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NASA NTRS2008

Logic Gates Made of N-Channel JFETs and Epitaxial Resistors

Prototype logic gates made of n-channel junction field-effect transistors (JFETs) and epitaxial resistors have been demonstrated, with a view toward eventual implementation of digital logic devices and systems in silicon carbide (SiC) integrated circuits (ICs). This development is intended to exploit the inherent ability of SiC electronic devices to function at temperatures from 300 to somewhat above 500 C and withstand large doses of ionizing radiation. SiC-based digital logic devices and systems could enable operation of sensors and robots in nuclear reactors, in jet engines, near hydrothermal vents, and in other environments that are so hot or radioactive as to cause conventional silicon electronic devices to fail. At present, current needs for digital processing at high temperatures exceed SiC integrated circuit production capabilities, which do not allow for highly integrated circuits. Only single to small number component production of depletion mode n-channel JFETs and epitaxial resistors on a single substrate is possible. As a consequence, the fine matching of components is impossible, resulting in rather large direct-current parameter distributions within a group of transistors typically spanning multiples of 5 to 10. Add to this the lack of p-channel devices to complement the n-channel FETs, the lack of precise dropping diodes, and the lack of enhancement mode devices at these elevated temperatures and the use of conventional direct coupled and buffered direct coupled logic gate design techniques is impossible. The presented logic gate design is tolerant of device parameter distributions and is not hampered by the lack of complementary devices or dropping diodes. In addition to n-channel JFETs, these gates include level-shifting and load resistors (see figure). Instead of relying on precise matching of parameters among individual JFETS, these designs rely on choosing the values of these resistors and of supply potentials so as to make the circuits perform the desired functions throughout the ranges over which the parameters of the JFETs are distributed. The supply rails V(sub dd) and V(sub ss) and the resistors R are chosen as functions of the distribution of direct-current operating parameters of the group of transistors used.

Krasowski, Michael J.↗

NASA NTRS2003

Radiation Risk Projections for Space Travel

Space travelers are exposed to solar and galactic cosmic rays comprised of protons and heavy ions moving with velocities close to the speed of light. Cosmic ray heavy ions are known to produce more severe types of biomolecular damage in comparison to terrestrial forms of radiation, however the relationship between such damage and disease has not been fully elucidated. On Earth, we are protected from cosmic rays by atmospheric and magnetic shielding, and only the remnants of cosmic rays in the form of ground level muons and other secondary radiations are present. Because human epidemiology data is lacking for cosmic rays, risk projection must rely on theoretical understanding and data from experimental models exposed to space radiation using charged particle accelerators to simulate space radiation. Although the risks of cancer and other late effects from cosmic rays are currently believed to present a severe challenge to space travel, this challenge is centered on our lack of confidence in risk projections methodologies. We review biophysics and radiobiology data on the effects of the cosmic ray heavy ions, and the current methods used to project radiation risks . Cancer risk projections are described as a product of many biological and physical factors, each of which has a differential range of uncertainty due to lack of data and knowledge. Risk projections for space travel are described using Monte-Carlo sampling from subjective error di stributions that represent the lack of knowledge in each factor that contributes to the projection model in order to quantify the overall uncertainty in risk projections. This analysis is applied to space mi ssion scenarios including lunar colony, deep space outpost, and a Mars mission. Results suggest that the number of days in space where cancer mortality risks can be assured at a 95% confidence level to be below the maximum acceptable risk for radi ation workers on Earth or the International Space Station is only on the order of 100-200 days. Approaches to reduce these unceI1ainties and mitigate risks are described.

