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DOE OSTI2022

CHIQUITA1 maintains the temporal transition between proliferation and differentiation in Arabidopsis thaliana

ABSTRACT Body size varies widely among species, populations and individuals, depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining kinematic and cell lineage-tracking studies, we found that the number of actively dividing cells in chiquita1-1 plants decreases prematurely compared with wild-type plants, suggesting CHIQ1 maintains the proliferative capacity in dividing cells and ensures that cells divide a specific number of times. CHIQ1 belongs to a plant-specific gene family of unknown molecular function and genetically interacts with three close members of its family to control the timing of proliferation exit. Our work reveals the interdependency between cellular and organ-level processes underlying final organ size determination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Metrology of Time-Domain Soft X-Ray Attosecond Pulses and Reevaluation of Pulse Durations of Three Recent Experiments

Attosecond pulses in the soft x-ray (SXR) to water-window energy region offer the tools for creating and studying target-specific localized inner-shell electrons or holes in materials, enabling monitoring or controlling charge and energy flows in a dynamic system on attosecond timescales. Recently, a number of laboratories have reported generation of continuum harmonics in the hundred-electron-volt to kilovolt region with few-cycle long-wavelength mid-infrared lasers. These harmonics have the bandwidth to support pulses with durations of a few to a few-ten attoseconds. But harmonics generated in a gas medium have attochirps that cannot be fully compensated by materials over a broad spectral range; thus, realistically what are the typical shortest attosecond pulses that one can generate? To answer this question, it is essential that the temporal attosecond pulses be accurately characterized. By reanalyzing the soft x-ray attosecond metrology reported in three recent experiments using a newly developed broadband phase retrieval algorithm, we demonstrate here that the generated attosecond pulses in the first two papers have durations of about 60 as, longer than what they have reported. Similarly, the duration from the third experiment is retrieved to be about half of the 322-as upper limit cited in that work. We also introduce the autocorrelation (AC) of the streaking spectrogram. By comparing the ACs from the experiments and from the retrieved SXR pulses, the accuracy of the retrieved results can be directly visualized. Our retrieval method is fast and accurate, and it shall provide a powerful tool for the metrology of the emerging few-ten-attosecond pulses.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

The role of oxygen in stimulating methane production in wetlands

Methane (CH 4 ), a potent greenhouse gas, is the second most important greenhouse gas contributor to climate change after carbon dioxide (CO 2 ). The biological emissions of CH 4 from wetlands are a major uncertainty in CH 4 budgets. Microbial methanogenesis by Archaea is an anaerobic process accounting for most biological CH 4 production in nature, yet recent observations indicate that large emissions can originate from oxygenated or frequently oxygenated wetland soil layers. To determine how oxygen (O 2 ) can stimulate CH 4 emissions, we used incubations of Sphagnum peat to demonstrate that the temporary exposure of peat to O 2 can increase CH 4 yields up to 2000-fold during subsequent anoxic conditions relative to peat without O 2 exposure. Geochemical (including ion cyclotron resonance mass spectrometry, X-ray absorbance spectroscopy) and microbiome (16S rDNA amplicons, metagenomics) analyses of peat showed that higher CH 4 yields of redox-oscillated peat were due to functional shifts in the peat microbiome arising during redox oscillation that enhanced peat carbon (C) degradation. Novosphingobium species with O 2 -dependent aromatic oxygenase genes increased greatly in relative abundance during the oxygenation period in redox-oscillated peat compared to anoxic controls. Acidobacteria species were particularly important for anaerobic processing of peat C, including in the production of methanogenic substrates H 2 and CO 2 . Higher CO 2 production during the anoxic phase of redox-oscillated peat stimulated hydrogenotrophic CH 4 production by Methanobacterium species. The persistence of reduced iron (Fe(II)) during prolonged oxygenation in redox-oscillated peat may further enhance C degradation through abiotic mechanisms (e.g., Fenton reactions). The results indicate that specific functional shifts in the peat microbiome underlie O 2 enhancement of CH 4 production in acidic, Sphagnum-rich wetland soils. They also imply that understanding microbial dynamics spanning temporal and spatial redox transitions in peatlands is critical for constraining CH 4 budgets; predicting feedbacks between climate change, hydrologic variability, and wetland CH 4 emissions; and guiding wetland C management strategies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

