Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
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60 APPLIED LIFE SCIENCES↗
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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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Addressing Coldwater Temperature Impairment in a Changing Climate
Climate change is concerning for fisheries professionals because increased water temperatures threaten coldwater habitats, which are vital to recreational and commercial fisheries and keystone species. The Clean Water Act provides a legal framework to identify and address water quality impairments including those associated with temperature. However, although this framework provides a basic strategy to identify impairments, develop total maximum daily loads, and reduce pollution, it does not explicitly consider the challenges of a changing climate in addressing water quality impairments. Clean Water Act administrators and fisheries professionals can facilitate temperature restoration planning and implementation using the Clean Water Act framework to link stakeholders to the management of coldwater resources. Stakeholder engagement and collaboration, robust local monitoring, and incorporating climate resilience into restoration planning and implementation will promote comprehensive management of temperature impairments and the effects of climate change on fisheries.
54 ENVIRONMENTAL SCIENCES↗
Electric field control of magnetism: multiferroics and magnetoelectrics
This article is written on behalf of a large number of colleagues, collaborators, and researchers in the field of complex oxides as well as current and former students and postdocs who continue to enable and undertake cutting-edge research in the field of multiferroics, magnetoelectrics, and the pursuit of electric-field control of magnetism. What we present is something that is extremely exciting from both a fundamental science and applications perspective and has the potential to revolutionize our world. Needless to say, to realize this potential will require numerous new innovations, both in the fundamental science arena as well as translating these scientific discoveries into real applications. Thus, this article will attempt to bridge the gap between fundamental condensed-matter physics and the actual manifestations of the physical concepts into real-life applications. Here, we hope this article will help spur more translational research within the broad materials physics community.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Materials for a Sustainable Microelectronics Future: Electric Field Control of Magnetism with Multiferroics
This article is written on behalf of many colleagues, collaborators, and researchers in the field of complex oxides as well as current and former students and postdocs who continue to enable and undertake cutting-edge research in the field of multiferroics, magnetoelectrics, and the pursuit of electric-field control of magnetism. What I present is something that is extremely exciting from both a fundamental science and applications perspective and has the potential to revolutionize our world, particularly from a sustainability perspective. To realize this potential will require numerous new innovations, both in the fundamental science arena as well as translating these scientific discoveries into real applications. Thus, this article will attempt to bridge the gap between fundamental materials physics and the actual manifestations of the physical concepts into real-life applications. Further, I hope this article will help spur more translational research within the broad materials community.
36 MATERIALS SCIENCE↗
Hackathon Speeds Progress Toward Climate Model Collaboration
Climate scientists collaborated in a nationwide event to analyze and compare archived Earth system model simulations and to generate input for the IPCC's upcoming climate change report.
54 ENVIRONMENTAL SCIENCES↗
Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data
Here, we present ECoG ClusterFlow, a novel interactive visual analysis tool for the exploration of high-resolution Electrocorticography (ECoG) data. Our system detects and visualizes dynamic high-level structures, such as communities, using the time-varying spatial connectivity network derived from the high-resolution ECoG data. ECoG ClusterFlow provides a multi-scale visualization of the spatio-temporal patterns underlying the time-varying communities using two views: 1) an overview summarizing the evolution of clusters over time and 2) a hierarchical glyph-based technique that uses data aggregation and small multiples techniques to visualize the propagation of clusters in their spatial domain. ECoG ClusterFlow makes it possible 1) to compare the spatio-temporal evolution patterns across various time intervals, 2) to compare the temporal information at varying levels of granularity, and 3) to investigate the evolution of spatial patterns without occluding the spatial context information. Lastly, we present case studies done in collaboration with neuroscientists on our team for both simulated and real epileptic seizure data aimed at evaluating the effectiveness of our approach.