Cucinotta, Francis↗

NASA NTRS2013

Spectrum for UAS Control and Non-Payload Communications

There is an increasing need to fly UAS in the NAS to perform missions of vital importance to National Security and Defense, Emergency Management, and Science as well as commercial applications (e.g. cargo transport). To enable integration of UAS into the National Airspace System, several critical technical barriers must be eliminated, including: Separation Assurance/Sense and Avoid - the uncertainty surrounding the ability to interoperate in ATC environments and maintain safe separation from other aircraft in the absence of an on-board pilot. Human Systems Integration - lack of standards and guidelines with respect to UAS display information as well as lack of Ground Control Station (GCS) design requirements to operate in the NAS. Certification - lack of airworthiness requirements and safety-related data specific to the full range of UAS, or for their avionics systems or other components. Communications - lack of standard, certifiable data links and aviation safety spectrum to operate such links for civil UAS control communications.

Kerczewski, Robert J.↗

NASA NTRS2013

The Pinnacles of Callisto

Many regions of Callisto feature an unusual landscape consisting of rolling dark plains with interspersed bright knobs (pinnacles) and ridges. In earlier work we interpreted the dark plains as dusty, mass-wasted residue from sublimation from volatile-rich bedrock and the bright knobs (often crater rims) as water ice accumulations at locations sheltered from thermal reradiation from the dusty residue. We simulated evolution of Callisto's craters as a combination of bedrock volatile sublimation, mass wasting of the dark, non-coherent residue, and redeposition of ice, and concluded that the ice pinnacles and ridges might be underlain by tens to hundreds of meters of ice. Here we report the initial work of a new study of pinnacles addressing additional questions: 1) Is there an evolutionary sequence starting, e.g., from a cratered initial surface through growth and formation of a dust mantle and pinnacles, to eventual loss of ice to sublimation resulting in just a dark, dusty surface? 2) What determines the areal density and spatial scale of pinnacles - volatile content of bedrock, crater density, surface age, broad-scale topographic setting? 3) Are pinnacles still forming? Several observations address these questions. In a few places scattered high-albedo blocks approx. 25-60 m in diameter occur in the vicinity of large icy pinnacles. We interpret these blocks to be remnants from the collapse of tall pinnacles that were undermined by mass wasting. Some high-relief icy knobs have developed a skeletonized planform due to mass wasting by avalanching, or perhaps to seeding of new sites of ice deposition on mass-wasted ice blocks. Some areas nearly lack fresh craters with well-defined ejecta and ice-free rims. This may imply rapid transformation of fresh craters by sublimation, mass wasting, and ice reprecipitation. In other areas small sharp-rimmed craters occur which lack ice pinnacles, but the craters nonetheless lack visible ejecta sheets. Our preliminary interpretation is that mass wasting is very efficient on Callisto, or alternatively the dust cover is very thick and lacks competent coarse materials.

