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NASA NTRSDate not supplied

Transcriptomics-based Machine Learning (ML) Analysis Predicts Space-Exposed Murine Livers

Limited sample sizes, high data dimensionality, and sensitivity to technical and biological variability of next generation sequencing (NGS), typically limits machine learning (ML) approaches in spaceflight studies that include radiation effects. However, pooling smaller studies while addressing intra- and inter-study variabilities allows for ML predictive modeling. Here, integration methods were applied to whole transcriptome shotgun sequencing (RNA-seq) data from six mouse liver GeneLab datasets (GLDS) (n ranging from 6 to 39 samples) from with a total of 81 spaceflight and ground-control samples to determine top features (i.e. genes) relevant to spaceflight including the effect of radiation exposure. RNASeq counts were normalized for each study, then merged and scaled across all datasets. Data dimensionality was reduced using a minimum redundancy maximum relevance (MRMR) methodology. Redundancy and relevance were computed using the Pearson correlation and F-statistic, respectively. The top 100 MRMR features were used to predict spaceflight vs. ground-control samples using Random Forest (RF), Support Vector Machine (SVM), and Linear Discriminant Analysis (LDA) classifiers with 5-fold cross validation (CV). Principal component analysis (PCA) on the complete feature set versus the MRMR features shows separation between spaceflight samples and ground controls (Figure 1A). The ML-based gene sets were compared against differential gene expression results obtained with DESeq2 from individual GLDS. Using all features or randomly sampled subsets at matching set sizes with MRMR, a maximum classifier accuracy of 69% on the test set over 5 folds. For all classifiers, CV training using at least the top 30 MRMR genes show minimum 89% accuracy and 0.95 AUC value on the test set over 5 folds (Figure 1B). Baseline set analysis on differentially expressed genes (DEGs) identified using padj ≤ 0.05 show 295 DEGs that overlap at least two studies and 13 DEGs that overlap three studies (Figure 1C). Set analysis between the top 100 MRMR features and the DEGs showed 47 genes that overlap at least one study and 24 genes that overlap two studies. Over-representation analysis showed overlapping biological processes related to fatty acid and lipid metabolism which may indicate these processes in the response to spaceflight stressors. MRMR feature selection for the selected ML methods improve performance relative to a classifier built on all features or randomly sampled subsets. Permutation feature importance within the decorrelated MRMR features showed concordance in feature ranking between ML methods. A challenge of applying ML methods across heterogeneous NGS data is accounting for signal:noise. Here, signal validation across studies was shown by intersecting sets between top MRMR genes and DEGs from DESeq2 analysis. Non-intersecting sets introduce opportunity to explore genes relevant to differentiating space flight exposed groups and implementing ML methods across existing NGS datasets may overcome sample size limitations.

Machine Learning↗

NASA NTRSDate not supplied

Transcriptomics-based Machine Learning Analysis Predicts Space-Exposed Murine Livers

Limited sample sizes, high data dimensionality, and sensitivity to technical and biological variability of next generation sequencing (NGS), typically limits machine learning (ML) approaches in spaceflight studies that include radiation effects. However, pooling smaller studies while addressing intra- and inter-study variabilities allows for ML predictive modeling. Here, integration methods were applied to whole transcriptome shotgun sequencing (RNA-seq) data from six mouse liver GeneLab datasets (GLDS) (n ranging from 6 to 39 samples) from with a total of 81 spaceflight and ground-control samples to determine top features (i.e. genes) relevant to spaceflight including the effect of radiation exposure. RNASeq counts were normalized for each study, then merged and scaled across all datasets. Data dimensionality was reduced using a minimum redundancy maximum relevance (MRMR) methodology. Redundancy and relevance were computed using the Pearson correlation and F-statistic, respectively. The top 100 MRMR features were used to predict spaceflight vs. ground-control samples using Random Forest (RF), Support Vector Machine (SVM), and Linear Discriminant Analysis (LDA) classifiers with 5-fold cross validation (CV). Principal component analysis (PCA) on the complete feature set versus the MRMR features shows separation between spaceflight samples and ground controls (Figure 1A). The ML-based gene sets were compared against differential gene expression results obtained with DESeq2 from individual GLDS. Using all features or randomly sampled subsets at matching set sizes with MRMR, a maximum classifier accuracy of 69% was shown on the test set over 5 folds. For all classifiers, CV training using at least the top 30 MRMR genes show minimum 89% accuracy and 0.95 AUC value on the test set over 5 folds (Figure 1B). Baseline set analysis on differentially expressed genes (DEGs) identified using padj ≤ 0.05 show 295 DEGs that overlap at least two studies and 13 DEGs that overlap three studies (Figure 1C). Set analysis between the top 100 MRMR features and the DEGs showed 47 genes that overlap at least one study and 24 genes that overlap two studies. Over-representation analysis showed overlapping biological processes related to fatty acid and lipid metabolism which may indicate these processes in the response to spaceflight stressors. MRMR feature selection for the selected ML methods improve performance relative to a classifier built on all features or randomly sampled subsets. Permutation feature importance within the decorrelated MRMR features showed concordance in feature ranking between ML methods. A challenge of applying ML methods across heterogeneous NGS data is accounting for signal:noise. Here, signal validation across studies was shown by intersecting sets between top MRMR genes and DEGs from DESeq2 analysis. Non-intersecting sets introduce opportunity to explore genes relevant to differentiating space flight exposed groups and implementing ML methods across existing NGS datasets may overcome sample size limitations.

