Dan Berrios

National Aeronautics and Space Administration · Intelligent Systems Division

Space biology research aims to understand fundamental spaceflight effects on organisms, develop foundational knowledge to support deep space exploration and, ultimately, bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals and humans for sustained multi-planetary life. To advance these aims, the field l...

Human exploration of deep space will involve missions of substantial distance and duration. To effectively mitigate health hazards, paradigm shifts in astronaut health systems are necessary to enable Earth-independent healthcare, rather than Earth-reliant. Here we present a summary of decadal recommendations from a workshop organized by NASA on art...

The era of high-throughput techniques created big data in the medical field and research disciplines. Machine intelligence (MI) approaches can overcome critical limitations on how those large-scale data sets are processed, analyzed, and interpreted. The 67th Annual Meeting of the Radiation Research Society featured a symposium on MI approaches to h...

Human space exploration beyond low Earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in data and space health systems are necessary to enable Earth-independence, rather than Earth-reliance. Promising developments in the fields of artificial intelligence and m...

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the fiel...

The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized temp...

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from space...

Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however,...

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from space...

The mission of NASA’s GeneLab database (https://genelab.nasa.gov/) is to collect, curate, and provide access to the genomic, transcriptomic, proteomic and metabolomic (so-called ‘omics’) data from biospecimens flown in space or exposed to simulated space stressors, maximizing their utilization. This large collection of data enables the exploration...

Performing biological experiments in space requires special accommodations and procedures to ensure that these investigations are performed effectively and efficiently. Moreover, given the infrequency of these experiments it is imperative that their impacts be maximized. The rapid advancement of omics technologies offers an opportunity to dramatica...

Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the "FAIRness" of NASA's GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omic...

Motivation: - To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms. Results: - The GeneLab Data System (GLDS) is an open access database containi...

NASA's Rodent Research (RR) project is playing a critical role in advancing biomedical research on the physiological effects of space environments. Due to the limited resources for conducting biological experiments aboard the International Space Station (ISS), it is imperative to use crew time efficiently while maximizing high‐quality science retur...

Translating fundamental biological discoveries from NASA Space Biology program into health risk from space flights has been an ongoing challenge. We propose to use NASA GeneLab database to gain new knowledge on potential systemic responses to space. Unbiased systems biology analysis of transcriptomic data from seven different rodent datasets reveal...

Accurate assessment of risks of long-term space missions is critical for human space exploration. It is essential to have a detailed understanding of the biological effects on humans living and working in deep space. Ionizing radiation from galactic cosmic rays (GCR) is a major health risk factor for astronauts on extended missions outside the prot...

NASA has a large range of custom-built and commercial data systems to support spaceflight programs. Some of the systems are re-used by many programs and projects over time. Management and systems engineering processes require integration of data across many of these systems, a difficult problem given the widely diverse nature of system interfaces a...

I. Abstract he development of increasingly sophisticated autonomous vehicles capable of being deployed from great distances and for extended periods of time brings new challenges, including tracing collaboratively made decisions regarding these assets and relating collected data to such decisions and their rationale. For scientific data gathering,...

NASA's Mobile Agents project leads coordinated planetary exploration simulations at the Mars Desert Research Station. Through ScienceOrganizer, a Web-based tool for organizing and providing contextual information for scientific data sets, remote teams of scientists access and annotate data sets, images, documents and other forms of scientific infor...

We describe a reference architecture for space information management systems that elegantly overcomes the rigid design of common information systems in many domains. The reference architecture consists of a set of flexible, reusable, independent models and software components that function in unison, but remain separately managed entities. The mai...

information sources, including databases, web servers, document repositories, ftp servers, special-purpose application servers, and Web service applications. For example, diagnosing a problem with the International Space Station (ISS) communications systems might require a flight controller to access multiple pieces of information, including the re...

NASA Ames' Mobile Agents Architecture is a distributed agent-based architecture, which integrates diverse mobile entities in a wide-area wireless system for lunar and planetary surface operations. Software agents, implemented in the Brahms multiagent language, run in Brahms virtual machines onboard laptops for space suits, robots, and surface habit...

InvestigationOrganizer (IO) is a collaborative semantic Web application designed to support mishap investigations, and has been used for accidents ranging from those involving only minor property damage to the loss of the Space Shuttle Columbia. The development and use of IO in support of these investigations has provided significant lessons about...

We have developed and tested an advanced EVA communications and computing system to increase astronaut self-reliance and safety, reducing dependence on continuous monitoring and advising from mission control on Earth. This system, called Mobile Agents (MA), is voice controlled and provides information verbally to the astronauts through programs cal...