bedrock volatile sublimation↗

NASA NTRS2015

Risk of Crew Adverse Health Event Due to Altered Immune Response

Determining the effect of space travel on the human immune system has proven to be extremely challenging. Limited opportunities for in-flight studies, varying mission durations, technical and logistical obstacles, small subject numbers, and a broad range of potential assays have contributed to this problem. Additionally, the inherent complexity of the immune system, with its vast array of cell populations, sub-populations, diverse regulatory molecules, and broad interactions with other physiological systems, makes determining precise variables to measure very difficult. There is also the challenge of determining the clinical significance of any observed immune alterations. Will such a change lead to disease, or is it a transient subclinical observation related to short-term stress? The effect of this problem may be observed by scanning publications associated with immunity and spaceflight, which began to appear during the 1970s. Although individually they are each valid studies, the comprehensive literature to date suffers from widely varying sampling methods and assay techniques, low subject counts, and sometimes a disparate focus on narrow aspects of immunity. The most clinically relevant data are derived from in-flight human studies, which have demonstrated altered cell-mediated immunity and reactivation of latent herpes viruses. Much more data are available from post-flight testing of humans, with clear evidence of altered cytokine production patterns, altered leukocyte distribution, continued latent viral reactivation, and evidence of dramatically altered virus-specific immunity. It is unknown if post-flight assessments relate to the in-flight condition or are a response to landing stress and readaptation. In-flight culture of cells has clearly demonstrated that immune cells are gravity-sensitive and display altered functional characteristics. It is unknown if these data are related to in vivo immune cell function or are an artifact of microgravity culture. Ground analog testing of humans and animals, as well as microgravity-analog cell culture, has demonstrated utility. However, in all cases, it is not known with certainty if these data would reflect similar testing during space travel. Given their ready availability, ground analogs may be extremely useful for assay development and the evaluation of potential countermeasures. In general, the evidence base suffers from widely disparate studies on small numbers of subjects that do not directly correlate well with each other or spaceflight itself. Also lacking are investigations of the effect of gender on adaption to spaceflight. This results in significant knowledge 'gaps' that must be filled by future studies to completely determine any clinical risk related to immunity for human exploration-class space missions. These gaps include a significant lack of in-flight data, particularly during long-duration space missions. The International Space Station represents an excellent science platform with which to address this knowledge gap. Other knowledge gaps include lack of a single validated ground analog for the phenomenon and a lack of flight-compatible laboratory equipment capable of monitoring astronauts (for either clinical or research purposes). However, enough significant data exist, as described in this manuscript, to warrant addressing this phenomenon during the utilization phase of the ISS. A recent Space Shuttle investigation has confirmed the 31 in-flight nature of immune dysregulation, demonstrating that it is not merely a post-flight phenomenon. Several current studies are ongoing onboard the ISS that should thoroughly characterize the phenomenon. NASA recognizes that if spaceflight-associated immune dysregulation persists during exploration flights in conjunction with other dangers, such as high-energy radiation, the result may be a significant clinical risk. This emphasizes the need for a continued integrated comprehensive approach to determining the effect of prolonged spaceflight, separated from transient launch and landing stresses, on human immunity. After such studies, the phenomenon will be understood, and, hopefully, a monitoring strategy will have been developed that could be used to monitor the effectiveness of countermeasure

Crucian, Brian↗

NASA NTRS2022

Risk of Performance and Behavioral Health Decrements Due to Inadequate Cooperation, Coordination, and Psychosocial Adaptions within a Team

