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All sources NASA NTRS DOE OSTI

DOE OSTI2017

Quantum Accelerators for High-performance Computing Systems

We define some of the programming and system-level challenges facing the application of quantum processing to high-performance computing. Alongside barriers to physical integration, prominent differences in the execution of quantum and conventional programs challenges the intersection of these computational models. Following a brief overview of the state of the art, we discuss recent advances in programming and execution models for hybrid quantum-classical computing. We discuss a novel quantum-accelerator framework that uses specialized kernels to offload select workloads while integrating with existing computing infrastructure. We elaborate on the role of the host operating system to manage these unique accelerator resources, the prospects for deploying quantum modules, and the requirements placed on the language hierarchy connecting these different system components. We draw on recent advances in the modeling and simulation of quantum computing systems with the development of architectures for hybrid high-performance computing systems and the realization of software stacks for controlling quantum devices. Finally, we present simulation results that describe the expected system-level behavior of high-performance computing systems composed from compute nodes with quantum processing units. We describe performance for these hybrid systems in terms of time-to-solution, accuracy, and energy consumption, and we use simple application examples to estimate the performance advantage of quantum acceleration.

Humble, Travis↗

DOE OSTI2026

Universal Jaynes-Cummings Control of an Oscillator

The Jaynes-Cummings (JC) interaction-the coherent exchange of excitations between a two-level system and a harmonic oscillator-is one of the fundamental interactions of quantum optics, realized across platforms such as cavity quantum electrodynamics, trapped ions, mechanical resonators, and superconducting circuits. Although JC interactions and qubit rotations form a universal gate set for oscillator control, practical implementations have not been demonstrated. Here we develop and experimentally demonstrate universal JC-based oscillator control by compiling arbitrary unitary gates into sequences of JC interactions and qubit rotations. In our experiment, the oscillator is realized using a mode of a high quality factor microwave cavity and the ancilla qubit using a superconducting transmon circuit, with the JC interaction implemented by a sideband interaction enabled by the Josephson nonlinearity. The native gates are constructed to be closed below a chosen cutoff photon number, encoding a qudit with suppressed leakage errors, while ancilla relaxation errors are detectable. We further find that the dispersive shift serves as a compilation resource that reduces circuit depths. We demonstrate universal qudit control and implement a single-qutrit gate set with a mean post-selected process fidelity of 96%, as well as ququart and ququint shift gates. These results establish Jaynes-Cummings control as a practical route to universal oscillator control, enabling programmable bosonic processors across a variety of quantum platforms.

Huang, Jordan [Rutgers U., Piscataway]↗

DOE OSTI2024

Antarctic Soils Select Copiotroph-Dominated Bacteria

The life strategies of bacterial communities determine their structure and function and are an important driver of biogeochemical cycling. However, the variations in these strategies under different soil resource conditions remain largely unknown. We explored the bacterial life strategies and changes in structure and functions between Antarctic soils and forest (temperate, subtropical, and tropical) soils. The results showed that the weighted mean rRNA operon copy number in temperate soils was 19.5% lower than that in Antarctic soils, whereas no significant differences were observed among Antarctic, subtropical, and tropical soils. An unexpected result was that bacterial communities in Antarctic soils tended to be copiotrophs, such as Actinobacteriota and Bacteroidota, whereas those in temperate soils tended to be oligotrophs, such as Acidobacteriota and Chloroflexi. Functional predictions showed that in comparison to copiotrophs in Antarctic soils, temperate-inhabiting oligotrophic bacteria exhibited an 84.2–91.1% lower abundance of labile C decomposition genes (hemicellulose, cellulose, monosaccharides, and disaccharides), whereas a 74.4% higher abundance of stable C decomposition (lignin). Genes involved in N cycling (nitrogen fixation, assimilatory nitrate reduction, and denitrification) were 24.3–64.4% lower in temperate soils than in Antarctic soils. Collectively, our study provides a framework for describing the life strategies of soil bacteria, which are crucial to global biogeochemical cycles.

