Search NASA⌕ Search

SEARCH · Search NASA

Results for “sample annotation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

161 records · Page 9

Facilitating Analysis of Multiple Partial Data Streams

Robotic Operations Automation: Mechanisms, Imaging, Navigation report Generation (ROAMING) is a set of computer programs that facilitates and accelerates both tactical and strategic analysis of time-sampled data especially the disparate and often incomplete streams of Mars Explorer Rover (MER) telemetry data described in the immediately preceding article. As used here, tactical refers to the activities over a relatively short time (one Martian day in the original MER application) and strategic refers to a longer time (the entire multi-year MER missions in the original application). Prior to installation, ROAMING must be configured with the types of data of interest, and parsers must be modified to understand the format of the input data (many example parsers are provided, including for general CSV files). Thereafter, new data from multiple disparate sources are automatically resampled into a single common annotated spreadsheet stored in a readable space-separated format, and these data can be processed or plotted at any time scale. Such processing or plotting makes it possible to study not only the details of a particular activity spanning only a few seconds, but also longer-term trends. ROAMING makes it possible to generate mission-wide plots of multiple engineering quantities [e.g., vehicle tilt as in Figure 1(a), motor current, numbers of images] that, heretofore could be found only in thousands of separate files. ROAMING also supports automatic annotation of both images and graphs. In the MER application, labels given to terrain features by rover scientists and engineers are automatically plotted in all received images based on their associated camera models (see Figure 2), times measured in seconds are mapped to Mars local time, and command names or arbitrary time-labeled events can be used to label engineering plots, as in Figure 1(b).

Maimone, Mark W.↗

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes

The gut microbiome plays a fundamental role in the human host’s overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn’s disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues. It has been difficult, however, to elucidate the overall functional characteristics of this relationship because the microbiota can vary substantially in composition for healthy humans and possibly even more in individuals with gut disease conditions such as Crohn’s disease. Overall, this suggests that microbial membership composition may not be the best way to characterize a phenotype. Alternatively, it seems to be more informative to examine and characterize the functional composition of a gut microbiome. Towards that end, this study examines 25 metaproteomes measured in several Crohn’s disease patients’ post-resection surgery across the course of 1 year, in order to examine persistence of microbial taxa, genes, proteins, and metabolic functional distributions across time in individuals whose microbiome might be more variable due to the gut disease condition. As a result, the measured metaproteomes were highly personalized, with all the temporally-related metaproteomes clustering most closely by individual. In general, the metaproteomes were remarkably distinct between individuals and to a lesser extent within individuals. This prompted a need to characterize the metaproteome at a higher functional level, which was achieved by annotating identified protein groups with KEGG orthologous groups to infer metabolic modules. At this level, similar and redundant metabolic functions across multiple phyla were observed across time and between individuals. Tracking through these various metabolic modules revealed a clear path from carbohydrate, lipid, and amino acid degradation to central metabolism and finally the production of fermentation products. In conclusion, the human gut metaproteome can vary quite substantially across time and individuals. However, despite substantial intra-individual variation in the metaproteomes, there is a clear persistence of conserved metabolic functions across time and individuals. Additionally, the persistence of these core functions is redundant across multiple phyla but is not always observable in the same sample. Finally, the gut microbiome’s metabolism is not driven by a set of discrete linear pathways but a web of interconnected reactions facilitated by a network of enzymes that connect multiple molecules across multiple pathways.

59 BASIC BIOLOGICAL SCIENCES↗

ROI-Finder : machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli ( E. Coli ), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗

Statistical Perspectives on Stratospheric Transport

Long-lived tropospheric source gases, such as nitrous oxide, enter the stratosphere through the tropical tropopause, are transported throughout the stratosphere by the Brewer-Dobson circulation, and are photochemically destroyed in the upper stratosphere. These chemical constituents, or "tracers" can be used to track mixing and transport by the stratospheric winds. Much of our understanding about the stratospheric circulation is based on large scale gradients and other spatial features in tracer fields constructed from satellite measurements. The point of view presented in this paper is different, but complementary, in that transport is described in terms of tracer probability distribution functions (PDFs). The PDF is computed from the measurements, and is proportional to the area occupied by tracer values in a given range. The flavor of this paper is tutorial, and the ideas are illustrated with several examples of transport-related phenomena, annotated with remarks that summarize the main point or suggest new directions. One example shows how the multimodal shape of the PDF gives information about the different branches of the circulation. Another example shows how the statistics of fluctuations from the most probable tracer value give insight into mixing between different regions of the atmosphere. Also included is an analysis of the time-dependence of the PDF during the onset and decline of the winter circulation, and a study of how "bursts" in the circulation are reflected in transient periods of rapid evolution of the PDF. The dependence of the statistics on location and time are also shown to be important for practical problems related to statistical robustness and satellite sampling. The examples illustrate how physically-based statistical analysis can shed some light on aspects of stratospheric transport that may not be obvious or quantifiable with other types of analyses. An important motivation for the work presented here is the need for synthesis of the large and growing database of observations of the atmosphere and the vast quantities of output generated by atmospheric models.

Sparling, L. C.↗

Automatic information extraction from childhood cancer pathology reports

The International Classification of Childhood Cancer (ICCC) facilitates the effective classification of a heterogeneous group of cancers in the important pediatric population. However, there has been no development of machine learning models for the ICCC classification. We developed deep learning-based information extraction models from cancer pathology reports based on the ICD-O-3 coding standard. In this article, we describe extending the models to perform ICCC classification. We developed 2 models, ICD-O-3 classification and ICCC recoding (Model 1) and direct ICCC classification (Model 2), and 4 scenarios subject to the training sample size. We evaluated these models with a corpus consisting of 29206 reports with age at diagnosis between 0 and 19 from 6 state cancer registries. Our findings suggest that the direct ICCC classification (Model 2) is substantially better than reusing the ICD-O-3 classification model (Model 1). Applying the uncertainty quantification mechanism to assess the confidence of the algorithm in assigning a code demonstrated that the model achieved a micro-F1 score of 0.987 while abstaining (not sufficiently confident to assign a code) on only 14.8% of ambiguous pathology reports. Our experimental results suggest that the machine learning-based automatic information extraction from childhood cancer pathology reports in the ICCC is a reliable means of supplementing human annotators at state cancer registries by reading and abstracting the majority of the childhood cancer pathology reports accurately and reliably.

60 APPLIED LIFE SCIENCES↗

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k -mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k -mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ~5% for virome and ~75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. Furthermore, for viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ~95% (whole genomes) down to ~80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses ‘hidden’ in diverse sequence datasets.

59 BASIC BIOLOGICAL SCIENCES↗

Semi-supervised permutation invariant particle-level anomaly detection

The development of analysis methods to distinguish potential beyond the Standard Model phenomena in a model-agnostic way can significantly enhance the discovery reach in collider experiments. However, the typical machine learning (ML) algorithms employed for this task require fixed length and ordered inputs that break the natural permutation invariance in collision events. To address this, a semi-supervised anomaly detection tool is presented that takes a variable number of particle-level inputs and leverages a signal model to encode this information into a permutation invariant, event-level representation via supervised training with a Particle Flow Network (PFN). Data events are then encoded into this representation and given as input to an autoencoder for unsupervised ANomaly deTEction on particLe flOw latent sPacE (ANTELOPE), classifying anomalous events based on a low-level and permutation invariant input modeling. Performance of the ANTELOPE architecture is evaluated on simulated samples of hadronic processes in a high energy collider experiment, showing good capability to distinguish disparate models of new physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Community-Driven Metadata Standards for Agricultural Microbiome Research

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research.

