Data for EMSL Project 61049 from April 2026
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Toyoda, Jason [Environmental Molecular Sciences La↗
SEARCH · Engineering Papers
Results for “network science”
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.
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Combining compositional data sets introduces error in covariance network reconstruction
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and interkingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.
59 BASIC BIOLOGICAL SCIENCES↗
Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer
Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin–antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.
59 BASIC BIOLOGICAL SCIENCES↗
Use of Nack Oriented Reliable Multicast (NORM) Protocol for Transport of Spacecraft Telemetry in Ground Networks
Frequently it is necessary to distribute spacecraft telemetry to multiple destinations on Internet Protocol (IP) networks. There are various methods of delivering this data, but when the data is high rate and there are many destinations IP multicast provides the best solution from a network perspective. However, IP multicast only supports the User Datagram Protocol (UDP) which is connectionless and unreliable. This nature of UDP and by extension the low priority treatment of UDP packets by some network hardware creates a difficult environment for distribution of high rate telemetry to a number of recipients over IP networks. NACK (Negative ACKnowledgment) Oriented Reliable Multicast (NORM) is defined by IETF (Internet Engineering Task Force) RFC (Request for Comments) 5740 in 2009 by B. Adamson et al. NORM provides a mechanism of retransmission and or forward error correction for UDP packets, potentially overcoming the limits of UDP for the transmission of spacecraft telemetry. Marshall Space Flight Center’s (MSFC) Huntsville Operations Support Center (HOSC) manages the delivery of the International Space Station (ISS) payload science and health data. The ISS IP Ground Routed (IIGoR) network provides the delivery of the data from the ground stations to the control centers. HOSC personnel have been experimenting with the use of NORM on the link between the ground stations and the front end processor equipment in Huntsville, AL.
Baldwin, Patrick A.↗
A Flexible Control Center Architecture for Support of Diverse Spaceflight Missions
The Ames Multi-Mission Operations Center (MMOC) enables and supports flight and science operations for Ames' spaceflight missions. The MMOC is composed of the facilities, networks, information technology equipment, software, and system administration services needed by flight projects to effectively and efficiently perform all mission functions, including planning, scheduling, command, telemetry processing, and science analysis. The MMOC's ready-to-use services reduce start-up time, shorten procurement and provisioning and allow mission planning efforts to focus more on science and less on infrastructure. The architecture of the MMOC was designed from the start for flexibility, so that it can readily support multiple missions of greatly varying size and complexity while simultaneously keeping costs low.
Differding, Joan C.↗
Advancing the understanding of coastal disturbances with a network-of-networks approach
Coastal ecosystems are at the nexus of many high priority challenges in environmental sciences, including predicting the influences of compounding disturbances exacerbated by climate change on biogeochemical cycling. Extreme events such as hurricanes, flooding, landslides, and wildfires influence biogeochemical cycling in these systems. However, while research in coastal science is fundamentally transdisciplinary – as drivers of biogeochemical and ecological processes often span scientific and environmental domains – traditional place-based approaches are still often employed to understand coastal ecosystems. In this perspective, we argue that integration among distributed research sites from a macrosystem perspective is crucial to understand how compounding disturbances affect coastal ecosystems. We identify a roadmap for the implementation of an integrated network-of-networks framework that leverages existing research network sites in coastal ecosystems to advance continental-scale process understanding for studying extreme events and global change. We also identify specific ways that existing research efforts can maximize mutual benefit, and where additional infrastructure investments might increase return-on-investment along the coast, using the coastal continental US as a case study.
Myers-Pigg, Allison N. [BATTELLE (PACIFIC NW LAB)]↗
Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana
Abstract Adverse environmental and pathophysiological situations can overwhelm the biosynthetic capacity of the endoplasmic reticulum (ER), igniting a potentially lethal condition known as ER stress. ER stress hampers growth and triggers a conserved cytoprotective signaling cascade, the unfolded protein response (UPR) for ER homeostasis. As ER stress subsides, growth is resumed. Despite the pivotal role of the UPR in growth restoration, the underlying mechanisms for growth resumption are yet unknown. To discover these, we undertook a genomics approach in the model plant species Arabidopsis thaliana and mined the gene reprogramming roles of the UPR modulators, basic leucine zipper28 (bZIP28) and bZIP60, in ER stress resolution. Through a network modeling and experimental validation, we identified key genes downstream of the UPR bZIP-transcription factors (bZIP-TFs), and demonstrated their functional roles. Our analyses have set up a critical pipeline for functional gene discovery in ER stress resolution with broad applicability across multicellular eukaryotes.
59 BASIC BIOLOGICAL SCIENCES↗
Exploring the binding properties and activities of ancestral expansins
Bacterial expansins are non-lytic proteins capable of loosening cellulose networks, offering promising applications in agriculture, biotechnology, and material science. Their ability to disrupt noncovalent interactions in biopolymer matrices such as cellulose and chitin positions them as valuable tools for upgrading abundant natural materials. However, their industrial use remains limited due to their relatively low wall-loosening activity compared to plant expansins. To address this limitation, we applied Ancestral Sequence Resurrection (ASR) to reconstruct and characterize ancient variants of the Bacillus subtilis expansin BsEXLX1. ASR is a powerful evolutionary tool that enables the inference and synthesis of ancestral proteins, allowing researchers to explore functional traits that may have been lost over time. This approach not only provides insights into protein evolution but also facilitates the design of proteins with enhanced properties, such as improved substrate affinity or structural stability. In this study, we combined biochemical and biophysical assays to evaluate the activity and binding behavior of ancestral expansins. Our results reveal that ancestral variants exhibit increased cellulose affinity, reduced binding to acidic polysaccharides, and greater salt resistance. Furthermore, these traits enhance their wall-loosening activity and demonstrate the utility of ASR in engineering surface-active proteins for industrial applications, particularly in biomass processing and cellulose modification.
