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DOE OSTI2017

N-Protonated Isomers and Coulombic Barriers to Dissociation of Doubly Protonated Ala{sub 8}Arg

Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules). To make progress, shortcuts are needed. Inspired by the popular mobile proton model, we have previously proposed a simplified theoretical model in which the gas-phase fragmentation pattern of protonated peptides reflects the relative stabilities of N-protonated isomers, thus avoiding the need for transition-state information. For singly protonated Ala{sub n} (n = 3–11), the resulting predictions were in qualitative agreement with the results from low-energy MS/MS experiments. Here, the comparison is extended to a model tryptic peptide, doubly protonated Ala{sub 8}Arg. This is of interest because doubly protonated tryptic peptides are the most important in proteomics. In comparison with experimental results, our model seriously overpredicts the degree of backbone fragmentation at N{sub 9}. We offer an improved model that corrects this deficiency. The principal change is to include Coulombic barriers, which hinder the separation of the product cations from each other. Coulombic barriers may be equally important in MS/MS of all multiply charged peptide ions. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Experimental Investigation of Mercury's Magma Ocean Viscosity: Implications for the Formation of Mercury's Cumulate Mantle, Its Subsequent Dynamic Evolution, and Crustal Petrogenesis

Mercury has a compositionally heterogeneous surface that was produced by different periods of igneous activity during Mercury’s history, perhaps suggesting heterogeneous mantle sources. Furthermore, understanding the structure of Mercury’s mantle formed during the planet’s magma ocean stage could help in developing a petrologic model for Mercury, and thus, its dynamic history in the context of crustal petrogenesis. We present results of falling sphere viscometry experiments on late stage Mercurian magma ocean analogue compositions. Owing to the presence of sulfur on the surface of Mercury, two compositions were tested, one with sulfur and one without. The liquids have viscosities of 0.6-3.9 (sulfur-bearing) and 0.6-10.9 Pa·s (sulfur-free), similar to an andesite at the tested experimental conditions (1.4-6.2 GPa, 1600-2000°C). We present new viscosity models that enable extrapolation beyond the experimental conditions and evaluate grain growth and the potential for crystal entrainment in a cooling, convecting magma ocean. We consider scenarios with and without a graphite flotation crust, which suggests two possible endmember outcomes for Mercury’s mantle structure. With a graphite flotation crust, crystallization of the mantle would be fractional with negatively buoyant minerals sinking to form a stratified cumulate pile according to the crystallization sequence. Without a flotation crust, crystals would largely remain entrained in the convecting liquid during solidification, producing a homogeneous mantle. In the context of these endmember models, the chemically heterogeneous surface could result from dynamical stirring or mixing of a mantle that was initially compositionally stratified, or from different extents of melting of a homogeneous mantle.

58 GEOSCIENCES↗

DOE OSTI2024

Interface Box for Dual Power Amplifier Modulators in Main Injector

The Proton Improvement Plan II (PIP-II) aims to enhance the current Fermilab particle accelerator complex to intensify and accelerate more beam. The project will power the beam as it heads from Illinois to the Deep Underground Neutrino Experiment (DUNE) in South Dakota by providing them with neutrinos. To intensify the beam, one of the PIP-II upgrades is to add a second power amplifier (PA) to the existing Main Injector cavities. In turn, this boosts the maximum output power to 400kW per station even though the PIP-II requirement is only 240kW. With more output power, more protons can be accelerated through the particle accelerator and in the case of the DUNE project, this is ideal given that the chance of a neutrino interacting with a proton or a neutron is one in ten billion. The power amplifier is added to the cavity and driven by the modulator. Within the modulator, the control unit receives input signals from the power supplies, moderates they are working properly, and controls the timing of the power up sequence. However, a challenge imposed by an additional PA was that the control unit could only read signals coming from the previous power supplies but not the additional second set. For this reason, the interface box was designed to facilitate the issue.

