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At least 721 records · Page 40

High-throughput, dynamic, multi-dimensional: an expanding repertoire of plant respiration measurements

A recent burst of technological innovation and adaptation has greatly improved our ability to capture respiration rate data from plant sources. At the tissue level, several independent respiration measurement options are now available, each with distinct advantages and suitability, including high-throughput sampling capacity. These advancements facilitate the inclusion of respiration rate data into large-scale biological studies such as genetic screens, ecological surveys, crop breeding trials, and multi-omics molecular studies. As a result, our understanding of the correlations of respiration with other biological and biochemical measurements is rapidly increasing. Difficult questions persist concerning the interpretation and utilization of respiration data; concepts such as allocation of respiration to growth versus maintenance, the unnecessary or inefficient use of carbon and energy by respiration, and predictions of future respiration rates in response to environmental change are all insufficiently grounded in empirical data. However, we emphasize that new experimental designs involving novel combinations of respiration rate data with other measurements will flesh-out our current theories of respiration. Furthermore, dynamic recordings of respiration rate, which have long been used at the scale of mitochondria, are increasingly being used at larger scales of size and time to reflect processes of cellular signal transduction and physiological response to the environment. Herein, we also highlight how respiratory methods are being better adapted to different plant tissues including roots and seeds, which have been somewhat neglected historically.

59 BASIC BIOLOGICAL SCIENCES↗

Multifidelity uncertainty quantification with models based on dissimilar parameters

Multifidelity uncertainty quantification (MF UQ) sampling approaches have been shown to significantly reduce the variance of statistical estimators while preserving the bias of the highest-fidelity model, provided that the low-fidelity models are well correlated. However, maintaining a high level of correlation can be challenging, especially when models depend on different input uncertain parameters, which drastically reduces the correlation. Existing MF UQ approaches do not adequately address this issue. In this work, we propose a new sampling strategy that exploits a shared space to improve the correlation among models with dissimilar parameterization. We achieve this by transforming the original coordinates onto an auxiliary manifold using the adaptive basis (AB) method (Tipireddy and Ghanem, 2014). The AB method has two main benefits: (1) it provides an effective tool to identify the low-dimensional manifold on which each model can be represented, and (2) it enables easy transformation of polynomial chaos representations from high- to low-dimensional spaces. This latter feature is used to identify a shared manifold among models without requiring additional evaluations. Here we present two algorithmic flavors of the new estimator to cover different analysis scenarios, including those with legacy and non-legacy high-fidelity (HF) data. We provide numerical results for analytical examples, a direct field acoustic test, and a finite element model of a nuclear fuel assembly. For all examples, we compare the proposed strategy against both single-fidelity and MF estimators based on the original model parameterization.

42 ENGINEERING↗

Algorithm 1049: The Delaunay Density Diagnostic

Accurate approximation of a real-valued function depends on two aspects of the available data: the density of inputs within the domain of interest and the variation of the outputs over that domain. There are few methods for assessing whether the density of inputs is sufficient to identify the relevant variations in outputs—i.e., the “geometric scale” of the function—despite the fact that sampling density is closely tied to the success or failure of an approximation method. In this article, we introduce a general purpose, computational approach to detecting the geometric scale of real-valued functions over a fixed domain using a deterministic interpolation technique from computational geometry. The algorithm is intended to work on scalar data in moderate dimensions (2–10). Our algorithm is based on the observation that a sequence of piecewise linear interpolants will converge to a continuous function at a quadratic rate (in L 2 norm) if and only if the data are sampled densely enough to distinguish the feature from noise (assuming sufficiently regular sampling). We present numerical experiments demonstrating how our method can identify feature scale, estimate uncertainty in feature scale, and assess the sampling density for fixed (i.e., static) datasets of input–output pairs. Finally, we include analytical results in support of our numerical findings and have released lightweight code that can be adapted for use in a variety of data science settings.