The Risk of Performance and Behavioral Health Decrements Due to Inadequate Cooperation, Coordination, Communication, and Psychosocial Adaptation within a Team (the Team Risk) is primarily performance-focused, with a secondary emphasis on behavioral health outcomes resulting from team performance and interpersonal interactions. Monitoring tools, measures, and countermeasures are aimed at enhancing team processes and team composition configurations to optimize team performance and functioning. Long-duration exploration missions (LDEMs) will include major challenges that could affect team performance, including social isolation, physical confinement, a small and diverse crew, communication delays between crew and ground, limited or no crew rotation or evacuation options, limited or no resupply, and a high-consequence environment. Each of these conditions will affect the crew’s coordination, cooperation, psychological well-being, and performance. Although the International Space Station (ISS) remains important for studies that require spaceflight testing and validation, the current conditions on the ISS do not adequately mimic the exploration environment that is required for National Aeronautics and Space Administration (NASA) teams research, and thus access to terrestrial or ground-based analogs of LDEM conditions is paramount. The emphasis on analogs for research is reflected in this updated evidence review of the Team Risk, and includes data from studies conducted at isolated, confined, extreme (ICE) environments (e.g., Antarctic stations), and from several mission simulation analogs such as the Human Exploration Research Analog (HERA) (HERA Experiment Information Package, 2014), also known as isolated, confined, controlled (ICC) environments. These studies have characterized many team factors regarding LDEMs, and the Team Risk has now matured from risk characterization to focusing more on countermeasure development. Because spaceflight evidence for team-level research is lacking, no reliable data is available to quantify the impact of team-level variables on individual and team-level outcomes during spaceflight missions. Until recently, no systematic attempt had been undertaken to measure the performance effects of team cohesion, team composition, team training, or team-related psychosocial adaptation during spaceflight. The Team Risk is a relatively young research area for NASA, with substantial growth only since the 2000s, and with limited access to spaceflight performance data. As a result, spaceflight evidence is lacking to identify specifically what team composition, level of training, amount of cohesion, or quality of psychosocial adaptation is necessary to reduce the risk of performance errors in space. However, astronaut journals and interviews and reports from spaceflight subject matter experts (SMEs) provide testimonies that team performance during spaceflight is important for mission success and to maintain crew health. Team spaceflight data is now being collected as part of the Spaceflight Standard Measures task (Clement, 2021)—a set of core measurements related to many human spaceflight risks that are collected from astronauts before, during, and after long-duration missions. The team-related standard measures focus on team cohesion, team performance, group living, team climate, and team processes. Collection of standard measures data is ongoing and published data is not yet available. Finally, although spaceflight evidence is lacking, evidence gleaned from ground studies and spaceflight analog studies will help close the gaps outlined in the Team Risk. Ground-based studies provide quantitative evidence for team functioning in ICE environments. Academic research on teams has produced dozens of meta-analyses that can be used to understand the general relationships among team inputs (e.g., team member characteristics and skills, job context), team processes, and emergent states (e.g., coordination, communication, cooperation, cohesion, trust, shared cognition), and team outcomes (e.g., effectiveness, errors, adaptation). Teams are complex, incorporating individual characteristics of team members, but also existing at a level that is greater than the sum of its parts. Therefore, the Team Risk must be integrated with other individual-focused NASA Human Research Program (HRP) risks, including Behavioral Medicine (BMed), Sleep, and Human-Systems Integration Architecture (HSIA), and emerging research indicates more integration may needed between the Team Risk and the physiologically oriented risks. Much of this integration occurs through the Human Systems Risk Board (HSRB). A lack of team functioning may be a stressor in some circumstances, but the team often acts as a countermeasure. For example, support for team leaders and teammates can facilitate individual functioning and encourage psychological and physically healthy behaviors and attitudes. However, more research is needed regarding teams during LDEMs and the remaining gaps in the research are described in the current report.

Lauren Blackwell Landon↗

NASA NTRSDate not supplied

Appetite and Food Intake During 11 Days of Mild Hypobaric Hypoxia

Introduction Reduced food consumption and loss of body mass and muscle mass have been observed during spaceflight. Hypoxic conditions that astronauts may encounter on exploration missions may further implicate satiety signals and dietary intake. Appetite, food intake, and satiety hormones were investigated under the conditions of mild hypoxia and high energy output during simulated extravehicular activity (EVA) to determine the adequacy of a mission relevant space food system to support energy balance and body composition. Methods Foods realistic to early Artemis missions was packed by meal for each subject for the 11-day test based on estimated energy requirements (EER) and estimated EVA caloric requirements. No hot water or food warmer was provided and only room temperature water was available to rehydrate food and beverages in-mission, mimicking plans for early Artemis missions. Measures included food records (pre-mission, in-mission); fasted body weight (pre-mission, in-mission); Dual-energy X-ray absorptiometry (DXA) (pre-mission, post-mission); subjective ratings and feedback of food acceptability, mealtime and meal preparation sufficiency, appetite, and nausea (in-mission); and circulating ghrelin and leptin concentration in fasted blood samples (pre-mission, in-mission: pre-post EVA). Results All subjects consumed fewer calories in-mission than predicted. On average, subjects consumed 341 calories less on EVA days compared to non-EVA days in-mission (p=0.0511). The total weight loss estimate from daily weight measurements (-1.1 kg, p=0.0028) is consistent with underconsumption and supported by DXA measurements (-1.3 kg total body mass, p=0.0123 and -1.6 kg fat mass, p=0.0016). In general, most foods that were consumed were given acceptable scores, but subject comments indicated that the most acceptable foods were those not intended to be heated. Comments also indicated that subjects found their favorite foods early in the mission and avoided the foods that they did not like throughout the mission. Habitability scores indicated that overall aspects of the food system were considered borderline or unacceptable over the length of this mission. Foods that caused gas were avoided pre-EVA to prevent discomfort during pressure changes. Average fruit and vegetable intake decreased during the mission, dropping from 4.8 servings/d pre-mission to 3.4 servings/d on non-EVA days in-mission (p=0.0872) and 2.3 servings on EVA days (p=0.0020). Fasting ghrelin concentrations tended to be lower pre-EVA and on non-EVA days when exposed to mild hypoxia compared to normoxic conditions pre-mission and post-EVA (p=0.0136). Fasting levels of leptin did not change. Discussion Food intake was reduced in-mission, resulting in a caloric deficit and weight loss for most subjects. Crew food and appetite ratings and comments indicated this was due to a combination of food choices, lack of preference, lack of preparation capability, lack of time for meal preparation, consumption, and cleanup, and physiological challenges with the changing pressure. The regulation of appetite stimulating hormone ghrelin, but not the appetite suppressor leptin, appeared to be sensitive to hypoxic conditions. Conclusions Food preparation capabilities and time for meals are important for promoting adequate food intake. Reduced appetite and food intake during missions may further be aggravated under hypoxic conditions through the suppression of ghrelin. Lack of time for meals on EVA days, and avoidance of potential gas-causing foods (e.g., health promoting fruits and vegetables) prior to EVAs, demonstrate the importance of scheduling ample recovery time between EVA days.

