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DOE OSTI2020

Neural networks for modeling and control of particle accelerators

Charged particle accelerators support a wide variety of scientific, industrial, and medical applications. They range in scale and complexity from systems with just a few components for beam acceleration and manipulation, to large scientific user facilities that span many kilometers and have hundreds-to-thousands of individually-controllable components. Specific operational requirements must be met by adjusting the many controllable variables of the accelerator. Meeting these requirements can be challenging, both in terms of the ability to achieve specific beam quality metrics in a reliable fashion and in terms of the time needed to set up and maintain the optimal operating conditions. One avenue toward addressing this challenge is to incorporate techniques from the fields of machine learning (ML) and artificial intelligence (AI) into the way particle accelerators are modeled and controlled. While many promising approaches within AI/ML could be used for particle accelerators, this dissertation focuses on approaches based on neural networks. Neural networks are particularly well-suited to modeling, control, and diagnostic analysis of nonlinear systems, as well as systems with large parameter spaces. They are also very appealing for their ability to process high-dimensional data types, such as images and time series (both of which are ubiquitous in particle accelerators). In this work, key studies that demonstrated the potential utility of modern neural network-based approaches to modeling and control of particle accelerators are presented. The context for this work is important: at the start of this work in 2012, there was little interest in AI/ML in the particle accelerator community, and many of the advances in neural networks and deep learning that enabled its present success had not yet been made at that time. As such, this work was both an exploration of possible application areas and a generator of proof-of-concept demonstrations in these areas.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Elucidating algal-bacterial community interactions by tracking volatile biomarkers (Final Report)

This feasibility study project aimed to lay further groundwork for studying and understanding how microorganisms interact with each other at the molecular level using model algal-bacterial co-cultures. A better understanding of such interactions is critical to optimizing and operating biotic platforms for a number of applications, including bioenergy, algal bioproducts and agriculture, and carbon capture. Here we explored the feasibility of characterizing and following these interactions by identifying and tracking volatile metabolites and biomarkers in the complex gaseous headspace of such cultures. We set up an experimental platform using a co-culture of Phaeodactylum tricornutum and Marinobacter subspecies 3-2 as a model system, used solid-phase microextraction fibers for volatile collection at various time points throughout culture growth, and employed gas chromatography mass spectrometry-based instrumentation available at LLNL for compound identification and quantification. We found that it is feasible to determine volatile profiles from the growth of Phaeodactylum tricornutum and Marinobacter subspecies 3-2 using our methodology and monitor profile changes over time. We also observed that volatiles distinguishing between cultures of the individual species and the co-cultures could be detected. We expect that results of this project will feed into the ongoing LLNL’s DOE BER funded Biofuels Scientific Focus Area (SFA) on algal-bacterial interactions and pave the way for future expanded volatile studies supported by DOE. The approach and technologies developed here would also be applicable and transferable to other microbial communities under study, such as cyanobacteria, rhizosphere communities and biofilms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2004

The Art of Space Flight Exercise Hardware: Design and Implementation

The design of space flight exercise hardware depends on experience with crew health maintenance in a microgravity environment, history in development of flight-quality exercise hardware, and a foundation for certifying proper project management and design methodology. Developed over the past 40 years, the expertise in designing exercise countermeasures hardware at the Johnson Space Center stems from these three aspects of design. The medical community has steadily pursued an understanding of physiological changes in humans in a weightless environment and methods of counteracting negative effects on the cardiovascular and musculoskeletal system. The effects of weightlessness extend to the pulmonary and neurovestibular system as well with conditions ranging from motion sickness to loss of bone density. Results have shown losses in water weight and muscle mass in antigravity muscle groups. With the support of university-based research groups and partner space agencies, NASA has identified exercise to be the primary countermeasure for long-duration space flight. The history of exercise hardware began during the Apollo Era and leads directly to the present hardware on the International Space Station. Under the classifications of aerobic and resistive exercise, there is a clear line of development from the early devices to the countermeasures hardware used today. In support of all engineering projects, the engineering directorate has created a structured framework for project management. Engineers have identified standards and "best practices" to promote efficient and elegant design of space exercise hardware. The quality of space exercise hardware depends on how well hardware requirements are justified by exercise performance guidelines and crew health indicators. When considering the microgravity environment of the device, designers must consider performance of hardware separately from the combined human-in-hardware system. Astronauts are the caretakers of the hardware while it is deployed and conduct all sanitization, calibration, and maintenance for the devices. Thus, hardware designs must account for these issues with a goal of minimizing crew time on orbit required to complete these tasks. In the future, humans will venture to Mars and exercise countermeasures will play a critical role in allowing us to continue in our spirit of exploration. NASA will benefit from further experimentation on Earth, through the International Space Station, and with advanced biomechanical models to quantify how each device counteracts specific symptoms of weightlessness. With the continued support of international space agencies and the academic research community, we will usher the next frontier in human space exploration.