TAILORED BIOBLENDSTOCKS WITH LOW ENVIRONMENTAL IMPACT TO OPTIMIZE MCCI ENGINES

The overall objective of the project is to develop and demonstrate a microalgae bio-blendstock with greater than 60% greenhouse gas reduction potential relative to petroleum diesel, that can reduce sooting propensity, increase cetane number and improve engine thermal efficiency relative to a baseline diesel engine operating on conventional fuel. Specific objectives include: (1) development of a new framework for both LCA and TEA that explicitly considers temporal variation in productivity and the frequency of crop loss; (2) determination of how fuel compounds that can be produced from the algal biomass can be ‘bio-tailored’ based on the species composition and biological production process, and subsequent processing via HTL to biocrude, and upgrading of the biocrude; (3) execution of a feedback loop (algae production  biocrude refining  combustion optimization  feedback to refining stage), for optimization of fuels for MCCI combustion; (4) optimization of MCCI combustion and emissions performance, accounting first for the biological processes that dictate the chemical composition of biocrude oil, and second for the subsequent chemical processes that comprise mixing controlled compression ignition combustion; (6) simulation of MCCI engine combustion processes to demonstrate the incorporation of relevant fuel chemistry that captures the specific impacts of optimized algal fuels.

09 BIOMASS FUELS↗

DOE OSTI2020

Tailored Bioblendstocks with Low Environmental Impact to Optimize MCCI Engines

09 BIOMASS FUELS↗

NASA NTRS1992

Role of atrial natriuretic peptide in systemic responses to acute isotonic volume expansion

A hypothesis is proposed that a temporal relationship exists between increases in cardiac filling pressure and plasma artrial natriuretic peptide (ANP) concentration and also between ANP elevation and vasodilation, fluid movement from plasma to interstitium, and increased urine volume (UV). To test the hypothesis, 30 ml/kg isotonic saline were infused in supine male subjects over 24 min and responses were monitored for 3 h postinfusion. Results show that at end infusion, mean arterial pressure (RAP), heart rate and plasma volume exhibited peak increases of 146, 23, and 27 percent, respectively. Mean plasma ANP and UV peaked (45 and 390 percent, respectively) at 30 min postinfusion. Most cardiovascular variables had returned toward control levels by 1 h postinfusion, and net reabsorption of extravascular fluid ensued. It is concluded that since ANP was not significantly increased until 30 min postinfusion, factors other than ANP initiate responses to intravascular fluid loading. These factors include increased vascular pressures, baroreceptor-mediated vasolidation, and hemodilution of plasma proteins. ANP is suggested to mediate, in part, the renal response to saline infusion.