Grace L Douglas↗

NASA NTRS2023

Appetite and Food Intake During 11 Days of Mild Hypobaric Hypoxia

Lichar Dillon↗

DOE OSTI2021

Overall equilibrium in the coupling of peridynamics and classical continuum mechanics

Coupling peridynamics based computational tools with those using classical continuum mechanics can be very beneficial, because it can provide a means to generate a computational method that combines the efficiency of classical continuum mechanics with the capability to simulate crack propagation, typical of peridynamics. This paper presents an overlooked issue in this type of coupled computational methods: the lack of overall equilibrium. This can be the case even if the coupling strategy satisfies the usual numerical tests involving rigid body motions as well as uniform and linear strain distributions. We focus our investigation on the lack of overall equilibrium in an approach to couple peridynamics and classical continuum mechanics recently proposed by the authors. In our examples, the magnitude of the out-of-balance forces is a fraction of a percent of the applied forces, but it cannot be assumed to be a numerical round-off error. We show analytically and numerically that the main reason for the existence of out-of-balance forces is a lack of balance between the local and nonlocal tractions at the coupling interface. This usually results from the presence of high-order derivatives of displacements in the coupling zone.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Aim18p and Aim46p are chalcone isomerase domain–containing mitochondrial hemoproteins in Saccharomyces cerevisiae

Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid–binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection

In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create "orthogonal" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling the mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here, we engineered the Escherichia coli ribosome to prevent binding of bS1 to the 30S subunit and separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomes in vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have an improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of binding of bS1 to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Observed and Bin Model Simulated Evolution of Drop Size Distributions in High-Based Cumulus Congestus Over the United Arab Emirates

This study examines microphysical processes in developing high-based cumulus congestus over the United Arab Emirates using aircraft observations and a large-eddy-simulation model with bin microphysics. A notable feature of this case is the lack of mm-sized drops despite having a liquid cloud layer >3.5 km deep, contrasting with copious large drops observed in maritime tropical cumulus congestus having a similar vertical extent. Modeled drop size distributions are similar to observations at various temperatures between 9.5 and –12°C, including the lack of mm-sized drops. Cloud dilution leads to low-to-moderate liquid water contents (~0.5–1.5 g m –3 ) in most of the cloud core, several times smaller than adiabatic values. Dilution is enhanced in the inflowing branch of the toroidal circulations associated with individual cloud thermals, which are favored regions for secondary droplet activation (activation above cloud base). Secondary activation in general contributes substantially to the droplet population. Turning it off leads to a sharp decrease in droplet concentration and increase in mean size aloft, but does little to increase rain drop production. Warm rain generation (or lack thereof) in this case is therefore determined more by the sub-cloud aerosol and the cloud base droplet size distribution (DSD) than DSD evolution aloft from secondary droplet activation. Decreasing the aerosol concentration by a factor of 10 greatly increases production of large drops via collision-coalescence. Thus, despite its high base (low temperatures) and substantial dilution, the simulated cloud is thermodynamically and dynamically capable of rapidly producing copious mm-sized drops from collision-coalescence under pristine aerosol conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

