Design and iterative decoding of networks of many small codes
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iterative decoding code graphs code networks molec↗
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Systemic Microgravity Response: Utilizing GeneLab to Develop Hypotheses for Spaceflight Risks
Biological risks associated with microgravity is a major concern for space travel. Although determination of risk has been a focus for NASA research, data examining systemic (i.e., multi- or pan-tissue) responses to space flight are sparse. The overall goal of our work is to identify potential master regulators responsible for such responses to microgravity conditions. To do this we utilized the NASA GeneLab database which contains a wide array of omics experiments, including data from: 1) different flight conditions (space shuttle (STS) missions vs. International Space Station (ISS); 2) different tissues; and 3) different types of assays that measure epigenetic, transcriptional, and protein expression changes. We have performed meta-analysis identifying potential master regulators involved with systemic responses to microgravity. The analysis used 7 different murine and rat data sets, examining the following tissues: liver, kidney, adrenal gland, thymus, mammary gland, skin, and skeletal muscle (soleus, extensor digitorum longus, tibialis anterior, quadriceps, and gastrocnemius). Using a systems biology approach, we were able to determine that p53 and immune related pathways appear central to pan-tissue microgravity responses. Evidence for a universal response in the form of consistency of change across tissues in regulatory pathways was observed in both STS and ISS experiments with varying durations; while degree of change in expression of these master regulators varied across species and strain, some change in these master regulators was universally observed. Interestingly, certain skeletal muscle (gastrocnemius and soleus) show an overall down-regulation in these genes, while in other types (extensor digitorum longus, tibialis anterior and quadriceps) they are up-regulated, suggesting certain muscle tissues may be compensating for atrophy responses caused by microgravity. Studying these organtissue-specific perturbations in molecular signaling networks, we demonstrate the value of GeneLab in characterizing potential master regulators associated with biological risks for spaceflight.
Microgravity↗
Enabling Model Organism and Commercial Astronaut Data Access Through the NASA Open Science Data Repository
NASA’s Open Science Data Repository (OSDR) brings together omics data from NASA’s GeneLab project and non-omics data, including physiological, phenotypic, imaging, and behavioral data from NASA’s Ames Life Sciences Data Archive (ALSDA) collected from decades of space biology research, providing open and FAIR (findable, accessible, interoperable, and reusable) access of these precious data to scientists world-wide. This rich source of meticulously curated metadata and data from spaceflight and analog studies has been mined by the scientific community resulting in dozens of high impact scientific publications that reveals a complex network of molecular and physiological effects of spaceflight across living systems, from microbes to plants, to mammals. Understanding how these effects translate to the human condition is critical as we move deeper into the era of commercial space travel. However, the integration of data, specifically omics data, from astronauts is particularly challenging due to their sensitive nature. OSDR has risen to this challenge by developing a mechanism to control access to identifiable levels of omics data, such as raw sequence data, while enabling public access to processed, unidentifiable, data and associated metadata that will allow the scientific community to interrogate human astronaut data alongside data from model organisms to begin answering these critical questions. The 2021 SpaceX Inspiration4 (I4) mission collected a comprehensive atlas of biological measurements from four civilian astronauts, providing a wealth of data to characterize the effects of spaceflight on the human body. These data include both non-omics and omics assays such as direct RNA sequencing (RNA-seq), single nuclei ATAC-seq and RNA-seq, metagenomics, proteomics, and comprehensive metabolic and cytokine panels, all of which have been integrated into the OSDR system across no less than 9 studies. Each study has been carefully curated using community-backed OSDR standards for sample and assay level metadata ensuring these data are findable and accessible. In addition to hosting both raw and processed data from the principal investigator team for each assay type, the GeneLab team plans to re-process the I4 omics data using GeneLab’s standard processing pipelines. The GeneLab processed data outputs will allow for comparisons across studies on OSDR and enable visualization of these data through the OSDR data visualization platform thereby enabling data reusability and interoperability. Here we describe the robust privacy and security protocols implemented by OSDR to safeguard sensitive health data from astronauts while facilitating metadata and processed data sharing for research purposes. We further provide a road map for navigating the vast amount of data provided for each I4 study on the OSDR, including experimental design, associated experiments, payloads, and missions, data generation and analysis protocols, and associated scientific articles. Additionally, we illustrate how to interrogate the standardized metadata provided in the sample and assay tables as well as various means to download and access the data including programmatically through the GeneLab Open API (GLOpenAPI). The open access of datasets in NASA’s OSDR provides a unique opportunity for the scientific community, as well as citizen scientists and students, to continue using OSDR resources to further unlock profound insights into the consequences of space travel on the human body. Through implementation of security measures to protect sensitive human data, the OSDR seeks to strengthen the science exchange between the Biological and Physical Sciences Program and the Human Research Program, per recommendation 4-1 of the 2023-2032 Decadal Survey, and encourage further sharing and dissemination of astronaut data to provide the scientific community with the resources needed to lay the groundwork for developing targeted mitigation strategies to help withstand the rigors of long-duration spaceflight.