59 BASIC BIOLOGICAL SCIENCES↗

Reporting Verification of BOP Shear Ram Capability: Requirements and Good Practices on Reporting Blowout Preventer (BOP) Shear Ram Capability for Outer Continental Shelf (OCS) Oil and Gas Operations

The Bureau of Safety and Environmental Enforcement (BSEE) Well Control Rule (Subpart G)1 became effective on July 28, 2016. This rule is part of the BSEE regulations pertaining to well control equipment used for oil and gas operations on the U.S. Outer Continental Shelf (OCS). More recently BSEE issue a proposed rule to amend portions of the 2016 well control rule. This proposed rule (now implemented) appeared in the Federal Register on May 18, 2018. This report was prepared late in the public comment period for the current rule and intended is a sample of desirable documentation of blind shear ram shear testing and associated regulatory requirements either in place or anticipated at the time of preparation. In accordance with this original rule and the proposed revisions, BSEE requests specific information regarding the capabilities of blind shear rams (BSR) in the Blowout Preventer (BOP). This information is required prior to beginning any operation involving the use of any BOP. More specifically, Title 30 CFR 250.732(b) of these regulations requires documentation of shear testing demonstrating the shearing and sealing capabilities of the BOP BSR. Such documentation is consistent with and complementary to other documentation verifying the designs of individual well control components and the overall BOP system. Verification demonstrates performance and reliability of the equipment based on a testing process that is repeatable and reproducible.2 This document, an annotated outline of verification documentation, arises from the combination of regulations and good practices concerning how to report BOP shear ram tests and third-party verification of BSR capability to support BSEE’s regulatory role.

03 NATURAL GAS↗

An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof

The Arabidopsis genome sequencing in 2000 gave to science the first blueprint of a vascular plant. Its successful completion also prompted the US National Science Foundation to launch the Arabidopsis 2010 initiative, the goal of which is to identify the function of each gene by 2010. In this study, an exhaustive analysis of The Institute for Genomic Research (TIGR) and The Arabidopsis Information Resource (TAIR) databases, together with all currently compiled EST sequence data, was carried out in order to determine to what extent the various metabolic networks from phenylalanine ammonia lyase (PAL) to the monolignols were organized and/or could be predicted. In these databases, there are some 65 genes which have been annotated as encoding putative enzymatic steps in monolignol biosynthesis, although many of them have only very low homology to monolignol pathway genes of known function in other plant systems. Our detailed analysis revealed that presently only 13 genes (two PALs, a cinnamate-4-hydroxylase, a p-coumarate-3-hydroxylase, a ferulate-5-hydroxylase, three 4-coumarate-CoA ligases, a cinnamic acid O-methyl transferase, two cinnamoyl-CoA reductases) and two cinnamyl alcohol dehydrogenases can be classified as having a bona fide (definitive) function; the remaining 52 genes currently have undetermined physiological roles. The EST database entries for this particular set of genes also provided little new insight into how the monolignol pathway was organized in the different tissues and organs, this being perhaps a consequence of both limitations in how tissue samples were collected and in the incomplete nature of the EST collections. This analysis thus underscores the fact that even with genomic sequencing, presumed to provide the entire suite of putative genes in the monolignol-forming pathway, a very large effort needs to be conducted to establish actual catalytic roles (including enzyme versatility), as well as the physiological function(s) for each member of the (multi)gene families present and the metabolic networks that are operative. Additionally, one key to identifying physiological functions for many of these (and other) unknown genes, and their corresponding metabolic networks, awaits the development of technologies to comprehensively study molecular processes at the single cell level in particular tissues and organs, in order to establish the actual metabolic context.

NASA Program Fundamental Space Biology↗

Methods for automated genome-scale metabolic model reconstruction

In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. We are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.

