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DOE OSTI2015

Cyanobacterial reuse of extracellular organic carbon in microbial mats

Cyanobacterial organic matter excretion is crucial to carbon cycling in many microbial communities, but the nature and bioavailability of this C depend on unknown physiological functions. Cyanobacteria-dominated hypersaline laminated mats are a useful model ecosystem for the study of C flow in complex communities, as they use photosynthesis to sustain a more or less closed system. Although such mats have a large C reservoir in the extracellular polymeric substances (EPSs), the production and degradation of organic carbon is not well defined. To identify extracellular processes in cyanobacterial mats, we examined mats collected from Elkhorn Slough (ES) at Monterey Bay, California, for glycosyl and protein composition of the EPS. We found a prevalence of simple glucose polysaccharides containing either α or β (1,4) linkages, indicating distinct sources of glucose with differing enzymatic accessibility. Using proteomics, we identified cyanobacterial extracellular enzymes, and also detected activities that indicate a capacity for EPS degradation. In a less complex system, we characterized the EPS of a cyanobacterial isolate from ES, ESFC-1, and found the extracellular composition of biofilms produced by this unicyanobacterial culture were similar to that of natural mats. By tracing isotopically labeled EPS into single cells of ESFC-1, we demonstrated rapid incorporation of extracellular-derived carbon. Taken together, these results indicate cyanobacteria reuse excess organic carbon, constituting a dynamic pool of extracellular resources in these mats.

Environmental Sciences & Ecology↗

DOE OSTI2025

Diet outperforms microbial transplant to drive microbiome recovery in mice

A high-fat, low-fibre Western-style diet (WD) induces microbiome dysbiosis characterized by reduced taxonomic diversity and metabolic breadth, which in turn increases risk for a wide array of metabolic, immune and systemic pathologies. Recent work has established that WD can impair microbiome resilience to acute perturbations such as antibiotic treatment, although little is known about the mechanism of impairment and the specific consequences for the host of prolonged post-antibiotic dysbiosis. Here, in this study, we characterize the trajectory by which the gut microbiome recovers its taxonomic and functional profile after antibiotic treatment in mice on regular chow (RC) or WD, and find that only mice on RC undergo a rapid successional process of recovery. Metabolic modelling indicates that a RC diet promotes the development of syntrophic cross-feeding interactions, whereas in mice on WD, a dominant taxon monopolizes readily available resources without releasing syntrophic byproducts. Intervention experiments reveal that an appropriate dietary resource environment is both necessary and sufficient for rapid and robust microbiome recovery, whereas microbial transplant is neither. Furthermore, prolonged post-antibiotic dysbiosis in mice on WD renders them susceptible to infection by the intestinal pathogen Salmonella enterica serovar Typhimurium. Our data challenge widespread enthusiasm for faecal microbiota transplant (FMT) as a strategy to address dysbiosis, and demonstrate that specific dietary interventions are, at a minimum, an essential prerequisite for effective FMT, and may afford a safer, more natural and less invasive alternative.

Kennedy, M. S. [University of Chicago, IL (United ↗

DOE OSTI2018

Utah FORGE: Drilling Data for Student Competition

Diagnostic drilling data (Pason log files) from Well 58-32 (previously labeled MU-ESW1), which was drilled near Milford Utah during Phase 2B of the FORGE Project to confirm geothermal reservoir characteristics met requirements for the final FORGE site. This dataset includes both raw, unprocessed drilling data recorded at 1Hz and a processed version downscaled to ~0.3m (1 ft) intervals. Diagnostic drilling data were collected to obtain useful information regarding the nature of the subsurface materials and performance of the drilling rig and drilling bits, including rate of penetration (ROP), weight on bit, temperature, pump pressure, etc.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions

Introduction Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress ( Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Methods Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing). Results Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density. Discussion These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

A review of initial investigations to utilize ERTS-1 data in determining the availability and distribution of living marine resources