Ayala, Diana↗

NASA NTRS2012

Real-Time X-ray Radiography Diagnostics of Components in Solid Rocket Motors

Solid rocket motors (SRMs) typically use nozzle materials which are required to maintain their shape as well as insulate the underlying support structure during the motor operation. In addition, SRMs need internal insulation materials to protect the motor case from the harsh environment resulting from the combustion of solid propellant. In the nozzle, typical materials consist of high density graphite, carbon-carbon composites and carbon phenolic composites. Internal insulation of the motor cases is typically a composite material with carbon, asbestos, Kevlar, or silica fibers in an ablative matrix such as EPDM or NBR. For both nozzle and internal insulation materials, the charring process occurs when the hot combustion products heat the material intensely. The pyrolysis of the matrix material takes away a portion of the thermal energy near the wall surface and leaves behind a char layer. The fiber reinforcement retains the porous char layer which provides continued thermal protection from the hot combustion products. It is of great interest to characterize both the total erosion rates of the material and the char layer thickness. By better understanding of the erosion process for a particular ablative material in a specific flow environment, the required insulation material thickness can be properly selected. The recession rates of internal insulation and nozzle materials of SRMs are typically determined by testing in some sort of simulated environment; either arc-jet testing, flame torch testing, or subscale SRMs of different size. Material recession rates are deduced by comparison of pre- and post-test measurements and then averaging over the duration of the test. However, these averaging techniques cannot be used to determine the instantaneous recession rates of the material. Knowledge of the variation in recession rates in response to the instantaneous flow conditions during the motor operation is of great importance. For example, in many SRM configurations the recession of the solid propellant grain can drastically alter the flow-field and effect the recession of internal insulation and nozzle materials. Simultaneous measurement of the overall erosion rate, the development of the char layer, and the recession of the char-virgin interface during the motor operation can be rather difficult. While invasive techniques have been used with limited success, they have serious drawbacks. Break wires or make wire sensors can be installed into a sufficient number of locations in the charring material from which a time history of the charring surface can be deduced. These sensors fundamentally alter the local structure of the material in which they are imbedded. Also, the location of these sensors within the material is not known precisely without the use of an X-ray. To determine instantaneous recession rates, real-time X-ray radiography (X-ray RTR) has been utilized in several SRM experiments at PSU. The X-ray RTR system discussed in this paper consists of an X-ray source, X-ray image intensifier, and CCD camera connected to a capture computer. The system has been used to examine the ablation process of internal insulation as well as nozzle material erosion in a subscale SRM. The X-ray source is rated to 320 kV at 10 mA and has both a large (5.5 mm) and small (3.0 mm) focal spot. The lead-lined cesium iodide X-ray image intensifier produces an image which is captured by a CCD camera with a 1,000 x 1,000 pixel resolution. To produce accurate imagery of the object of interest, the alignment of the X-ray source to the X-ray image intensifier is crucial. The image sequences captured during the operation of an SRM are then processed to enhance the quality of the images. This procedure allows for computer software to extract data on the total erosion rate and the char layer thickness. Figure 1 Error! Reference source not found.shows a sequence of images captured during the operation the subscale SRM with the X-ray RTR system. The X-rayTR system, alignment procedure, uncertainty determination, and image analysis process will be discussed in detail in the full manuscript.

Cortopassi, A. C.↗

NASA NTRS2017

Pressure-Fed LOX/LCH4 Reaction Control System for Spacecraft: Transient Modeling and Thermal Vacuum Hotfire Test Results