The anomaly of the CMB power with the latest Planck data

Abstract The lack of power anomaly is an unexpected feature observed at large angular scales in the maps of Cosmic Microwave Background (CMB) produced by the COBE, WMAP andPlancksatellites. This signature, which consists in a missing of power with respect to that predicted by the ΛCDM model, might hint at a new cosmological phase before the standard inflationary era.The main point of this paper is taking into account the latestPlanckpolarisation data to investigate how the CMB polarisation improves the understanding of this feature. With this aim, we apply to the latestPlanckdata, both PR3 (2018) and PR4 (2020) releases, a new class of estimators capable of evaluating this anomaly by considering temperature and polarisation data both separately and in a jointly way. This is the first time that the PR4 dataset has been used to study this anomaly. To critically evaluate this feature, taking into account the residuals of known systematic effects present in thePlanckdatasets, we analyse the cleaned CMB maps using different combinations of sky masks, harmonic range and binning on the CMB multipoles.Our analysis shows that the estimator based only on temperature data confirms the presence of a lack of power with a lower-tail-probability (LTP), depending on the component separation method, ≤ 0.33% and ≤ 1.76% for PR3 and PR4, respectively. To our knowledge, the LTP≤ 0.33% for the PR3 dataset is the lowest one present in the literature obtained fromPlanck2018 data, considering thePlanckconfidence mask. We find significant differences between these two datasets when polarisation is taken into account most likely due to a different level of systematics. Especially, the analysis with PR3 data, unlike that with PR4, seems to point towards a lack of power at large scales also for polarisation.Moreover, we also show that for the PR3 dataset the inclusion of the subdominant polarisation information provides estimates that are less likely accepted in a ΛCDM cosmological model than the only-temperature analysis over the entire harmonic-range considered. In particular, at ℓ max = 26, we found that no simulation has a value as low as the data for all the pipelines.

Astronomy & Astrophysics↗

DOE OSTI2021

Simulations of future particle accelerators: issues and mitigations

The ever increasing demands placed upon machine performance have resulted in the need for more comprehensive particle accelerator modeling. Computer simulations are key to the success of particle accelerators. Many aspects of particle accelerators rely on computer modeling at some point, sometimes requiring complex simulation tools and massively parallel supercomputing. Examples include the modeling of beams at extreme intensities and densities (toward the quantum degeneracy limit), and with ultra-fine control (down to the level of individual particles). In the future, adaptively tuned models might also be relied upon to provide beam measurements beyond the resolution of existing diagnostics. Much time and effort has been put into creating accelerator software tools, some of which are highly successful. However, there are also shortcomings such as the general inability of existing software to be easily modified to meet changing simulation needs. In this paper possible mitigating strategies are discussed for issues faced by the accelerator community as it endeavors to produce better and more comprehensive modeling tools. This includes lack of coordination between code developers, lack of standards to make codes portable and/or reusable, lack of documentation, among others.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Abstract Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2024

Explaining Health Risk Behaviors in the U.S. with Social Deprivation at Local and Regional Levels

