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DOE OSTI2024

Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater

Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Comparison of the Antiviral Activity of Remdesivir, Chloroquine, and Interferon-β as Single or Dual Agents Against the Human Beta-Coronavirus OC43

The human beta-coronavirus strain, OC43, provides a useful model for testing the antiviral activity of various agents. We compared the activity of several antiviral drugs against OC43, including remdesivir, chloroquine, interferon (IFN)-β, IFN-λ1, and IFN-λ4, in two distinct cell types: human colorectal carcinoma cell line (HCT-8 cells) and normal human bronchial epithelial (NHBE) cells. We also tested whether these agents mediate additive, synergistic, or antagonistic activity against OC43 infection when used in combination. When used as single agents, remdesivir exhibited stronger antiviral activity than chloroquine, and IFN-β exhibited stronger activity than IFN-λ1 or IFN-λ4 against OC43 in both HCT-8 and NHBE cells. Anakinra (IL-1 inhibitor) and tocilizumab (IL-6 inhibitor) did not mediate any antiviral activity. The combination of IFN-β plus chloroquine or remdesivir resulted in higher synergy scores and higher expression of IFN-stimulated genes than did IFN-β alone. In contrast, the combination of remdesivir plus chloroquine resulted in an antagonistic interaction in NHBE cells. Our findings indicate that the combined use of IFN-β plus remdesivir or chloroquine induces maximal antiviral activity against human coronavirus strain OC43 in primary human respiratory epithelial cells. Furthermore, our experimental OC43 virus infection model provides an excellent method for evaluating the biological activity of antiviral drugs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

GraphCH: A Deep Framework for Assessing Cyber-Human Aspects in Insider Threat Detection

Insider threat is one of the most damaging cyber attacks that could cause the loss of intellectual property and enterprise data security breaches. Action sequence data such as host logs are used to investigate such threats and develop anomaly-based AI detectors. However, insider threat actions are similar to legitimate user activities, causing AI detectors to fail and suffer from high false alarm rates. Therefore, user cyber activity logs are inadequate to fully unfold insider threats. In this study, we adopt human psychological principles of risk-taking and impulsiveness along with host data to assess the influence and usefulness of human behavioral aspects in insider threat detection. Here, we hypothesize that individuals' impulsive and risk-taking behavior correlates with cyberspace activities. To validate our hypothesis, we conducted an IRB-approved study recruiting 35 participants who work in a large U.S. university and collected their cyber and psychological data for 90 days. Host and human-behavioral data analysis and mapping indicate that impulsive and risk-taking users trigger more system errors causing (un)intentional insider threats and are susceptible to attackers' social engineering and cognitive hacking. Utilizing cyber-human aspects, we introduce a Cyber-Human Graph Neural Network (GNN) based framework GraphCH to identify abnormal user behaviors and detect insider threats.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Human Host Cellular Response to HCoV-229E Infection Transcriptomics (ACS-DP1)

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Human Host Cellular Response to HCoV-229E Infection Proteomics (ACS-JM-DP2)

The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected immortalized human lung epithelial cells (A549) (MOI 5) nuclear extracts, immortalized human lung fibroblasts cells (MRC5) (MOI5) nuclear extracts, and primary human airway epithelial (HAE) (MOI 3) cells from lung tissue and processed for proteome analysis. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files and supporting metadata materials. Experimental proteomics samples were prepared using Limited Proteolysis (LiP) methods for Label-free quantification (LFQ) and global proteomic evaluation. Sample data was acquired using a Q-Exactive HF-X mass spectrometer and was processed and compiled using MaxQuant software (v.1.6.17.0). Processed proteomic data downloads include a sample naming key, processed MaxQuant results/parameters, and protein annotated relative abundance files. See corresponding primary data accessions below and Viral Experiment LiP Analysis source code supporting data transparency and reuse. Experimental transcriptomics samples were collected in parallel and processed for RNA sequencing (RNA-Seq) as summarized under ACS-DP1 (https://data.pnnl.gov/group/nodes/dataset/34069).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Human-Centric Lighting: Foundational Considerations and a Five-Step Design Process

At its best, human-centric lighting considers the visual and non-visual effects of light in support of positive human outcomes. At its worst, it is a marketing phrase used to healthwash lighting products or lighting design solutions. There is no doubt that environmental lighting contributes to human health, but how might one practice human-centric lighting given both the credible potential and the implausible hype? Marketing literature is filled with promises. Technical lighting societies have summarized the science but have not yet offered design guidance. Meanwhile, designers are in the middle, attempting to distinguish credible knowledge from that which is dubious to make design decisions that affect people directly. This article is intended to: (1) empower the reader with fundamental understandings of ways in which light affects health; (2) provide a process for human-centric lighting design that can dovetail with the decision-making process that is already a part of a designer's workflow.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Investigating the impact of environmental factors on West Nile virus human case prediction in Ontario, Canada