Machine Learning↗

NASA NTRS2017

Variability and Trends in the Arctic Sea Ice Cover: Results from Different Techniques

Variability and trend studies of sea ice in the Arctic have been conducted using products derived from the same raw passive microwave data but by different groups using different algorithms. This study provides consistency assessment of four of the leading products, namely, Goddard Bootstrap (SB2), Goddard NASA Team (NT1), EUMETSAT Ocean and Sea Ice Satellite Application Facility (OSI-SAF 1.2), and Hadley HadISST 2.2 data in evaluating variability and trends in the Arctic sea ice cover. All four provide generally similar ice patterns but significant disagreements in ice concentration distributions especially in the marginal ice zone and adjacent regions in winter and meltponded areas in summer. The discrepancies are primarily due to different ways the four techniques account for occurrences of new ice and meltponding. However, results show that the different products generally provide consistent and similar representation of the state of the Arctic sea ice cover. Hadley and NT1 data usually provide the highest and lowest monthly ice extents, respectively. The Hadley data also show the lowest trends in ice extent and ice area at negative 3.88 percent decade and negative 4.37 percent decade, respectively, compared to an average of negative 4.36 percent decade and negative 4.57 percent decade for all four. Trend maps also show similar spatial distribution for all four with the largest negative trends occurring at the Kara/Barents Sea and Beaufort Sea regions, where sea ice has been retreating the fastest. The good agreement of the trends especially with updated data provides strong confidence in the quantification of the rate of decline in the Arctic sea ice cover.

Arctic↗

NASA NTRS1996

Quantitative changes of GABA-immunoreactive cells in the hindlimb representation of the rat somatosensory cortex after 14-day hindlimb unloading by tail suspension

The present study was aimed at evaluating quantitatively gamma-aminobutyric acid (GABA) immunoreactivity in the hindlimb representation of the rat somatosensory cortex after 14 days of hindlimb unloading by tail suspension. A reduction in the number of GABA-immunoreactive cells with respect to the control animals was observed in layer Va and Vb. GABA-containing terminals were also reduced in the same layers, particularly those terminals surrounding the soma and apical dendrites of pyramidal cells in layer Vb. On the basis of previous morphological and behavioral studies of the neuromuscular system of hindlimb-suspended animals, it is suggested that the unloading due to hindlimb suspension alters afferent signaling and feedback information from intramuscular receptors to the cerebral cortex due to modifications in the reflex organization of hindlimb muscle groups. We propose that the reduction in immunoreactivity of local circuit GABAergic neurons and terminals is an expression of changes in their modulatory activity to compensate for the alterations in the afferent information.

Non-NASA Center↗

NASA NTRS2013

A Semantic Basis for Proof Queries and Transformations

We extend the query language PrQL, designed for inspecting machine representations of proofs, to also allow transformation of proofs. PrQL natively supports hiproofs which express proof structure using hierarchically nested labelled trees, which we claim is a natural way of taming the complexity of huge proofs. Query-driven transformations enable manipulation of this structure, in particular, to transform proofs produced by interactive theorem provers into forms that assist their understanding, or that could be consumed by other tools. In this paper we motivate and define basic transformation operations, using an abstract denotational semantics of hiproofs and queries. This extends our previous semantics for queries based on syntactic tree representations.We define update operations that add and remove sub-proofs, and manipulate the hierarchy to group and ungroup nodes. We show that