59 BASIC BIOLOGICAL SCIENCES↗

RU Net for Automatic Characterization of TRISO Fuel Cross Sections

TRistructural ISOtropic (TRISO) particle fuel is a type of nuclear fuel known for its high-temperature and high-burnup performance. Each sub-millimeter diameter TRISO particle consists of uranium-oxycarbide (UCO) or UO2 fuel kernel, coated with buffer, inner pyrolytic carbon (IPyC), silicon carbide (SiC), and outer pyrolytic carbon (OPyC) layers. The SiC layer acts as the main containment barrier for the TRISO particle to retain the fission products, while the IPyC and OPyC layers provide additional barriers to the release of fission products, especially fission gases. During irradiation, phenomena like kernel swelling, buffer densification, and IPyC fracture may impact fuel performance. Post-irradiation microscopy on entire compact cross sections or samples of individual particles deconsolidated from compacts is often used to identify these irradiation-induced changes in morphology. However, each fuel compact generally contains thousands of TRISO particles. To get statistical information on these phenomena, it is cumbersome work if done manually. For example, to get information about swelling/densification behaviors of different layers or kernels after irradiation, researchers previously manually measured the perimeter of each TRISO layer in hundreds of particles after four rounds of iterative grinding and polishing encompassing more than 2000 cross-section images for a total of four fuel compacts. To attempt to reduce the subjectivity inherent in that process and accelerate data analysis, we conducted a study on the automatic TRISO layer segmentation on cross-sectional microscopic images using Convolutional Neural Networks (CNNs). CNNs are a class of machine learning algorithms specifically designed for processing structured grid data that have gained popularity in recent years due to their remarkable performance in various computer vision tasks, including image classification, object detection, and image segmentation. In this research, we have generated the large irradiated TRISO layer dataset with more than 2000 cross-section TRISO microscopic images and the corresponding annotated images. Based on these annotated images, we have employed different CNNs for automatic segmentation of different TRISO layers. These include RU-Net (developed in this study), as well as three existing architectures: U-Net, Residual Network (ResNet), and Attention U-Net. The preliminary results show that the model based on RU-Net has the best performance in terms of intersection-over-union (IoU). Through the aid of these CNN models, we can expedite the analysis of TRISO particle cross-sections, significantly reducing the manual labor involved and improving the objectivity of the segmentation results.

Convolutional Neural Networks↗

X-HAB 2020: AR Field Treks Summary and Conclusions

As part of the FY20 X-Hab Challenge, BLiSS sought to create an Augmented Reality (AR) toolkit to help with analog field trek operations under the supervision of the Solar System Exploration Research Virtual Institute (SSERVI). These treks are operational and technical demonstrations at space-like destinations on Earth to test current extra-vehicular activity (EVA) techniques. While BLiSS as an organization has experience studying operational tasks such as this, it has never developed AR software at this scale. For that reason, another team at the University was brought on to work in parallel. The Collaborative Lab for Advancing Work in Space (CLAWS) is a veteran group of the NASA Spacesuit User Interface Technologies for Students (SUITS) challenge in which Hololens displays for astronauts are created within a year. The operational and technological pairing was ideally suited for tackling this problem. The team divided its responsibilities so that BLiSS would handle the research required to shape the project. As this deliverable had an end user, it was decided that interviewing these field geologists and operations specialists would provide the best insight. These interviews paired with literature review would reveal niche applications for AR that remained within feasible bounds. These science-driven EVAs in unknown terrain require more flexible tools than the current generation of EVA assistants. Rather than focus on sequential instructions, there instead needs to be a broad toolkit that's only called upon in specific instances. This AR Toolkit for Lunar Astronauts and Scientists (ATLAS) became the development goal of the project: create a non-intrusive assembly of tools that could be accessed in AR on the field. The current ATLAS design makes use of a geospatially and temporally annotated eld note system called GeoNotes. This allows for data to be collected and coordinated in a way that's synchronized across time, space, and different users. A Mission Control Center (MCC) and Mobile Support Equipment (MSE) were all needed to transport the AR headset into the field with the user. A network infrastructure was designed and set up within the University to enable this functionality. The software is based on a Protocol-Module structure that allows for modular development of each capability. A Protocol Manager coordinates different protocols that make use of modules. Each module tackles a different individual task while the protocol puts each one to use. The protocol manager coordinates when these are called to be used. This software is hosted on a head-mounted display (HMD) with the MCC acting as support from afar. While the software would be unit-tested at each level and each hardware component verified, a final demonstration would serve to prove the system's capabilities: an analog field trek. The team would prepare to support a user in a remote location from the MCC back at the University. A local area near campus would be tested before going out to do sample field geology further away. This unfortunately became impossible with the arrival of COVID-19. Access to all of the facilities to complete the project as planned were shut down. Our team was scattered across the globe and forced to complete the rest virtually. Adjustments were made to produce a small virtual concept in Adobe XD in the meantime. Even digital surveys were created based on the NASA task-load index (TLX) originally intended for testing actual users. The goal shifted towards completing software and getting feedback on the user interfaces (UI) and user experiences (UX). This team has reformed in response to COVID and its focus has shifted to what can be done remotely. There is still an intention to finish the original deliverable described in this report. The work has been expanded beyond the original X-Hab challenge and has instead become its own research e ort to be continued afterwards. This report collects the processes and knowledge gained from a year of studying and working at this problem with two teams. It should preserve it for the time until the world returns to normal and work can resume. CLAWS will be taking over full responsibility from that point forward, eventually surpassing the original needs of the project. While this document captures the work done towards an eventual end, the CLAWS team has written their own proposal alongside it. It outlines a new future for ATLAS beyond X-Hab, BLiSS, and hopefully beyond COVID-19. This project began as a vague goal hoping to place a new technology into the unique setting of exploration science. The project has since comfortably taken root and will hopefully bloom over the next year.

