Connecting soils to life in conservation planning, nutrient cycling, and planetary science
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58 GEOSCIENCES↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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A geometric framework for momentum-based optimizers for low-rank training
Low-rank pre-training and fine-tuning have recently emerged as promising techniques for reducing the computational and storage costs of large neural networks. Training low-rank parameterizations typically relies on conventional optimizers such as heavy ball momentum methods or Adam. In this work, we identify and analyze potential difficulties that these training methods encounter when used to train low-rank parameterizations of weights. In particular, we show that classical momentum methods can struggle to converge to a local optimum due to the geometry of the underlying optimization landscape. To address this, we introduce novel training strategies derived from dynamical low-rank approximation, which explicitly account for the underlying geometric structure. Our approach leverages and combines tools from dynamical low-rank approximation and momentum-based optimization to design optimizers that respect the intrinsic geometry of the parameter space. We validate our methods through numerical experiments, demonstrating faster convergence, and stronger validation metrics at given parameter budgets.
Schotthoefer, Steffen [ORNL] (ORCID:00000002156965↗
Science Breakthroughs 2030. Final report
Agriculture is a fundamental societal activity, characterized by many different landscapes, crops, markets, and participants. Food, agricultural, and biofuels products are central to the daily life of all citizens, though most do not recognize the fragility of the environment that brings forth this abundance. As is noted in the 2012 report from the President's Council of Advisors on Science and Technology, Agricultural Preparedness and the United States Agricultural Research Enterprise (PCAST, 2012) the food and agricultural system faces constant challenges in: Managing new pests, pathogens, and invasive plants. Increasing the efficiency of water use. Growing food in a changing climate. Reducing the environmental footprint of agriculture. Managing the production of bioenergy. Producing safe and nutritious food. Assisting with global food security and maintaining abundant yields. Science Breakthroughs 2030 was organized to identify the most compelling research directions in food and agriculture, in particular those empowered by the application of insights and tools from disciplines of science and engineering not typically associated with food and agricultural research. A committee appointed by the Chairman of the National Research Council explored ideas for research directions with input from the scientific community, with the objective of producing a report describing ambitious and achievable scientific pathways to address major problems and create new opportunities in food and agriculture. Following numerous meetings, a jamboree, and town hall, the appointed committee prepared a report that has subsequently become a reference for federal agencies supporting research in the food and agricultural space. It highlights five key areas for research investment with broad application across food and agriculture: integrated systems research; sensor development; data mining and information sciences, genomics; and the microbiome.
09 BIOMASS FUELS↗
Beneficial Use Impairments, Degradation of Aesthetics, and Human Health: A Review
In environmental programs and blue/green space development, improving aesthetics is a common goal. There is broad interest in understanding the relationship between ecologically sound environments that people find aesthetically pleasing and human health. However, to date, few studies have adequately assessed this relationship, and no summaries or reviews of this line of research exist. Therefore, we undertook a systematic literature review to determine the state of science and identify critical needs to advance the field. Keywords identified from both aesthetics and loss of habitat literature were searched in PubMed and Web of Science databases. After full text screening, 19 studies were included in the review. Most of these studies examined some measure of greenspace/bluespace, primarily proximity. Only one study investigated the impacts of making space quality changes on a health metric. The studies identified for this review continue to support links between green space and various metrics of health, with additional evidence for blue space benefits on health. No studies to date adequately address questions surrounding the beneficial use impairment degradation of aesthetics and how improving either environmental quality (remediation) or ecological health (restoration) efforts have impacted the health of those communities.
60 APPLIED LIFE SCIENCES↗
Accelerating Biological Insight for Understudied Genes
Synopsis The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.
Zoology↗
Selective consolidation of learning and memory via recall-gated plasticity
In a variety of species and behavioral contexts, learning and memory formation recruits two neural systems, with initial plasticity in one system being consolidated into the other over time. Moreover, consolidation is known to be selective; that is, some experiences are more likely to be consolidated into long-term memory than others. Here, we propose and analyze a model that captures common computational principles underlying such phenomena. The key component of this model is a mechanism by which a long-term learning and memory system prioritizes the storage of synaptic changes that are consistent with prior updates to the short-term system. This mechanism, which we refer to as recall-gated consolidation, has the effect of shielding long-term memory from spurious synaptic changes, enabling it to focus on reliable signals in the environment. We describe neural circuit implementations of this model for different types of learning problems, including supervised learning, reinforcement learning, and autoassociative memory storage. These implementations involve synaptic plasticity rules modulated by factors such as prediction accuracy, decision confidence, or familiarity. We then develop an analytical theory of the learning and memory performance of the model, in comparison to alternatives relying only on synapse-local consolidation mechanisms. We find that recall-gated consolidation provides significant advantages, substantially amplifying the signal-to-noise ratio with which memories can be stored in noisy environments. We show that recall-gated consolidation gives rise to a number of phenomena that are present in behavioral learning paradigms, including spaced learning effects, task-dependent rates of consolidation, and differing neural representations in short- and long-term pathways.
