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Tracking Community Building in Open Science

Open Science is enabled by a vibrant community of researchers who regularly engage with the data, from its production to its organization, curation, archiving, dissemination, analysis, and publication. This presentation will examine community building in open science. The NASA Open Science Data Repository (OSDR) makes data available to the public following the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles. OSDR takes open science further with the OS Analysis Working Groups (AWGs) that facilitate community development and promotion. The primary activity of each AWG is to establish and validate analytical processes to generate higher-order data from data housed in OSDR. There are a number of these groups on various topics, including the Animal AWG, Plant AWG, Microbial AWG, Multi-Omics AWG, AI/ML AWG, and the Ames Life Sciences Data Archive (ALSDA) AWG. The international volunteers participating in these AWGs come from academia, citizen science initiatives, industry, and government. They include researchers, principal investigators, professors, trained hobbyists, and students from various domains and disciplines. Anyone may request to join the AWGs, and membership requests are vetted monthly by the group organizers before granting admission. Core to membership is demonstrated expertise through records of training, integrity, work in the professed domain(s), and good community standing. Regular virtual meetings are held for each AWG, with a varying cadence depending on the group's needs and goals. AWG communities share their expertise in research including cutting edge tools, software, frameworks, data formats, and libraries accelerating research collectively. This collaborative approach helps community members cross technology gaps and identify emerging challenges. These diverse communities encompass a wide range of individuals hailing from various sectors within the Science Mission Directorate and beyond. They serve as a means to promote and enhance transparency, accessibility, and inclusion. An annual AWG Symposium brings contributors together in person. Participation in AWGs can be synchronous or asynchronous, with some groups performing most of their work in off hours. Participants gain valuable skills and connections that allow them to add value to their communities and new organizations that they join, resulting in an expanded return on investment for the space life science community. Open science is increasingly a federal mandate and initiatives like NASA's Transform to Open Science and instruments like the Decadal Survey of Biological and Physical Sciences in Space demonstrate the need to carefully consider best practices in this domain. Here, we present greater detail about the makeup and participation metrics of the various AWGs affiliated with OSDR and details of successful peer-reviewed publication campaigns.

Christina M Johnson↗
NASA NTRS2003

Evaluating Corn (Zea Mays L.) N Variability Via Remote Sensed Data

Transformations and losses of nitrogen (N) throughout the growing season can be costly. Methods in place to improve N management and facilitate split N applications during the growing season can be time consuming and logistically difficult. Remote sensing (RS) may be a method to rapidly assess temporal changes in crop N status and promote more efficient N management. This study was designed to evaluate the ability of three different RS platforms to predict N variability in corn (Zea mays L.) leaves during vegetative and early reproductive growth stages. Plots (15 x 15m) were established in the Coastal Plain (CP) and Appalachian Plateau (AP) physiographic regions each spring from 2000 to 2002 in a completely randomized design. Treatments consisted of four N rates (0, 56, 112, and 168 kg N/ha) applied as ammonium nitrate (NH4N03) replicated four time. Spectral measurements were acquired via spectroradiometer (lambda = 350 - 1050 nm), Airborne Terrestrial Applications Sensor (ATLAS) (lambda = 400 - 12,500 nm), and the IKONOS satellite (lambda = 450 - 900 nm). Spectroradiometer data were collected on a biweekly basis from V4 through R1. Due to the nature of - satellite and aircraft acquisitions, these data were acquired per availability. Chlorophyll meter (SPAD) and tissue N were collected as ancillary data along with each RS acquisition. Results showed vegetation indices derived from hand-held spectroradiometer measurements as early as V6-V8 were linearly related to yield and tissue N content. ATLAS data was correlated with tissue N at the AP site during the V6 stage (r2 = 0.66), but no significant relationships were observed at the CP site. No significant relationships were observed between plant N and IKONOS imagery. Using a combination of the greenness vegetation index (GNDVI) and the normalized difference vegetation index (NDVI), RS data acquired via ATLAS and the spectroradiometer could be used to evaluate tissue N variability and estimate corn yield variability under ideal growing conditions.