Alex Sena↗

Longitudinal analysis of host protein serum signatures of treatment and recovery in pulmonary tuberculosis

A better understanding of treatment progression and recovery in pulmonary tuberculosis (TB) infectious disease is crucial. This study analyzed longitudinal serum samples from pulmonary TB patients undergoing interventional treatment to identify surrogate markers for TB-related outcomes. Serum that was collected at baseline and 8, 17, 26, and 52 weeks from 30 TB patients experiencing durable cure were evaluated and compared using a sensitive LC-MS/MS proteomic platform for the detection and quantification of differential host protein signatures relative to timepoint. The global proteome signature was analyzed for statistical differences across the time course and between disease severity and treatment groups. A total of 676 proteins showed differential expression in the serum over these timepoints relative to baseline. Comparisons to understand serum protein dynamics at 8 weeks, treatment endpoints at 17 and 26 weeks, and post-treatment at 52 weeks were performed. The largest protein abundance changes were observed at 8 weeks as the initial effects of antibiotic treatment strongly impacted inflammatory and immune modulated responses. However, the largest number of proteome changes was observed at the end of treatment time points 17 and 26 weeks respectively. Post-treatment 52-week results showed an abatement of differential proteome signatures from end of treatment, though interestingly those proteins uniquely significant at post-treatment were almost exclusively downregulated. Patients were additionally stratified based upon disease severity and compared across all timepoints, identifying 461 discriminating proteome signatures. These proteome signatures collapsed into discrete expression profiles with distinct pathways across immune activation and signaling, hemostasis, and metabolism annotations. Insulin-like growth factor (IGF) and Integrin signaling maintained a severity signature through 52 weeks, implying an intrinsic disease severity signature well into the post-treatment timeframe. Previous proteome studies have primarily focused on the 8-week timepoint in relation to culture conversion status. While this study confirms previous observations, it also highlights some differences. The inclusion of additional end of treatment and post-treatment time points offers a more comprehensive assessment of treatment progression within the serum proteome. Examining the expression dynamics at these later time periods will help in the investigation of relapse patients and has provided indicative markers of response and recovery.