97 MATHEMATICS AND COMPUTING↗

Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces – part II

The modeling of the near-field interaction in the scattering-type scanning near-field optical microscope (s-SNOM) is rapidly advancing, although an accurate yet versatile modeling framework that can be easily adapted to various complex situations is still lacking. In this work, we propose a time-efficient numerical scheme in the quasi-electrostatic limit to capture the tip-sample interaction in the near field. This method considers an extended tip geometry, which is a significant advantage compared to the previously reported method based on the point-dipole approximation. Using this formalism, we investigate, among others, nontrivial questions such as uniaxial and biaxial anisotropy in the near-field interaction, the relationship between various experimental parameters (e.g. tip radius, tapping amplitude, etc.), and the tip-dependent spatial resolution. The demonstrated method further sheds light on the understanding of the contrast mechanism in s-SNOM imaging and spectroscopy, while also representing a valuable platform for future quantitative analysis of the experimental observations.

Chen, Xinzhong (ORCID:0000000261033848)↗

Leaf gas exchange and fitted parameters, San Lorenzo, Panama, 2020

This data package contains photosynthetic CO2 response curves (ACi curves), light response curves (AQ curves), dark adapted dark respiration, conductance curves, and survey measurements for leaves measured at the San Lorenzo forest canopy crane site, Panama (PA-SLZ) from January to March 2020. Leaves were sampled from both the top of the canopy and multiple heights within the canopy from 10 vertical profiles and included around 50 species. In addition, six core species were also measured, from the top of the canopy. Fitted maximum carboxylation rate (Vcmax), maximum electron transport rate (Jmax), and triose phosphate utilization rate (TPU) were derived from measured data as well as the convexity, light use efficiency, apparent quantum yield, and Rdark. The measurements can also be used to derive the conductance parameters g0 and g1 of stomatal model. All the gas exchange data and metadata are presented in .csv files and complete instrument output are included in .zip folders. Data and metadata meet the ESS-DIVE leaf-level gas exchange reporting format requirements. The protocol details are provided as pdf documents. In addition to gas exchange data described here these samples were also used for measurement of leaf optical properties, carbon and nitrogen content, and leaf mass per unit leaf area (LMA) these data can be cross linked using the unique sample ID and are provided in separate related data packages. Sample information including canopy elevation and leaf area index (LAI) can be found in the related “Leaf and canopy traits” data package.

54 ENVIRONMENTAL SCIENCES↗

Active Learning for Rapid Targeted Synthesis of Compositionally Complex Alloys

The next generation of advanced materials is tending toward increasingly complex compositions. Synthesizing precise composition is time-consuming and becomes exponentially demanding with increasing compositional complexity. An experienced human operator does significantly better than a novice but still struggles to consistently achieve precision when synthesis parameters are coupled. The time to optimize synthesis becomes a barrier to exploring scientifically and technologically exciting compositionally complex materials. This investigation demonstrates an active learning (AL) approach for optimizing physical vapor deposition synthesis of thin-film alloys with up to five principal elements. We compared AL-based on Gaussian process (GP) and random forest (RF) models. The best performing models were able to discover synthesis parameters for a target quinary alloy in 14 iterations. We also demonstrate the capability of these models to be used in transfer learning tasks. RF and GP models trained on lower dimensional systems (i.e., ternary, quarternary) show an immediate improvement in prediction accuracy compared to models trained only on quinary samples. Furthermore, samples that only share a few elements in common with the target composition can be used for model pre-training. We believe that such AL approaches can be widely adapted to significantly accelerate the exploration of compositionally complex materials.

Chemistry↗

Method and apparatus for a Fabry-Perot multiple beam fringe sensor

A method and the resulting apparatus for implementing a unique multiple beam fringe sensor that is adapted to be interfaced with a low cost, compact fiber optic transmission system in order to provide an accurate digital representation of a physical parameter (e.g. temperature) of a remote sample. The sensor is fabricated so as to include a Fabry-Perot gap formed between the ends of two mated optical fibers. By examining the optical characteristics of light that is transmitted through the Fabry-Perot sensor gap, an indication of gap width can be ascertained. Accordingly, a change in Fabry-Perot sensor gap width is related to a change in the particular physical parameter to be measured.

