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All sources NASA NTRS DOE OSTI

DOE OSTI2023

A framework for materials informatics education through workshops

The burgeoning field of materials informatics necessitates a focus on educating the next generation of materials scientists in the concepts of data science, artificial intelligence (AI), and machine learning (ML). In addition to incorporating these topics in undergraduate and graduate curricula, regular hands-on workshops present the most effective medium to initiate researchers to informatics and have them start applying the best AI/ML tools to their own research. With the help of the Materials Research Society (MRS), members of the MRS AI Staging Committee, and a dedicated team of instructors, we successfully conducted workshops covering the essential concepts of AI/ML as applied to materials data, at both the Spring and Fall Meetings in 2022, with plans to make this a regular feature in future meetings. Here, in this article, we discuss the importance of materials informatics education via the lens of these workshops, including details such as learning and implementing specific algorithms, the crucial nuts and bolts of ML, and using competitions to increase interest and participation.

36 MATERIALS SCIENCE↗

NASA NTRS2006

Comprehensive Environmental Informatics System (CEIS) Integrating Crew and Vehicle Environmental Health

Integrated Vehicle Health Management (IVHM) systems have been pursued as highly integrated systems that include smart sensors, diagnostic and prognostics software for assessments of real-time and life-cycle vehicle health information. Inclusive to such a system is the requirement to monitor the environmental health within the vehicle and the occupants of the vehicle. In this regard an enterprise approach to informatics is used to develop a methodology entitled, Comprehensive Environmental Informatics System (CEIS). The hardware and software technologies integrated into this system will be embedded in the vehicle subsystems, and maintenance operations, to provide both real-time and life-cycle health information of the environment within the vehicle cabin and of its occupants. This comprehensive information database will enable informed decision making and logistics management. One key element of the CEIS is interoperability for data acquisition and archive between environment and human system monitoring. With comprehensive components the data acquired in this system will use model based reasoning systems for subsystem and system level managers, advanced on-board and ground-based mission and maintenance planners to assess system functionality. Knowledge databases of the vehicle health state will be continuously updated and reported for critical failure modes, and routinely updated and reported for life cycle condition trending. Sufficient intelligence, including evidence-based engineering practices which are analogous to evidencebased medicine practices, will be included in the CEIS to result in more rapid recognition of off-nominal operation to enable quicker corrective actions. This will result from better information (rather than just data) for improved crew/operator situational awareness, which will produce significant vehicle and crew safety improvements, as well as increasing the chance for mission success, future mission planning as well as training. Other benefits include improved reliability, increase safety in operations and cost of operations. The cost benefits stem from significantly reduced processing and operations manpower, predictive maintenance for systems and subjects. The improvements in vehicle functionality and cost will result from increased prognostic and diagnostic capability due to the detailed total human exploration system health knowledge from CEIS. A collateral benefit is that there will be closer observations of the vehicle occupants as wrist watch sized devices are worn for continuous health monitoring. Additional database acquisition will stem from activities in countermeasure practices to ensure peak performance capability by occupants of the vehicle. The CEIS will provide data from advanced sensing technologies and informatics modeling which will be useful in problem troubleshooting, and improving NASA s awareness of systems during operation.

Nall, Mark E.↗

NASA NTRS2006

Paradigm Shift in Data Content and Informatics Infrastructure Required for Generalized Constitutive Modeling of Materials Behavior

Materials property information such as composition and thermophysical/mechanical properties abound in the literature. Oftentimes, however, the corresponding response curves from which these data are determined are missing or at the very least difficult to retrieve. Further, the paradigm for collecting materials property information has historically centered on (1) properties for materials comparison/selection purposes and (2) input requirements for conventional design/analysis methods. However, just as not all materials are alike or equal, neither are all constitutive models (and thus design/ analysis methods) equal; each model typically has its own specific and often unique required materials parameters, some directly measurable and others indirectly measurable. Therefore, the type and extent of materials information routinely collected is not always sufficient to meet the current, much less future, needs of the materials modeling community. Informatics has been defined as the science concerned with gathering, manipulating, storing, retrieving, and classifying recorded information. A key aspect of informatics is its focus on understanding problems and applying information technology as needed to address those problems. The primary objective of this article is to highlight the need for a paradigm shift in materials data collection, analysis, and dissemination so as to maximize the impact on both practitioners and researchers. Our hope is to identify and articulate what constitutes "sufficient" data content (i.e., quality and quantity) for developing, characterizing, and validating sophisticated nonlinear time- and history-dependent (hereditary) constitutive models. Likewise, the informatics infrastructure required for handling the potentially massive amounts of materials data will be discussed.