Beyene, Nahom M.↗

DOE OSTI2024

Evaluation of data collection bias of third molar stages of mineralisation for age estimation in the living

Abstract Age assessment of the living is a fundamental procedure in the process of human identification, in order to guarantee fair treatment of individuals, which has ethical, civil, legal, and medical repercussions. The careful selection of the appropriate methods requires evaluation of several parameters: accuracy, precision of the method, as well as its reproducibility. The approach proposed by Mincer et al. adapted from Demirjian et al. exploring third molar mineralisation, is one of the most frequently considered for age estimation of the living. Thus, this work aims to assess potential bias in the data collection when applying the classification stages for dental mineralisation adapted by Mincer et al. A total of 102 orthopantomographs, of clinical origin, belonging to individuals aged between 12 and 25 years ($ \bar{\textit x} $ = 20.12 years, SD = 3.49 years; 65 females, 37 males, all of Portuguese nationality) were included and a retrospective analysis performed by five observers with different levels of experience (high, average, and basic). The performance and agreement between five observers were evaluated using Weighted Cohen’s Kappa and the Intraclass Correlation Coefficient. To access the influence of impaction on third molar classification, variables were tested using ordinal logistic regression Generalised Linear Model. It was observed that there were variations in the number of teeth identified among the observers, but the agreement levels ranged from moderate to substantial (0.4–0.8). Upon closer examination of the results, it was observed that although there were discernible differences between highly experienced observers and those with less experience, the gap was not as significant as initially hypothesised, and a greater disparity between the classifications of the upper (0.24–0.49) and lower third molars (>0.55) was observed. When bone superimposition is present, the classification process is not significantly influenced; however, variation in teeth angulation affects the assessment. The results suggest that with an efficient preparation, the level of experience as a factor can be overcome. Mincer and colleague's classification system can be replicated with ease and consistency, even though the classification of upper and lower third molars presents distinct challenges.

de Oliveira Santos, Inês (ORCID:0000000267324347)↗

DOE OSTI2024

Evaluation of GlassNet for physics-informed machine learning of glass stability and glass-forming ability

Glassy materials form the basis of many modern applications, including nuclear waste immobilization, touch-screen displays, and optical fibers, and also hold great potential for future medical and environmental applications. However, their structural complexity and large composition space make design and optimization challenging for certain applications. Of particular importance for glass processing and design is an estimate of a given composition's glass-forming ability (GFA). However, there remain many open questions regarding the underlying physical mechanisms of glass formation, especially in oxide glasses. It is apparent that a proxy for GFA would be highly useful in glass processing and design, but identifying such a surrogate property has proven itself to be difficult. While glass stability (GS) parameters have historically been used as a GFA surrogate, recent research has demonstrated that most of these parameters are not accurate predictors of the GFA of oxide glasses. Here, in this work, we explore the application of an open-source pre-trained neural network model, GlassNet, that can predict the characteristic temperatures necessary to compute GS with reasonable performance and assess the feasibility of using these physics-informed machine learning (PIML)-predicted GS parameters to estimate GFA. In doing so, we track the uncertainties at each step of the computation—from the original ML prediction errors to the compounding of errors during GS estimation, and finally to the final estimation of GFA. While GlassNet exhibits reasonable accuracy on all individual properties, we observe a large compounding of error in the combination of these individual predictions for the PIML prediction of GS, finding that random forest models offer similar accuracy to GlassNet. We also break down the performance of GlassNet on different glass families and find that the error in GS prediction is correlated with the error in crystallization peak temperature prediction. Lastly, we utilize this finding to assess the relationship between top-performing GS parameters and GFA for two ternary glass systems: sodium borosilicate and sodium iron phosphate glasses. We conclude that to obtain true ML predictive capability of GFA, significantly more data needs to be collected.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Single‐Cell Nanodroplet Processing Proteomics Pipeline for Analysis of Human‐Derived Microglia