An integrated cryogenic liquid oxygen, liquid methane (LOX/LCH4) reaction control system (RCS) was tested at NASA Glenn Research Center's Plum Brook Station in the Spacecraft Propulsion Research Facility (B-2) under vacuum and thermal vacuum conditions. The RCS is a subsystem of the Integrated Cryogenic Propulsion Test Article (ICPTA), a pressure-fed LOX/LCH4 propulsion system composed of a single 2,800 lbf main engine, two 28 lbf RCS engines, and two 7 lbf RCS engines. Propellants are stored in four 48 inch diameter 5083 aluminum tanks that feed both the main engine and RCS engines in parallel. Helium stored cryogenically in a composite overwrapped pressure vessel (COPV) flows through a heat exchanger on the main engine before being used to pressurize the propellant tanks to a design operating pressure of 325 psi. The ICPTA is capable of simultaneous main engine and RCS operation. The RCS engines utilize a coil-on-plug (COP) ignition system designed for operation in a vacuum environment, eliminating corona discharge issues associated with a high voltage lead. There are two RCS pods on the ICPTA, with two engines on each pod. One of these two engines is a heritage flight engine from Project Morpheus. Its sea level nozzle was removed and replaced by an 85:1 nozzle machined using Inconel 718, resulting in a maximum thrust of 28 lbf under altitude conditions. The other engine is a scaled down version of the 28 lbf engine, designed to match the core and overall mixture ratios as well as other injector characteristics. This engine can produce a maximum thrust of 7 lbf with an 85:1 nozzle that was additively manufactured using Inconel 718. Both engines are film-cooled and capable of limited duration gas-gas and gas-liquid operation, as well as steady-state liquid-liquid operation. Each pod contains one of each version, such that two engines of the same thrust level can be fired as a couple on opposite pods. The RCS feed system is composed of symmetrical 3/8 inch lines that tap off of the main propellant manifold to send LOX and LCH4 outboard to the RCS pods. A Thermodynamic Vent System (TVS) is used to condition propellants at each pod by venting through an orifice and then routing the cold expansion products back through tubing that is welded along a large portion of the main RCS feed lines. Prior to final installation on the ICPTA, the RCS engines were tested in a small vacuum chamber at the Johnson Space Center (JSC) Energy Systems Test Area (ESTA) to verify functionality of the new COP ignition system and check out operation of the vacuum nozzles. After engine-level testing, the RCS engines were installed on the vehicle and a series of integrated hot-fire tests were performed at JSC consisting of various pulsing and steady-state firings as well as integrated main engine/RCS operation. The ICPTA was then integrated into the Plum Brook B-2 facility for vacuum and thermal/vacuum testing. Testing in the B-2 facility was composed of multiple thermal and pressure environments. The first set of tests were performed under ambient temperature and altitude pressure conditions. These tests consisted of a range of minimum impulse bit (MIB) pulsing sequences with low duty cycle, analogous to a coast phase in which the RCS is primarily used for station keeping. The primary goal of this sequence is to understand how propellant conditions were effected without an active TVS. In this scenario, consistent gas-gas operation is desirable since it results in a smaller MIB and more efficient propellant consumption. Multiple skin thermocouples are mounted on the feedlines, in addition to a submerged thermocouple on each commodity, in order to gather thermal data on the system. Higher duty cycle pulsing tests were then performed, analogous to an ascent or landing mission phase. The primary goal of this sequence was to examine how well the engines self-conditioned without active TVS when starting from a quiescent state. The TVS was then activated during some tests to demonstrate the capability to quickly condition the engines for higher pulsing demand scenarios. A thermocouple at the TVS outlet allows for the calculation of energy absorbed by the vented propellant. Lastly, tests with longer pulses and multiple engines firing either in sequence or simultaneously were run in order to gather transient system response data on waterhammer. Six total high-speed pressure transducers are installed on the RCS system, one sensor at the end of each propellant manifold line on the pods, and one at the tap-off location for each commodity. This will allow for the accurate characterization of waterhammer in the system under various propellant conditions and firing sequences. Other instrumentation for this test series includes nozzle throat thermocouples, chamber pressure measurement, heat soakback measurement, and tank wall plume impingement temperature measurement. The next set of tests were performed to demonstrate simultaneous main engine and RCS operation. Data from this test will be used to examine if there is any change to nominal operation of the RCS as a result of feed system interaction or other phenomenon. Some of these tests began under high vacuum conditions (target ambient pressure less than 1x10(exp -3) torr) and others began at altitude conditions. The last set of tests were performed with the B-2 cold wall active. Under these tests, many of the same low duty cycle MIB tests were repeated in order to characterize how propellant conditions changed with the lower heat leak. In this scenario the RCS manifold experiences much less heat leak, resulting in a change to how well the engines self-condition. As a result, an increase in maximum waterhammer pressures and a change in natural frequency of the system was expected due to higher density propellants. The lower heat leak should also result in a change to the MIB pulse profile, and data will be examined to understand how MIB repeatability is affected in the different operating environments. Parallel to the test efforts, a set of transient model development efforts were made to predict RCS performance. The primary effort was aimed at producing a SINDA/FLUINT model to predict propellant conditioning up to the engine inlet as a function of different environmental and operating parameters, with the goal of predicting chamber pressure, TVS performance, and propellant consumption over time. Preliminary results for this effort will be presented in comparison with test data. Additional modeling efforts were made using SINDA/FLUINT to predict waterhammer in the system since the software is capable of handling multiphase transient fluid dynamics. These results will be compared with the high-speed pressure transducer test data for validation purposes.