Watenpaugh, Donald E.↗

NASA NTRS1993

Galileo SSI lunar observations: Copernican craters and soils

The Galileo spacecraft completed its first Earth-Moon flyby (EMI) in December 1990 and its second flyby (EM2) in December 1992. Copernican-age craters are among the most prominent features seen in the SSI (Solid-State Imaging) multispectral images of the Moon. The interiors, rays, and continuous ejecta deposits of these youngest craters stand out as the brightest features in images of albedo and visible/1-micron color ratios (except where impact melts are abundant). Crater colors and albedos (away from impact melts) are correlated with their geologic emplacement ages as determined from counts of superposed craters; these age-color relations can be used to estimate the emplacement age (time since impact event) for many Copernican-age craters on the near and far sides of the Moon. The spectral reflectivities of lunar soils are controlled primarily by (1) soil maturity, resulting from the soil's cumulative age of exposure to the space environment; (2) steady-state horizontal and vertical mixing of fresh crystalline materials ; and (3) the mineralogy of the underlying bedrock or megaregolith. Improved understanding of items (1) and (2) above will improve our ability to interpret item (3), especially for the use of crater compositions as probes of crustal stratigraphy. We have examined the multispectral and superposed crater frequencies of large isolated craters, mostly of Eratosthenian and Copernican ages, to avoid complications due to (1) secondaries (as they affect superposed crater counts) and (2) spatially and temporally nonuniform regolith mixing from younger, large, and nearby impacts. Crater counts are available for 11 mare craters and 9 highlands craters within the region of the Moon imaged during EM1. The EM2 coverage provides multispectral data for 10 additional craters with superposed crater counts. Also, the EM2 data provide improved spatial resolution and signal-to-noise ratios over the western nearside.

Mcewen, A. S.↗

NASA NTRS1993

MAX-91: Polarimetric SAR results on Montespertoli site

The polarimetric Synthetic Aperture Radar (SAR) is a powerful sensor for high resolution ocean and land mapping and particularly for monitoring hydrological parameters in large watersheds. There is currently much research in progress to assess the SAR operational capability as well as to estimate the accuracy achievable in the measurements of geophysical parameters with the presently available airborne and spaceborne sensors. An important goal of this research is to improve our understanding of the basic mechanisms that control the interaction of electro-magnetic waves with soil and vegetation. This can be done both by developing electromagnetic models and by analyzing statistical relations between backscattering and ground truth data. A systematic investigation, which aims at a better understanding of the information obtainable from the multi-frequency polarimetric SAR to be used in agro-hydrology, is in progress by our groups within the framework of SIR-C/X-SAR Project and has achieved a most significant milestone with the NASA/JPL Aircraft Campaign named MAC-91. Indeed this experiment allowed us to collect a large and meaningful data set including multi-temporal multi-frequency polarimetric SAR measurements and ground truth. This paper presents some significant results obtained over an agricultural flat area within the Montespertoli site, where intensive ground measurements were carried out. The results are critically discussed with special regard to the information associated with polarimetric data.

Baronti, S.↗

DOE OSTI2022

Formal verification and validation of run-to-completion style state charts using Event-B

State chart notations with ‘run to completion’ semantics are popular with engineers for designing controllers that react to environment events with a sequence of state transitions but lack formal refinement and rigorous verification methods. State chart models are typically used to design complex control systems that respond to environmental triggers with a sequential process. The model is usually constructed at a concrete level and verified and validated using animation techniques relying on human judgement. Event-B, on the other hand, is based on refinement from an initial abstraction and is designed to make formal verification by automatic theorem provers feasible. Abstraction and formal verification provide greater assurance that critical (e.g. safety or security) properties are not violated by the control system. In this paper, we introduce a notion of refinement into a ‘run to completion’ state chart modelling notation and leverage Event-B’s tool support for theorem proving. We describe the difficulties in translating ‘run to completion’ semantics into Event-B refinements and suggest a solution. We illustrate our approach and show how models can be validated at different refinement levels using our scenario checker animation tools. We show how critical invariant properties can be verified by proof despite the reactive nature of the system and how behavioural aspects of the system can be verified by testing the expected reactions using a temporal logic, model checking approach. To verify liveness, we outline a proof that the run to completion is deadlock-free and converges to complete the run.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Unified many-worlds browsing of arbitrary physics-based animations