Proof Queries↗

NASA NTRS1994

Program Helps Design Tests Of Developmental Software

Computer program called "A Formal Test Representation Language and Tool for Functional Test Designs" (TRL) provides automatic software tool and formal language used to implement category-partition method and produce specification of test cases in testing phase of development of software. Category-partition method useful in defining input, outputs, and purpose of test-design phase of development and combines benefits of choosing normal cases having error-exposing properties. Traceability maintained quite easily by creating test design for each objective in test plan. Effort to transform test cases into procedures simplified by use of automatic software tool to create cases based on test design. Method enables rapid elimination of undesired test cases from consideration and facilitates review of test designs by peer groups. Written in C language.

Hops, Jonathan↗

NASA NTRS2019

Predictive Modeling for Differential Diagnosis and Mortality Risk Assessment

The prevalence of electronic health record (EHR) systems has brought prodigious biomedical informatics opportunity. Automated machine learning methods can effectively utilize such data and have become common tools for healthcare predictive modeling. Researches in medical informatics have explored the potential of deep learning and classical models in emergent care scenarios. In particular, predicting differential diagnoses for admissions have proven useful in decreasing unnecessary lab tests and improving inpatient triage decision-making. Moreover, identification of high-risk patients for in-hospital mortality is vitally important to maximize allocation of medical resources.The Medical Information Mart for Intensive Care (MIMIC-III) database, containing de-identified critical care inpatient was used in our study. This data set captures hospital patient laboratory measurements, pharmacologic prescriptions, diagnostic data and procedure event recordings. When considering adult patients and discounting admissions with ICU length of stay less than 24 hours, there were 37,787 unique admissions and 30,414 total patients. We examined the top 25 most prevalent ICD-9 group-level disease specificities in MIMIC-III using a multi-label classification model. In-hospital mortality was modeled as binary classification with 4,155 (13%) adult patients that expired, of which 3,138 (75.5%) were in the ICU setting. The metrics AUC, F1 score, sensitivity and specificity values calculated for each disease label measured prediction performance.The usage of ICD-9 group codes reduced feature dimension from 14,567 to 942 and greatly improved distribution of patient diagnostic categories. Disease temporal patterns were captured by considering the most frequently sampled 6 vital signs and 13 laboratory values. Missing data were imputed at each time-stamp. Time-series raw hourly average values were converted into 5 summary features (mean, standard deviation, number of observations, min & max values). Patient demographic variables such as age, gender, marital status and ethnicity were also factored into the modeling. Choi et al showed that contextual embedding of medical data, diagnostic and procedural codes alone can predict future diagnoses with sensitivity as high as 0.79. We utilized an embedding technique called word2vec which allowed sparse representations of medical history to be transformed into dense word vectors. The mappings captured contextual information by treating each admission as a sentence and learning the most likely neighboring words in a sliding window fashion. Binary and multi-label classification was achieved via collapse models, which do not consider temporal information, as well as recurrent neural networks with regularization, Softmax output layer activation together with categorical cross-entropy as the loss function.

US Army collaboration↗

NASA NTRS1992

Toward domain-specific design environments: Some representation ideas from the telecommunications domain

ACME is an experimental environment for investigating new approaches to modeling and analysis of system requirements and designs. ACME is built on and extends object-oriented conceptual modeling techniques and knowledge representation and reasoning (KRR) tools. The most immediate intended use for ACME is to help represent, understand, and communicate system designs during the early stages of system planning and requirements engineering. While our research is ostensibly aimed at software systems in general, we are particularly motivated to make an impact in the telecommunications domain, especially in the area referred to as Intelligent Networks (IN's). IN systems contain the software to provide services to users of a telecommunications network (e.g., call processing services, information services, etc.) as well as the software that provides the internal infrastructure for providing the services (e.g., resource management, billing, etc.). The software includes not only systems developed by the network proprietors but also by a growing group of independent service software providers.