Atwell, Matthew J.↗

NASA NTRSDate not supplied

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields in the last two decades, in part thanks to an increasing culture of open data sharing and reuse. Due to its capability for identifying complex relationships and patterns, AI/ML methodology is particularly well suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are many key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Even with the positive culture of Open Science and data sharing, inexperienced researchers working quickly without proper checks can produce models that perform poorly outside of the immediate training dataset. Lessons learned from biological AI/ML research indicate that Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Andrew Casaletto↗

DOE OSTI2024

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Data-Driven Modeling and Correction of Vehicle Dynamics

We develop a data-driven framework for learning and correcting nonautonomous vehicle dynamics. Physics-based vehicle models are often simplified for tractability and therefore exhibit inherent model-form uncertainty, motivating the need for data-driven correction. Moreover, nonautonomous dynamics are governed by time-dependent control inputs, which pose challenges in learning predictive models directly from temporal snapshot data. To address these, we reformulate the vehicle dynamics via a local parameterization of the time-dependent inputs, yielding a modified system composed ofa sequence of local parametric dynamical systems. Here, we approximate these parametric systems using two complementary approaches. First, we employ the dimension reduction and interpolation in parameter space (DRIPS) methodology to construct efficient linear surrogate models, equipped with lifted observable spaces and manifold-based operator interpolation. This enables data-efficient learning of vehicle models whose dynamics admit accurate linear representations in the lifted spaces. Second, for more strongly nonlinear systems, we employ flow map learning (FML), a deep neural network (DNN) approach that approximates the parametric evolution map without requiring special treatment of nonlinearities. We further extend FML with a transfer-learning-based model correction procedure, enabling the correction of misspecified prior models using only a sparse set of high-fidelity or experimental measurements, without assuming a prescribed form for the correction term. Through a suite of numerical experiments on unicycle, simplified bicycle, and slip-based bicycle models, we demonstrate that DRIPS offers robust and highly data-efficient learning of nonautonomous vehicle dynamics, while FML provides expressive nonlinear modeling and effective correction of model-form errors under severe data scarcity.

data-driven modeling↗

NASA NTRS2000

Plant chimeric Ca2+/Calmodulin-dependent protein kinase. Role of the neural visinin-like domain in regulating autophosphorylation and calmodulin affinity

Chimeric Ca(2+)/calmodulin-dependent protein kinase (CCaMK) is characterized by a serine-threonine kinase domain, an autoinhibitory domain, a calmodulin-binding domain and a neural visinin-like domain with three EF-hands. The neural visinin-like Ca(2+)-binding domain at the C-terminal end of the CaM-binding domain makes CCaMK unique among all the known calmodulin-dependent kinases. Biological functions of the plant visinin-like proteins or visinin-like domains in plant proteins are not well known. Using EF-hand deletions in the visinin-like domain, we found that the visinin-like domain regulated Ca(2+)-stimulated autophosphorylation of CCaMK. To investigate the effects of Ca(2+)-stimulated autophosphorylation on the interaction with calmodulin, the equilibrium binding constants of CCaMK were measured by fluorescence emission anisotropy using dansylated calmodulin. Binding was 8-fold tighter after Ca(2+)-stimulated autophosphorylation. This shift in affinity did not occur in CCaMK deletion mutants lacking Ca(2+)-stimulated autophosphorylation. A variable calmodulin affinity regulated by Ca(2+)-stimulated autophosphorylation mediated through the visinin-like domain is a new regulatory mechanism for CCaMK activation and calmodulin-dependent protein kinases. Our experiments demonstrate the existence of two functional molecular switches in a protein kinase regulating the kinase activity, namely a visinin-like domain acting as a Ca(2+)-triggered switch and a CaM-binding domain acting as an autophosphorylation-triggered molecular switch.

NASA Discipline Plant Biology↗

DOE OSTI2021

Thermal Chemistry of Nickel Diketonate Atomic Layer Deposition (ALD) Precursors on Tantalum and Silicon Oxide Surfaces

The mechanism of the thermal conversion of both bis(2,2,6,6-tetramethyl-3,5-heptanedionato)nickel(II) (Ni(TMHD) 2 ) and the protonated ligand (TMHD-H) adsorbed on TaO x and SiO 2 /TaO x surfaces was characterized under ultrahigh vacuum (UHV) by a combination of temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS) experiments. In this work, A stepwise decomposition was observed with Ni(TMHD) 2 encompassing at least four different stages: (1) a ligand loss, to release TMHD-H; (2) a surprising ligand fractioning via the scission of an inner C–C bond within the central β-diketonate moiety to produce an aldehyde (pivaldehyde) and a ketone (pinacolone); (3) further ligand splitting following a more extensive cracking to yield an olefin (from dehydrogenation of the terminal tert-butyl group), carbon monoxide, and adsorbed methylene groups; and finally, (4) the loss of one oxygen atom from the remaining ligands to produce the corresponding enone. As these conversions take place, the Ni ion is reduced, first to a partially oxidized intermediate, as the first ligand is removed, and then to its metallic state as the remaining organic fragments migrate to the surface. A similar sequence was seen on both surfaces, but with the transitions taking place at higher temperatures on SiO 2 . The implications of these results to the surface chemistry of other ALD precursors and to the design of ALD processes are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRSDate not supplied