SemanticOrganizer is a collaborative knowledge management system designed to support distributed NASA projects, including multidisciplinary teams of scientists, engineers, and accident investigators. The system provides a customizable, semantically structured information repository that stores work products relevant to multiple projects of differin...

While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still unclear. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without sig...

Information needs in clinical practice take the form of specific questions about a given clinical situation, and are best satisfied by concise and specific information retrieval. We sought to develop a comprehensive set of generic queries for information retrieval from electronic medical information resources. We collected one hundred and ten real-...

While there are now a number of languages and frameworks that enable the SemanticOrganizer network.

To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and...

Information needs in clinical practice take the form of specific questions about a given clinical situation, and are best satisfied by concise and specific information retrieval. We sought to develop a comprehensive set of generic queries for information retrieval from electronic medical information resources. We collected one hundred and ten real-...

During the last three years, we have developed and described components of ELBook, a semantically based information-retrieval system [1-4]. Using these components, domain experts can specify a query model, indexers can use the query model to index documents, and end-users can search these documents for instances of indexed queries.

We report our experience with a statistically based method of generating sentence-level indexing based on identified UMLS concepts and query and vector-space models. We evaluated the system using the consensus markup of two domain experts as the gold standard. UMLS concepts identified both from HTML headings and in paragraph text were valuable in p...

Indexing medical text in journals or in textbooks requires a tremendous amount of resources. We tested two algorithms for automatically indexing nouns, noun-modifier, noun phrases and inferring selected binary relations between UMLS concepts in a textbook of infectious disease. Sixty-six percent of nouns and nounmodifiers and 81% of noun phrases we...

Indexing medical text in journals or textbooks requires a tremendous amount of resources. We tested two algorithms for automatically indexing nouns, noun-modifiers, and noun phrases, and inferring selected binary relations between UMLS concepts in a textbook of infectious disease. Sixty-six percent of nouns and noun-modifiers and 81% of noun phrase...

Our group has built an information retrieval system based on a complex semantic markup of medical textbooks. We describe the construction of a set of web-based knowledge-acquisition tools that expedites the collection and maintenance of the concepts required for text markup and the search interface required for information retrieval from the marked...

We describe the construction of MYCIN II, a prototype system that provides for content-based markup and search of a forthcoming clinical therapeutics textbook, Antimicrobial Therapy and Vaccines. Existing commercial search technology for digital references utilizes generic tools such as textword-based searches with geographical or statistical refin...

The information needs of practicing clinicians frequently require textbook or journal searches.(1) Making these sources available in electronic form improves the speed of these searches, but precision (i.e., the fraction of relevant to total documents retrieved) remains low. Improving the traditional keyword search by transforming search terms into...

To determine the diagnostic accuracy of an investigational test for human immunodeficiency virus (HIV) envelope antibodies in urine. Matched blood and urine specimens were tested for HIV by two independent laboratories, both of which were blinded to all results at the other site. Duplicate positive enzyme-linked immunoassay (EIA) results were confi...

To determine the costs and outcomes associated with intensive care unit (ICU) admission for patients with acquired immunodeficiency syndrome (AIDS)-related Pneumocystis carinii pneumonia (PCP), and severe respiratory failure. Survival and cost-effectiveness analysis. A large municipal teaching hospital serving an indigent population. Consecutive pa...

To determine the prevalence of testing for human immunodeficiency virus (HIV) antibody among adults with various risk factors for infection, particularly those residing in large metropolitan areas where the bulk of cases of acquired immunodeficiency syndrome (AIDS) have occurred. A nationwide, population-based telephone survey eliciting testing, se...

Objective. —To determine the prevalence of testing for human immunodeficiency virus (HIV) antibody among adults with various risk factors for infection, particularly those residing in large metropolitan areas where the bulk of cases of acquired immunodeficiency syndrome (AIDS) have occurred.Design. —A nationwide, population-based telephone survey...

We surveyed men and women aged 21 to 34 years to determine the rates of human immunodeficiency virus (HIV) antibody testing in blacks and whites of diverse education levels in four US cities. Responses to the anonymous, mailed questionnaire were received from 90% of 777 white women, 64% of 734 black women, 79% of 677 white men, and 48% of 541 black...

Domestic violence is a pervasive and frequently unrecognized cause of injury among women. We reviewed data from standardized interviews with 218 women who presented to an emergency department with injuries due to domestic violence. Victims ranged in age from 16 to 66 years and constituted a wide range of socioeconomic and ethnic backgrounds. Domest...

The Mars Society's Desert Research Station (MDRS) Rotation 38, April 3-17, 2005, was dedicated to field tests of NASA's Mobile Agents EVA communications system. MDRS provided an excellent, cost-effective venue for bringing together teams from NASA Ames and Johnson Space Center, including six distinct projects, in an intensive two weeks of system in...