James, Kenneth A.↗

A Year of Progress: NASA's Space Launch System Approaches Critical Design Review

NASA's Space Launch System (SLS) made significant progress on the manufacturing floor and on the test stand in 2014 and positioned itself for a successful Critical Design Review in mid-2015. SLS, the world's only exploration-class heavy lift rocket, has the capability to dramatically increase the mass and volume of human and robotic exploration. Additionally, it will decrease overall mission risk, increase safety, and simplify ground and mission operations - all significant considerations for crewed missions and unique high-value national payloads. Development now is focused on configuration with 70 metric tons (t) of payload to low Earth orbit (LEO), more than double the payload of the retired Space Shuttle program or current operational vehicles. This "Block 1" design will launch NASA's Orion Multi-Purpose Crew Vehicle (MPCV) on an uncrewed flight beyond the Moon and back and the first crewed flight around the Moon. The current design has a direct evolutionary path to a vehicle with a 130t lift capability that offers even more flexibility to reduce planetary trip times, simplify payload design cycles, and provide new capabilities such as planetary sample returns. Every major element of SLS has successfully completed its Critical Design Review and now has hardware in production or testing. In fact, the SLS MPCV-to-Stage-Adapter (MSA) flew successfully on the Exploration Flight Test (EFT) 1 launch of a Delta IV and Orion spacecraft in December 2014. The SLS Program is currently working toward vehicle Critical Design Review in mid-2015. This paper will discuss these and other technical and programmatic successes and challenges over the past year and provide a preview of work ahead before the first flight of this new capability.

Askins, Bruce↗

ASGarD: Adaptive Sparse Grid Discretization

Many areas of science exhibit physical processes that are described by high dimensional partial differential equations (PDEs), e.g., the 4D, 5D and 6D models describing magnetized fusion plasmas, models describing quantum chemistry, or derivatives pricing. Such problems are affected by the so-called “curse of dimensionality” where the number of degrees of freedom (or unknowns) required to be solved for scales as N D where N is the number of grid points in any given dimension D. A simple, albeit naive, 6D example is demonstrated in the left panel of Figure 1. With N = 1000 grid points in each dimension, the memory required just to store the solution vector, not to mention forming the matrix required to advance such a system in time, would exceed an exabyte - and also the available memory on the largest of supercomputers available today. The right panel of Figure 1 demonstrates potential savings for a range of problem dimensionalities and grid resolution. While there are methods to simulate such high-dimensional systems, they are mostly based on Monte-Carlo methods, which rely on a statistical sampling such that the resulting solutions include noise. Since the noise in such methods can only be reduced at a rate proportional to $\sqrt{N_p}$ where N p is the number of Monte-Carlo samples, there is a need for continuum, or grid/mesh-based methods for high-dimensional problems, which both do not suffer from noise and bypass the curse of dimensionality. We present a simulation framework that provides such a method using adaptive sparse grids.

97 MATHEMATICS AND COMPUTING↗

A Methodology for determining optimal milling parameters for low-taper microtensile sample production

Femtosecond lasers are beginning to see an increase in interest for industrial and high throughput microsample milling applications. Despite this, much of the literature regarding removal rate studies for ultrashort pulse laser milling continues to focus on single-pulse or similar experiments that have a very small time on target. The material volume removal rates of femtosecond milling can vary wildly depending on parameters like laser scan speed, hatch spacing, z-axis step size, and pulses on the material. Currently, there is no established methodology for determining the optimal values of these parameters for micromilling applications. This methodology was developed in this study. The methodology consists of a pulse study, a repeat study, and a z-step study that will return the milling parameters that resulted in the largest volume removal rate for the laser used for this research. The methodology was created for the laser system used in this study, and was tested on 316 Stainless Steel, but was developed in such a way that it may be adapted to any material, and with some tweaking of variables might be used in other laser systems. The laser system used in this study utilizes a novel positioning stage that introduces 6 degrees of freedom to the translation of laser samples, being able to tilt and move in all three axes. Using both the developed methodology and the unique capabilities of the laser microtensile samples were produced with taper angles of <1° in 316 Stainless Steel.