Amanda Marie Saravia-butler↗
Enabling Model Organism and Commercial Astronaut Data Access Through the NASA Open Science Data Repository
NASA’s Open Science Data Repository (OSDR) brings together omics data from NASA’s GeneLab project and non-omics data, including physiological, phenotypic, imaging, and behavioral data from NASA’s Ames Life Sciences Data Archive (ALSDA) collected from decades of space biology research, providing open and FAIR (findable, accessible, interoperable, and reusable) access of these precious data to scientists world-wide. This rich source of meticulously curated metadata and data from spaceflight and analog studies has been mined by the scientific community resulting in dozens of high impact scientific publications that reveals a complex network of molecular and physiological effects of spaceflight across living systems, from microbes to plants, to mammals. Understanding how these effects translate to the human condition is critical as we move deeper into the era of commercial space travel. However, the integration of data, specifically omics data, from astronauts is particularly challenging due to their sensitive nature. OSDR has risen to this challenge by developing a mechanism to control access to identifiable levels of omics data, such as raw sequence data, while enabling public access to processed, unidentifiable, data and associated metadata that will allow the scientific community to interrogate human astronaut data alongside data from model organisms to begin answering these critical questions. The 2021 SpaceX Inspiration4 (I4) mission collected a comprehensive atlas of biological measurements from four civilian astronauts, providing a wealth of data to characterize the effects of spaceflight on the human body. These data include both non-omics and omics assays such as direct RNA sequencing (RNA-seq), single nuclei ATAC-seq and RNA-seq, metagenomics, proteomics, and comprehensive metabolic and cytokine panels, all of which have been integrated into the OSDR system across no less than 9 studies. Each study has been carefully curated using community-backed OSDR standards for sample and assay level metadata ensuring these data are findable and accessible. In addition to hosting both raw and processed data from the principal investigator team for each assay type, the GeneLab team plans to re-process the I4 omics data using GeneLab’s standard processing pipelines. The GeneLab processed data outputs will allow for comparisons across studies on OSDR and enable visualization of these data through the OSDR data visualization platform thereby enabling data reusability and interoperability. Here we describe the robust privacy and security protocols implemented by OSDR to safeguard sensitive health data from astronauts while facilitating metadata and processed data sharing for research purposes. We further provide a road map for navigating the vast amount of data provided for each I4 study on the OSDR, including experimental design, associated experiments, payloads, and missions, data generation and analysis protocols, and associated scientific articles. Additionally, we illustrate how to interrogate the standardized metadata provided in the sample and assay tables as well as instructions for how to download and access the data. The I4 datasets described here re present the first ever comprehensive collection of commercial astronaut data.
Amanda M Saravia-Butler↗
A genomic regulatory network for development
Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.
Non-NASA Center↗
Network rupture and the flow of concentrated polymer solutions.
Network rupture hypothesis and molecular structure considerations used in obtaining constitutive equations for flow of polymer melts and solutions
Tanner, R. I.↗
Network rupture and the flow of concentrated polymer solutions.
Network rupture hypothesis and molecular structure considerations used in obtaining constitutive equations for flow of polymer melts and solutions
Tanner, R. I.↗
Machine Learning in Atomistic Simulations for Additive Manufacturing Alloys
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Additive manufacturing↗
Network Security via Biometric Recognition of Patterns of Gene Expression
Molecular biology provides the ability to implement forms of information and network security completely outside the bounds of legacy security protocols and algorithms. This paper addresses an approach which instantiates the power of gene expression for security. Molecular biology provides a rich source of gene expression and regulation mechanisms, which can be adopted to use in the information and electronic communication domains. Conventional security protocols are becoming increasingly vulnerable due to more intensive, highly capable attacks on the underlying mathematics of cryptography. Security protocols are being undermined by social engineering and substandard implementations by IT (Information Technology) organizations. Molecular biology can provide countermeasures to these weak points with the current security approaches. Future advances in instruments for analyzing assays will also enable this protocol to advance from one of cryptographic algorithms to an integrated system of cryptographic algorithms and real-time assays of gene expression products.
cybersecurity↗
Network Security via Biometric Recognition of Patterns of Gene Expression
Molecular biology provides the ability to implement forms of information and network security completely outside the bounds of legacy security protocols and algorithms. This paper addresses an approach which instantiates the power of gene expression for security. Molecular biology provides a rich source of gene expression and regulation mechanisms, which can be adopted to use in the information and electronic communication domains. Conventional security protocols are becoming increasingly vulnerable due to more intensive, highly capable attacks on the underlying mathematics of cryptography. Security protocols are being undermined by social engineering and substandard implementations by IT organizations. Molecular biology can provide countermeasures to these weak points with the current security approaches. Future advances in instruments for analyzing assays will also enable this protocol to advance from one of cryptographic algorithms to an integrated system of cryptographic algorithms and real-time expression and assay of gene expression products.