60 APPLIED LIFE SCIENCES↗
NRAP-Open-IAM: NRAP Open Source Integrated Assessment Model
Note: This is the last version (a2.6.1) of NRAP-Open-IAM released during NRAP Phase II in 2022. The latest version of NRAP-Open-IAM is available here: https://edx.netl.doe.gov/dataset/phase-iii-nrap-open-iam NRAP-Open-IAM is an open-source software product that enables quantification of containment effectiveness and leakage risk at storage sites in the context of system uncertainties and variability. NRAP-Open-IAM represents the next-generation in a line of systems-based computational models developed for quantitative geological carbon storage (GCS) risk assessment. The model comprises a set of reduced-order and analytical models of various components of the GCS system, potential leakage pathways, receptors of concern including impact to groundwater resources and the atmosphere, a framework to support stochastic simulation, time stepping, uncertainty quantification, other analytical functionality for scenario and risk-performance evaluation, and a basic graphical user interface to support scenario development, data input simulation definition, and basic post-processing and results display. As the NRAP Open-IAM functionality continues to evolve, we continue to add to its capability to develop quantitative, probabilistic, and time-dependent profiles of the evolution of risk at a GCS site and evaluate the influence of uncertain parameters on uncertainty in predicted risk. It can be used to quantify the dynamics of reservoir saturation plume and pressure-affected area, for evaluation of the area of potential groundwater impact (i.e., Area of Review) and monitoring requirements to support cost and regulatory analysis, and for consideration of different post-injection site care and closure scenarios. This submission contains the current version of NRAP-Open-IAM available for evaluation and testing. To use the NRAP-Open-IAM, download the source code (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/4c24a3da-3b40-4ffe-9892-c807ae9f8760) then open the NRAP-Open-IAM user's guide (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669) to read more about the tool. Installation instructions for Windows, Mac, and Linux can be found in the "installers" folder of the extracted NRAP-Open-IAM folder and describe setup of environment (e.g., Python libraries) needed for proper work of the tool. Test of installation can be done by running "python openiam_setup_tests.py" in the "setup" folder. The installation test also runs a test suite to see if the NRAP-Open-IAM has been installed correctly. To run the test suite separately, run "python iam_test.py" in the "test" folder. User's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669 Developer's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/3bc6ee7d-609d-4eb6-80ba-fa6130ee0313 Reservoir simulation data used in some examples distributed with NRAP-Open-IAM: - Kimberlina: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/eb62cece-61b2-4037-9b6d-32407dde2ab8 - Kimberlina (compartmentalized): https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/366f9530-3b32-4b84-affe-ab2df1d9a8b5 - FutureGen 2.0: https://edx.netl.doe.gov/dataset/futuregen-2-0-1008-simulation-reservoir-lookup-table NRAP-Open-IAM GitLab repository: https://gitlab.com/NRAP/OpenIAM Related publications: - Bacon, D., Yonkofski, C., Brown, C., Demirkanli, D. and Whiting, J., 2019. Risk-based post injection site care and monitoring for commercial-scale carbon storage: Reevaluation of the FutureGen 2.0 site using NRAP-Open-IAM and DREAM. International Journal of Greenhouse Gas Control 90: 102784. - Bacon, D. Demirkanli, D., and White, S., 2020. Probabilistic risk-based Area of Review (AoR) determination for a deep-saline carbon storage site. International Journal of Greenhouse Gas Control 102: 103153. - Harp, D., Oldenburg, C., and Pawar, R., 2019. A metric for evaluating conformance robustness during geologic CO2 sequestration operations. International Journal of Greenhouse Gas Control 85: 100-108. - Lackey, G., Vasylkivska, V., Huerta, N., King, S., and Dilmore, R., 2019. Managing well leakage risks at a geologic carbon storage site with many wells, International Journal of Greenhouse Gas Control, 88 :182-194. - Vasylkivska, V., Dilmore, R., Lackey, G., Zhang, Y., King, S., Bacon, D., Chen, B., Mansoor, K., and Harp, D., 2021. NRAP-Open-IAM: A flexible open-source integrated assessment model for geologic carbon storage risk assessment and management, Environmental Modelling & Software, 143: 105114. Presentations: - Chen, B., Harp, D., and Pawar, R., A data assimilation approach (ES-MDA) coupling with NRAP-Open-IAM for quantifying uncertainty reduction in geological CO2 sequestration. AGUFM 2019: T44A-02. - Chen, B., and Harp, D., Improving risk analysis precision for geologic CO2 sequestration by quantifying the uncertainty reduction before and after acquiring monitoring data. 14th Greenhouse Gas Control Technologies Conference, Melbourne, Australia, 2018, pp. 21-26. - Harp, D., National Risk Assessment Partnership Task 2: Containment Assurance. No. LA-UR-19-28654, Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2019. - Vasylkivska, V., King, S., Bacon, D., Harp, D., Chen, B., Mansoor, K., Onishi, T., Yang, Y., Zhang, Y., and Keating, E., NRAP-Open-IAM: An open-source integrated assessment model, poster, Mastering the Subsurface Through Technology Innovation, Partnerships and Collaboration: Carbon Storage and Oil and Natural Gas Technologies Review Meeting, Pittsburgh, PA, August 13-16, 2018. - Vasylkivska, V., Lackey, G., King, S., Wentworth, A., Huerta, N., Creason, C., DiGiulio, J., Yang, Y., and Dilmore, R., Long-term risk analysis of a geologic