Microbiology↗

DOE OSTI2020

A Comparison of DER Voltage Regulation Technologies Using Real-Time Simulations

Grid operators are now considering using distributed energy resources (DERs) to provide distribution voltage regulation rather than installing costly voltage regulation hardware. DER devices include multiple adjustable reactive power control functions, so grid operators have the difficult decision of selecting the best operating mode and settings for the DER. In this work, we develop a novel state estimation-based particle swarm optimization (PSO) for distribution voltage regulation using DER-reactive power setpoints and establish a methodology to validate and compare it against alternative DER control technologies (volt–VAR (VV), extremum seeking control (ESC)) in increasingly higher fidelity environments. Distribution system real-time simulations with virtualized and power hardware-in-the-loop (PHIL)-interfaced DER equipment were run to evaluate the implementations and select the best voltage regulation technique. Each method improved the distribution system voltage profile; VV did not reach the global optimum but the PSO and ESC methods optimized the reactive power contributions of multiple DER devices to approach the optimal solution.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

Sequential Perturbation-based FDIA Detection using DERs for Unbalanced Distribution System

The power distribution system with its reliance on automated monitoring and control infrastructure makes it a complicated cyber-physical system and vulnerable to various cyber-attacks. This paper proposes a moving target defense inspired false data injection attack (FDIA) detection mechanism for an unbalanced distribution system. In the proposed grid diagnosis service framework, the distribution system operator judiciously manipulates power outputs of a subset of inverter-based distribution energy resources (DERs) to create secret low magnitude voltage perturbations which are inconsequential to the normal operation of the grid. A mixed-integer-linear-programming algorithm is developed to select the optimal set of DERs that can create a voltage perturbation signal of the required magnitude at each sensor location at a minimum cost. Then, a sequential detector is applied that detects for the FDIA as measurements are received from individual sensors. The performance of the proposed perturbation-based FDIA detection framework is demonstrated via simulation of the IEEE 123 bus test system.

Attack Detection↗

DOE OSTI2022

Comprehensive Study of the Potential of Extracting and Processing Critical Minerals from Coal-Based Resources - Phase I

The Phase I report prepared for the Department of Energy addresses U.S. Executive Order 13817 titled A Federal Strategy to Ensure Secure and Reliable Supplies of Critical Minerals, issued on December 20, 2017, that lists 35 critical minerals that are vulnerable to supply disruption. A comprehensive review of each of the minerals was conducted to determine the criticality based primarily on extractability from coal-based resources. Several other factors were also considered such as gaps in supply and demand, use in current technology, and the existence of viable substitutes. It was determined that the critical minerals that show highest potential for extraction from coal-based resources are lithium, rare earth elements (REEs), cobalt, and manganese. All four of the critical minerals listed serve an important role in the technology industry, have few substitutes, and have a heavy import reliance. Most notably are lithium, which is widely used in the electric vehicle industry, and the REEs which can be found in virtually all electronic devices. The research of critical mineral extraction from coal-based resources was completed using a combination of literature review from public sources as well as cooperation from coal mines and power plants across the United States. Samples collected from six different geographical locations across the U.S. were subjected to sample preparation (i.e., pH measurement, moisture content, particle size analysis) and characterization studies using Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS) and Scanning Electron Microscopy, Energy Dispersive X-Ray Spectroscopy (SEM-EDX) instruments. 27 samples of coal waste materials such as refuse, sludge, and fly ash were tested to characterize the rare earth element concentration by total rare earth elements (TREEs), heavy rare earth elements (HREEs), and light rare earth elements (LREEs). Of the 27 samples tested, 22 contained a TREE concentration higher than the threshold of 300 ppm, which is considered a viable feedstock material. 3 samples contained less than 300 ppm of TREEs; however, they were within 20 ppm of the threshold, and could potentially be considered viable sources in the future pending the advancement of more efficient extraction technologies. 2 of the 27 samples had significantly low TREE concentrations, which does not imply any potential for being a source for REEs. For the minerals identified as most critical in the literature review, a conceptual process flow diagram (PFD) was developed for their extraction from different coal-based feedstocks. The process targets selective recovery of one commodity (i.e., rare earths, lithium, cobalt, and manganese) via several hydrometallurgical separation methods. By identifying potentially extractable coal-based critical mineral resources, a study of the current and future market environments for each critical mineral, and a review of current processing methodologies for critical mineral extraction from coal-based resources, the foundation has been laid to further characterize and explore new resources and extraction techniques. As reliance on technologies in industries such as the production of electronic devices, batteries, and alloys containing critical minerals utilizing critical minerals continues to increase, a sound understanding of our nation’s dependence on and even the global criticality of certain critical minerals, will serve as a catalyst for innovation in virtually all fields of science.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2022

Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters

The one-carbon recursive ketoacid elongation pathway is responsible for making various branched-chain amino acids, aldehydes, alcohols, and acetate esters in living cells. Controlling selective microbial biosynthesis of these target molecules at high efficiency is challenging due to enzyme promiscuity, regulation, and metabolic burden. In this study, we present a systematic modular design approach to control proteome reallocation for selective microbial biosynthesis of branched-chain acetate esters. Through pathway modularization, we partitioned the branched-chain ester pathways into four submodules including keto-isovalerate submodule for converting pyruvate to keto-isovalerate, ketoacid elongation submodule for producing longer carbon-chain keto-acids, ketoacid decarboxylase submodule for converting ketoacids to alcohols, and alcohol acyltransferase submodule for producing branched-chain acetate esters by condensing alcohols and acetyl-CoA. By systematic manipulation of pathway gene replication and transcription, enzyme specificity of the first committed steps of these submodules, and downstream competing pathways, we demonstrated selective microbial production of isoamyl acetate over isobutyl acetate. In this work, we found that the optimized isoamyl acetate pathway globally redistributed the amino acid fractions in the proteomes and required up to 23-31% proteome reallocation at the expense of other cellular resources, such as those required to generate precursor metabolites and energy for growth and amino acid biosynthesis. From glucose fed-batch fermentation, the engineered strains produced isoamyl acetate up to a titer of 8.8 g/L (> 0.25 g/L toxicity limit), a yield of 0.22 g/g (61% of maximal theoretical value), and 86% selectivity, achieving the highest titers, yields and selectivity of isoamyl acetate reported to date.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2018

NASA Pilot-Engaged Expert Response Using IBM Watson Technology: Prototype Evaluation of Knowledge Retrieval System

NASA Langley Research Center and IBM have been investigating the use of IBM Watson technology in aerospace research and development. One application of Watson technology is the Pilot-Engaged Expert Response (PEER) use case. The PEER system is envisioned as an in-cockpit advisor that will act as a source of situationally-relevant information for pilots and other flight crew members to assist in decision making about real-time events and situations that arise in the course of aircraft operations. PEER will make available vast stores of knowledge and information quickly and directly, putting important informational resources where they are needed most. IBM has worked with NASA to develop an architecture and articulate a roadmap for the development of the PEER system. That vision is built around Watson Discovery Advisor (WDA) software solution, derived from IBM's Jeopardy!-winning automatic question answering system. PEER makes use of WDA's sophisticated question-answering capabilities as its core, adding important User Interface components and other customizations for the cockpit environment, including communication with flight systems and other external data sources. The development plan for PEER includes four development stages, with the current project constituting the first phase. In this project, a prototype instance of PEER was successfully adapted to the aviation domain, enabling users to ask questions about aviation topics and receive useful and accurate answers to these questions. Major tasks accomplished include the development of procedures for domain adaptation through automatic lexicon extraction from domain glossaries; generation of question-answer training data which was used to train the system; and assessment of the effectiveness of domain adaptation, which showed a dramatic improvement in the ability of the PEER system to answer domain-relevant questions. In addition, the vision for the PEER system was pushed forward by the articulation of a plan for the automatic enhancement of question-answering with contextual information. This initial phase focused on two main goals: 1) the targeted domain adaptation of the underlying WDA system to the aviation domain; and, 2) the design of the software systems needed to leverage flight-contextual data. Domain adaptation of the WDA system proceeds via three main activities: Domain data ingestion, lexical customization and model training. A textual corpus consisting of 1,147 individual documents with more than 7.5 million words of text was ingested into the system and this served as the basis of all further development. A domain lexicon of over 3,500 aviation-domain terms was semi-automatically generated from domain documents and used to train the system. In addition, a set of over 500 question-answer (QA) pairs relevant to the PEER use case was developed; these were used to train and assess the system. These important first steps established the basis for the PEER system. In addition, steps were taken towards the integration of the PEER system into the cockpit environment with the development of a functional design for the Contextual Data Augmentation (CDA) subsystem. This subsystem brings to bear contextual data to improve system responses. It has three main submodules: the Contextual Data Collection module, the Contextual Data Selection module, and the Contextual QA Augmentation module. These modules form a processing pipeline that addresses the problems associated with automatically integrating information from external resources into the knowledge-retrieval mechanism.