Single-cell omics tools provide unique insights into heterogeneous cell populations and their responses to stimuli. For example, single-cell RNA sequencing has identified several transcriptionally distinct populations of microglia, which are resident immune cells of the central nervous system (CNS) that are responsive to CNS injury, infection, and neurodegeneration. To date, single-cell studies of microglia have focused on RNA-sequencing or cytometry by time of flight (CyTOF), which provide indirect readouts of protein abundance or quantification of a limited number of targets. Herein, we present a workflow based on FACS-assisted isolation, cryopreservation, and nanodroplet-based processing for single-cell mass spectrometry proteomics analysis of the postmortem human brain cortex-derived microglia. From a single microglial cell, 1039 proteins could be identified on average. As a proof-of-principle, we applied single-cell proteomics for exploring the heterogeneity of brain microglia at the cellular level. This pilot proteomics data partially recapitulates the prior microglia subtypes. Specifically, we determined that mitochondrial proteins, in particular members of NADH dehydrogenase (Complex I), cytochrome b-c1 (Complex III), cytochrome c oxidase (Complex IV), F1-ATPase (Complex V), and Na+/K+-ATPase complex, drive variation across microglia. This pipeline offers the potential for identifying functionally and analytically relevant protein targets for microglia in Alzheimer's disease and other neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2016

Levitation Technology in International Space Station Research

The International Space Station (ISS) is a unique multidisciplinary orbiting laboratory for science and technology research, enabling discoveries that benefit life on Earth and exploration of the universe. ISS facilities for containerless sample processing in Materials Science experiments include levitation devices with specimen positioning control while reducing containment vessel contamination. For example, ESA's EML (ElectroMagnetic Levitator), is used for melting and solidification of conductive metals, alloys, or semiconductors in ultra-high vacuum, or in high-purity gaseous atmospheres. Sample heating and positioning are accomplished through electromagnetic fields generated by a coil system. EML applications cover investigation of solidification and microstructural formation, evaluation of thermophysical properties of highly reactive metals (whose properties can be very sensitive to contamination), and examination of undercooled liquid metals to understand metastable phase convection and influence convection on structural changes. MSL utilization includes development of novel light-weight, high-performance materials. Another facility, JAXA's ELF (Electrostatic Levitation Furnace), is used to perform high temperature melting while avoiding chemical reactions with crucibles by levitating a sample through Coulomb force. ELF is capable of measuring density, surface tension, and viscosity of samples at high temperatures. One of the initial ELF investigations, Interfacial Energy-1, is aimed at clarification of interfacial phenomena between molten steels and oxide melts with industrial applications in control processes for liquid mixing. In addition to these Materials Science facilities, other ISS investigations that involve levitation employ it for biological research. For example, NASA's "Magnetic 3D Culturing and Bioprinting" investigation uses magnetic levitation for three-dimensional culturing and positioning of magnetized cells to generate spheroid assemblies for biomedical applications. Levitation is also used as a modeled microgravity ground analog in the NASA OsteoOmics ISS investigation, which tests whether magnetic levitation accurately simulates microgravity conditions by studying gravitational regulation of osteoblast and osteoclast genomics and metabolism. Elucidating the cellular mechanisms of bone loss in microgravity contributes to the understanding of bone loss in medical disorders on Earth, which may lead to development of preventive or therapeutic countermeasures. Thus, the ISS state-of-the-art laboratory offers various levitation capability platforms with applications for innovative research in Materials and Life Sciences disciplines, with benefits for humanity.

