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At least 739 records · Page 41

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DOE OSTI2021

Source:sink imbalance detected with leaf and canopy-level spectroscopy in a field-grown crop

The finely-tuned balance between sources and sinks determines plant resource partitioning and regulates growth and development. Understanding and measuring metabolic indicators of source or sink limitation forms a vital part of global efforts to increase crop yield for future food security. Here, we measured metabolic profiles of Cucurbita pepo (zucchini) grown in the field under carbon sink limitation and control conditions. We demonstrate that these profiles can be measured non-destructively using hyperspectral reflectance at both leaf and canopy scales. Total non-structural carbohydrates (TNC) increased 82% in sink-limited plants; leaf mass per unit area (LMA) increased 38%; free amino acids increased 22%. Partial least-squares regression models link these measured functional traits with reflectance data, enabling high-throughput estimation of traits comprising the sink limitation response. Leaf- and canopy-scale models for TNC had R 2 values of 0.93 and 0.64 and %RMSE of 13% and 38% respectively. For LMA, R 2 values were 0.91 and 0.60 and %RMSE 7% and 14%; for free amino acids, R 2 was 0.53 and 0.21 with %RMSE 20% and 26%. Remote sensing can enable accurate, rapid detection of sink limitation in the field at the leaf and canopy scale, greatly expanding our ability to understand and measure metabolic responses to stress.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Insights into the thermo-hydraulic properties of compacted MX80 bentonite during hydration under elevated temperature

In high-level radioactive waste geological repositories, compacted bentonite undergoes coupled thermo-hydraulic processes due to heat released from a central waste canister and groundwater imbibition from the surrounding host rock. An understanding of these processes is essential for long-term simulations of radionuclide migration and canister corrosion, which requires an understanding of temperature effects on the coupled thermo-hydraulic properties governing these processes. In this study, a tank-scale radial infiltration test was used to investigate water imbibition processes in compacted bentonite under a central heater temperature of 200 °C that simulates high thermal gradients in a repository. Interpretation of this test focuses on evaluation of the liquid water wetting front during hydration and the interpretation of the temperature-dependent transient soil water retention curve (SWRC), thermal conductivity function (TCF), and hydraulic conductivity function (HCF). The SWRC during imbibition follows a temperature-dependent wetting path. Temperature effects on the hydraulic conductivity of bentonite in saturated conditions had the greatest effect on the shape of the HCF, with minimal temperature effects at higher suctions. The transient thermal conductivity data matched well with a new TCF linked with the SWRC shape. Although the bentonite layer was restrained, local deformations during hydration may have affected the shapes of the TCF and HCF.

Engineering↗

DOE OSTI2021

Vulcan Digital Engineering Application

The application is being developed with the goal of preventing the entropy of all the different single purpose applications. This application utilizes a framework that enables different file formats to be read and understood through plugins dynamically loaded to the main application containing the framework. The main application provides interoperability to all the different plugins, this allows each file format to convert to every other file format that has been read. There is no theoretical limit to the number of plugins that can be used by the application. Even though the plugins may be individually written and serve a purpose like single use scripts, the plugins can only be used with the main application, this forces the application and plugins to be linked. In theory this will force better data management, or at least the bundling of the main application with the plugins.

Lehmer, JacobP↗

DOE OSTI2018

EGS Collab Experiment 1: In-situ observation of pre-, co- and post-seismic shear slip preceding hydraulic fracturing

Understanding the initiation and arrest of earthquakes is one of the long-standing challenges of seismology. Here we report on direct observations of borehole displacement by a meter-sized shear rupture induced by pressurization of metamorphic rock at 1.5 km depth. We observed the acceleration of sliding, followed by fast co-seismic slip and a transient afterslip phase. Total displacements were about 7, 5.5 and 9.5 micrometers, respectively for the observed pre-slip, co-seismic slip and afterslip. The observed pre-slip lasted about 0.4 seconds. Co-seismic slip was recorded by the 1 kHz displacement recording and a 12-component array of 3-C accelerometers sampled at 100 kHz. The observed afterslip is consistent with analytical models of arrest in a velocity-strengthening region and subsequent stress relaxation. The observed slip vector agrees with the activation of a bedding plane within the phyllite, which is corroborated by relocated seismic events that were observed during the later stages of the injection experiment. This submission includes the pressure and deformation data recorded by the SIMFIP probe during the first injection at the 164 ft (50 m) notch of borehole E1-I. The injection was performed on on 05/22/2018 as part of Experiment 1 of the EGS Collab project. This data accompanies a manuscript submitted to GRL, linked in this submission.

