scenarios. Additionally, we show how the proposed method can promote increased experimental investigation into the likelihood of hazard and exposure parameters and highlight the parameters where uncertainty should be reduced, leading to more targeted risk research and more precise characterizations of risk.
  • Cyanobacteria Harmful Algal Blooms (HABs) and US Army Engineer Research and Development Center (ERDC): Research and Services

    Abstract: This factsheet details the research and services available from the US Army Engineer Research and Development Center–Environmental Laboratory’s Harmful Algal Blooms team.
  • Geotechnical Effects on Fiber Optic Distributed Acoustic Sensing Performance

    Abstract: Distributed Acoustic Sensing (DAS) is a fiber optic sensing system that is used for vibration monitoring. At a minimum, DAS is composed of a fiber optic cable and an optic analyzer called an interrogator. The oil and gas industry has used DAS for over a decade to monitor infrastructure such as pipelines for leaks, and in recent years changes in DAS performance over time have been observed for DAS arrays that are buried in the ground. This dissertation investigates the effect that soil type, soil temperature, soil moisture, time in-situ, and vehicle loading have on DAS performance for fiber optic cables buried in soil. This was accomplished through a field testing program. Signal to Noise Ratio (SNR) of the DAS response was used for all the tests to evaluate the system performance. The results of the impact testing program indicated that the portions of the array in gravel performed more consistently over time. The results also indicated that time DAS performance does change somewhat over time. Performance variance increased in new portions of array in all material types through time. Overall, this dissertation provides guidance that can help inform the civil engineering community with respect to installation design recommendations related to DAS used for infrastructure monitoring.
  • Spatial Variability of Coastal Foredune Evolution, Part A: Timescales of Months to Years

    Abstract: Coastal foredunes are topographically high features that can reduce vulnerability to storm-related flooding hazards. While the dominant aeolian, hydrodynamic, and ecological processes leading to dune growth and erosion are fairly well-understood, predictive capabilities of spatial variations in dune evolution on management and engineering timescales (days to years) remain relatively poor. In this work, monthly high-resolution terrestrial lidar scans were used to quantify topographic and vegetation changes over a 2.5 year period along a micro-tidal intermediate beach and dune. Three-dimensional topographic changes to the coastal landscape were used to investigate the relative importance of environmental, ecological, and morphological factors in controlling spatial and temporal variability in foredune growth patterns at two 50 m alongshore stretches of coast. Despite being separated by only 700 m in the alongshore, the two sites evolved differently over the study period. The northern dune retreated landward and lost volume, whereas the southern dune prograded and vertically accreted. The largest differences in dune response between the two sections of dunes occurred during the fall storm season, when each of the systems’ geomorphic and ecological properties modulated dune growth patterns. These findings highlight the complex eco-morphodynamic feedback controlling dune dynamics across a range of spatial scales.
  • VI Preferential Pathways: Rule or Exception

    Abstract: Trichloroethylene (TCE) releases from leaks and spills next to a large government building occurred over several decades with the most recent event occurring 20 years ago. In response to a perceived conventional vapor intrusion (VI) issue a sub-slab depressurization system (SSDS) was installed 6 years ago. The SSDS is operating within design limits and has achieved building TCE vapor concentration reductions. However, subsequent periodic TCE vapor spikes based on daily HAPSITE™ measurements indicate additional source(s). Two rounds of smoke tests conduct-ed in 2017 and 2018 involved introduction of smoke into a sanitary sewer and storm drain manholes located on effluent lines coming from the building until smoke was observed exiting system vents on the roof. Smoke testing revealed many leaks in both the storm sewer and sanitary sewer systems within the building. Sleuthing of the VI source term using a portable HAPSITE™ indicate elevated vapor TCE levels correspond with observed smoke emanation from utility lines. In some instances, smoke odors were perceived but no leak or suspect pipe was identified suggesting the odor originates from an unidentified pipe located behind or enclosed in a wall. Sleuthing activities also found building roof materials explain some of the elevated TCE levels on the 2nd floor. A relationship was found between TCE concentrations in the roof truss area, plenum space above 2nd floor offices, and breathing zone of 2nd floor offices. Installation of an external blower in the roof truss space has greatly reduced TCE levels in the plenum and office spaces. Preferential VI pathways and unexpected source terms may be overlooked mechanisms as compared to conventional VI.
  • Deep Learning-Based Structure-Activity Relationship Modeling for Multi-Category Toxicity Classification: A Case Study of 10K Tox21 Chemicals with High-Throughput Cell-Based Androgen Receptor Bioassay Data