Guinart-Ramirez, Y.↗

NASA NTRS2016

Closed Loop Control Compact Exercise Device for Use on MPCV

Long duration space travel to Mars or to an asteroid will expose astronauts to extended periods of reduced gravity. To combat spaceflight physiological deconditioning, astronauts will use resistive and aerobic exercise regimens for the duration of the space flight to minimize the loss of bone density, muscle mass and aerobic capacity that occurs during exposure to a reduced gravity environment. Unlike the International Space Station (ISS), the mass and volume available for an exercise device in the next generation of spacecraft is limited. Therefore, compact exercise device prototypes are being developed for human in the loop evaluations. The NASA Human Research Program (HRP) is managing Advanced Exercise Concepts (AEC) requirements development and candidate technology maturation for all exploration mission profiles from Multi-Purpose Crew Vehicle (MPCV) exploration missions (e.g., EM-2, up to 21 day) to Mars Transit (up to 1000 day) missions. Numerous technologies have been considered and evaluated against HRP-approved functional requirements and include flywheel, pneumatic and closed-loop microprocessor-controlled motor driven power plants. Motor driven technologies offer excellent torque density and load accuracy characteristics as well as the ability to create custom mechanical impedance (the dynamic relationship between force and velocity) and custom load versus position exercise algorithms. Further, closed-loop motor-driven technologies offer the ability to monitor exercise dose parameters and adapt to the needs of the crewmember for real time optimization of exercise prescriptions. A simple proportional-integral-derivative (PID) controller is demonstrated in a prototype motor driven exercise device with comparison to resistive static and dynamic load set points and aerobic work rate targets. The resistive load term in the algorithm includes a constant force component (Fcmg) as well as inertial component (Fima) and a discussion of system tuning is presented in terms of addressing key functional requirements and human interfaces. The device aerobic modality is modelled as a rowing exercise using ground data sets obtained from Concept 2 rowers as well as competitive rowing1. A discussion of software and electronic implementations are presented which demonstrate unique approaches to meeting the constrained mass, volume and power requirements of the MPCV. . In addition to utilizing traditional PID control, controllers utilizing state feedback with gains solved using a Linear Quadratic Regulator will be developed. Controllability and observability will be utilized to investigate the need for state measurement in the design. As the control system directly interacts with human test subjects, robust methods such as H-infinity are also being investigated.1. Kleshnev V. Biomechanics. In: Rowing, Handbook of Sports Medicine and Science. ed. by Secher N., Voliantis S. IOC Medical Commission, Blackwell Pub. pp. 22-34, 2007

microgravity↗

DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗

NASA NTRS2013

Challenges of Integrating NASAs Space Communication Networks

The transition to new technology, innovative ideas, and resistance to change is something that every industry experiences. Recent examples of this shift are changing to using robots in the assembly line construction of automobiles or the increasing use of robotics for medical procedures. Most often this is done with cost-reduction in mind, though ease of use for the customer is also a driver. All industries experience the push to increase efficiency of their systems; National Aeronautics and Space Administration (NASA) and the commercial space industry are no different. NASA space communication services are provided by three separately designed, developed, maintained, and operated communications networks known as the Deep Space Network (DSN), Near Earth Network (NEN) and Space Network (SN). The Space Communications and Navigation (SCaN) Program is pursuing integration of these networks and has performed a variety of architecture trade studies to determine what integration options would be the most effective in achieving a unified user mission support organization, and increase the use of common operational equipment and processes. The integration of multiple, legacy organizations and existing systems has challenges ranging from technical to cultural. The existing networks are the progeny of the very first communication and tracking capabilities implemented by NASA and the Jet Propulsion Laboratory (JPL) more than 50 years ago and have been customized to the needs of their respective user mission base. The technical challenges to integrating the networks are many, though not impossible to overcome. The three distinct networks provide the same types of services, with customizable data rates, bandwidth, frequencies, and so forth. The differences across the networks have occurred in effort to satisfy their user missions' needs. Each new requirement has made the networks more unique and harder to integrate. The cultural challenges, however, have proven to be a significant obstacle for integration. Over the past few decades of use, user missions and network personnel alike have grown accustomed to the processes by which services are provided by the NASA communications and navigation networks. The culture established by each network has created several challenges that need to be overcome in order to effectively integrate the networks. As with any change, there has been resistance, an apprehension to explore automation of existing processes, and a working environment that attempts to indirectly influence change without mandating compliance. Overcoming technical and cultural challenges is essential to successfully integrating the networks and although the challenges are numerous, the integration of the networks promises a more efficient space communications network for NASA and its customers, as well as potential long-term cost savings to the agency. This paper, Challenges of Integrating NASA Legacy Communications Networks, will provide a brief overview of the current NASA space communications networks as well as the an overview of the process implemented while performing the SCaN Trade Studies and an introduction to the requirements driving integration of the SCaN Networks. This paper will describe in detail the challenges experienced, both technical and cultural, while working with NASA space communications network-specific personnel. The paper will also cover lessons learned during the performance of architecture trade studies and provide recommendations for ways to improve the process.