Barker, Zachary Wayne↗

Sandwich Hybridization Assay for In Situ Real-Time Cyanobacterial Detection and Monitoring: A Review

As cyanobacterial harmful algal bloom (cHAB) events increase in scale, severity, frequency, and duration around the world, rapid and accurate monitoring and characterization tools have become critically essential for regulatory and management decision-making. The composition of cHAB-forming cyanobacteria community can change significantly over time and space and be altered by sample preservation and transportation, making in situ monitoring necessary to obtain real-time and localized information. Sandwich hybridization assay (SHA) utilizes capture oligonucleotide probes for sensitive detection of target-specific nucleic acid sequences. As an amplification-free molecular biology technology, SHA can be adapted for in-situ, real-time or near real-time detection and qualitatively or semi-quantitatively monitoring of cHAB-forming cyanobacteria, owing to its characteristics such as being rapid, portable, inexpensive, and amenable to automation, high sensitivity, specificity and robustness, and multiplexing (i.e., detecting multiple targets simultaneously). Despite its successful application in the monitoring of marine and freshwater phytoplankton, there is still room for improvement. The ability to identify a cHAB community rapidly would decrease delays in cyanotoxin analyses, reduce costs, and increase sample throughput, allowing for timely actions to improve environmental and human health and the understanding of short- and long-term bloom dynamics. Real-time detection and quantitation of HAB-forming cyanobacteria is essential for improving environmental and public health and reducing associated costs. We review and propose to apply SHA for in situ cHABs monitoring.

59 BASIC BIOLOGICAL SCIENCES↗

Confidence-Based Buffer for Strategic Deconfliction with Probabilistic Operational Intent

This paper presents a methodology to expand the 95% confidence level of the elliptical geometry given by Unmanned Aircraft System (UAS) operators planning to fly Beyond Visual Line of Sight (BVLOS) to any confidence level before being fed to the strategic deconfliction (SD) module, effectively increasing the separation buffer between Operational Intents (OIs). To assess the performance of this approach, it is integrated within an adaptation of the Rolling Horizon with K-Position Search volume-based strategic deconfliction approach, previously developed at NASA Ames, preventing the 4D overlapping of OIs shaped by ellipses instead of traditional blocks. Safety and efficiency metrics are evaluated through the deconfliction of four simulated package delivery route network structures across the San Francisco Metropolitan Area with increasing numbers of crossing waypoints (network complexity). Safety assessment entails the in-house creation of a metric to quantify collision occurrences per flight hour based on the frequency at which the probabilistic operational volume segments are sampled, whereas efficiency is measured using ground delay. Results indicate that the largest buffer growth occurs when increasing the confidence level beyond 99.9% and demonstrate the negative impact of network complexity on both metrics, regardless of the OI geometry. Further, the ellipse-based SD adaptation more accurately estimates temporal separation at crossings, allowing deconflicted vehicles to be closer together. It is concluded that the proposed methodology enables the desired confidence level to serve as an effective controller of buffer size.

strategic deconfliction↗

Confidence-Based Buffer for Strategic Deconfliction with Probabilistic Operational Intent

This paper presents a methodology to expand the 95% confidence level of the elliptical geometry given by Unmanned Aircraft System (UAS) operators planning to fly Beyond Visual Line of Sight (BVLOS) to any confidence level before being fed to the strategic deconfliction (SD) module, effectively increasing the separation buffer between Operational Intents (OIs). To assess the performance of this approach, it is integrated within an adaptation of the Rolling Horizon with K-Position Search volume-based strategic deconfliction approach, previously developed at NASA Ames, preventing the 4D overlapping of OIs shaped by ellipses instead of traditional blocks. Safety and efficiency metrics are evaluated through the deconfliction of four simulated package delivery route network structures across the San Francisco Metropolitan Area with increasing numbers of crossing waypoints (network complexity). Safety assessment entails the in-house creation of a metric to quantify collision occurrences per flight hour based on the frequency at which the probabilistic operational volume segments are sampled, whereas efficiency is measured using ground delay. Results indicate that the largest buffer growth occurs when increasing the confidence level beyond 99.9% and demonstrate the negative impact of network complexity on both metrics, regardless of the OI geometry. Further, the ellipse-based SD adaptation more accurately estimates temporal separation at crossings, allowing deconflicted vehicles to be closer together. It is concluded that the proposed methodology enables the desired confidence level to serve as an effective controller of buffer size.

safety↗

Wavelet-Based Interpolation and Representation of Non-Uniformly Sampled Spacecraft Mission Data