Sullivan, D. G.↗
NASA NTRS2003

Command Interface ASIC - Analog Interface ASIC Chip Set

A command interface application-specific integrated circuit (ASIC) and an analog interface ASIC have been developed as a chip set for remote actuation and monitoring of a collection of switches, which can be used to control generic loads, pyrotechnic devices, and valves in a high-radiation environment. The command interface ASIC (CIA) can be used alone or in combination with the analog interface ASIC (AIA). Designed primarily for incorporation into spacecraft control systems, they are also suitable for use in high-radiation terrestrial environments (e.g., in nuclear power plants and facilities that process radioactive materials). The primary role of the CIA within a spacecraft or other power system is to provide a reconfigurable means of regulating the power bus, actuating all valves, firing all pyrotechnic devices, and controlling the switching of power to all switchable loads. The CIA is a mixed-signal (analog and digital) ASIC that includes an embedded microcontroller with supporting fault-tolerant switch control and monitoring circuitry that is capable of connecting to a redundant set of interintegrated circuit (I(sup 2)C) buses. Commands and telemetry requests are communicated to the CIA. Adherence to the I(sup 2)C bus standard helps to reduce development costs by facilitating the use of previously developed, commercially available components. The AIA is a mixed-signal ASIC that includes the analog circuitry needed to connect the CIA to a custom higher powered version of the I(sup 2)C bus. The higher-powered version is designed to enable operation with bus cables longer than those contemplated in the I(sup 2)C standard. If there are multiple higher-power I(sup 2)C-like buses, then there must an AIA between the CIA and each such bus. The AIA includes two identical interface blocks: one for the side-A I(sup 2)C clock and data buses and the other for the side B buses. All the AIAs on each side are powered from a common power converter module (PCM). Sides A and B of the I(sup 2)C buses are electrically isolated from each other (see figure). They are also isolated from the CIA by use of transformer coupling of signals between the AIA blocks and the CIA.

Ruiz, Baldes↗
NASA NTRS1988

Assessment of an apparent relationship between availability of soluble carbohydrates and reduced nitrogen during floral initiation in tobacco

Daily relative accumulation rate of soluble carbohydrates (RARS) and reduced nitrogen (RARN) in the shoot, as estimates of source strength, were compared with daily relative growth rates (RGR) of the shoot, as an estimate of sink demand, during floral transformation in apical meristems of tobacco (Nicotiana tabacum 'NC 2326') grown at day/night temperatures of 18/14, 22/18, 26/22, 30/26, and 34/30 C. Source strength was assumed to exceed sink demand for either carbohydrates or nitrogen when the ratio of RARS/RGR or RARN/RGR was greater than unity, and sink demand was assumed to exceed source strength when the ratio was less than unity. Time of floral initiation, which was delayed up to 21 days with increases in temperature over the experimental range, was associated with intervals in which source strength of either carbohydrate or nitrogen exceeded sink demand, while sink demand for the other exceeded source strength. Floral initiation was not observed during intervals in which source strengths of both carbohydrates and nitrogen were greater than or less than sink demand. These results indicate that floral initiation is responsive to an imbalance in the relative availabilities of carbohydrate and nitrogen.

NASA Discipline Life Support Systems↗
NASA NTRS1995

Vegetation species composition and canopy architecture information expressed in leaf water absorption measured in the 1000 nm and 2200 spectral region by an imaging spectrometer

Plant species composition and plant architectural attributes are critical parameters required for the measuring, monitoring, and modeling of terrestrial ecosystems. Remote sensing is commonly cited as an important tool for deriving vegetation properties at an appropriate scale for ecosystem studies, ranging from local to regional and even synoptic scales. Classical approaches rely on vegetation indices such as the normalized difference vegetation index (NDVI) to estimate biophysical parameters such as leaf area index or intercepted photosynthetically active radiation (IPAR). Another approach is to apply a variety of classification schemes to map vegetation and thus extrapolate fine-scale information about specific sites to larger areas of similar composition. Imaging spectrometry provides additional information that is not obtainable through broad-band sensors and that may provide improved inputs both to direct biophysical estimates as well as classification schemes. Some of this capability has been demonstrated through improved discrimination of vegetation, estimates of canopy biochemistry, and liquid water estimates from vegetation. We investigate further the potential of leaf water absorption estimated from Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data as a means for discriminating vegetation types and deriving canopy architectural information. We expand our analysis to incorporate liquid water estimates from two spectral regions, the 1000-nm region and the 2200-nm region. The study was conducted in the vicinity of Jasper Ridge, California, which is located on the San Francisco peninsula to the west of the Stanford University campus. AVIRIS data were acquired over Jasper Ridge, CA, on June 2, 1992, at 19:31 UTC. Spectra from three sites in this image were analyzed. These data are from an area of healthy grass, oak woodland, and redwood forest, respectively. For these analyses, the AVIRIS-measured upwelling radiance spectra for the entire Jasper Ridge scene were transformed to apparent surface reflectance using a radiative transfer code-based inversion algorithm.