This study was initiated in July 1972 to determine the reliability of satellite and high altitude sensors to provide data about oceanographic parameters in coastal waters; demonstrate the use of remotely sensed oceanographic information to predict the distribution and abundance of adult menhaden; and, demonstrate the potential of using satellite acquired information for improving the harvest and management of a fishery resource. The study focused on coastal are as in the north central portion of the Gulf of Mexico including parts of Alabama, Mississippi and Louisiana. The area used in the final analysis was limited to the Mississippi Sound, which is approximately 145 kilometers (90 miles) long and 16 kilometers (10 miles) wide, has an average water depth of about 3.7 meters (12 feet), and in general characterizes an estuarine environment.

Stevenson, W. H.↗

NASA NTRS1988

Massive parallelism in the future of science

Massive parallelism appears in three domains of action of concern to scientists, where it produces collective action that is not possible from any individual agent's behavior. In the domain of data parallelism, computers comprising very large numbers of processing agents, one for each data item in the result will be designed. These agents collectively can solve problems thousands of times faster than current supercomputers. In the domain of distributed parallelism, computations comprising large numbers of resource attached to the world network will be designed. The network will support computations far beyond the power of any one machine. In the domain of people parallelism collaborations among large groups of scientists around the world who participate in projects that endure well past the sojourns of individuals within them will be designed. Computing and telecommunications technology will support the large, long projects that will characterize big science by the turn of the century. Scientists must become masters in these three domains during the coming decade.

Denning, Peter J.↗

NASA NTRS2001

Four Generations of Maintenance Resource Management Programs in the United States: An Analysis of the Past, Present, and Future

This paper analyzes four generations of Maintenance Resource Management (MRM) programs implemented by aviation maintenance organizations in the United States. Data collected from over ten years of survey research and field observations are used for this analysis; they are presented in a case-study format. The first three generations of MRM programs were episodic efforts to increase safety through teamwork, focus group discussions, and awareness courses, respectively. Now, the fourth generation programs, characterized by a commitment to long-term communication and behavioral changes in maintenance, are set to build on those earlier generations, toward a culture of mutual trust between mechanics, their managers, and regulators.

Taylor, James C.↗

NASA NTRS2003

Requirements Development for the NASA Advanced Engineering Environment (AEE)

The requirements development process for the Advanced Engineering Environment (AEE) is presented. This environment has been developed to allow NASA to perform independent analysis and design of space transportation architectures and technologies. Given the highly collaborative and distributed nature of AEE, a variety of organizations are involved in the development, operations and management of the system. Furthermore, there are additional organizations involved representing external customers and stakeholders. Thorough coordination and effective communication is essential to translate desired expectations of the system into requirements. Functional, verifiable requirements for this (and indeed any) system are necessary to fulfill several roles. Requirements serve as a contractual tool, configuration management tool, and as an engineering tool, sometimes simultaneously. The role of requirements as an engineering tool is particularly important because a stable set of requirements for a system provides a common framework of system scope and characterization among team members. Furthermore, the requirements provide the basis for checking completion of system elements and form the basis for system verification. Requirements are at the core of systems engineering. The AEE Project has undertaken a thorough process to translate the desires and expectations of external customers and stakeholders into functional system-level requirements that are captured with sufficient rigor to allow development planning, resource allocation and system-level design, development, implementation and verification. These requirements are maintained in an integrated, relational database that provides traceability to governing Program requirements and also to verification methods and subsystem-level requirements.