09 BIOMASS FUELS↗
Active and transfer learning with partially Bayesian neural networks for materials and chemicals
This work demonstrates the applicability of partially Bayesian neural networks (PBNNs) to active and transfer learning within materials science and chemistry domains, combining reliable uncertainty quantification (UQ) with NN flexibility.
36 MATERIALS SCIENCE↗
Physics-Informed Neural Network with Fourier Features for Radiation Transport in Heterogeneous Media
Not Available
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Space programs summary no. 37-32, volume vi for the period january 1, 1965 to february 28, 1965. space exploration programs and space sciences
Space exploration programs and space science - lunar and planetary-interplanetary programs, deep space network, and supporting activities
DEEP SPACE↗
Center for Aeronautics and Space Information Sciences
This report summarizes the research done during 1991/92 under the Center for Aeronautics and Space Information Science (CASIS) program. The topics covered are computer architecture, networking, and neural nets.
Flynn, Michael J.↗
Ultrastable reference frequency distribution utilizing a fiber optic link
The Frequency Standards Laboratory at the Jet Propulsion Laboratory (JPL) is responsible for the generation and distribution of ultra-stable reference frequency in NASA's Deep Space Network (DSN). Certain assemblies and components of the Radio Science and VLBI systems are located in the cones of tracking antennas hundreds of meters from the Frequency and Timing Subsystem's frequency standards. The very stringent requirements of these users challenge the performance of state-of-the-art frequency sources as well as the associated signal distribution system. The reference frequency distribution system described is designed around a low temperature coefficient of delay (TCD) optical fiber. On-site measurements of the fiber optic link alone indicate 100 MHz phase noise performance on the order of -120 dBc at 1 Hz from the carrier and Allan deviation on the order of parts in 10(exp 16) at 1000 seconds averaging time. The measured phase noise and stability of the link indicate that the performance characteristics of the hydrogen maser frequency standards are not degraded by the distribution system. Thus, optical fibers and electro-optic devices as distribution media appear to be a viable alternative to the classical coaxial cable distribution systems.
Calhoun, Malcolm↗
Data Analysis of a Space Experiment: Common Software Tackles Uncommon Task
Presented here are the software adaptations developed by laboratory scientists to process the space experiment data products from three experiments on two International Microgravity Laboratory Missions (IML-1 and IML-2). The challenge was to accommodate interacting with many types of hardware and software developed by both European Space Agency (ESA) and NASA aerospace contractors, where data formats were neither commercial nor familiar to scientists. Some of the data had been corrupted by bit shifting of byte boundaries. Least-significant/most-significant byte swapping also occurred as might be expected for the various hardware platforms involved. The data consisted of 20 GBytes per experiment of both numerical and image data. A significant percentage of the bytes were consumed in NASA formatting with extra layers of packetizing structure. It was provided in various pieces to the scientists on magnetic tapes, Syquest cartridges, DAT tapes, CD-ROMS, analog video tapes, and by network FIP. In this paper I will provide some science background and present the software processing used to make the data useful in the months after the missions.
Wilkinson, R. Allen↗
Phoning Home from Mars in 2025
It's spring at Martian Outpost 3, the year 2025. The Universe Cup's on later today, and next week little Suzie celebrates her fourth birthday. Fortunately, this football fan and parent will be able to participate in both of these activities, albeit at a slight time delay, due completely to the sophisticated, high-speed quasi-real-time multimedia/navigation MarsNet surrounding Mars and tying it to Earth. Capable of moving gigabits a second in either direction, the network supports not only the multiple manned and robotic science needs of teams and devices encircling Mars, but also the very real human need for communication.
Adams, J.↗
P2P Technology for High-Performance Computing: An Overview
The transition from cluster computing to peer-to-peer (P2P) high-performance computing has recently attracted the attention of the computer science community. It has been recognized that existing local networks and dedicated clusters of headless workstations can serve as inexpensive yet powerful virtual supercomputers. It has also been recognized that the vast number of lower-end computers connected to the Internet stay idle for as long as 90% of the time. The growing speed of Internet connections and the high availability of free CPU time encourage exploration of the possibility to use the whole Internet rather than local clusters as massively parallel yet almost freely available P2P supercomputer. As a part of a larger project on P2P high-performance computing, it has been my goal to compile an overview of the 2P2 paradigm. I have studied various P2P platforms and I have compiled systematic brief descriptions of their most important characteristics. I have also experimented and obtained hands-on experience with selected P2P platforms focusing on those that seem promising with respect to P2P high-performance computing. I have also compiled relevant literature and web references. I have prepared a draft technical report and I have summarized my findings in a poster paper.
Follen, Gregory J.↗
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↗
Environmental Effects on the Stability of Optical Fibers Used for Reference Frequency Distribution
The frequency Standards Laboratory at the Jet Propulsion Laboratory (JPL) is responsible for the generation and distribution of ultra-stabel reference frequencies in NASA's Deep Space Network (DSN).Certain assemblies and components of the Radio Science and VLBI systems are located in the cones of tracking antennas hundreds of meters from the Frequency and Timing Subsystem's frequency standards.
Environmental Effects↗