cybersecurity↗
Neural network error correction for solving coupled ordinary differential equations
A neural network is presented to learn errors generated by a numerical algorithm for solving coupled nonlinear differential equations. The method is based on using a neural network to correctly learn the error generated by, for example, Runge-Kutta on a model molecular dynamics (MD) problem. The neural network programs used in this study were developed by NASA. Comparisons are made for training the neural network using backpropagation and a new method which was found to converge with fewer iterations. The neural net programs, the MD model and the calculations are discussed.
Shelton, R. O.↗
Mechanical and swelling behaviour of well characterized polybutadiene networks
Endlinking of hydroxyl-terminated polybutadiene with the appropriate isocyanate has been used to prepare well characterized networks. Two networks have been studied with molecular weights of the prepolymers being 6100 and 2400 g/mole by g.p.c. Cylindrical specimens were prepared and the derivatives of the stored energy function with respect to the stretch invariants were determined by torque and normal force measurements in torsion. From these data the Valanis-Landel (1967) stored energy function derivatives w-prime(lambda) were determined for both networks. The stored energy function for the junction constraint model of Flory (1953, 1977, 1979, 1985) which is a special form of the Valanis-Landel function, has been fitted to that determined from the experiments. The contributions to the stored energy function from the phantom network and from the junction constraints respectively do not agree with predictions from the topologies of the networks. In spite of this, the form of w-prime(lambda) for the junction constraint model gives an excellent 'curve fit' to the data. Comparison is also made with equilibrium swelling.
Mckenna, Gregory B.↗
Bonding by Hydroxide-Catalyzed Hydration and Dehydration
A simple, inexpensive method for bonding solid objects exploits hydroxide-catalyzed hydration and dehydration to form silicate-like networks in thin surface and interfacial layers between the objects. The method can be practiced at room temperature or over a wide range of temperatures. The method was developed especially to enable the formation of precise, reliable bonds between precise optical components. The bonds thus formed exhibit the precision and transparency of bonds formed by the conventional optical-contact method and the strength and reliability of high-temperature frit bonds. The method also lends itself to numerous non-optical applications in which there are requirements for precise bonds and/or requirements for bonds, whether precise or imprecise, that can reliably withstand severe environmental conditions. Categories of such non-optical applications include forming composite materials, coating substrates, forming laminate structures, and preparing objects of defined geometry and composition. The method is applicable to materials that either (1) can form silicate-like networks in the sense that they have silicate-like molecular structures that are extensible into silicate-like networks or (2) can be chemically linked to silicate-like networks by means of hydroxide-catalyzed hydration and dehydration. When hydrated, a material of either type features surface hydroxyl (-OH) groups. In this method, a silicate-like network that bonds two substrates can be formed either by a bonding material alone or by the bonding material together with material from either or both of the substrates. Typically, an aqueous hydroxide bonding solution is dispensed and allowed to flow between the mating surfaces by capillary action. If the surface figures of the substrates do not match precisely, bonding could be improved by including a filling material in the bonding solution. Preferably, the filling material should include at least one ingredient that can be hydrated to have exposed hydroxyl groups and that can be chemically linked, by hydroxide catalysis, to a silicate-like network. The silicate-like network could be generated in situ from the filling material and/or substrate material, or could be originally present in the bonding material.
Gwo, Dz-Hung↗
Molecular Dynamics Investigation of the Structural and Mechanical Properties of Off-Stoichiometric Epoxy Resins
Molecular dynamic (MD) simulations were performed to compute the mechanical properties of off-stoichiometric epoxy resins as a function of hardener/epoxy mixture ratio (r). Properties were characterized in relation to their microscopic structures. Such resins have been used recently for adhesive-free bonding of large-scale composite structures using the co-curing-ply method. In this process, two partially precured composite panels with hardener-poor (HP) off-stoichiometric resins are coupled with ply(ies) of complementary hardener-rich (HR) formulations and then cured simultaneously. This bonding process has the potential to produce reliable and certifiable composite joints without the need for additional fasteners, which are often required for many conventional bonding methods because even small amounts of contamination can cause a weak bond. The reflow and mixing of the HP/HR resin in this bonding process result in a joint with no discernable interface that should not be susceptible to surface contamination. However, incomplete mixing of the two offset resins may result in chemical heterogeneity of the cured polymeric joint. Thus, different r values may be obtained across the joint. Classical MD simulations were performed to compute the Young’s modulus of polymers with different r values and correlate their properties to network structures. High stiffness was associated with molecular packing due to chemical crosslinking, leading to a single network structure. Moreover, the networks became denser as the ratio approached the stoichiometric value r = 1. Thus, the r = 1 systems were single clusters, with high stiffness, high molecular weight, and a high degree of crosslinking. Structural properties such as radius of gyration and mean square displacement were determined to investigate the variation in the stiffness with respect to r. This MD simulation study was validated with experimental measurements.