Rogers, Eric↗

NASA NTRS2011

Ares I-X Range Safety Analyses Overview

Ares I-X was the first test flight of NASA's Constellation Program's Ares I Crew Launch Vehicle designed to provide manned access to low Earth orbit. As a one-time test flight, the Air Force's 45th Space Wing required a series of Range Safety analysis data products to be developed for the specified launch date and mission trajectory prior to granting flight approval on the Eastern Range. The range safety data package is required to ensure that the public, launch area, and launch complex personnel and resources are provided with an acceptable level of safety and that all aspects of prelaunch and launch operations adhere to applicable public laws. The analysis data products, defined in the Air Force Space Command Manual 91-710, Volume 2, consisted of a nominal trajectory, three sigma trajectory envelopes, stage impact footprints, acoustic intensity contours, trajectory turn angles resulting from potential vehicle malfunctions (including flight software failures), characterization of potential debris, and debris impact footprints. These data products were developed under the auspices of the Constellation's Program Launch Constellation Range Safety Panel and its Range Safety Trajectory Working Group with the intent of beginning the framework for the operational vehicle data products and providing programmatic review and oversight. A multi-center NASA team in conjunction with the 45th Space Wing, collaborated within the Trajectory Working Group forum to define the data product development processes, performed the analyses necessary to generate the data products, and performed independent verification and validation of the data products. This paper outlines the Range Safety data requirements and provides an overview of the processes established to develop both the data products and the individual analyses used to develop the data products, and it summarizes the results of the analyses required for the Ares I-X launch.

Starr, Brett R.↗

NASA NTRS2011

Ares I-X Range Safety Flight Envelope Analysis

Starr, Brett R.↗

NASA NTRS2018

Additive Construction with Mobile Emplacement: Multifaceted Planetary Construction Materials Development

The National Aeronautics and Space Administration's Additive Construction with Mobile Emplacement (ACME) project is developing construction materials with which infrastructure elements, including habitats, will be additively constructed for planetary surface missions. These materials must meet requirements such as the ability to be produced from available in-situ resources to eliminate the cost of launching materials from Earth, the ability to be emplaced via three dimensional building techniques, the ability to resist aging in extreme environments including radiation and micrometeorite bombardment, and the ability to provide the necessary structural integrity for a given building. This paper reviews the constraints placed on such planetary construction materials and details the work of the ACME team in characterizing materials that could one day construct planetary surface structures on Mars or the Moon. Material compositions, compressive strength, and requirements for additive construction on planetary surfaces are discussed. Due to the multifunctional requirements of the material, an optimization is necessary to balance between the site-specific regolith composition, emplacement via additive construction techniques, and characteristics of the final structure.

simulant↗

DOE OSTI2021

Limitations of Hartree–Fock with quantum resources

The Hartree–Fock problem provides the conceptual and mathematical underpinning of a large portion of quantum chemistry. As efforts in quantum technology aim to enhance computational chemistry algorithms, the Hartree–Fock method, central to many other numerical approaches, is a natural target for quantum enhanced algorithms. While quantum computers and quantum simulation offer many prospects for the future of modern chemistry, the non-deterministic polynomial-complete Hartree–Fock problem is not a likely candidate. Here, we highlight this fact from a number of perspectives including computational complexity, practical examples, and the full characterization of energy landscapes for simple systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Large-scale parametric modeling of spent nuclear fuel dynamics in the 30 cm package drop scenario

Packages used to transport spent nuclear fuel (SNF) are required by the U.S. Code of Federal Regulations 10 CFR 71.71 to demonstrate satisfactory performance during a drop scenario. While the CFR is meant to ensure safe package function, it does not evaluate survival of the SNF within. The U.S. Department of Energy Spent Fuel and Waste Science and Technology program is working on closing the knowledge gap related to the response of SNF to external mechanical loads, including the hypothetical 30 cm package drop scenario in the CFR. In support of this effort, LS-DYNA finite element simulations were developed by Pacific Northwest National Laboratory (PNNL) to model generic drop scenarios at both the package and fuel assembly level. The models were validated against one-third scale package and full scale fuel assembly drop test data and were exercised to predict fuel cladding strains in a narrow range of model configurations. This work describes a large-scale parametric study conducted by PNNL using the previously developed and validated PWR finite element model, with the addition of a new generic BWR assembly model. The motivation for the parametric study was to characterize the broad range of SNF responses in the 30 cm package drop scenario. This was accomplished by varying the drop orientation, fuel assembly type (17x17 PWR and 10x10 BWR), burnup, cladding temperature, spacer grid buckling load, package mass, impact limiter stiffness, and mechanical gap conditions within the basket. A MATLAB framework was developed to automate LS-DYNA model generation and execution on PNNL institutional computing resources. In total, over 2000 simulations were performed. For each simulation, the SNF response was quantified in terms of permanent grid deformation, fuel rod contact pressure, and strains within the fuel rods, guide tubes, and water rods. The results provide valuable insight into the range of responses that could be reasonably expected from SNF in the hypothetical drop scenario, as well as the sensitivity to each input parameter. The results of this parametric study are a key component of the testing and modeling strategy the Spent Fuel and Waste Science and Technology program is using to close the external loads knowledge gap.