59 BASIC BIOLOGICAL SCIENCES↗

Flight Mechanics Modeling and Simulation of the Earth Entry System

Introduction: The Mars Sample Return (MSR) Campaign being planned by NASA and ESA has the ambitious goal to return Mars samples back to Earth. This international collaboration had developed a concept of operations that included a ESA-designed Earth Return Orbiter (ERO) and NASA-designed Capture, Containment, and Return System (CCRS). The Earth Entry System (EES), consisting of a protective aeroshell that houses the samples as well as sample containment vessels, would conduct entry, descent, and landing (EDL) on a direct Earth trajectory. The EES would enter on a spin-stabilized ballistic trajectory with the goal to passively achieve aerodynamic stability throughout all regions of flight. The EDL sequence would end with the EES impacting the soft playa soil of the Utah Test and Training Range (UTTR). As of the submission of this abstract, the MSR campaign is undergoing a re-architecture leading to a pause in EES development. However, the novel approaches developed in flight mechanics modeling and simulation can significantly benefit the greater IPPW community in the development of Earth return vehicles. This paper will present the latest state of EES flight mechanics modeling and simulation. The paper will highlight the simulation architecture developed and key lessons learned from understanding of EDL trajectory sensitivities. Modeling and Simulation: Figure 1 provides a high-level concept of operations for the approach, entry, descent, and landing (AEDL) phase of the CCRS-portion of MSR. The objective of EES flight mechanics is to model and simulate the EES trajectory from ERO separation to ground impact at UTTR. A variety of flight mechanics simulation models were utilized to model both exo-atmopsheric and atmospheric portions of flight. 42, a 6-DOF simulation developed at Goddard Space Flight Center, is utilized for propagating the attitude of EES during exo-atmospheric flight. 42 allows for a variety of spin eject mechanism scenarios to be simulated for analysis. 10 minutes prior to entry, the 42 states are handed off to the EDL sims. The prime EDL sim utilized by EES is the Program to Optimize Simulated Trajectories II (POST2), a 6-DOF sim developed at Langley Research Center, and the independent verification and validation EDL sim utilized is DSENDS, a 6-DOF sim developed at Jet Propulsion Laboratory. Figure 2 provides a visualization of the flight mechanics simulation model flow through various points in the AEDL phase. Due to the existence of a variety of sim models, the EES flight mechanics team developed processes for data hand-off. These processes included the development of a centralized coordinate frame document, utilization of a single, centralized simulation input document for all sims to reference, and hand-off files containing both the technical data to be ingested by other flight mechanics sims as well as annotations of modeling assumptions utilized to generate the data. Figure~\ref{fig:post2simarchitecture} provides an overview of the POST2 sim architecture wherein POST2 ingests numerous subsystem models and input files. The dispersed state file generated by MONTE provides the position/velocity state of the trajectory while the 42 Handoff file provides the attitude. The aerodynamics database, delivered by the EES aeroscience team, is utilized to simulate the aerodynamic forces and moments experienced during EDL. A custom atmosphere model, developed by EES atmosphere team, is utilized to simulate the anticipated atmosphere environment around the region of Earth through which the EES trajectory flys. These inputs and subsystem models can be varied depending on the AEDL flight mechanics scenario being simulated. Monte Carlo simulations are utilized to generate statistical AEDL performance metrics in the form of scorecards and violin plots. Furthermore, outputs from the POST2 simulation are utilized for follow-on analyses including aerothermal and landing performance. \section{Flight Mechanics Lessons Learned} Though the EES flight mechanics team uncovered a variety of lessons learned through the analysis conducted to support CCRS through preliminary design review, this paper will highlight the most important lessons. A key AEDL performance goal is to ensure the landing footprint of EES remains on the UTTR south range. A common modeling strategy used in EDL analysis is One-Variable-At-a-Time (OVAT). OVAT analysis provides insight into the key drivers that affect AEDL performance metrics. Figure 3 shows the landing ellipses for single dispersion sources as compared to the baseline aggregate of all dispersions. The figure shows that atmosphere winds alone dominate the size of the footprint ellipse (note: EES does not use a parachute unlike previous Earth-return missions and is in wind-driven free fall for ~5min). The significance of the wind led the EES flight mechanics team to pursue the development of a Custom Atmosphere Model [4], in lieu of EarthGRAM [1], built on actual radiosonde wind measurements around the UTTR-region. This decision was driven by the realism in the generated footprint ellipses and lessons-learned from Stardust [5]. These findings will be invaluable for future Earth-return missions in providing an early understanding of the key drivers affecting footprint size and modeling considerations for which to account. Another lesson learned is tied to the AEDL performance goal of achieving passive stability throughout all regions of flight. It is well understood that blunt-body aeroshells are less stable as they transition from supersonic to subsonic. Eliminating a backshell does help improvestability; however, other phenomena such as roll-induced instability during terminal descent can still arise. The EES flight mechanics team developed stability metrics as tools to better understand the causes of and better predict the onset of dynamic instability. These tools were built upon analytical models developed by Jaffe [3] and Murphy [2]. The tools were shown to both be very accurate in correlation with actual unstable cases and useful in developing stability margin policies based on the vehicle design and simulation considerations (e.g. sphere-cone angle change, mass change, wind turbulence). These tools allowed for the current EES design to demonstrate the ability to achieve passive stability and can be an invaluable tool for consideration in the design of parachute-less Earth-return vehicles.

Rohan Deshmukh↗