CO2 storage project during the post-injection period, SIAM Conference on Computational Science and Engineering, Spokane, WA, February 25-March 1, 2019. - Vasylkivska, V., Overview of the NRAP-Open-IAM tool for carbon storage (beta release), 2019 Annual NRAP Tool Users Meeting, Pittsburgh, PA, August 27, 2019. - Vasylkivska, V., Bacon, D., Chen, B., Dilmore, R., Harp, D., King, S., Lackey, G., Lindner, E., Liu, G., Mansoor, K. and Zhang, Y., NRAP-Open-IAM: A new, open-source code for integrated assessment of geologic carbon storage containment effectiveness and leakage risk, poster, American Geophysical Union Fall Meeting 2020 (virtual meeting), December 2020. - Vasylkivska, V., NRAP open-source integrated assessment model and relevant application, oral presentation, NRAP workshop "NRAP Tools for Geologic Carbon Storage Risk-Based Decision Making" held in conjunction with Groundwater Protection Council (GWPC) 2021 Annual Forum (virtual meeting), Salt Lake City, UT, September 2021. - Vasylkivska, V., NRAP-Open-IAM: open-source integrated assessment model, digital poster/demonstration, software demonstration session, 2022 Carbon Management Project Review Meeting, August 16, 2022
AoR↗
2013 Building America Research Planning Meeting Summary
The Building America (BA) Research Planning Meeting was held October 28-30, 2013, in Washington, DC. This meeting provides one opportunity each year for the research teams, national laboratories and Department of Energy (DOE) managers to meet in person to share the most pertinent information and collaboration updates. This report documents the presentations, highlights key program updates, and outlines next steps for the program.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Phase II: Automated System for Aneuploidy Detection in Sperm Final Report CRADA No. TC-1554-98
This was a collaborative effort between the University of California, Lawrence Livermore National Laboratory (LLNL) and Cellomics, Inc. (formerly BioDx and Biological Detection, Inc.) to develop an automated system for detecting human sperm aneuploidy. Aneuploidy (an abnormal number of chromosomes) is one of the major categories of chromosomally abnormal sperm, which results in chromosomally defective pregnancies and babies. An automated system would be used for testing the effects of toxic agents and for other research and clinical applications. This collaborated effort was funded by a National Institutes of Environmental Health Services, Phase II, Small Business Innovation Research Program (SBIR) grant to Cellornics (Contract No. N44-ES-82004).
59 BASIC BIOLOGICAL SCIENCES↗
DOE's 449 MHz Wind Profiling Radars on the U.S. West Coast: Annual Report for Fiscal Year 2016
The three coastal wind profilers and associated meteorological instruments located in Forks, WA, Astoria, OR, and North Bend, OR, provide important observations at high temporal and vertical spatial resolution to characterize the meteorological inflow to the western region of the United States. These instruments have been operating for a year or more, and furnish boundary conditions for the modeling efforts of the WFIP2 project. The data have been delivered to archives at both NOAA and the DOE A2e DAP at a data recovery rate in excess of 98%. Site maintenance activities have been relatively minor, with a few component replacements and repairs to RASS foam. Bird mortality surveys have found no bird nests or carcasses, and the U.S. Fish and Wildlife Service has regularly been provided survey reports. This project represents a successful collaboration between PNNL and NOAA to procure, test, deploy, maintain, and operate three 449 MHz radar wind profilers.
54 ENVIRONMENTAL SCIENCES↗
Evaluation of the Lawrence Livermore Microbal Detection Array at the Statens Serum Institut
This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Statens Serum Institut to evaluate and transition the Lawrence Livermore Microarray Detection Array (LLMDA) analysis software package, the Composite Likelihood Maximization method (CLiMax) to the SSI. The SSI is a public enterprise under the Danish Ministry of Health that operates a microbiology reference laboratory for the Danish population and analyzes tens to thousands of human clinical samples annually. SSI has been collaborating with the LLNL team for several years to use the LLMDA to analyze viral and bacterial infections from human clinical samples. The collaboration has resulted in two joint publications thus far, describing improvements to LLMDA sample preparation, and the utility of the LLMDA for detecting emerging viruses in clinical samples.
59 BASIC BIOLOGICAL SCIENCES↗
Monitoring and Enhancing Plant Productivity
Researchers at Los Alamos National Laboratory are developing extensive capabilities to improve plant drought tolerance; water and nutrient use efficiency and reduce greenhouse gas emissions from agriculture and natural systems. By monitoring plant function, stress responses, water and nutrient use, greenhouse gas emissions, and analyzing rhizosphere and plant microbiomes, results have shown improved plant performance and stress tolerance, production of plant pro- and prebiotics, and ability to control greenhouse gas emissions from indoor and outdoor agricultural systems. We seek a commercialization partner to fund precision agriculture specific research & development (R&D) through a Cooperative Research and Development Agreement (CRADA). Our goal is to further research and develop our laboratory scale capabilities with a collaborative partner to achieve two goals: 1) reduce the use of water and fertilization in agricultural systems; and 2) create carbon neutral food and energy technologies to support precision agriculture at commercial scale.