Machine learning↗

DOE OSTI2014

Benefits of Greenhouse Gas Mitigation on the Supply, Management, and Use of Water Resources in the United States

Climate change impacts on water resources in the U.S. are likely to be far-reaching and substantial, because the water sector spans many parts of the economy, from supply and demand for agriculture, industry, energy production, transportation and municipal use to damages from natural hazards. This paper provides impact and damage estimates from five water resource-related models in the CIRA frame work, addressing drought risk, flooding damages, water supply and demand, and global water scarcity. The four models differ in the water system assessed, their spatial scale, and the units of assessment, but together they provide a quantitative and descriptive richness in characterizing water resource sector effects of climate change that no single model can capture. The results also address the sensitivity of these estimates to greenhouse gas emission scenarios, climate sensitivity alternatives, and global climate model selection. While calculating the net impact of climate change on the water sector as a whole may be impractical, because each of the models applied here uses a consistent set of climate scenarios, broad conclusions can be drawn regarding the patterns of change and the benefits of GHG mitigation policies for the water sector. Two key findings emerge: 1) climate mitigation policy substantially reduces the impact of climate change on the water sector across multiple dimensions; and 2) the more managed the water resources system, the more tempered the climate change impacts and the resulting reduction of impacts from climate mitigation policies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

NASA NTRS1992

To build a mine: Prospect to product

The terrestrial definition of ore is a quantity of earth materials containing a mineral that can be extracted at a profit. While a space-based resource-gathering operation may well be driven by other motives, such an operation should have the most favorable cost-benefit ratio possible. To this end, principles and procedures already tested by the stringent requirements of the profit motive should guide the selection, design, construction, and operation of a space-based mine. Proceeding from project initiation to a fully operational mine requires several interacting and overlapping steps, which are designed to facilitate the decision process and insure economic viability. The steps to achieve a fully operational mine are outlined. Presuming that the approach to developing nonterrestrial resources will parallel that for developing mineral resources on Earth, we can speculate on some of the problems associated with developing lunar and asteroidal resources. The baseline for our study group was a small lunar mine and oxygen extraction facility. The development of this facility is described in accordance with the steps outlined.

Gertsch, Richard E.↗

DOE OSTI2024

Investigating Mountain Watershed Headwater‐To‐Groundwater Connections, Water Sources, and Storage Selection Behavior With Dynamic‐Flux Particle Tracking