Health risk behaviors are precursors to many chronic health outcomes, and hence, they pose a challenge to public health. Social deprivation undoubtedly creates circumstances that limit access to healthy habits. Moreover, broad regional effects (weather patterns, political ideology, social norms), and local characteristics (cultural notions and barriers, urban places) also influence lifestyle choices and must be accounted for to truly understand the impact of social deprivation on risky behaviors. This research fills the knowledge gap in epidemiological modeling of health risk behaviors by leveraging machine learning to find associations between social deprivation and health risk behaviors, when adjusted by regional and local effects. Four health risk behaviors, namely, binge drinking, smoking, lack of sleep, and lack of physical activity from the CDC PLACES project are considered in a single framework to understand and compare the interplay between local/regional characteristics and seven measures of social deprivation. Our results indicate that local and/or regional factors rise to the top for three out of four risk behaviors (binge drinking, smoking and lack of sleep) out-competing social deprivation measures. Un-entangling the geographical effects reveals that poverty, educational attainment and non-employment are the three deprivation measures most significantly associated with all four health risk factors. The research thus indicates that public health policies to promote healthy lifestyle behaviors must seek to remedy social deprivation, but using socially and culturally sensitive interventions.

Gokhale, Swapna↗

DOE OSTI2023

Pickaxe: a Python library for the prediction of novel metabolic reactions

Abstract Background Biochemical reaction prediction tools leverage enzymatic promiscuity rules to generate reaction networks containing novel compounds and reactions. The resulting reaction networks can be used for multiple applications such as designing novel biosynthetic pathways and annotating untargeted metabolomics data. It is vital for these tools to provide a robust, user-friendly method to generate networks for a given application. However, existing tools lack the flexibility to easily generate networks that are tailor-fit for a user’s application due to lack of exhaustive reaction rules, restriction to pre-computed networks, and difficulty in using the software due to lack of documentation. Results Here we present Pickaxe, an open-source, flexible software that provides a user-friendly method to generate novel reaction networks. This software iteratively applies reaction rules to a set of metabolites to generate novel reactions. Users can select rules from the prepackaged JN1224min ruleset, derived from MetaCyc, or define their own custom rules. Additionally, filters are provided which allow for the pruning of a network on-the-fly based on compound and reaction properties. The filters include chemical similarity to target molecules, metabolomics, thermodynamics, and reaction feasibility filters. Example applications are given to highlight the capabilities of Pickaxe: the expansion of common biological databases with novel reactions, the generation of industrially useful chemicals from a yeast metabolome database, and the annotation of untargeted metabolomics peaks from an E. coli dataset. Conclusion Pickaxe predicts novel metabolic reactions and compounds, which can be used for a variety of applications. This software is open-source and available as part of the MINE Database python package ( https://pypi.org/project/minedatabase/ ) or on GitHub ( https://github.com/tyo-nu/MINE-Database ). Documentation and examples can be found on Read the Docs ( https://mine-database.readthedocs.io/en/latest/ ). Through its documentation, pre-packaged features, and customizable nature, Pickaxe allows users to generate novel reaction networks tailored to their application.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Multi-scale Multi-physics Scientific Machine Learning for Water Cycle Extreme Events Identification, Labelling, Representation, and Characterization

Impacts of climate are usually felt through extreme events such as droughts, floods, thunderstorms, windstorms, wildfires, and so on, that are intimately tied to the water cycle. Predicting the frequency and severity of extreme events under climate change remains a significant challenge; meanwhile, the mechanisms and impacts of these extremes are far from well understood. There are several major science challenges: (1) Lack of labelled extreme events data and missing standards in defining extremes; (2) Computational demand of high-resolution ensemble climate modeling; (3) Modeling the multiscale multi-physics hierarchical structure of compound extremes; (4) Lack of understanding of mechanisms of extreme events; (5) Large uncertainty in extreme events impacts on infrastructure; (6) Subjective assessment of weather-related risk from seasonal to multi-decadal time scales and lack of metrics for risk assessment and mitigation control.

54 ENVIRONMENTAL SCIENCES↗