A well-documented problem in the analysis of data collected by spacecraft instruments is the need for an accurate, efficient representation of the data set. The data may suffer from several problems, including additive noise, data dropouts, an irregularly-spaced sampling grid, and time-delayed sampling. These data irregularities render most traditional signal processing techniques unusable, and thus the data must be interpolated onto an even grid before scientific analysis techniques can be applied. In addition, the extremely large volume of data collected by scientific instrumentation presents many challenging problems in the area of compression, visualization, and analysis. Therefore, a representation of the data is needed which provides a structure which is conducive to these applications. Wavelet representations of data have already been shown to possess excellent characteristics for compression, data analysis, and imaging. The main goal of this project is to develop a new adaptive filtering algorithm for image restoration and compression. The algorithm should have low computational complexity and a fast convergence rate. This will make the algorithm suitable for real-time applications. The algorithm should be able to remove additive noise and reconstruct lost data samples from images.

Bose, Tamal↗

*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments

Background: Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. Findings: We first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality. Conclusions: We present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts.

59 BASIC BIOLOGICAL SCIENCES↗

A probabilistic inverse prediction method for predicting plutonium processing conditions

In the past decade, nuclear chemists and physicists have been conducting studies to investigate the signatures associated with the production of special nuclear material (SNM). In particular, these studies aim to determine how various processing parameters impact the physical, chemical, and morphological properties of the resulting special nuclear material. By better understanding how these properties relate to the processing parameters, scientists can better contribute to nuclear forensics investigations by quantifying their results and ultimately shortening the forensic timeline. This paper aims to statistically analyze and quantify the relationships that exist between the processing conditions used in these experiments and the various properties of the nuclear end-product by invoking inverse methods. In particular, these methods make use of Bayesian Adaptive Spline Surface models in conjunction with Bayesian model calibration techniques to probabilistically determine processing conditions as an inverse function of morphological characteristics. Not only does the model presented in this paper allow for providing point estimates of a sample of special nuclear material, but it also incorporates uncertainty into these predictions. This model proves sufficient for predicting processing conditions within a standard deviation of the observed processing conditions, on average, provides a solid foundation for future work in predicting processing conditions of particles of special nuclear material using only their observed morphological characteristics, and is generalizable to the field of chemometrics for applicability across different materials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Biological sampling and cleaning device

Flowing-liquid cleaner may be used to gently dislodge and remove 98 percent of biological particulates from surfaces. Cleaner may retain up to 90 percent of removed particulates for later analysis. If retention is not required, unit may be adapted to clean only. Cleaner is applicable wherever very clean surface is desired.

Scheider, H. W.↗

Renal effects of fresh water-induced hypo-osmolality in a marine adapted seal

With few exceptions, marine mammals are not exposed to fresh water; however quantifying the endocrine and renal responses of a marine-adapted mammal to the infusion of fresh water could provide insight on the evolutionary adaptation of kidney function and on the renal capabilities of these mammals. Therefore, renal function and hormonal changes associated with fresh water-induced diuresis were examined in four, fasting northern elephant seal ( Mirounga angustirostris) (NES) pups. A series of plasma samples and 24-h urine voids were collected prior to (control) and after the infusion of water. Water infusion resulted in an osmotic diuresis associated with an increase in glomerular filtration rate (GFR), but not an increase in free water clearance. The increase in excreted urea accounted for 96% of the increase in osmotic excretion. Following infusion of fresh water, plasma osmolality and renin activity decreased, while plasma aldosterone increased. Although primary regulators of aldosterone release (Na(+), K(+) and angiotensin II) were not significantly altered in the appropriate directions to individually stimulate aldosterone secretion, increased aldosterone may have resulted from multiple, non-significant changes acting in concert. Aldosterone release may also be hypersensitive to slight reductions in plasma Na(+), which may be an adaptive mechanism in a species not known to drink seawater. Excreted aldosterone and urea were correlated suggesting aldosterone may regulate urea excretion during hypo-osmotic conditions in NES pups. Urea excretion appears to be a significant mechanism by which NES pups sustain electrolyte resorption during conditions that can negatively affect ionic homeostasis such as prolonged fasting.

NASA Center ARC↗