West Nile virus is the most common mosquito borne disease in North America and the leading cause of viral encephalitis. West Nile virus is primarily transmitted between birds and mosquitoes while humans are incidental, dead-end hosts. Climate change may increase the risk of human infections as climatic variables have been shown to affect the mosquito life cycle, biting rate, incubation period of the disease in mosquitoes, and bird migration patterns. We develop a zero-inflated Poisson model to investigate how human West Nile virus case counts vary with respect to mosquito abundance and infection rates, bird abundance, and other environmental covariates. We use a Bayesian paradigm to fit our model to data from 2010–2019 in Ontario, Canada. Our results show mosquito infection rate, temperature, precipitation, and crow abundance are positively correlated with human cases while NDVI and robin abundance are negatively correlated with human cases. We find the inclusion of spatial random effects allows for more accurate predictions, particularly in years where cases are higher. Our model is able to accurately predict the magnitude and timing of yearly West Nile virus outbreaks and could be a valuable tool for public health officials to implement prevention strategies to mitigate these outbreaks.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

INVESTIGATION OF HUMAN RELIABILITY ANALYSIS METHODS FOR ANALYZING PRE-INITIATORS

As a type of human actions defined in human reliability analysis (HRA), pre-initiator refers to the human actions that may lead to the unavailability of systems, typically committed during maintenance, test, or calibration. This paper investigates representative HRA methods used for analyzing pre-initiators. The HRA methods are Technique for Human Error Rate Prediction (THERP), Korean Standard HRA (K-HRA) and Standard Plant Risk HRA (SPAR-H). In this paper, characteristics of each HRA method are compared for qualitative and quantification aspects. Two pre-initiators, i.e., a calibration task and a valve restoration task, are analyzed using the HRA methods to compare human error probabilities. Then, insights from the analysis and additional research requirements are discussed in this paper.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2022

A Framework to Integrate Human Reliability Data Obtained from Different Sources Based on the Complexity Scores of Proceduralized Tasks

For many decades, PSA (Probabilistic Safety Assessment) or PRA (Probabilistic Risk Assessment) techniques have been used to enhance the operational safety of nuclear power plants (NPPs) based on the consideration of potential hazards that could result in an unexpected consequence. As human error is one of the potential hazards, diverse human reliability analysis (HRA) methods have been proposed to provide a systematic way to estimate the likelihood of human errors (i.e., human error probability, HEP) in specific task contexts. Accordingly, it is evident that the quality of HRA results strongly depends on the credibility of HEP estimations. This implies that, in terms of enhancing this credibility, the collection of raw information (HRA data) that is helpful for understating when and why human errors occur is a crucial issue. In order to address this issue, in this study, the feasibility of a framework to integrate HRA data obtained from different sources is investigated based on the complexity of proceduralized tasks.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

Human Factors Challenges in Modernizing Nuclear Power Plant Control Rooms

Jeffrey Joe has been invited to give a presentation entitled, “Human Factors Challenges in Modernizing Nuclear Power Plant Control Rooms,” at the 2024 Human Systems Symposium. Experts conducting human factors and human systems research will gather and share research at this conference. This conference is a good opportunity to develop new business for INL via research collaborations, as attendees exchange knowledge and explore the latest trends, advancements, and challenges in the field of human systems research across the DOE national laboratories.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

Human Factors Design for Particle Accelerator Control Room Interfaces

Fermilab, the birthplace of many scientific discoveries in physics and particle accelerator sciences, is in the midst of a widescale modernization effort. The Accelerator Control Operations Research Network (ACORN project’s goal is to modernize the accelerator control system by replacing end-of-life power supplies and enhance future operations of the Fermilab accelerator complex with megawatt particle beams. Within ACORN, opportunities for process improvement concerning software development, human-system interface design, and task performance are also being considered. Human factors researchers from Idaho National Laboratory in collaboration with usability experts from Fermilab, are currently investigating human-centered design improvements for the accelerator control system. For example, substantial tribal knowledge and memory recall are required to effectively operate the accelerator system. This contributes to high cognitive workload and potential burnout of accelerator operators. Developing guidance for consistent visual and functional design enables a more intuitive interaction and relieves operators of cognitive burden. Additionally, developing more intuitive and integrated interfaces can also lead to improved accelerator efficacy by empowering operators with greater understanding and control of the systems. The challenge in developing such interfaces is in designing for a wide variety of user goals, system specifications, and level of experience in users. The challenges need to be met while e also considering the maintainability of the control system. The purpose of this paper is to detail the human factors process and design within the ACORN project, describe results gathered thus far, and discuss the larger implications for this work.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Vertebrate and invertebrate competition for carrion in human‐impacted environments depends on abiotic factors