GL4U: Bioinformatics training for students and educators using space omics data

NASA’s GeneLab project provides researchers open access to space-relevant experiment multi-omics data that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – training of trainers), in which participants learn to analyze GeneLab’s space-relevant omics data. The GL4U direct training pilot program was conducted in June 2021. During the pilot, students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrated the capacity of GL4U for training young scientists and encouraging data re-use. During the educator pilot, scheduled for June 2022, educators will receive materials and training to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative.

Amanda Marie Saravia-butler↗

NASA NTRSDate not supplied

GL4U: Bioinformatics Training for Students and Educators Using Space Omics Data

Amanda Marie Saravia-butler↗

NASA NTRS2006

Built But Not Used, Needed But Not Built: Ground System Guidance Based On Cassini-Huygens Experience

These reflections share insight gleaned from Cassini-Huygens experience in supporting uplink operations tasks with software. Of particular interest are developed applications that were not widely adopted and tasks for which the appropriate application was not planned. After several years of operations, tasks are better understood providing a clearer picture of the mapping of requirements to applications. The impact on system design of the changing user profile due to distributed operations and greater participation of scientists in operations is also explored. Suggestions are made for improving the architecture, requirements, and design of future systems for uplink operations.

telecommunications↗

NASA NTRS2006

Built But Not Used, Needed But Not Built: Ground System Guidance Based On Cassini-Huygens Experience

telecommunications↗

NASA NTRS2026

Controlled Parametric Forcing During Directional Solidification of a Bulk Organic Alloy Under Microgravity

The response of dendritic microstructures to step-like pulling velocity conditions is investigated using microgravity directional solidification experiments conducted on DECLIC-DSI combined with phase-field simulations. Under a constant pulling velocity of 1.5 µm/s, the evolution toward steady-state growth is characterized in terms of primary spacing, dendrite drift, and tip dynamics. For the first time, side-view observations enabled direct measurement of tip radius and sidebranching frequency. When step-like oscillations of the pulling velocity are imposed, the dendritic array exhibits a strongly period-dependent response: short periods lead to rapid tip adaptation, whereas longer periods induce a phase lag between tip position and morphology, resulting in progressive tip flattening and, above a critical period, interface destabilization and dendrite splitting. Quantitative phase-field simulations, including a realistic thermal field and stochastic noise, reproduce the experimental observations and provide insight into the governing mechanisms, highlighting the role of characteristic relaxation times, sequence-dependent effects, and the irreversible reorganization of the microstructure following splitting.

Microgravity↗

DOE OSTI2023

A General Framework for Progressive Data Compression and Retrieval

In scientific simulations, observations, and experiments, the transfer of data to and from disk and across networks has become a major bottleneck for data analysis and visualization. Compression techniques have been employed to tackle this challenge, but traditional lossy methods often demand conservative error tolerances to meet the numerical accuracy requirements of both anticipated and unknown data analysis tasks. Progressive data compression and retrieval has emerged as a promising solution, where each analysis task dictates its own accuracy needs. However, few analysis algorithms inherently support progressive data processing, and adapting compression techniques, file formats, client/server frameworks, and APIs to support progressivity can be challenging. Here, this paper presents a framework that enables progressive-precision data queries for any data compressor or numerical representation. Our strategy hinges on a multi-component representation that successively reduces the error between the original and compressed field, allowing each field in the progressive sequence to be expressed as a partial sum of components. We have implemented this approach with four established scientific data compressors and assessed its effectiveness using real-world data sets from the SDRBench collection. The results show that our framework competes in accuracy with the standalone compressors it is based upon. Additionally, (de)compression time is proportional to the number of components requested by the user. Finally, our framework allows for fully lossless compression using lossy compressors when a sufficient number of components are employed.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data

High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

RNA-seq↗