Reinert, Jessica M.↗

NASA NTRS2013

Challenges of Integrating NASA's Space Communications Networks

Systems Integration↗

NASA NTRS2020

Preparing for Human Missions to Mars: The role of ISS and Artemis as Analogs for Research and Technology Testing

The hazards of spaceflight to the human system are present in in varying degrees on different spaceflight platforms: altered gravity, isolation and confinement, distance from Earth, radiation, and hostile closed environments. A strategic view of the fidelity of hazards experienced on different platforms can shape the testing plans for human research and technology demonstration related to crew health and performance. Working across the international partnership, the International Space Station (ISS) is planning periods of modified operations to improve the fidelity of Mars simulations. To understand transit durations as an independent variable, a series of 1-year, 6-month and 30-45 day missions are being planned on ISS. Standard measurements across ISS missions of different durations, lunar missions and ground analogs offers the opportunity to distinguish different hazards and their effects in the context of the relevance to future mission concepts. The ISS partnership is planning for additional test cases that are aligned with Mars mission plans. (1) Evaluating crew performance capabilities when transitioning to gravity after long durations in microgravity representative of a Mars transit. (2) Simulating crew medical care under Mars-like autonomous operations. (3) Identification and testing of operations under communications delay and autonomy expected for Mars missions and the linked effects on behavioral health and performance of the crew. Artemis missions serve as a valuable analogs for Mars surface operations, with partial gravity and deep space radiation hazards, but with crewmembers that are probably more physically capable than their counterparts would be after a Mars transit. Getting unobtrusive data from early Artemis missions, and knowledge gained from operational experience as Artemis operations develop can improve engineering design, medical requirements and countermeasures, and ultimately ensure mission success on Mars. Linking Mars architectures with the plans and capabilities for ISS and Artemis allows us to plan to most operationally relevant tests of crew health and performance on current spaceflight missions to inform planning for future missions to Mars. By using human spaceflight platforms as well as ground simulation in an integrated way, the international community can improve exploration readiness, develop countermeasures and reduce risks of future human space missions.

International Space Station↗

DOE OSTI2023

Mathematical solutions in internal dose assessment: A comparison of Python-based differential equation solvers in biokinetic modeling