Abstract Climate change will impact mountain watershed streamflow both directly—with changing precipitation amounts and variability—and indirectly—through temperature shifts altering snowpack, melt, and evapotranspiration. To understand how these complex processes will affect ecosystem functioning and water resources, we need tools to distinguish connections between water sources (rain/snowmelt), groundwater storage, and exit fluxes (streamflow/evapotranspiration), and to determine how these connections change seasonally and as climate shifts. Here, we develop novel watershed‐scale approaches to understand water source, storage, and exit flux connections using a dynamic‐flux particle tracking model (EcoSLIM) applied in California's Cosumnes Watershed, which connects the Sierra Nevada and Central Valley. This work develops new visualizations and applications to provide mechanistic understanding that underpins the interpretation of isotopic field data at watershed scales to distinguish sources, flow paths, residence times, and storage selection. In our simulations, streamflow comes primarily from snow‐derived water while evapotranspiration generally comes from rain. Most streamflow starts above 1,000 m while evapotranspiration is sourced relatively evenly across the watershed and is generally younger than streamflow. Modeled streamflow consists primarily of water sourced from precipitation in the previous 5 years but before the current water year, while ET consists primarily of water from precipitation in the current water year. ET, and to a lesser extent streamflow, are both younger than water in groundwater storage. However, snowmelt‐derived streamflow preferentially discharges older water from snow‐derived storage. Dynamic‐flux particle tracking and new approaches presented here enable novel model‐tracer comparisons in large‐scale watersheds to better understand watershed behavior in a changing climate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Decadal-Scale Hydrothermal Alteration of Basalt: Implications for Long-Term Reactivity in Subsurface Technologies

Global demands to secure critical mineral supply chains and managing water resources require innovative resource management strategies. Subsurface basalt reservoirs offer a dual-purpose application, where CO2 enhanced critical metal recovery can be coupled with water remediation strategies for the extraction of economically important and environmentally relevant elements. This study utilizes static batch experiments conducted on Columbia River Basalt Group samples to evaluate long-term fluid–rock interactions relevant to coupled subsurface applications. Samples were reacted under elevated temperature and pressure conditions, for 296 and 4,061 days, providing a unique dataset to assess geochemical evolution, element partitioning, and aqueous chemistry over decadal timescales. The alteration was dominated by silicate, aluminosilicate, and oxide phases. Progressive hydrothermal alteration increased the cation exchange capacity through the formation of secondary minerals (e.g. clays and zeolites), influencing solute retention, ion exchange behavior, and aqueous chemistry. Grain-scale and bulk analyses revealed selective cation release and retention patterns, establishing a mechanistic baseline for predicting element mobility. These geochemical constraints inform the prospective use of CO2-enhanced metal recovery for critical resources (e.g. Co, Ni, Mn, Mg, Ti, Fe) and associated water-quality impacts, providing a foundation for the design and management of engineered fluid–rock systems in basalt reservoirs.

Gibson, Marie N.↗

DOE OSTI2021

Modeling Variable Renewable Energy and Storage in the Power Sector

The emergence of variable renewable energy and battery storage technologies have fundamentally transformed the electric power sector and generated demand for analysis to understand their roles in future energy systems. Although unique characteristics of these resources are well-recognized and require more sophisticated methodologies to capture effectively, guidance is limited on best practices and research gaps. This paper selectively reviews recent literature and draws upon our collective modeling experience to offer recommendations to analysts and consumers of model outputs on approaches for modeling variable renewable energy and storage in long-term electric sector models. We focus on regional- and national-scale models with technological, temporal, and spatial detail given their prevalence in planning and policy analysis, though insights are applicable in other settings. The review highlights how the research frontier has advanced in representing renewables and energy storage over the past decade; however, given the many considerations involved with appropriately capturing salient economic and operational characteristics of renewables, there is a gap between commonly used models and state-of-the-art methods. Model simplifications can materially impact policy analysis associated with power sector decarbonization and high renewables deployment, and improving model representations of variable renewables can enhance insights for policymakers and other stakeholders. This review can point the way for improved methods for established models and designs for emerging ones.

energy and environmental policy↗

DOE OSTI2015

ATLAS FTK Challenge: Simulation of a Billion-fold Hardware Parallelism

During the current LHC shutdown period the ATLAS experiment will upgrade the Trigger and Data Acquisition system to include a hardware tracker coprocessor: the Fast TracKer (FTK). The FTK receives data from the 80 million of channels of the ATLAS silicon detector, identifying charged tracks and reconstructing their parameters at a rate of up to 100 KHz and within 100 microseconds. To achieve this performance, the FTK system identifies candidate tracks utilizing the computing power of a custom ASIC chip with associative memory (AM) designed to perform “pattern matching” at very high speed; track parameters are then calculated using modern FPGAs. A detailed simulation of this massive system has been developed with the goal of supporting the hardware design and studying its impact in the ATLAS online event selection at high LHC luminosities. We present the issues related to emulating FTK on a general-purpose CPU platform, using ATLAS computing Grid resources, and the solutions developed in order to mitigate these problems and allow the studies required to support the system design, construction and installation.