Arnold, S. M.↗

NASA NTRS2009

NASA Biomedical Informatics Capabilities and Needs

To improve on-orbit clinical capabilities by developing and providing operational support for intelligent, robust, reliable, and secure, enterprise-wide and comprehensive health care and biomedical informatics systems with increasing levels of autonomy, for use on Earth, low Earth orbit & exploration class missions. Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information. The end objective of biomedical informatics is the coalescing of data, knowledge, and the tools necessary to apply that data and knowledge in the decision-making process, at the time and place that a decision needs to be made.

Johnson-Throop, Kathy A.↗

NASA NTRS2014

Earth Science Informatics Comes of Age

The volume and complexity of Earth science data have steadily increased, placing ever-greater demands on researchers, software developers and data managers tasked with handling such data. Additional demands arise from requirements being levied by funding agencies and governments to better manage, preserve and provide open access to data. Fortunately, over the past 10-15 years significant advances in information technology, such as increased processing power, advanced programming languages, more sophisticated and practical standards, and near-ubiquitous internet access have made the jobs of those acquiring, processing, distributing and archiving data easier. These advances have also led to an increasing number of individuals entering the field of informatics as it applies to Geoscience and Remote Sensing. Informatics is the science and technology of applying computers and computational methods to the systematic analysis, management, interchange, and representation of data, information, and knowledge. Informatics also encompasses the use of computers and computational methods to support decisionmaking and other applications for societal benefits.

Jodha, Siri↗

DOE OSTI2023

Empowering Women in Biomedical Informatics: Pivoting for Success in the Post-Pandemic World

The COVID-19 pandemic and the isolation measures implemented to contain its spread have exacerbated pre-existing barriers to advancement for women in biomedical informatics. In 2020, the Women in AMIA (WIA) Networking, Mentoring, and Lifecycle Committee administered a survey to identify resources and needs to assist women in informatics. Part of this survey identified several factors impacted by the pandemic: 1) work-life boundaries disappeared and caring for family while working from home became increasingly challenging; 2) isolation, stress and safety of well-being was heightened during the pandemic impacting physical and mental health; 3) diverse working environment and modality brought unforeseen challenges in collaborations and unified communications. These challenges present an opportunity for promoting career development for women professionals in biomedical informatics. This WIA-sponsored panel brings together leaders in the field to highlight their personal experiences and strategies to support women professionals.

Dua, Prerna↗

DOE OSTI2015

An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics

Comprehensive MS analysis of peptidome, the intracellular and intercellular products of protein degradation, has the potential to provide novel insights on endogenous proteolytic processing and their utility in disease diagnosis and prognosis. Along with the advances in MS instrumentation, a plethora of proteomics data analysis tools have been applied for direct use in peptidomics; however an evaluation of the currently available informatics pipelines for peptidomics data analysis has yet to be reported. In this study, we set off by evaluating the results of several popular MS/MS database search engines including MS-GF+, SEQUEST and MS-Align+ for peptidomics data analysis, followed by identification and label-free quantification using the well-established accurate mass and time (AMT) tag and newly developed informed quantification (IQ) approaches, both based on direct LC-MS analysis. Our result demonstrated that MS-GF+ outperformed both SEQUEST and MS-Align+ in identifying peptidome peptides. Using a database established from the MS-GF+ peptide identifications, both the AMT tag and IQ approaches provided significantly deeper peptidome coverage and less missing value for each individual data set than the MS/MS methods, while achieving robust label-free quantification. Besides having an excellent correlation with the AMT tag quantification results, IQ also provided slightly higher peptidome coverage than AMT. Taken together, we propose an optimal informatics pipeline combining MS-GF+ for initial database searching with IQ (or AMT) for identification and label-free quantification for high-throughput, comprehensive and quantitative peptidomics analysis.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2017