Abstract In biokinetic modeling systems employed for radiation protection, biological retention and excretion have been modeled as a series of discretized compartments representing the organs and tissues of the human body. Fractional retention and excretion in these organ and tissue systems have been mathematically governed by a series of coupled first-order ordinary differential equations (ODEs). The coupled ODE systems comprising the biokinetic models are usually stiff due to the severe difference between rapid and slow transfers between compartments. In this study, the capabilities of solving a complex coupled system of ODEs for biokinetic modeling were evaluated by comparing different Python programming language solvers and solving methods with the motivation of establishing a framework that enables multi-level analysis. The stability of the solvers was analyzed to select the best performers for solving the biokinetic problems. A Python-based linear algebraic method was also explored to examine how the numerical methods deviated from an analytical or semi-analytical method. Results demonstrated that customized implicit methods resulted in an enhanced stable solution for the inhaled 60 Co (Type M) and 131 I (Type F) exposure scenarios for the inhalation pathway of the International Commission on Radiological Protection (ICRP) Publication 130 Human Respiratory Tract Model (HRTM). The customized implementation of the Python-based implicit solvers resulted in approximately consistent solutions with the Python-based matrix exponential method ( expm ). The differences generally observed between the implicit solvers and expm are attributable to numerical precision and the order of numerical approximation of the numerical solvers. This study provides the first analysis of a list of Python ODE solvers and methods by comparing their usage for solving biokinetic models using the ICRP Publication 130 HRTM and provides a framework for the selection of the most appropriate ODE solvers and methods in Python language to implement for modeling the distribution of internal radioactivity.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2021

COVID-19 Evidence Accelerator: A parallel analysis to describe the use of Hydroxychloroquine with or without Azithromycin among hospitalized COVID-19 patients

Background: The COVID-19 pandemic remains a significant global threat. However, despite urgent need, there remains uncertainty surrounding best practices for pharmaceutical interventions to treat COVID-19. In particular, conflicting evidence has emerged surrounding the use of hydroxychloroquine and azithromycin, alone or in combination, for COVID-19. The COVID-19 Evidence Accelerator convened by the Reagan-Udall Foundation for the FDA, in collaboration with Friends of Cancer Research, assembled experts from the health systems research, regulatory science, data science, and epidemiology to participate in a large parallel analysis of different data sets to further explore the effectiveness of these treatments. Methods: Electronic health record (EHR) and claims data were extracted from seven separate databases. Parallel analyses were undertaken on data extracted from each source. Each analysis examined time to mortality in hospitalized patients treated with hydroxychloroquine, azithromycin, and the two in combination as compared to patients not treated with either drug. Cox proportional hazards models were used, and propensity score methods were undertaken to adjust for confounding. Frequencies of adverse events in each treatment group were also examined. Results: Neither hydroxychloroquine nor azithromycin, alone or in combination, were significantly associated with time to mortality among hospitalized COVID-19 patients. No treatment groups appeared to have an elevated risk of adverse events. Conclusion: Administration of hydroxychloroquine, azithromycin, and their combination appeared to have no effect on time to mortality in hospitalized COVID-19 patients. Continued research is needed to clarify best practices surrounding treatment of COVID-19.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Transcript and blood-microbiome analysis towards a blood diagnostic tool for goats affected by Haemonchus contortus

The Alpine goat (Capra aegagrus hircus) is parasitized by the barber pole worm (Haemonchus contortus). Hematological parameters from transcript and metagenome analysis in the host are reflective of infestation. We explored comparisons between blood samples of control, infected, infected zoledronic acid-treated, and infected antibody (anti-γδ T cells) treated wethers under controlled conditions. Seven days post-inoculation (dpi), we identified 7,627 transcripts associated with the different treatment types. Microbiome measurements at 7 dpi revealed fewer raw read counts across all treatments and a less diverse microbial flora than at 21 dpi. This study identifies treatment specific transcripts and an increase in microflora abundance and diversity as wethers age. Further, F/B ratio reflect health, based on depression or elevation above thresholds defined by the baseline of non-infected controls. Forty Alpine wethers were studied where blood samples were collected from five goats in four treatment groups on 7 dpi and 21 dpi. Transcript and microbiome profiles were obtained using the Partek Flow (St. Louis, Missouri, USA) software suites pipelines. Inflammation comparisons were based on the Firmicutes/Bacteriodetes ratios that are calculated as well as the reduction of microbial diversity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Assessing complexity and dynamics in epidemics: geographical barriers and facilitators of foot-and-mouth disease dissemination