15 GEOTHERMAL ENERGY↗

DOE OSTI2016

SUMMIT v2.1 Summary Report

Standard Unified Modeling Mapping and Integration Toolkit (SUMMIT) is a software capability developed by Sandia National Laboratories (SNL) under the direction and funding of the Department of Homeland Security (DHS), Science and Technology Directorate (S&T). SUMMIT is a scalable platform technology for linking together “best-in-class” models, data, and simulation tools to enable analysts, emergency planners and incident managers to more effectively, economically, and rapidly prepare, analyze, train, and respond to real or potential incidents. The SUMMIT software architecture was created under the Integrated Modeling, Mapping, and Simulation (IMMS) Project and was motivated by the issuance of Homeland Security Presidential Directive 8 (HSPD-8) which called for continuous improvement of our Nation’s preparedness to respond to catastrophic events. Furthermore, a state-of-the-art training and exercise facility called the National Exercise Simulation Center (NESC) was established within the Federal Emergency Management Agency (FEMA) headquarters.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

REopt Model Overview and Example Use Cases [Slides]

REopt(R) is a mixed-integer optimization model that minimizes the lifecycle cost of serving energy loads at a site. This work provides and introduction to the model along with its key workflow, techno-economic inputs, key outputs, and key caveats for readers to understand REopt the when, why, how of using this model. This resource also includes helpful links related to REopt model and the data sources it uses during the optimization.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2015

Hexokinase 1 is required for glucose-induced repression of bZIP63 , At5g22920 , and BT2 in Arabidopsis

Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes ( bZIP63 , At5g22920 , BT2 , MGD2 , and TPS9 ) in Arabidopsis thaliana . In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/ transporting proteins ( adg1 , sex1 , sus1-4 , sus5/6 , and tpt2 ), including also hexokinase1 (HXK1) loss- and gain-of-function plants— gin2.1 and oe3.2 , respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63 , At5g22920 , and BT . The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Altogether, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63 , At5g22920 , and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Dynamic graph system for a semantic database

A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Dynamic graph system for a semantic database

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Cosmic-Ray Moisture Probe on North Slope of Alaska Field Campaign Report

In September of 2014 a wide-area snow monitoring device was installed at the U.S. Department of Energy (DOE)’s Barrow, Alaska Atmospheric Radiation Measurement (ARM) Climate Research Facility site. The device is special in that it uses measurements of cosmic-ray neutrons as a proxy for snow water equivalent (SWE) depth. A unique characteristic of the technology is that it integrates over a wide area (as much as 40 ha), in contrast to conventional ground-based technologies, which essentially give point samples. Conventional point-scale technologies are problematic in the Arctic, both because extreme weather conditions are taxing on equipment, and because point measurements can fail to accurately characterize the average SWE over a larger area, even when excellent precision is obtained. The sensor installed in Barrow is, by far, the northernmost of a constellation of sites that makeup the U.S. COsmic ray Soil Moisture Observing System (COSMOS). The sensor is used for SWE measurements in winter and soil moisture measurements in summer. The ability of this type of sensor to operate in the Arctic had not been verified until now. The cosmic-ray sensor was installed on a tripod located approximately 150 m south of the ARM User Facility (Figure 1), and within boundaries of land managed by the ARM Facility. The sensor consists of both “bare” and “moderated” channels, where the moderated channel is the primary output used to calculate SWE. A QDL2100 data logger with pressure sensor was located inside of the User Facility, and a Campbell CS215 temperature and humidity sensor was attached to a rail on the upper deck of the User Facility, to enable near-real-time absolute humidity corrections to the data. The cosmic-ray sensors are connected to the data logger using an armored Cat5e cable that lies on top of the tundra. Data are retrieved hourly via Iridium satellite link.

"North Slope of Alaska, Barrow, soil moisture, cos↗

DOE OSTI2018

Bandwidth preemption for high-priority data transfer on dedicated channels

Bandwidth reservation has been increasingly used to provide QoS for various network applications. To accommodate a high-priority bandwidth reservation request (BRR), the bandwidth scheduler sometimes needs to preempt existing bandwidth reservations that have been made for BRRs with a lower priority, which is traditionally known as connection preemption. When such preemption is unavoidable, one primary goal of bandwidth scheduling is to minimize the disruption to existing reservations. In this paper, we study the problem of bandwidth reservation preemption for two types of BRRs, bandwidth- and data transfer oriented, respectively, on one given link of the scheduling network with two different objectives: (i) minimize the number and then the total bandwidth of existing bandwidth reservations to be preempted, and (ii) minimize the total bandwidth and then the number of existing bandwidth reservations to be preempted. We prove these four problems to be NP-complete and propose a heuristic algorithm for each. We also design baseline heuristic algorithms for performance comparison. Extensive simulation results show that the proposed heuristic algorithms outperform those in comparison.