Greenspan, Sol↗

NASA NTRS2019

Method for Tracking and Communicating Aggregate Risk Through the Use of Model-Based Systems Engineering (MBSE) Tools

Large, complex projects can identify a significant number and variety of risks, throughout the project life cycle. These risks are analyzed, mitigated, closed or accepted as independent uncertainties. Once closed or accepted, it is easy for projects to lose awareness of their impact. In reality, each of these risks contributes some amount to the overall risk posture of the project. The ability to track and effectively communicate this aggregate risk has represented a challenge to project management. There have been previous attempts to create a schema to communicate the aggregate effect of risks, without notable success. Most of these attempts have centered on some additive metric derived from the scoring of likelihood and consequence values. This, in and of itself, is a logical approach, but all too often the scores were then aggregated to a level where all context was lost. One weakness has been a lack of attempt to create linkages or logical groups of the risks upon which useful aggregation could then occur. The overall move to model-based (systems) engineering (MBSE) has opened up a vast frontier of opportunities to better integrate all project data. MBSE provides an underlying layer that links data items to each other. Objectives link to requirements, which then link to functions, functions to physical architecture items, and so on, as far down as projects want to model. While it started with a focus on modeling requirements based on things like use cases, efforts are now underway to integrate safety and mission assurance (S&MA) information and analyses, such as risks. This effort, called Model Based Mission Assurance (MBMA), is yielding models that are more useful and are a more accurate representations of the systems. MBSE models, with this ability to link related items, provide a new means of tracking and communicating aggregate risks. In the proposed method, risks are added into the models as distinct items, having attributes that communicate a scoring derived from the likelihood and consequence values as charted on the standard NASA 5x5 risk matrix. Like earlier efforts, each box in the 5x5 has an associated scoring, which may include both a current score and potential post-mitigation/control score. The risk items are then linked to elements of the model, such as system objectives/goals, requirements, functions, or physical architecture items, with "Risk to" relationships. These risks will then be communicated by use of reports generated from the model, detailing all risks and/or hazards linked to model elements. These reports can include aggregate impacts, including a current scoring and potential future state scoring based on the planned mitigations and/or controls. These reports will show all risks, open, accepted, and closed, linked to project objectives or requirements. When run as part of an upcoming risk acceptance discussion, these reports will serve to remind the team of all previous risks that relate to the effected portion of the system. When included as part of periodic program or project reviews, risk reviews, and safety reviews, this method can improve the overall understanding of the system's true risk posture. This proposed method takes full advantage of the advances that modern modeling techniques provide, with a minimal investment of additional time. Utilizing the model environment also enables a near constant access to current state of aggregate risks.

model based mission assurance↗

NASA NTRS1999

Digital Earth Initiative: A Joint Interagency Program

The Digital Earth is a virtual representation of our planet that enables a person to explore and interact with the vast amounts of natural and cultural information gathered about the Earth. The Digital Earth comprises data interfaces and standards enabling access to geo-referenced data from remote sensing, cartographic, demographic, medical, and other sources to respond to questions posed by the user. In a recent address at the California Science Center in Los Angeles, Vice President Al Gore articulated a Digital Earth Vision. That vision spoke to developing a multi-resolution, three-dimensional representation of the planet, into which we can roam and zoom into vast quantities of embedded geo-referenced data. The vision was not limited to moving through space but also allowing travel over a time-line, which can be set for days, years, centuries, or even geological epochs. As prototypes become available, it would also be possible to interact with the Digital Earth in multiple places around the country with access to high-speed networks and at a more limited level of access over the Internet. NASA was asked by the Vice President to lead an interagency initiative that would take steps to bring this vision to the public. This talk describes the start-up and plans of the Digital Earth Interagency Working Group in the formulation of its charter, an architecture reference model for Digital Earth, public/private partnerships, cooperative agreement notices, Digital Earth prototypes, and testbeds. Animations employing technologies for virtual roaming and zooming through multi-resolution satellite data set as prototype systems will be presented along with examples of potential user scenarios. Plans for engaging academia and industry in implementing the Digital Earth initiative will be discussed.

Halem, Milton↗

NASA NTRS2019

Exploiting the Convergence of Evidence in Satellite Data for Advanced Weather Index Insurance Design