Introduction: Physical and non-physical processes that occur in nature may influence biological processes, such as dissemination of infectious diseases. However, such processes may be hard to detect when they are complex systems. Because complexity is a dynamic and non-linear interaction among numerous elements and structural levels in which specific effects are not necessarily linked to any one specific element, cause-effect connections are rarely or poorly observed. Methods: To test this hypothesis, the complex and dynamic properties of geo-biological data were explored with high-resolution epidemiological data collected in the 2001 Uruguayan foot-and-mouth disease (FMD) epizootic that mainly affected cattle. County-level data on cases, farm density, road density, river density, and the ratio of road (or river) length/county perimeter were analyzed with an open-ended procedure that identified geographical clustering in the first 11 epidemic weeks. Two questions were asked: (i) do geo-referenced epidemiologic data display complex properties? and (ii) can such properties facilitate or prevent disease dissemination? Results: Emergent patterns were detected when complex data structures were analyzed, which were not observed when variables were assessed individually. Complex properties–including data circularity–were demonstrated. The emergent patterns helped identify 11 counties as ‘disseminators’ or ‘facilitators’ (F) and 264 counties as ‘barriers’ (B) of epidemic spread. In the early epidemic phase, F and B counties differed in terms of road density and FMD case density. Focusing on non-biological, geographical data, a second analysis indicated that complex relationships may identify B-like counties even before epidemics occur. Discussion: Geographical barriers and/or promoters of disease dispersal may precede the introduction of emerging pathogens. If corroborated, the analysis of geo-referenced complexity may support anticipatory epidemiological policies.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2014

Assessing the Effect of Spaceflight on the Propensity for Astronauts to Develop Disk Herniation

BACKGROUND: A previous study [1] reported that the instantaneous risk of developing a Herniated Nucleus Pulposus (HNP) was higher in astronauts who had flown at least one mission, as compared with those in the corps who had not yet flown. However, the study only analyzed time to HNP after the first mission (if any) and did not account for the possible effects of multiple missions. While many HNP's occurred well into astronauts' careers or in some cases years after retirement, the higher incidence of HNPs relatively soon after completion of space missions appears to indicate that spaceflight may lead to an increased risk of HNP. The purpose of this study was to support the Human System Risk Board assessment of back pain, evaluate the risk of injury due to dynamic loads, and update the previous dataset which contained events up to December 31, 2006. METHODS: Data was queried from the electronic medical record and provided by the Lifetime Surveillance of Astronaut Health. The data included all 330 United States astronauts from 1959 through February 2014. Cases were confirmed by Magnetic Resonance Imaging, Computerized Tomography, Myelography, operative findings, or through clinical confirmation with a neurologist or neurosurgeon. In this analysis, astronauts who had an HNP at selection into the corps or had an HNP diagnosis prior to their first flight were excluded. The statistical challenges in using the available data to separate effects of spaceflight from those associated with general astronaut training and lifestyle on propensity to develop HNPs are many. The primary outcome is reported date of first HNP (if any), which at best is only an approximation to the actual time of occurrence. To properly analyze this data with a survival analysis model, one must also know the "exposure" time - i.e. how long each astronaut has been at risk for developing an HNP. If an HNP is reported soon after a mission, is it mission caused or general? If the former, exposure time should be counted from the time of landing (assuming the risk of HNP occurring during a mission is zero). If the latter, exposure time should be counted from the time of selection; however we can't directly know which one to use. In our analysis we take both of these possibilities into account with a competing risks model, wherein two distinct stochastic processes are going on: TG = time to HNP (general) and TS = time to HNP (spaceflight). Under this type of model, whichever of these occurs first is what we observe; in other words we don't observe TG or TS, only min(TG, TS). Here, we parameterized the model in terms of separate Weibull hazard functions for each process and estimated all parameters using maximum likelihood. In addition, we allowed for a "cured fraction" - i.e. the possibility that some astronauts may never develop an HNP. RESULTS: Results will include a depiction of the competing hazard functions as well as a probability curve for the relative likelihood that an HNP reported at a given time after a mission is actually mission caused. Other factors, such as dwell time in microgravity and vehicle landing environment will be explored. An overall assessment as to whether spaceflight truly exacerbates HNP risk will be made.

Feiveson, A. H.↗

DOE OSTI2021

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy

Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.

60 APPLIED LIFE SCIENCES↗