Manually tuning physics-based animation parameters to explore a simulation outcome space or achieve desired motion outcomes can be notoriously tedious. This problem has motivated many sophisticated and specialized optimization-based methods for fine-grained (keyframe) control, each of which are typically limited to specific animation phenomena, usually complicated, and, unfortunately, not widely used. In this paper, we propose Unified Many-Worlds Browsing (UMWB), a practical method for sample-level control and exploration of physics-based animations. Our approach supports browsing of large simulation ensembles of arbitrary animation phenomena by using a unified volumetric WORLDPACK representation based on spatiotemporally compressed voxel data associated with geometric occupancy and other low-fidelity animation state. Beyond memory reduction, the WORLDPACK representation also enables unified query support for interactive browsing: it provides fast evaluation of approximate spatiotemporal queries, such as occupancy tests that find ensemble samples ("worlds") where material is either IN or NOT IN a user-specified spacetime region. WORLDPACKS also support real-time hardware-accelerated voxel rendering by exploiting the spatially hierarchical and temporal RLE raster data structure. Our UMWB implementation supports interactive browsing (and offline refinement) of ensembles containing thousands of simulation samples, and fast spatiotemporal queries and ranking. We show UMWB results using a wide variety of physics-based animation phenomena---not just JELL-O ® .

Computer Science↗

NASA NTRS1975

An automated atmospheric sampling system operating on 747 airliners

An air sampling system that automatically measures the temporal and spatial distribution of selected particulate and gaseous constituents of the atmosphere has been installed on a number of commercial airliners and is collecting data on commercial air routes covering the world. Measurements of constituents related to aircraft engine emissions and other pollutants are made in the upper troposphere and lower stratosphere (6 to 12 km) in support of the Global Air Sampling Program (GASP). Aircraft operated by different airlines sample air at latitudes from the Arctic to Australia. This system includes specialized instrumentation for measuring carbon monoxide, ozone, water vapor, and particulates, a special air inlet probe for sampling outside air, a computerized automatic control, and a data acquisition system. Air constituents and related flight data are tape recorded in flight for later computer processing on the ground.

Perkins, P.↗

DOE OSTI2024

Climate, Hydrology, and Nutrients Control the Seasonality of Si Concentrations in Rivers

Abstract The seasonal behavior of fluvial dissolved silica (DSi) concentrations, termedDSi regime, mediates the timing of DSi delivery to downstream waters and thus governs river biogeochemical function and aquatic community condition. Previous work identified five distinct DSi regimes across rivers spanning the Northern Hemisphere, with many rivers exhibiting multiple DSi regimes over time. Several potential drivers of DSi regime behavior have been identified at small scales, including climate, land cover, and lithology, and yet the large‐scale spatiotemporal controls on DSi regimes have not been identified. We evaluate the role of environmental variables on the behavior of DSi regimes in nearly 200 rivers across the Northern Hemisphere using random forest models. Our models aim to elucidate the controls that give rise to (a) average DSi regime behavior, (b) interannual variability in DSi regime behavior (i.e., Annual DSi regime), and (c) controls on DSi regime shape (i.e., minimum and maximum DSi concentrations). Average DSi regime behavior across the period of record was classified accurately 59% of the time, whereas Annual DSi regime behavior was classified accurately 80% of the time. Climate and primary productivity variables were important in predicting Average DSi regime behavior, whereas climate and hydrologic variables were important in predicting Annual DSi regime behavior. Median nitrogen and phosphorus concentrations were important drivers of minimum and maximum DSi concentrations, indicating that these macronutrients may be important for seasonal DSi drawdown and rebound. Our findings demonstrate that fluctuations in climate, hydrology, and nutrient availability of rivers shape the temporal availability of fluvial DSi.

Environmental Sciences & Ecology↗

DOE OSTI2024

Physiological Adaptations to Progressive Endurance Exercise Training in Adult and Aged Rats: Insights from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