Abstract Human altered landscapes have caused declines in the diversity of wildlife where behaviorally plastic species (i.e., mesocarnivores and invasive species) tend to monopolize these areas and consume predictable and readily accessible food resources, such as human food waste and carrion. Increased consumption of carrion by vertebrates and invasive invertebrate species can alter population dynamics of native necrophagous insects relying on these resources. We tested the hypothesis that vertebrate scavengers and invasive species reduce blow fly (1) ability to use carrion and (2) reproduction in human‐impacted environments in central Texas, USA, with season, habitat (field and wooded landscapes), and carrion type (species of carrion and coat color) acting synergistically. Vertebrate scavengers in this habitat, of which 75% of the documented species were mesocarnivores and obligate scavengers, consumed 100% of carrion during the winter and 62% during summer despite having low species richness (2–5 species). Of the remaining carcasses available for arthropod activity during summer, the invasive red imported fire ant, Solenopsis invicta (Hymenoptera: Formicidae), monopolized 34%, and blow flies (e.g., Lucilia eximia and Chrysomya rufifacies [Diptera: Calliphoridae]) were only able to colonize 25%. Approximately 90% of carrion that was utilized by blow flies was co‐colonized by fire ants, and subsequent production of adult blow flies experienced up to a ninefold reduction in production compared with carcasses that were not scavenged by vertebrates or fire ants. Our results demonstrate oviposition resources used by blow flies in environments altered by human activity are reduced significantly by vertebrate scavengers and an invasive ant species. Future research should determine whether competitive interactions between vertebrate and invasive ant competitors for access to carrion resources have population‐level impacts to blow flies in human‐mediated ecosystems, or whether blow flies are able to shift to other resources to maintain sustainable populations and continue providing ecosystem services, such as pollination.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

A treatment-effect model to quantify human dimensions of disaster impacts: the case of Hurricane Maria in Puerto Rico

Here, we propose a supervised learning approach using publicly available panel data to statistically quantify the specific manifestations of human impacts of an extreme event, such as changes number of suicides, substance abuse, excess mortality, and unemployment. This allows us to conceptually focus our framework on human impacts and how by attributing them to disaster events along widely accepted psychological, economic, and social dimensions. Our modified treatment-effect model allows counterfactual baseline conditions to be posited for each manifestation from which an aggregated quantitative multi-faceted measure of human impacts can be determined. The developed statistical methodology could be beneficial to policymakers who must allocate scarce resources to those communities in greater need. We illustrate the applicability of our approach using annual and monthly panel data from 2012 to 2018 encompassing the 2017 Hurricane Maria event across various municipalities in Puerto Rico. Our statistical modeling methodology stands apart since (i) it explicitly and more realistically captures the effect of different human-oriented manifestations of an actual event and (ii) it is flexible enough to accommodate individual preferences of various stakeholders in how they assign importance to multiple manifestations of human impacts.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Challenges in predicting protein-protein interactions of understudied viruses: Arenavirus-human interactions

Understanding protein-protein interactions (PPIs) between viruses and host organisms is crucial for uncovering infection mechanisms and identifying potential therapeutic targets. The ability to generalize PPI predictive models across understudied viruses presents a significant challenge. In this work, we use arenavirus-human PPIs to illustrate the difficulties associated with model generalization, which are compounded by a lack of both positive and negative data. We employ a Transfer Learning approach to investigate arenavirus-human PPIs by utilizing models trained on better-studied virus-human and human-human PPIs. Additionally, we curate and assess four types of negative sampling datasets to evaluate their impact on model performance. Despite the overall high accuracies (93–99 %) and AUPRC scores (0.8–0.9) appearing promising, further analysis indicates that these performance metrics can be misleading due to data leakage, data bias, and overfitting, especially concerning under-represented viral proteins. We reveal these gaps and assess the impact of data imbalance using standard k-fold cross-validation and Independent Blind Testing with a Balanced Dataset, resulting in a drop in accuracy below 50 %. We propose a viral protein-specific evaluation framework that categorizes viral proteins into majority and minority classes based on their representation in the dataset, enabling comparison of model performance across these groups using balanced accuracies. This framework offers a more robust evaluation of model generalizability, addressing biases inherent in standard evaluation techniques and paving the way for more reliable PPI prediction models for understudied viruses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