The goal of drought-related weather index insurance (WII) is to protect smallholder farmers against the risk of weather shocks and to increase their agricultural productivity. Estimates of precipitation and vegetation greenness are the two dominant satellite datasets. However, ignoring additional moisture- and energy-related processes that influence the response of vegetation to rainfall leads to an incomplete representation of the hydrologic cycle. This study evaluates the added value of considering multiple independent satellite-based variables to design, calibrate, and validate weather insurance indices on the African continent. The satellite data include two rainfall datasets, soil moisture, the evaporative stress index (ESI), and vegetation greenness. We limit artificial advantages by resampling all datasets to the same spatial (0.25°) and temporal (monthly) resolution, although datasets with a higher spatial resolution might have an added value, if considered as the single source of information for localized applications. A higher correlation coefficient between the moisture-focused variables and the normalized difference vegetation index (NDVI), an indicator for vegetation vigor, provides evidence for the datasets’ capability to capture agricultural drought conditions on the ground. The Climate Hazards Group Infrared Precipitation with Stations (CHIRPS) rainfall dataset, soil moisture, and ESI show higher correlations with the (lagged) NDVI in large parts of Africa, for different land covers and various climate zones, than the African Rainfall Climatology, version 2 (ARC2), rainfall dataset, which is often used in WII. A comparison to drought years as reported by farmers in Ethiopia, Senegal, and Zambia indicates a high “hit rate” of all satellite-derived anomalies regarding the detection of severe droughts but limitations regarding moderate drought events.

drought↗

NASA NTRS2010

BGen: A UML Behavior Network Generator Tool

BGen software was designed for autogeneration of code based on a graphical representation of a behavior network used for controlling automatic vehicles. A common format used for describing a behavior network, such as that used in the JPL-developed behavior-based control system, CARACaS ["Control Architecture for Robotic Agent Command and Sensing" (NPO-43635), NASA Tech Briefs, Vol. 32, No. 10 (October 2008), page 40] includes a graph with sensory inputs flowing through the behaviors in order to generate the signals for the actuators that drive and steer the vehicle. A computer program to translate Unified Modeling Language (UML) Freeform Implementation Diagrams into a legacy C implementation of Behavior Network has been developed in order to simplify the development of C-code for behavior-based control systems. UML is a popular standard developed by the Object Management Group (OMG) to model software architectures graphically. The C implementation of a Behavior Network is functioning as a decision tree.

Huntsberger, Terry↗

NASA NTRS1990

Dynamics and configurations of galaxy triplets

The purpose is to infer the probable dynamical states of galaxy triplets by the observed data on their configurations. Two methods are proposed for describing the distributions of the triplet configuration parameters characterizing a tendency to alignment and hierarchy: (1) obtaining a representative sample of configurations and determining its statistical parameters (moments and percentages); and (2) dividing the region of possible configurations of triple systems (Agekian and Anosova, 1967) into a set of segments and finding the probabilities for the configurations to find themselves in each of them. Both these methods allow representation of the data by numerical simulations as well as observations. The effect of projection was studied. It rather overestimates the alignment and hierarchy of the triple systems. Among the parameters of interest there are found some parameters that are least sensitive to projection effects. The samples consist of simulated galaxy triplets (with hidden mass) as well as of 46 probably physical triple galaxies (Karachentseva et al., 1979). The observed triples as well as numerical models show a tendency to alignment. The triple galaxies do not show any tendency to hierarchy (formation of the temporary binaries), but this tendency may be present for simulated triplets without significant dark matter. The significant hidden mass (of order ten times the total mass of a triplet) decreases the probability of forming a binary and so weakens the hierarchy. Small galaxy groups consisting of 3 to 7 members are probably the most prevalent types of galaxy aggregate (Gorbatsky, 1987). Galaxy triplets are the simplest groups, but dynamically nontrivial ones.

Anosova, Joanna P.↗

NASA NTRS1997

Root-Raised Cosine Filter Implementation That Uses Canonical Signed Digits for High-Speed Digital Filter Applications