High-content image informatics of the structural nuclear protein NuMA parses trajectories for stem/progenitor cell lineages and oncogenic transformation

Stem and progenitor cells that exhibit significant regenerative potential and critical roles in cancer initiation and progression remain difficult to characterize. Cell fates are determined by reciprocal signaling between the cell microenvironment and the nucleus; hence parameters derived from nuclear remodeling are ideal candidates for stem/progenitor cell characterization. Here we applied high-content, single cell analysis of nuclear shape and organization to examine stem and progenitor cells destined to distinct differentiation endpoints, yet undistinguishable by conventional methods. Nuclear descriptors defined through image informatics classified mesenchymal stem cells poised to either adipogenic or osteogenic differentiation, and oligodendrocyte precursors isolated from different regions of the brain and destined to distinct astrocyte subtypes. Nuclear descriptors also revealed early changes in stem cells after chemical oncogenesis, allowing the identification of a class of cancer-mitigating biomaterials. To capture the metrology of nuclear changes, we developed a simple and quantitative “imaging-derived” parsing index, which reflects the dynamic evolution of the high-dimensional space of nuclear organizational features. A comparative analysis of parsing outcomes via either nuclear shape or textural metrics of the nuclear structural protein NuMA indicates the nuclear shape alone is a weak phenotypic predictor. In contrast, variations in the NuMA organization parsed emergent cell phenotypes and discerned emergent stages of stem cell transformation, supporting a prognosticating role for this protein in the outcomes of nuclear functions. - Highlights: • High-content analysis of nuclear shape and organization classify stem and progenitor cells poised for distinct lineages. • Early oncogenic changes in mesenchymal stem cells (MSCs) are also detected with nuclear descriptors. • A new class of cancer-mitigating biomaterials was identified based on image informatics. • Textural metrics of the nuclear structural protein NuMA are sufficient to parse emergent cell phenotypes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗

NASA NTRS1994

Informatics in Turkey

In the last twenty years the rapid change in the informatics sector has had economic and social impact on private and government activities. The Supreme Council for Science and Technology of Turkey assigned highest priority to the informatics in its meeting in February 1993. With this advice TUBITAK (The Scientific and Technical Research Council of Turkey) intends to give a strong impulse to development of a research policy in this field.

Cakir, Serhat↗

NASA NTRS2007

Translational Research from an Informatics Perspective

Clinical and translational research (CTR) is an essential part of a sustainable global health system. Informatics is now recognized as an important en-abler of CTR and informaticians are increasingly called upon to help CTR efforts. The US National Institutes of Health mandated biomedical informatics activity as part of its new national CTR grant initiative, the Clinical and Translational Science Award (CTSA). Traditionally, translational re-search was defined as the translation of laboratory discoveries to patient care (bench to bedside). We argue, however, that there are many other kinds of translational research. Indeed, translational re-search requires the translation of knowledge dis-covered in one domain to another domain and is therefore an information-based activity. In this panel, we will expand upon this view of translational research and present three different examples of translation to illustrate the point: 1) bench to bedside, 2) Earth to space and 3) academia to community. We will conclude with a discussion of our local translational research efforts that draw on each of the three examples.

Bernstam, Elmer↗

NASA NTRS2012

Bridging Informatics and Earth Science: a Look at Gregory Leptoukh's Contributions

With the tragic passing this year of Gregory Leptoukh, the Earth and Space Sciences community lost a tireless participant in--and advocate for--science informatics. Throughout his career at NASA, Dr. Leptoukh established a theme of bridging the gulf between the informatics and science communities. Nowhere is this more evident than his leadership in the development of Giovanni (GES DISC Interactive Online Visualization ANd aNalysis Infrastructure). Giovanni is an online tool that serves to hide the often-complex technical details of data format and structure, making science data easier to explore and use by Earth scientists. To date Giovanni has been acknowledged as a contributor in 500-odd scientific articles. In recent years, Leptoukh concentrated his efforts on multi-sensor data inter-comparison, merging and fusion. This work exposed several challenges at the intersection of data and science. One of these was the ease with which a naive user might generate spurious comparisons, a potential hazard that was the genesis of the Multi-sensor Data Synergy Advisor (MDSA). The MDSA uses semantic ontologies and inference rules to organize knowledge about dataset quality and other salient characteristics in order to advise users on potential caveats for comparing or merging two datasets. Recently, Leptoukh also led the development of AeroStat, an online Giovanni instance to investigate aerosols via statistics from station and satellite comparisons and merged maps of data from more than one instrument. Aerostat offers a neural net based bias adjustment to harmonize the data by removing systematic offsets between datasets before merging. These examples exhibit Leptoukh's talent for adopting advanced computer technologies in the service of making science data more accessible to researchers. In this, he set an example that is at once both vital and challenging for the ESSI community to emulate.