Green, Robert O.↗
NASA NTRS2009

Simulation of TGF-Beta Activation by Low-Dose HZE Radiation in a Cell Culture

High charge (Z) and energy (E) (HZE) nuclei comprised in the galactic cosmic rays are main contributors to space radiation risk. They induce many lesions in living matter such as non-specific oxidative damage and the double-strand breaks (DSBs), which are considered key precursors of early and late effects of radiation. There is increasing evidence that cells respond collectively rather than individually to radiation, suggesting the importance of cell signaling1. The transforming growth factor (TGF ) is a signaling peptide that is expressed in nearly all cell type and regulates a large array of cellular processes2. TGF have been shown to mediate cellular response to DNA damage3 and to induce apoptosis in non-irradiated cells cocultured with irradiated cells4. TFG molecules are secreted by cells in an inactive complex known as the latency-associated peptide (LAP). TGF is released from the LAP by a conformational change triggered by proteases, thrombospondin-1, integrins, acidic conditions and .OH radical5. TGF then binds to cells receptors and activates a cascade of events mediated by Smad proteins6, which might interfere with the repair of DNA. Meanwhile, increasingly sophisticated Brownian Dynamics (BD) algorithms have appeared recently in the literature7 and can be applied to study the interaction of molecules with receptors. These BD computer models have contributed to the elucidation of signal transduction, ligand accumulation and autocrine loops in the epidermal growth factor (EGF) and its receptor (EFGR) system8. To investigate the possible roles of TGF in an irradiated cell culture, our Monte-Carlo simulation codes of the radiation track structure9 will be used to calculate the activation of TFG triggered by .OH produced by low doses of HZE ions. The TGF molecules will then be followed by a BD algorithm in a medium representative of a cell culture to estimate the number of activated receptors.

Plante, Ianik↗
NASA NTRS1995

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

Non-NASA Center↗
NASA NTRS1999

Nutrient-substituted hydroxyapatites: synthesis and characterization

Incorporation of Mg, S, and plant-essential micronutrients into the structure of synthetic hydroxyapatite (HA) may be advantageous for closed-loop systems, such as will be required on Lunar and Martian outposts, because these apatites can be used as slow-release fertilizers. Our objective was to synthesize HA with Ca, P, Mg, S, Fe, Cu, Mn, Zn, Mo, B, and Cl incorporated into the structure, i.e., nutrient-substituted apatites. Hydroxyapatite, carbonate hydroxyapatite (CHA), nutrient-substituted hydroxyapatite (NHA), and nutrient-substituted carbonate hydroxyapatite (NCHA) were synthesized by precipitating from solution. Chemical and mineralogical analysis of precipitated samples indicated a considerable fraction of the added cations were incorporated into HA, without mineral impurities. Particle size of the HA was in the 1 to 40 nm range, and decreased with increased substitution of nutrient elements. The particle shape of HA was elongated in the c-direction in unsubstituted HA and NHA but more spherical in CHA and NCHA. The substitution of cations and anions in the HA structure was confirmed by the decrease of the d[002] spacing of HA with substitution of ions with an ionic radius less than that of Ca or P. The DTPA-extractable Cu ranged from 8 to 8429 mg kg-1, Zn ranged from 57 to 1279 mg kg-1, Fe from 211 to 2573 mg kg-1, and Mn from 190 to 1719 mg kg-1, depending on the substitution level of each element in HA. Nutrient-substituted HA has the potential to be used as a slow-release fertilizer to supply micronutrients, S, and Mg in addition to Ca and P.

NASA Discipline Life Support Systems↗