Kadooka, Kevin↗

DOE OSTI2023

Discrete Measurements of the Least Horizontal Principal Stress from Core Data: An Application of Viscoelastic Stress Relaxation

Summary The emerging Paradox Oil Play in southeastern Utah is among the most significant unconventional plays in the western USA. The mean total undiscovered oil resources within just the Pennsylvanian Cane Creek interval of the Paradox Basin are believed to exceed 215 million barrels. However, to date, less than 5% (~9 million barrels) of the total Cane Creek resource has been produced from fewer than 40 wells, and only approximately one-half of those are horizontal wells. More than 95% of production is from the central Cane Creek Unit (CCU). Natural fractures are a key feature of many production wells, but stimulation by induced hydraulic fractures is not consistently successful. We hypothesize that more effective production in this play will rely on better fundamental characterization, especially on better quantification of the state of stress. Approximately 110 ft of core, well logs, and a diagnostic fracture injection test (DFIT) were acquired from the State 16-2 well within the CCU. With these data, we applied two methods to constrain and clarify the state of stress. The first technique, the Simpson’s coefficient method, provides lower bounds on the two horizontal principal stresses and relies on only limited data. Alternatively, the viscoelastic stress relaxation (VSR) method is used to estimate the least horizontal principal stress, building on observations that principal stresses become more isotropic as the viscous behavior of a rock is more pronounced. Results of these two methods support the hypothesis that the state of stress in the CCU of the Paradox Basin is nearly lithostatic and isotropic. Other factors consistent with this hypothesis include high formation pore pressure, which tends to reduce the possible stress states by changing the frictional failure equilibrium; lack of induced fractures in the core, which should be present in the case of stress anisotropy; and interbedded halite layers, which given their high degree of ductility, probably lead to greater VSR for the entire sedimentary package.

Energy & Fuels↗

DOE OSTI2016

A Review of Current Machine Learning Methods Used for Cancer Recurrence Modeling and Prediction

Cancer has been characterized as a heterogeneous disease consisting of many different subtypes. The early diagnosis and prognosis of a cancer type has become a necessity in cancer research. A major challenge in cancer management is the classification of patients into appropriate risk groups for better treatment and follow-up. Such risk assessment is critically important in order to optimize the patient’s health and the use of medical resources, as well as to avoid cancer recurrence. This paper focuses on the application of machine learning methods for predicting the likelihood of a recurrence of cancer. It is not meant to be an extensive review of the literature on the subject of machine learning techniques for cancer recurrence modeling. Other recent papers have performed such a review, and I will rely heavily on the results and outcomes from these papers. The electronic databases that were used for this review include PubMed, Google, and Google Scholar. Query terms used include “cancer recurrence modeling”, “cancer recurrence and machine learning”, “cancer recurrence modeling and machine learning”, and “machine learning for cancer recurrence and prediction”. The most recent and most applicable papers to the topic of this review have been included in the references. It also includes a list of modeling and classification methods to predict cancer recurrence.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Towards improved and more routine Earth system model evaluation in CMIP