Source record↗

NASA NTRS2014

Advanced Extravehicular Mobility Unit Informatics Software Design

This is a description of the software design for the 2013 edition of the Advanced Extravehicular Mobility Unit (AEMU) Informatics computer assembly. The Informatics system is an optional part of the space suit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and caution and warning information. In the future it will display maps with GPS position data, and video and still images captured by the astronaut.

extravehicular mobility units↗

NASA NTRS2013

Climate Informatics

The impacts of present and potential future climate change will be one of the most important scientific and societal challenges in the 21st century. Given observed changes in temperature, sea ice, and sea level, improving our understanding of the climate system is an international priority. This system is characterized by complex phenomena that are imperfectly observed and even more imperfectly simulated. But with an ever-growing supply of climate data from satellites and environmental sensors, the magnitude of data and climate model output is beginning to overwhelm the relatively simple tools currently used to analyze them. A computational approach will therefore be indispensable for these analysis challenges. This chapter introduces the fledgling research discipline climate informatics: collaborations between climate scientists and machine learning researchers in order to bridge this gap between data and understanding. We hope that the study of climate informatics will accelerate discovery in answering pressing questions in climate science.

Climate change↗

NASA NTRS2016

Advanced Spacesuit Informatics Software Design for Power, Avionics and Software Version 2.0

A description of the software design for the 2016 edition of the Informatics computer assembly of the NASAs Advanced Extravehicular Mobility Unit (AEMU), also called the Advanced Spacesuit. The Informatics system is an optional part of the spacesuit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and warning information. It also provides an interface to the suit mounted camera for recording still images, video, and audio field notes.

Instrumentation↗

NASA NTRS2023

Trades, Architecture, and Design of the Joint Augmented Reality Visual Informatics (Joint AR) Product

Future expeditions will enable exploration and study of the planetary surfaces of the Moon and Mars by performing extravehicular activity (EVA) operations. Present-day International Space Station (ISS) EVA operations require an intricate and tight choreography of crew, space suits, tools, systems, and flight teams to plan, train, and execute with limited advanced informatics. Additionally, EVA operations, aside from the Apollo Lunar surface missions, have predominately focused on maintenance and construction tasks where success criteria are clearly measurable. However, future exploration missions expect to enable crew to carry out scientific objectives in increasingly Earth-independent ways. In this paper, the Joint Augmented Reality Visual Informatics System (Joint AR) characterizes the design space for developing a modular augmented reality (AR) device for a spacesuit form factor that can support crew decision-making for EVA. This paper highlights the project’s experience with a product-focused management style and use-case centered systems engineering approach to iteratively design, build, and test. The Joint AR product features were defined via trade studies and market analysis of previous EVA display efforts, various AR components such as optics, commercial AR systems, light engines, data interfaces, graphics engine software and analog test beds. We outline the defining architectural design decisions, including safety criticality considerations, suit mounting interfaces, computer architectures, and partnership contracting mechanisms. The outcomes of these studies, architecture decisions, and management requirements result in a recommended design which is the Joint AR product. We discuss the evolution, development of these system components, and what work remains. We hope to share a unified understanding of various design decisions and how they impact the future of crew members’ access to data during Lunar and Martian EVAs. This ongoing effort can enable a community-wide discovery process toward realizing necessary AR features and capabilities for future missions.

Augmented Reality↗

NASA NTRS2023

Trades, Architecture, and Design of the Joint Augmented Reality Visual Informatics System (Joint AR) Product

Paromita Mitra↗

NASA NTRS2023

Trades, Architecture, and Design of the Joint Augmented Reality Visual Informatics System (Joint AR) Product

Paromita Mitra↗