NASA Lewis Research Center's Space Communications Division has been investigating high-speed digital filters that can operate at a higher speed than those in current use for a digital modulator and demodulator (modem). Using the Canonical Signed Digits (CSD) number representation for filter coefficients is a very effective way to increase the filter's speed while reducing complexity in the digital filter hardware design. This approach is a good alternative to using an expensive parallel-processing design technique or custom, application-specific integrated circuits. Such integrated circuits may not be suitable for applications that require filter speeds faster than what application-specific integrated circuits digital signal processors can offer for a dedicated channel. When a communication channel is a dedicated, multiplication process--a costly, time-consuming process--it can be greatly simplified by a replacement of the filter coefficients with CSD numbers. A computer code written with the MATLAB software package runs the program and generates CSD-represented filter coefficients that are based on minimizing minimum mean square errors. Also, the Alta Group of Cadence's Signal Processing Workstation is used to simulate and analyze the CSD filter responses. The impulse response of the root-raised cosine filter that is used as a base model is defined. From this filter, a set of coefficients is sampled and stored in a file. For the all coefficients, the optimal CSD number for each coefficient is searched on the basis of the minimum-mean-square-errors criterion. Because the distribution of CSD numbers is not uniform, quantization errors tend to be bigger for coefficients greater than 1/2. To offset errors that occur in a region of coefficients between 1/2 to 1 and to better represent fractions with CSD numbers, an extra nonzero digit is allowed for any coefficients exceeding 1/2. This will greatly improve frequency response as well as intersymbol interference at the receiver. The frequency response of a set of collected CSD-represented filter coefficients was compared with the same filter that was conventionally implemented. Analyses show CSD-implemented filters perform as well as conventional filters. Comparison of eye diagrams and bit-error-rate curves between CSD filters and traditionally implemented filters are almost indistinguishable. However, filter complexity was reduced from almost 3.5 to 1 for CSD filters. Complete computer simulation results are available. In the near future, work will focus on building actual working digital filter hardware in a field programmable gate array (FPGA).

Kim, Heechul↗

NASA NTRS2006

Evaluation of Mesoscale Model Phenomenological Verification Techniques

Forecasters at the Spaceflight Meteorology Group, 45th Weather Squadron, and National Weather Service in Melbourne, FL use mesoscale numerical weather prediction model output in creating their operational forecasts. These models aid in forecasting weather phenomena that could compromise the safety of launch, landing, and daily ground operations and must produce reasonable weather forecasts in order for their output to be useful in operations. Considering the importance of model forecasts to operations, their accuracy in forecasting critical weather phenomena must be verified to determine their usefulness. The currently-used traditional verification techniques involve an objective point-by-point comparison of model output and observations valid at the same time and location. The resulting statistics can unfairly penalize high-resolution models that make realistic forecasts of a certain phenomena, but are offset from the observations in small time and/or space increments. Manual subjective verification can provide a more valid representation of model performance, but is time-consuming and prone to personal biases. An objective technique that verifies specific meteorological phenomena, much in the way a human would in a subjective evaluation, would likely produce a more realistic assessment of model performance. Such techniques are being developed in the research community. The Applied Meteorology Unit (AMU) was tasked to conduct a literature search to identify phenomenological verification techniques being developed, determine if any are ready to use operationally, and outline the steps needed to implement any operationally-ready techniques into the Advanced Weather Information Processing System (AWIPS). The AMU conducted a search of all literature on the topic of phenomenological-based mesoscale model verification techniques and found 10 different techniques in various stages of development. Six of the techniques were developed to verify precipitation forecasts, one to verify sea breeze forecasts, and three were capable of verifying several phenomena. The AMU also determined the feasibility of transitioning each technique into operations and rated the operational capability of each technique on a subjective 1-10 scale: (1) 1 indicates that the technique is only in the initial stages of development, (2) 2-5 indicates that the technique is still undergoing modifications and is not ready for operations, (3) 6-8 indicates a higher probability of integrating the technique into AWIPS with code modifications, and (4) 9-10 indicates that the technique was created for AWIPS and is ready for implementation. Eight of the techniques were assigned a rating of 5 or below. The other two received ratings of 6 and 7, and none of the techniques a rating of 9-10. At the current time, there are no phenomenological model verification techniques ready for operational use. However, several of the techniques described in this report may become viable techniques in the future and should be monitored for updates in the literature. The desire to use a phenomenological verification technique is widespread in the modeling community, and it is likely that other techniques besides those described herein are being developed, but the work has not yet been published. Therefore, the AMIU recommends that the literature continue to be monitored for updates to the techniques described in this report and for new techniques being developed whose results have not yet been published. 111

Lambert, Winifred↗

NASA NTRS2018

Calculating the Modal Mineralogy of Aubrite Meteorites Using X-Ray Computed Tomography