59 BASIC BIOLOGICAL SCIENCES↗
Coupling Waste Feedstocks to Microbial Protein for a Circular Food System
The global food system is responsible for approximately 34% of annual greenhouse gas (GHG) emissions and up to 85% of water consumption. This critical sector suffers from intensive and inefficient land and water use, the generation of multiple (solid, liquid, and gaseous) waste streams, and high fuel, fertilizer, and pesticide consumption. The production of waste-derived microbial protein (MP) represents a promising alternative for reducing the environmental impacts of protein production relative to conventional agriculture. MP can be mass-produced in volumetrically scalable cultivation processes on short timescales, enabling facile up-scaling with lower greenhouse gas emissions, land use, and water impacts than animal and, in some cases, plant protein production. MP can also be produced from waste feedstocks, diverting waste from landfills or the natural environment. Here, we present the availability and suitability of waste feedstocks for MP production, as well as the fermentation and downstream processes required to convert MP into human food products. We discuss the challenges and opportunities facing waste-derived bacterial MP and highlight key areas for innovation in both the microbiology and process design space for a more sustainable and circular food system.
BASIC BIOLOGICAL SCIENCES,ENERGY PLANNING, POLICY,↗
Studies of Alternative Ventilation Configurations to Mitigate Airborne Exposure Risks in Office Spaces
The objective of this study was to evaluate the impact of alternative ventilation configurations on airflow patterns and potential exposure risks in office spaces. Two existing conference rooms at Sandia NM were modeled using Computational Fluid Dynamics (CFD) simulations to characterize airflow patterns and potential airborne exposure risks in well-mixed and once-through (through-flow) ventilation conditions. Multiple scenarios were studied to evaluate the impact of occupancy, Plexiglass barriers, and a modified-return airflow configuration. Experimental and visualization tests were also conducted to validate the well-mixed and through-flow models and findings. The simulations demonstrated that the modified-return airflow configuration that promoted through-flow conditions reduced pathogen concentrations within the space compared to the well-mixed airflow configuration; occupancy reduction only reduced the number of exposed individuals, and Plexiglass barriers had almost no effect. The experimentally measured air speeds at nine anemometer locations generally matched the simulated airflow velocities, and a fog-purge visualization test was also consistent with simulated results of plume movement and dissipation. The visualization tests demonstrated improvements in air change rate with the modified return, which promoted through-flow conditions, versus the original well-mixed ventilation configuration. The results of this study demonstrate that minor modifications to a space that promote through-flow conditions can improve air quality and reduce pathogen concentrations. Additional airflow modeling and testing of alternative occupied space configurations are recommended to further inform room designs that mitigate airborne exposure risks for occupants.
42 ENGINEERING↗
Moon, Mars and Minds: Evaluating Parkinson’s disease mortality among U.S. radiation workers and veterans in the million person study of low-dose effects
Background: Radiation is one of the most important stressors related to missions in space beyond Earth’s orbit. Epidemiologic studies of exposed workers have reported elevated rates of Parkinson’s disease. The importance of cognitive dysfunction related to low-dose rate radiation in humans is not defined. A meta-analysis was conducted of six cohorts in the Million Person Study (MPS) of low-dose health effects to learn whether there is consistent evidence that Parkinson’s disease is associated with radiation dose to brain. Materials and methods: The MPS evaluates all causes of death among U.S. radiation workers and veterans, including Parkinson’s disease. Systematic and consistent methods are applied to study all categories of workers including medical radiation workers, industrial radiographers, nuclear power plant workers, atomic veterans, and Manhattan Projects workers at the Los Alamos National Laboratory and at Rocky Flats. Consistent methods for all cohorts are used to estimate organ-specific doses and to obtain vital status and cause of death. Results: The meta-analysis include 6 cohorts within the MPS, consisting of 517,608 workers and 17,219,001 person-years of observation. The mean dose to brain ranged from 6.9 to 47.6 mGy and the maximum dose from 0.76 to 2.7 Gy. Five of the 6 cohorts revealed positive associations with Parkinson’s disease. The overall summary estimate from the meta-analysis was statistically significant based on 1573 deaths due to Parkinson’s disease. The summary excess relative risk at 100 mGy was 0.17 (95% CI: 0.05; 0.29). Conclusions: Parkinson’s disease was positively associated with radiation in the MPS cohorts indicating the need for careful evaluation as to causality in other studies, delineation of possible mechanisms, and assessing possible implications for space travel as well as radiation protection guidance for terrestrial workers.