Chang Woon Jang↗
Development and Application of Tools to Characterize the Oxidative Degradation of AP/HTPB/Al Propellants in a Propellant Reliability Study
The oxidative thermal aging of a crosslinked hydroxyl-terminated polybutadiene (HTPB)/isophorone diisocyanate (IPDI) polyurethane rubber was studied at temperatures between 25 C and 125 C. Changes in tensile elongation, mechanical hardening, polymer network properties, density, O2 permeation, and molecular chain dynamics were investigated as a function of age. The techniques used include solvent swelling, detailed modulus profiling, and NMR relaxation measurements. The Arrhenius methodology, which normally assumes a linear extrapolation of high temperature aging data, is critically evaluated by using extensive data superposition and highly sensitive oxygen consumption measurements. Significant curvature in the Arrhenius diagram of these oxidation rates is observed to be similar to previous results found for other rubber materials that have been evaluated by this technique. Preliminary gel/network properties suggest that crosslinking is the dominant process at higher temperatures. The effect on the oxidation rate of the binder when other constituents found in propellants are present, such as ammonium perchlorate, plasticizer and aluminum powder, is presented.
Celina, Mathew↗
Interactions of Hydrazine and Blowby Gases
The interactions between hydrazine and blowby gases from pyrovalves was explored in this research project. Investigating the decomposition chemistry of hydrazine through detailed chemical kinetic modeling is a project started last summer while participating in the Summer Faculty Fellowship program. During the 1999-2000 academic year, the chemical kinetic mechanism for hydrazine decomposition developed while a SFF at NASA's White Sands Test Facility was further revised and validated against the limited experimental data in the literature. This mechanism was then used in assessing the effects of blowby gas species on hydrazine decomposition. The combustion products introduced into the fuel line by pyrovalve actuation consist primarily of hydrogen gas. Hydrogen is also a product of the decomposition of hydrazine. Additional gaseous chemical species are introduced into the fuel, as well as metals and metal salts that deposit onto the walls of the fuel line. The deposition process is undoubtedly very rapid, and exothermic. Therefore, the major focus of this summer's work was examining the effects of hydrogen presence on hydrazine decomposition, with some representative calculations including the remaining gaseous species found to exist in blowby gases. Since hydrogen is a product of hydrazine decomposition, all reactions necessary to evaluate its effect on hydrazine decomposition chemistry were in the original mechanism developed. However, the mechanism needed to be considerably expanded to include the reactions of the other gaseous blowby species with hydrazine, all the intermediate species formed in its decomposition, and each other. The expanded mechanism consists of 70 species interacting via a network of 452 reactions. Calculations with molecular hydrogen introduced into hydrazine gas in an inert bath gas indicate that H2 presence as an initial reactant in substantial amounts can dramatically impact the decomposition process for hydrazine. The other gaseous blowby species (CO, CO2, H2O, CH4, O2, and N2) were found to have little effect compared to the inclusion of hydrogen itself as an initial reagent. This result is undoubtedly due, in part, to the fact that the blowby gas used in these calculations consisted of 94.6% H2. A more rigorous examination of the behavior of the full detailed mechanism under a variety of conditions was not performed.
Meagher, Nancy E.↗
Ion Composition in Saturn's Plasma Environment: Early Results from the Cassini Plasma Spectrometer
Prior to Cassini s arrival at Saturn, most of what was known about the composition of the plasma in Saturn s environment was derived from limited measurements by Pioneer 11 and Voyager 1 and 2 in 1979-1981[1-3]. The measurements reported here were made by the Cassini Plasma Spectrometer (CAPS) [4] during the first two Cassini orbits, including the closest approach to Saturn and the rings during the tour, and a close flyby of Titan. The CAPS instrument resolves ion energy/charge from 1 V to 50 kV and ion mass/charge from 1 to approx.100 amu/e, and it measures electron energy from 1 eV to 28 keV. Initial composition measurements of Saturn s magnetosphere show that protons dominate outside approx.8 R(sub s), while inside this radius the plasma is dominated by a mix of water-derived ions and N(+). Over the A and B rings a plasma layer is observed composed of O2(+) and O(+) . The close passage near Titan shows a rich network of both positive and negative molecular ions. We report preliminary analysis of these and other composition findings.
Reisenfeld, D. B.↗
Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering
Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.
Dhaeseleer, Patrik↗