While regular physical activity is a cornerstone of health, wellness, and vitality, the impact of endurance exercise training on molecular signaling within and across tissues remains to be delineated. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to characterize molecular networks underlying the adaptive response to exercise. Here, we describe the endurance exercise training studies undertaken by the Preclinical Animal Sites Studies component of MoTrPAC, in which we sought to develop and implement a standardized endurance exercise protocol in a large cohort of rats. To this end, Adult (6-mo) and Aged (18-mo) female (n = 151) and male (n = 143) Fischer 344 rats were subjected to progressive treadmill training (5 d/wk, ~70%–75% VO 2 max) for 1, 2, 4, or 8 wk; sedentary rats were studied as the control group. A total of 18 solid tissues, as well as blood, plasma, and feces, were collected to establish a publicly accessible biorepository and for extensive omics-based analyses by MoTrPAC. Treadmill training was highly effective, with robust improvements in skeletal muscle citrate synthase activity in as little as 1–2 wk and improvements in maximum run speed and maximal oxygen uptake by 4–8 wk. For body mass and composition, notable age- and sex-dependent responses were observed. This work in mature, treadmill-trained rats represents the most comprehensive and publicly accessible tissue biorepository, to date, and provides an unprecedented resource for studying temporal-, sex-, and age-specific responses to endurance exercise training in a preclinical rat model.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

A tissue‐resolved, network‐based transcriptomic framework for abiotic stress responses in sorghum

Developing climate‐resilient crops requires a detailed understanding of stress‐induced gene expression dynamics, as maladaptive responses can compromise their productivity and survival. Sorghum, a globally important cereal with exceptional tolerance to multiple abiotic stresses, provides a powerful system for investigating these dynamics. However, how stress type, tissue specificity, and temporal progression jointly shape transcriptomic responses in crops remains poorly understood. Here, we present a comparative, time‐resolved transcriptomic atlas of sorghum responses to drought, heat, and salinity stress across shoot and root tissues. Integrative analyses revealed that tissue specificity is the dominant determinant of abiotic stress‐induced gene reprogramming across all three stresses. Building on these global comparisons, we focused on heat stress, as it elicited the most coherent and pronounced transcriptional and regulatory responses, enabling deeper network‐level interrogation. Co‐expression network analysis identified tissue‐specific modules enriched for phytohormone‐responsive genes, while gene regulatory network (GRN) mapping and cistrome analyses uncovered transcription factors (TFs) controlling key hub genes within these modules. Together, this study provides a foundational transcriptomic and network‐based resource for dissecting the regulatory architecture of abiotic stress responses in sorghum and offers prioritized candidates for future functional validation and engineering of climate‐resilient crops.

abiotic stress↗

NASA NTRS2014

Data Automata in Scala

The field of runtime verification has during the last decade seen a multitude of systems for monitoring event sequences (traces) emitted by a running system. The objective is to ensure correctness of a system by checking its execution traces against formal specifications representing requirements. A special challenge is data parameterized events, where monitors have to keep track of the combination of control states as well as data constraints, relating events and the data they carry across time points. This poses a challenge wrt. efficiency of monitors, as well as expressiveness of logics. Data automata is a form of automata where states are parameterized with data, supporting monitoring of data parameterized events. We describe the full details of a very simple API in the Scala programming language, an internal DSL (Domain-Specific Language), implementing data automata. The small implementation suggests a design pattern. Data automata allow transition conditions to refer to other states than the source state, and allow target states of transitions to be inlined, offering a temporal logic flavored notation. An embedding of a logic in a high-level language like Scala in addition allows monitors to be programmed using all of Scala's language constructs, offering the full flexibility of a programming language. The framework is demonstrated on an XML processing scenario previously addressed in related work.

runtime verification↗

NASA NTRS2022

Assimilation of Sea Ice Thickness Derived from Cryosat-2 Along-Track Freeboard Measurements into the Met Office's Forecast Ocean Assimilation Model (FOAM)