60 APPLIED LIFE SCIENCES↗
ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design
Abstract Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical ‘starters’ and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.
59 BASIC BIOLOGICAL SCIENCES↗
Constraints and variation in food web link-species space
Predicting food web structure in future climates is a pressing goal of ecology. These predictions may be impossible without a solid understanding of the factors that structure current food webs. Here, the most fundamental aspect of food web structure—the relationship between the number of links and species—is still poorly understood. Some species interactions may be physically or physiologically ‘forbidden'—like consumption by non-consumer species—with possible consequences for food web structure. We show that accounting for these ‘forbidden interactions' constrains the feasible link-species space, in tight agreement with empirical data. Rather than following one particular scaling relationship, food webs are distributed throughout this space according to shared biotic and abiotic features. Our study provides new insights into the long-standing question of which factors determine this fundamental aspect of food web structure.
59 BASIC BIOLOGICAL SCIENCES↗
Physical Sciences Vistas Issue 3 2021
In this issue, highlights of our contributions to mission operations include descriptions of the following. • How exact and scrupulous planning in concert with sophisticated science enabled a first-ever direct measurement of a radionuclide with a half-life as short as six days. The work, which included operations at the Los Alamos Neutron Science Centers (LANSCE) Weapons Neutron Research Facility and the Isotope Production Facility’s hot cell facility, is a boon for both astrophysics and weapons science. • An introduction to Christie Davis and her role in ensuring the Lab’s execution of simultaneous excellence. • A look at progress by AOT’s Target and Experimental Support Team in reclaiming long-dormant space in a radiological controlled area for new work improving target systems for the Lujan Center. • A story showcasing a cross-organizational effort to minimize the directorate’s legacy and environmental footprint. Staff from across the Lab joined together to ensure the safe and efficient disposal of Rocky Flats legacy waste stored in a transportainer at the Target Fabrication Facility. • How the Lab’s Utilities and Infrastructure experts collaborated with stakeholders in our directorate to safety execute preventive maintenance on the LANSCE mesa’s large electrical substation. The Safe Conduct of Research principles provided a common framework for the planning and process. • A description of the resources called upon and the procedures undertaken by MPA to inventory the division’s time-sensitive chemicals, including the careful and conscientious response of an alert team member when something seemed amiss.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
An integrated Imaging and Modeling Toolbox for Accelerated Development of Root-focused Crops at Field Scales
This project, led by Yuxin Wu at the LBNL, was proposed to develop an integrated imaging-modeling toolbox allowing for accelerated development of root-focused crops at field scales. Our approach is based on a novel root phenotyping method we termed Tomographic Electrical Rhizosphere Imaging (TERI), which provides advanced phenotyping of key root traits by sensing the electrical impedance response of roots and soil to external electrical excitations, and mapping these responses to root and soil properties. The role of Noble Research Institute in this project is to assist TERI model establishment and validation by collecting various above- and below-ground traits data from container- and field-grown plants (mainly wheat). Over the last three years, Noble Research Institute has conducted 3 phases of experiments as proposed including: (Phase 1) greenhouse and hoop-house experiments in wheat and pecan plants grown under controlled container-grown conditions; (Phase 2) space-planted individual plant field experiment using different wheat varieties; and (Phase 3) small-plot planted field experiment using different wheat varieties, as well as using different small grains species including wheat, rye, triticale, oat and barley for increasing plant variation.