Rao, Nageswara↗

DOE OSTI2024

Utah FORGE: Direct Shear Test Data for Investigating Seismic Precursors to Shear Failure of Fractures

This dataset includes results of direct shear tests to investigate the mechanical and geophysical response of dry and saturated fractures in Indiana limestone and Sierra White granite. Direct shear tests were performed on tensile-induced fractures in Indiana limestone and Sierra White granite in a custom water-pressurized chamber. The provided Excel files include the representative seismic wave signals and the normalized wave amplitudes of ultrasonic wave transducers. A link to the published journal article presenting the data and describing the experiment in detail is provided as well.

15 GEOTHERMAL ENERGY↗

DOE OSTI2017

The cyclophilin D/Drp1 axis regulates mitochondrial fission contributing to oxidative stress-induced mitochondrial dysfunctions in SH-SY5Y cells

Oxidative stress plays a central role in the pathogenesis of various neurodegenerative diseases. Increasing evidences have demonstrated that structural abnormalities in mitochondria are involved in oxidative stress related nerve cell damage. And Drp1 plays a critical role in mitochondrial dynamic imbalance insulted by oxidative stress-derived mitochondria. However, the status of mitochondrial fusion and fission pathway and its relationship with mitochondrial properties such as mitochondrial membrane permeability transition pore (mPTP) have not been fully elucidated. Here, we demonstrated for the first time the role of Cyclophilin D (CypD), a crucial component for mPTP formation, in the regulation of mitochondrial dynamics in oxidative stress treated nerve cell. We observed that CypD-mediated phosphorylation of Drp1 and subsequently augmented Drp1 recruitment to mitochondria and shifts mitochondrial dynamics toward excessive fission, which contributes to the mitochondrial structural and functional dysfunctions in oxidative stress-treated nerve cells. CypD depletion or over expression accompanies mitochondrial dynamics/functions recovery or aggravation separately. We also demonstrated first time the link between the CypD to mitochondrial dynamics. Our data offer new insights into the mechanism of mitochondrial dynamics which contribute to the mitochondrial dysfunctions, specifically the role of CypD in Drp1-mediated mitochondrial fission. The protective effect of CsA, or other molecules affecting the function of CypD hold promise as a potential novel therapeutic strategy for governing oxidative stress pathology via mitochondrial pathways. - Highlights: • Demonstrated first time the link between the mPTP to mitochondrial dynamics. • The role of Cyclophilin D in the regulation of Drp1-mediated mitochondrial fission. • CsA as a potential target for governing oxidative stress related neuropathology.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Leaf sample detail, Feb2016-May2016, PA-SLZ, PA-PNM, PA-BCI: Panama

This data package contains details of the date, location, species and photographs of leaf samples collected on a monthly basis from Feb to May 2016 from Parque Natural Metropolitano (PA-PNM), Barro Colorado Island (PA-BCI) and Bosque Protector San Lorenzo (PA-SLZ) in Panama. Data from BCI only available for March. This data was collected as part of the 2016 El Niño-Southern Oscillation (ENSO) campaign. Included in this data package are an Excel file with data (2016ENSO_Panama_LeafSamples) and two Excel files with associated metadata. Sample photos are included in five zip files, organized by month and site. Also included is a Word document (Metadata_description_2016_ENSO_Panama) with details such as data collection methods, equipment used, and site information. Data to be used as a reference to linking related datasets including leaf water potential, leaf spectra, LMA, gas exchange and leaf chemistry (CHN, NSC). Most leaves were sampled from sunlit canopy trees. VERSION 2 update. The identification of a species from the PNM site has been corrected as follows: the identification of the tree initially identified as Pseudosamanea guachapele (ALBIED) has been revised to Albizia adinocephala (ALBIAD). The updated data package includes revised data, metadata and protocol documents updated to reflect this change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