The feasibility of assimilating sea ice thickness (SIT) observations derived from CryoSat-2 along-track measurements of sea ice freeboard is successfully demonstrated using a 3D-Var assimilation scheme, NEMOVAR, within the Met Office's global, coupled ocean–sea-ice model, Forecast Ocean Assimilation Model (FOAM). The CryoSat-2 Arctic freeboard measurements are produced by the Centre for Polar Observation and Modelling (CPOM) and are converted to SIT within FOAM using modelled snow depth. This is the first time along-track observations of SIT have been used in this way, with other centres assimilating gridded and temporally averaged observations. The assimilation leads to improvements in the SIT analysis and forecast fields generated by FOAM, particularly in the Canadian Arctic. Arctic-wide observation-minus-background assimilation statistics for 2015–2017 show improvements of 0.75 m mean difference and 0.41 m root-mean-square difference (RMSD) in the freeze-up period and 0.46 m mean difference and 0.33 m RMSD in the ice break-up period. Validation of the SIT analysis against independent springtime in situ SIT observations from NASA Operation IceBridge (OIB) shows improvement in the SIT analysis of 0.61 m mean difference (0.42 m RMSD) compared to a control without SIT assimilation. Similar improvements are seen in the FOAM 5 d SIT forecast. Validation of the SIT assimilation with independent Beaufort Gyre Exploration Project (BGEP) sea ice draft observations does not show an improvement, since the assimilated CryoSat-2 observations compare similarly to the model without assimilation in this region. Comparison with airborne electromagnetic induction (Air-EM) combined measurements of SIT and snow depth shows poorer results for the assimilation compared to the control, despite covering similar locations to the OIB and BGEP datasets. This may be evidence of sampling uncertainty in the matchups with the Air-EM validation dataset, owing to the limited number of observations available over the time period of interest. This may also be evidence of noise in the SIT analysis or uncertainties in the modelled snow depth, in the assimilated SIT observations, or in the data used for validation. The SIT analysis could be improved by upgrading the observation uncertainties used in the assimilation. Despite the lack of CryoSat-2 SIT observations available for assimilation over the summer due to the detrimental effect of melt ponds on retrievals, it is shown that the model is able to retain improvements to the SIT field throughout the summer months due to prior, wintertime SIT assimilation. This also results in regional improvements to the July modelled sea ice concentration (SIC) of 5 % RMSD in the European sector, due to slower melt of the thicker sea ice.

Emma K. Fiedler↗

DOE OSTI2023

Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase

The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen–deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein–solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation ( E a ) for the Stokes shifts decay rates and the millisecond C–H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.

Science & Technology - Other Topics↗

DOE OSTI2022

Sink or source? Insights into the behavior of copper and zinc in the sediment porewater of a constructed wetland by peepers

The H-02 free water surface constructed wetland has been applied to remove heavy metals, mainly copper (Cu) and zinc (Zn), from wastewater on the Savannah River Site (Aiken, SC, USA). More and more studies focus on the metal behavior between the sediment and the overlying water, which directly reflects the stability of metals after sedimentation in constructed wetlands. This study focused on the biogeochemical pathways in metal bioavailability and remobilization in the sediment after metals were removed from the overlying water. The dialysis sampling devices (peepers) were used to collect porewater samples from eight depths in the sediment for the measurement of Cu, Zn, dissolved organic carbon (DOC), and major anions (sulfate and chloride). Surface water samples were also collected for the measurement of Cu, Zn, DOC, and anions. Different temporal trends were observed for dissolved Cu between the surface and bottom waters, but not for dissolved Zn. There were no obvious changes in porewater metal concentrations with increasing depths in the sediment. Sediment served as a sink for Cu as only 3% of porewater samples showed higher labile Cu concentrations than the surface water during the entire year. Furthermore, sediment served as a source for Zn in summer and winter as 32% of porewater samples showed higher labile Zn concentrations than the surface water, and these samples were collected at all sediment depths. We think the seasonal changes in the behaviors of Cu and Zn were primarily controlled by the sulfur dynamics and the metal removal processes in the constructed wetland, as well as the different complexing chemistry between Cu and Zn. Also, our study supports that peeper is a powerful tool for studying the biogeochemistry of metals in the sediment.

54 ENVIRONMENTAL SCIENCES↗