In vitro effects of cannabidiol and its main metabolites in mouse and human Sertoli cells

Cannabidiol (CBD) is a major cannabinoid present in extracts of the plant Cannabis sativa (marijuana). While the therapeutic effects of CBD on epilepsy have been demonstrated, less is understood regarding its potential adverse effects. Recent studies revealed that CBD induced toxicity in the male reproductive system of animal models. In this study, we used TM4, an immortalized mouse Sertoli cell line, and primary human Sertoli cells to evaluate the toxicities of CBD and its main metabolites, 7-carboxy-CBD and 7-hydroxy-CBD. CBD induced concentration- and time-dependent cytotoxicity in mouse and human Sertoli cells, which mainly resulted from the inhibition of the G1/S-phase cell cycle transition. CBD also inhibited DNA synthesis and downregulated key cell cycle proteins. Moreover, CBD reduced the mRNA and protein levels of a functional marker, Wilms’ tumor 1. Similar to CBD, 7-carboxy-CBD and 7-hydroxy-CBD inhibited cellular proliferation and decreased DNA synthesis. 7-Carboxy-CBD was less cytotoxic than CBD, while 7-hydroxy-CBD showed comparable cytotoxicity to CBD in both mouse and human Sertoli cells. Compared to mouse Sertoli cells, CBD, 7-hydroxy-CBD, and 7-carboxy-CBD were more cytotoxic in human Sertoli cells. Finally, our results indicate that CBD and its main metabolites can inhibit cell proliferation in mouse and human Sertoli cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation

Human uracil DNA-glycosylase (UDG) is the prototypic and first identified DNA glycosylase with a vital role in removing deaminated cytosine and incorporated uracil and 5-fluorouracil (5-FU) from DNA. UDG depletion sensitizes cells to high APOBEC3B deaminase and to pemetrexed (PEM) and floxuridine (5-FdU), which are toxic to tumor cells through incorporation of uracil and 5-FU into DNA. To identify small-molecule UDG inhibitors for pre-clinical evaluation, we optimized biochemical screening of a selected diversity collection of >3,000 small-molecules. We found aurintricarboxylic acid (ATA) as an inhibitor of purified UDG at an initial calculated IC 50 < 100 nM. Subsequent enzymatic assays confirmed effective ATA inhibition but with an IC50 of 700 nM and showed direct binding to the human UDG with a K D of <700 nM. ATA displays preferential, dose-dependent binding to purified human UDG compared to human 8-oxoguanine DNA glycosylase. ATA did not bind uracil-containing DNA at these concentrations. Yet, combined crystal structure and in silico docking results unveil ATA interactions with the DNA binding channel and uracil-binding pocket in an open, destabilized UDG conformation. Biologically relevant ATA inhibition of UDG was measured in cell lysates from human DLD1 colon cancer cells and in MCF-7 breast cancer cells using a host cell reactivation assay. Collective findings provide proof-of-principle for development of an ATA-based chemotype and “door stopper” strategy targeting inhibitor binding to a destabilized, open pre-catalytic glycosylase conformation that prevents active site closing for functional DNA binding and nucleotide flipping needed to excise altered bases in DNA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Characterization of the procoagulant phenotype of amniotic fluid across gestation in rhesus macaques and humans

Background: Amniotic fluid (AF) plays a key role in fetal development, yet the evolving composition of AF and its effects of hemostasis and thrombosis are poorly understood. Objectives: Here, we aim to determine how the evolving molecular composition of AF relates to its procoagulant properties. Methods: We analyzed the proteomes, lipidomes and procoagulant properties of AF obtained by amniocentesis from rhesus macaque and human pregnancies at gestational-age matched timepoints. Results When added to human plasma, both rhesus and human AF accelerated clotting time and fibrin generation. We identified proteomic modules associated with clotting time and enriched for coagulation-related pathways. Proteins known to be involved in hemostasis were highly correlated with each other and their intensity of expression varied across gestation in both rhesus and humans. Inhibition of contact pathway did not affect the procoagulant effect of AF. Blocking tissue factor pathway inhibitor reversed the ability of AF to block the generation of FXa. The prothrombinase activity of AF was inhibited by phospholipid inhibitors. The levels of phosphatidylserine in AF were inversely correlated with clotting time. AF promoted platelet activation and secretion in plasma. Conclusions: The addition of AF to plasma enhances coagulation in a manner dependent on phospholipids as well as the presence of proteases and other proteins that directly regulate coagulation. We describe a correlation between clotting time and expression of coagulation proteins and phosphatidylserine in both rhesus and human AF, supporting the use rhesus models for future studies of AF biology.

amniotic fluid↗