The aubrites are a group of differentiated meteorites that formed in extremely reducing conditions, with oxygen fugacities (ƒO2) ranging from ~2 to ~6 log units below the Iron-Wüstite buffer. At these extreme conditions, elements that are lithophile (silica-loving) on Earth can behave as chalcophiles (sulfur-loving) or siderophiles (metal-loving), and FeO-poor silicates and exotic sulfides can form. Elemental partitioning among minerals at these conditions are still not well understood, thus studying aubrites could help better constrain elemental behavior. Only 30 aubrites exist; however, they display various textures, which can be difficult to identify in small samples. Identifying composite clasts can help in understanding the igneous history of the aubrite parent bodies. In order to distinguish different minerals and textures in larger samples, we use X-ray computed tomography (XCT), which is a useful, non-destructive analysis that can produce a 3D representation of a meteorite's textures, structures, and modal mineralogy. This study investigates the Norton County aubrite using XCT. Norton County is a fragmental impact breccia aubrite, and was an observed fall with a main mass of 1.1 tons. This large amount of material offers an opportunity to investigate a great volume of reduced, aubritic sample and study a more diverse variety of clasts. Here we report XCT results of two samples of Norton County (NC 15417) in order to constrain the 3D modal mineralogy of silicates, sulfides, and metals, and to identify unique clasts within the matrix.

Wilbur, Zoe↗

NASA NTRS1995

The scheme machine: A case study in progress in design derivation at system levels

The Scheme Machine is one of several design projects of the Digital Design Derivation group at Indiana University. It differs from the other projects in its focus on issues of system design and its connection to surrounding research in programming language semantics, compiler construction, and programming methodology underway at Indiana and elsewhere. The genesis of the project dates to the early 1980's, when digital design derivation research branched from the surrounding research effort in programming languages. Both branches have continued to develop in parallel, with this particular project serving as a bridge. However, by 1990 there remained little real interaction between the branches and recently we have undertaken to reintegrate them. On the software side, researchers have refined a mathematically rigorous (but not mechanized) treatment starting with the fully abstract semantic definition of Scheme and resulting in an efficient implementation consisting of a compiler and virtual machine model, the latter typically realized with a general purpose microprocessor. The derivation includes a number of sophisticated factorizations and representations and is also deep example of the underlying engineering methodology. The hardware research has created a mechanized algebra supporting the tedious and massive transformations often seen at lower levels of design. This work has progressed to the point that large scale devices, such as processors, can be derived from first-order finite state machine specifications. This is roughly where the language oriented research stops; thus, together, the two efforts establish a thread from the highest levels of abstract specification to detailed digital implementation. The Scheme Machine project challenges hardware derivation research in several ways, although the individual components of the system are of a similar scale to those we have worked with before. The machine has a custom dual-ported memory to support garbage collection. It consists of four tightly coupled processes--processor, collector, allocator, memory--with a very non-trivial synchronization relationship. Finally, there are deep issues of representation for the run-time objects of a symbolic processing language. The research centers on verification through integrated formal reasoning systems, but is also involved with modeling and prototyping environments. Since the derivation algebra is basd on an executable modeling language, there is opportunity to incorporate design animation in the design process. We are looking for ways to move smoothly and incrementally from executable specifications into hardware realization. For example, we can run the garbage collector specification, a Scheme program, directly against the physical memory prototype, and similarly, the instruction processor model against the heap implementation.

Johnson, Steven D.↗

NASA NTRS2018

GeneLab Analysis Working Group Kick-Off Meeting

Goals to achieve for GeneLab AWG - GL vision - Review of GeneLab AWG charter Timeline and milestones for 2018 Logistics - Monthly Meeting - Workshop - Internship - ASGSR Introduction of team leads and goals of each group Introduction of all members Q/A Three-tier Client Strategy to Democratize Data Physiological changes, pathway enrichment, differential expression, normalization, processing metadata, reproducibility, Data federation/integration with heterogeneous bioinformatics external databases The GLDS currently serves over 100 omics investigations to the biomedical community via open access. In order to expand the scope of metadata record searches via the GLDS, we designed a metadata warehouse that collects and updates metadata records from external systems housing similar data. To demonstrate the capabilities of federated search and retrieval of these data, we imported metadata records from three open-access data systems into the GLDS metadata warehouse: NCBI's Gene Expression Omnibus (GEO), EBI's PRoteomics IDEntifications (PRIDE) repository, and the Metagenomics Analysis server (MG-RAST). Each of these systems defines metadata for omics data sets differently. One solution to bridge such differences is to employ a common object model (COM) to which each systems' representation of metadata can be mapped. Warehoused metadata records are then transformed at ETL to this single, common representation. Queries generated via the GLDS are then executed against the warehouse, and matching records are shown in the COM representation (Fig. 1). While this approach is relatively straightforward to implement, the volume of the data in the omics domain presents challenges in dealing with latency and currency of records. Furthermore, the lack of a coordinated has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

GeneLab↗