A browser-based tool for visualization and analysis of diffusion MRI data

Human neuroscience research faces several challenges with regards to reproducibility. While scientists are generally aware that data sharing is important, it is not always clear how to share data in a manner that allows other labs to understand and reproduce published findings. Here we report a new open source tool, AFQ-Browser, that builds an interactive website as a companion to a diffusion MRI study. Because AFQ-Browser is portable—it runs in any web-browser—it can facilitate transparency and data sharing. Moreover, by leveraging new web-visualization technologies to create linked views between different dimensions of the dataset (anatomy, diffusion metrics, subject metadata), AFQ-Browser facilitates exploratory data analysis, fueling new discoveries based on previously published datasets. In an era where Big Data is playing an increasingly prominent role in scientific discovery, so will browser-based tools for exploring high-dimensional datasets, communicating scientific discoveries, aggregating data across labs, and publishing data alongside manuscripts.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Complexation of NpO 2 + with Amine-Functionalized Diacetamide Ligands in Aqueous Solution: Thermodynamic, Structural, and Computational Studies

Complexation of Np(V) with three structurally related amine-functionalized diacetamide ligands, including 2,2'-azanediylbis( N, N'-dimethylacetamide) (ABDMA), 2,2'-(methylazanediyl)bis( N, N'-dimethylacetamide) (MABDMA), and 2,2'-(benzylazanediyl)bis( N, N'-dimethylacetamide) (BnABDMA), in aqueous solutions was investigated. The stability constants of two successive complexes, namely, NpO 2 L + and NpO 2 L 2 + , where L stands for the ligands, were determined by absorption spectrophotometry. The results suggest that the stability constants of corresponding Np(V) complexes follow the trend: MABDMA > ABDMA ≈ BnABDMA. The data are discussed in terms of the basicity of the ligands and compared with those for the complexation of Np(V) with an ether oxygen-linked diacetamide ligand. Extended X-ray absorption fine structure data indicate that, similar to the complexation with Nd 3+ and UO 2 2+ , the ligands coordinate to NpO 2 + in a tridentate mode through the amine nitrogen and two oxygen atoms of the amide groups. Furthermore, computational results, in conjunction with spectrophotometric data, verify that the 1:2 complexes (NpO 2 (L) 2 + ) in aqueous solutions are highly symmetric with Np at the inversion center, so that the f-f transition of Np(V) is forbidden and NpO 2 (L) 2 + does not display significant absorption in the near-IR region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Understanding the Response of Photosynthetic Metabolism in Tropical Forests to Seasonal Climate Variations

We propose a study focused on the basic question: What controls the response of photosynthesis in Amazonian forests to seasonal variations in climate? This question, despite its apparent simplicity, remains difficult for modern earth system models to answer, and is also the subject of continuing controversy in the remote-sensing literature. For example, in the modeling arena, four cutting-edge earth system models (ESM’s) show significant divergence in their seasonal patterns of photosynthesis from observed whole-system photosynthetic fluxes at two sites in the central Amazon. The overall objective of the project is to guide improvements in earth system models of tropical forest photosynthesis by collecting and integrating a suite of observations to 1) test several hypotheses (three core, conceptual hypotheses for explaining observed photosynthetic seasonality and a methodological hypotheses for scaling from leaves to canopy with hyperspectral cameras), and 2) perform a synthesis activity that applies our empirical work to earth system models of terrestrial carbon cycling. The project will provide an extensive suite of new and unique datasets that enable us to fill, through advanced modeling techniques and analysis, critical knowledge gaps in current understanding of what controls the response of canopy photosynthesis and related functions in Amazonian forests to seasonal variation in climate. Three major types of datasets and data products will be delivered: (1) in situ leaf and tree-scale measurements from intensive ecophysiological and ecohydological field campaigns, (2) time-series observations of leaf-to-crown scale forest reflectance properties and atmospheric radiation from two innovative, ground-based imaging sensors (respectively, the Hyperspectral Vegetation Imaging System and the High Dynamic Range All-Sky Imaging System), and (3) results from state-of-the-art models of 3-dimensional canopy processes for radiative transfer and photosynthesis that integrate and link our observations to tropical forest processes. These data products and the improved knowledge we achieve with them will contribute to testing and improving the treatment of tropical forest processes in ESMs. They will contribute data to and leverage related data from of the GOAmazon campaign, and make significant contributions to support the overall goals of GOAmazon. This work will also help establish a foundation for the Next Generation Ecosystem Experiments (NGEE) in the Tropics.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning

The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4-5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models.

60 APPLIED LIFE SCIENCES↗