60 APPLIED LIFE SCIENCES↗
OrganiCam: First Camera for Noncontact Biodetection in Space
Los Alamos National Laboratory designed a compact laser-induced fluorescence imaging camera with Raman spectrometer to identify organic molecules and biosignatures in environments such as Martian caves, icy-moons, and asteroid surfaces. OrganiCam is the primary instrument on the Laser-Induced Fluorescence Exploration of Caves for Organics and Volatiles using an Elevated Platform (LIFE COVE) NASA mission concept. OrganiCam could also determine if instruments being sent into space for NASA are sterile and analyze samples returned to Earth. OrganiCam’s robust design for extreme environments, portability, simple operation, and low power requirement build on LANL’s 50+ years designing robotic instruments for space applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational Modeling To Adapt Neutralizing Antibody
Monoclonal antibodies (mAbs) is the leading therapy for viral infections because it provides immediate protection and can be administered at higher levels than in a natural immune response. Finding mAbs that neutralize a broad spectrum of viral targets has proven difficult because many species and strains exist and blanket targeting is a slow and laborious process to experimentally screen 108 variants. A new method is needed to rapidly redesign mAbs for homologous targets. This project speeds up redesign using structure-based computational design to reduce the mAbs search space to a manageable level and screen mutants at a much higher rate than in experiments. Computation will also provide critical knowledge about the fundamental interactions. The project will adapt S230, a human antibody that neutralizes SARS-CoV, to neutralize SARS-COV-2.
60 APPLIED LIFE SCIENCES↗
Wind turbine blade material in the United States: Quantities, costs, and end-of-life options
Wind energy has experienced enormous growth in the past few decades; as a result, there are thousands of wind turbines around the world that will reach the end of their design lifetimes in the coming years. Much of the material in those turbines can be recycled using conventional processes, but the composite material that is the main component of the blades is more challenging to recycle. In the United States, turbine blades may be disposed of in landfills, adding a new solid waste stream to the material already being landfilled. This paper presents a spatially resolved estimate of the mass and volume of wind turbine blade waste in each state by 2050 and compares these amounts to estimates of the remaining landfill capacity by state. In this work, we estimate costs for each stage of the disposal process to indicate cost levels for alternatives. Assuming a 20-year turbine lifetime, the cumulative blade waste in 2050 is approximately 2.2 million tons. This value represents approximately 1% of remaining landfill capacity by volume, or 0.2% by mass. We also find that the current cost of disposing of blades in large segments or through grinding is relatively low in comparison to the overall life-cycle cost of energy. Based on these findings, landfill space constraints and disposal costs appear unlikely to motivate a change in waste handling strategies under current policy conditions. Instead, more profound shifts in recycling technologies, blade materials, or policy may be needed to move towards a circular economy for wind turbine blades.
17 WIND ENERGY↗
GAHLS: an optimized graph analytics based high level synthesis framework
The urgent need for low latency, high-compute and low power on-board intelligence in autonomous systems, cyber-physical systems, robotics, edge computing, evolvable computing, and complex data science calls for determining the optimal amount and type of specialized hardware together with reconfigurability capabilities. With these goals in mind, we propose a novel comprehensive graph analytics based high level synthesis (GAHLS) framework that efficiently analyzes complex high level programs through a combined compiler-based approach and graph theoretic optimization and synthesizes them into message passing domain-specific accelerators. This GAHLS framework first constructs a compiler-assisted dependency graph (CaDG) from low level virtual machine (LLVM) intermediate representation (IR) of high level programs and converts it into a hardware friendly description representation. Next, the GAHLS framework performs a memory design space exploration while account for the identified computational properties from the CaDG and optimizing the system performance for higher bandwidth. The GAHLS framework also performs a robust optimization to identify the CaDG subgraphs with similar computational structures and aggregate them into intelligent processing clusters in order to optimize the usage of underlying hardware resources. Finally, the GAHLS framework synthesizes this compressed specialized CaDG into processing elements while optimizing the system performance and area metrics. Evaluations of the GAHLS framework on several real-life applications (e.g., deep learning, brain machine interfaces) demonstrate that it provides 14.27× performance improvements compared to state-of-the-art approaches such as LegUp 6.2.
97 MATHEMATICS AND COMPUTING↗
2024 International Conference on Microbiome Engineering (ICME)
The 2024 International Conference on Microbiome Engineering (ICME) took place November 12-14 at Tufts University in Medford, MA. ICME connects experts from academia and industry to share the most recent developments in the field of microbiome engineering. This includes genetically engineered organisms that function within microbiomes, control of microbiomes through environmental/nutrient modifications, and inference of engineering principles from analysis of synthetic and natural microbiomes. The conference is unique and distinct from other microbiome conferences in that it specifically highlights the integration of engineering design principles with microbiome research (others are more focused on basic biological principles). The conference thus integrates synthetic biology, systems biology, microbial ecology, and bioinformatics across a range of application spaces from the environment to manufacturing, food, and human health. This project utilized support from the Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) to help trainees and early career faculty attend ICME.
60 APPLIED LIFE SCIENCES↗