    Abstract: Deep learning (DL) has attracted the attention of computational toxicologists as it offers a potentially greater power for in silico predictive toxicology than existing shallow learning algorithms. However, contradicting reports have been documented. To further explore the advantages of DL over shallow learning, we conducted this case study using two cell-based androgen receptor (AR) activity datasets with 10K chemicals generated from the Tox21 program. A nested double-loop cross-validation approach was adopted along with a stratified sampling strategy for partitioning chemicals of multiple AR activity classes (i.e., agonist, antagonist, inactive, and inconclusive) at the same distribution rates amongst the training, validation and test subsets. Deep neural networks (DNN) and random forest (RF), representing deep and shallow learning algorithms, respectively, were chosen to carry out structure-activity relationship-based chemical toxicity prediction. Results suggest that DNN significantly outperformed RF (p < 0.001, ANOVA) by 22–27% for four metrics (precision, recall, F-measure, and AUPRC) and by 11% for another (AUROC). Further in-depth analyses of chemical scaffolding shed insights on structural alerts for AR agonists/antagonists and inactive/inconclusive compounds, which may aid in future drug discovery and improvement of toxicity prediction modeling.
  • Influence of High Volumes of Silica Fume on the Rheological Behavior of Oil Well Cement Pastes

    Abstract: Specialized classes of concrete, such as ultra-high-performance concrete, use volumes of silica fume in concrete that are higher than those in conventional concrete, resulting in increased water demand and mixing difficulty. This study considered the effects of eight different silica fumes in three dosages (10%, 20%, 30%) with three w/b (0.20, 0.30, 0.45) on rheological behavior as characterized by the Herschel-Bulkley model. Results indicated that the specific source of silica fume used, in addition to dosage and w/b, had a significant effect on the rheological behavior. As such, all silica fumes cannot be treated as equivalent or be directly substituted one for another without modification of the mixture proportion. The rheology of cement pastes is significantly affected by the physical properties of silica fume more so than any chemical effects.
  • 2017 Hurricane Season: Recommendations for a Resilient Path Forward for the Marine Transportation System

    Abstract: In October 2017, the Coordinating Board of the US Committee on the Marine Transportation System (MTS) tasked the MTS Resilience Integrated Action Team (RIAT) to identify the impacts, best practices, and lessons learned by federal agencies during the 2017 hurricane season. The RIAT studied the resiliency of the MTS by targeting its ability to prepare, respond, recover, and adapt to and from disruptions by turning to the collective knowledge of its members. Utilizing interagency data calls and a targeted workshop, the RIAT gauged the disruptive effect of the 2017 hurricane season and how Hurricanes Harvey, Irma, and Maria affected the operating status of at least 45 US ports across three major regions. This report identifies recommendations to better understand how the MTS can prepare for future storms and identifies activities by federal agencies that are contributing towards resilience. Such actions include hosting early pre-storm preparedness meetings, prioritizing communication between agencies and information distribution, and maintaining or updating existing response plans. Recommendations also target challenges experienced such as telecommunication and prioritization assistance to ports and critical infrastructure. Finally, the report offers opportunities to minimize the impacts experienced from storms and other disruptions to enhance the resilience of the MTS and supporting infrastructure.
  • An Epigenetic Modeling Approach for Adaptive Prognostics of Engineered Systems

    Abstract: Prognostics and health management (PHM) frameworks are widely used in engineered systems, such as manufacturing equipment, aircraft, and vehicles, to improve reliability, maintainability, and safety. Prognostic information for impending failures and remaining useful life is essential to inform decision-making by enabling cost versus risk estimates of maintenance actions. These estimates are generally provided by physics-based or data-driven models developed on historical information. Although current models provide some predictive capabilities, the ability to represent individualized dynamic factors that affect system health is limited. To address these shortcomings, we examine the biological phenomenon of epigenetics. Epigenetics provides insight into how environmental factors affect genetic expression in an organism, providing system health information that can be useful for predictions of future state. The means by which environmental factors influence epigenetic modifications leading to observable traits can be correlated to circumstances affecting system health. In this paper, we investigate the general parallels between the biological effects of epigenetic changes on cellular DNA to the influences leading to either system degradation and compromise, or improved system health. We also review a variety of epigenetic computational models and concepts, and present a general modeling framework to support adaptive system prognostics.
  • Hydrocarbon Treatability Study of Antarctica Soil with Fenton’s Reagent

    Abstract: The study objectives were to determine the effectiveness of Fenton’s Reagent and Modified Fenton’s Reagent in reducing Total Petroleum Hydrocarbon (TPH) concentrations in petroleum-contaminated soil from McMurdo Station, Antarctica. Comparisons of the contaminated soils were made, and a treatability study was completed and documented. This material was presented at the Association for Environmental Health and Sciences Foundation (AEHS) 30th Annual International Conference on Soil, Water, Energy, and Air (Virtual) on March 25, 2021.