Distributed Computing↗

DOE OSTI2017

Identification and recovery of rare-earth permanent magnets from waste electrical and electronic equipment

Highlights: • Different WEEE were analyzed and the rare-earth permanent magnets were collected. • Chemical composition evolution of Nd-Fe-B alloys over the years is illustrated. • Loudspeakers from laptops and loudspeakers from flat TV contained Nd-Fe-B magnets. • The amount of Nd-Fe-B could double if the loudspeakers streams are included. - Abstract: Nd-Fe-B permanent magnets are a strategic material for a number of emerging technologies. They are a key component in the most energy efficient electric motors and generators, thus, they are vital for energy technologies, industrial applications and automation, and future forms of mobility. Rare earth elements (REEs) such as neodymium, dysprosium and praseodymium are also found in waste electrical and electronic equipment (WEEE) in volumes that grow with the technological evolution, and are marked as critical elements by the European Commission due to their high economic importance combined with significant supply risks. Recycling could be a good approach to compensate for the lack of rare earths (REs) on the market. However, less than 1% of REs are currently being recycled, mainly because of non-existing collection logistics, lack of information about the quantity of RE materials available for recycling and recycling-unfriendly product designs. To improve these lack of information, different waste streams of electrical and electronic equipment from an industrial recycling plant were analyzed in order to localize, identify and collect RE permanent magnets of the Nd-Fe-B type. This particular type of magnets were mainly found in hard disk drives (HDDs) from laptops and desktop computers, as well as in loudspeakers from compact products such as flat screen TVs, PC screens, and laptops. Since HDDs have been investigated thoroughly by many authors, this study focusses on other potential Nd-Fe-B resources in electronic waste. The study includes a systematic survey of the chemical composition of the Nd-Fe-B magnets found in the selected waste streams, which illustrates the evolution of the Nd-Fe-B alloys over the years. The study also provides an overview over the types of magnets integrated in different waste electric and electronic equipment.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Thiol-Functionalized Adsorbents through Atomic Layer Deposition and Vapor-Phase Silanization for Heavy Metal Ion Removal

The removal of toxic heavy metal ions from water resources is crucial for environmental protection and public health. In this study, we address this challenge by developing a surface functionalization technique for the selective adsorption of these contaminants. Our approach involves atomic layer deposition (ALD) followed by vapor-phase silanization of porous substrates. We utilized porous silica gel powder (similar to 100 mu m particles, 89 m 2 /g surface area, similar to 30 nm pores) as an initial substrate. This powder was first coated with similar to 0.5 nm ALD Al 2 O 3 , followed by vapor-phase grafting of a thiol-functional silane. The modified powder, particularly in acidic conditions (pH = 4), showed high selectivity in adsorbing Cd(II), As(V), Pb(II), Hg(II), and Cu(II) heavy metal ions in mixed ion solutions over common benign ions (e.g., Na, K, Ca, and Mg). Langmuir adsorption isotherms and breakthrough adsorption studies were conducted to assess heavy metal binding affinity and revealed the order of Cd(II) < Pb(II) < Cu(II) < As(V) < Hg(II), with a significantly higher affinity for As(V) and Hg(II) ions. Time-dependent uptake studies demonstrated rapid removal of heavy metal ions from aqueous environments, with Hg(II) exhibiting the fastest adsorption kinetics on thiol-modified surfaces. Finally, these findings highlight the potential of ALD and vapor-phase silanization to create effective adsorbents for the targeted removal of hazardous contaminants from water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Missing microbial eukaryotes and misleading meta-omic conclusions

Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

59 BASIC BIOLOGICAL SCIENCES↗