The Coupled Model Intercomparison Project (CMIP) has successfully provided the climate community with a rich collection of simulation output from Earth system models (ESMs) that can be used to understand past climate changes and make projections and uncertainty estimates of the future. Confidence in ESMs can be gained because the models are based on physical principles and reproduce many important aspects of observed climate. More research is required to identify the processes that are most responsible for systematic biases and the magnitude and uncertainty of future projections so that more relevant performance tests can be developed. At the same time, there are many aspects of ESM evaluation that are well established and considered an essential part of systematic evaluation but have been implemented ad hoc with little community coordination. Given the diversity and complexity of ESM analysis, we argue that the CMIP community has reached a critical juncture at which many baseline aspects of model evaluation need to be performed much more efficiently and consistently. We provide a perspective and viewpoint on how a more systematic, open, and rapid performance assessment of the large and diverse number of models that will participate in current and future phases of CMIP can be achieved, and announce our intention to implement such a system for CMIP6. Accomplishing this could also free up valuable resources as many scientists are frequently "re-inventing the wheel" by re-writing analysis routines for well-established analysis methods. A more systematic approach for the community would be to develop and apply evaluation tools that are based on the latest scientific knowledge and observational reference, are well suited for routine use, and provide a wide range of diagnostics and performance metrics that comprehensively characterize model behaviour as soon as the output is published to the Earth System Grid Federation (ESGF). The CMIP infrastructure enforces data standards and conventions for model output and documentation accessible via the ESGF, additionally publishing observations (obs4MIPs) and reanalyses (ana4MIPs) for model intercomparison projects using the same data structure and organization as the ESM output. This largely facilitates routine evaluation of the ESMs, but to be able to process the data automatically alongside the ESGF, the infrastructure needs to be extended with processing capabilities at the ESGF data nodes where the evaluation tools can be executed on a routine basis. Efforts are already underway to develop community-based evaluation tools, and we encourage experts to provide additional diagnostic codes that would enhance this capability for CMIP. And, at the same time, we encourage the community to contribute observations and reanalyses for model evaluation to the obs4MIPs and ana4MIPs archives. The intention is to produce through the ESGF a widely accepted quasi-operational evaluation framework for CMIP6 that would routinely execute a series of standardized evaluation tasks. Over time, as this capability matures, we expect to produce an increasingly systematic characterization of models which, compared with early phases of CMIP, will more quickly and openly identify the strengths and weaknesses of the simulations. This will also reveal whether long-standing model errors remain evident in newer models and will assist modelling groups in improving their models. Finally, this framework will be designed to readily incorporate updates, including new observations and additional diagnostics and metrics as they become available from the research community.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Results for the January 2023 Semiannual Tank 50 Salt Solution Sample

In this Technical Report, the chemical and radionuclide contaminant results from the January 2023 Semiannual sample of Tank 50 salt solution are presented in tabulated form. The information from this characterization will be used by Savannah River Mission Completion (SRMC) for the transfer of aqueous waste from Tank 50 to the Saltstone Production Facility (SPF), where the waste will be treated and disposed in the Saltstone Disposal Facility. This Technical Report compares results, where applicable, to SPF Waste Acceptance Criteria (WAC) LIMITS and TARGETS that were established at the time the Tank 50 sample was obtained.1 The chemical and radionuclide contaminant results from the characterization of the January 2023 semiannual sampling of Tank 50 were requested by SRMC personnel via a Task Technical Request (TTR)2 and details of the testing are presented in the Savannah River National Laboratory (SRNL) Task Technical and Quality Assurance Plan (TTQAP).3 This Technical Report is part of Deliverable 2 relating to Task 1 from the SRMC request.2 Data pertaining to the regulatory limits for Resource Conservation and Recovery Act (RCRA) metals per Task 2 from the SRMC request will be obtained semiannually for the January 2023 and July 2023 Tank 50 samples.

Crawford, Charles L.↗