54 ENVIRONMENTAL SCIENCES↗
FY21 Report on Activities for EBS International
This report summarizes the FY21 Activities for EBS International Collaborations Work Package. The international collaborations work packages aim to leverage knowledge, expertise, and tools from the international nuclear waste community, as deemed relevant according to SFWST “roadmap” priorities. This report describes research and development (R&D) activities conducted during fiscal year 2021(FY21) specifically related to the Engineered Barrier System (EBS) R&D Work Package in the Spent Fuel and Waste Science and Technology (SFWST) Campaign supported by the United States (U.S.) Department of Energy (DOE). It fulfills the SFWST Campaign deliverable M4SF- 21SN010308062. The R&D activities described in this report focus on understanding EBS component evolution and interactions within the EBS, as well as interactions between the host media and the EBS. A primary goal is to advance the development of process models that can be implemented directly within the Generic Disposal System Analysis (GDSA) platform or that can contribute to the safety case in some manner such as building confidence, providing further insight into the processes being modeled, establishing better constraints on barrier performance, etc. Sandia National Laboratories is participating in THM modeling in the international projects EBS Task Force and DECOVALEX 2023. EBS Task Force, Task 11 is on modeling of laboratory-scale High Temperature Column Test conducted at Lawrence Berkeley National Laboratory. DECOVALEX 2023, Task C is on THM modeling of the full-scale emplacement experiment (FE experiment) at the Mont Terri Underground Rock Laboratory, Switzerland. This report summarizes Sandia’s progress in the modeling studies of DECOVALEX 2023, Task C. Modeling studies related to the High Temperature Column Test will be documented in future reports.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
High throughput single cell multiomics platform [Abstract]
In this collaborative project, PNNL and Scienion will co-develop an integrated microfluidic technology to co-measure the transcriptome and proteome in single cells. The technology will enable us to efficiently separate proteins from mRNA transcripts between two microchips, barcode the molecules, and measure them separately with next-generation sequencing and mass spectrometry, respectively. Multicellular organisms contain diverse cell types and tremendous cell-to-cell heterogeneity that dictates a multitude of biological functions in both physiological and pathological environments. Even in the case of microbes, these genetically identical organisms can randomly differentiate into many subpopulations that assume different roles for the survival of the community. Bulk-scale measurements are insufficient to resolve such complexities. The development and applications of high throughput single-cell omics technologies have transformed our understanding of cellular heterogeneities and their differential responses to internal signaling events or external stimulations. Despite these advances, most current single-cell omic technologies provide information on only one type of biomolecule. Perse, such measurements provide incomplete information because the cell phenotype is determined by multiple layers of biomolecules and the interplay between genome, epigenome, transcriptome, and proteome. For example, mRNA abundance in one cell can not be precisely referred to the corresponding DNA and protein in other cells because of the potential subtle difference in genotype (e.g., somatic mutation or copy number variation) or phenotype (external microenvironment and cell-cell interactions). As such, parallel measurement of multiple biomolecules in the same single cells can offer unique advantages compared with measuring them separately in different single cells. Scienion is a world-leading biotech company focusing on precision liquid handling and its application in single-cell whole-genome sequencing and RNA sequencing. PNNL is the leading institution in ultrasensitive mass spectrometry, microfluidics, and untargeted single-cell proteomics (scProteomics). This collaboration will facilitate a unique fusion between scTranscriptomics capability at Scienion and scProteomics capabilities at PNNL to, for the first time, perform both untargeted transcriptomics and proteomics from the same single cells.
59 BASIC BIOLOGICAL SCIENCES↗
Wind Energy Instrumentation Development Roadmap
The current instrumentation for observing the complex flow fields in and around wind plants struggles to match the fidelity of existing simulation tools. As a result, these measurement limitations create a hurdle for validating and assessing the quality of the wind plant numerical models. This roadmap for instrumentation development recommendations was created to offer guidance on narrowing the gap between measurement and simulation fidelity. A process was established to identify where gaps in instrumentation exist for wind energy test campaigns by analyzing the capabilities of instrumentation for capturing the various important phenomena at the necessary resolution for both the science goal and validation objectives. To this end, a multi-disciplinary team of experts on instrumentation, wind energy, and atmospheric science was assembled to identify these significant instrumentation needs. A recommendation for instrumentation to be developed is provided, and the framework developed through this process is expected to be useful to the design of future test campaigns. The mapping tools developed for this process will be distributed as part of a future International Energy Agency Wind Technology Collaboration Program task on instrumentation development.
17 WIND ENERGY↗
RD53 analog front-end processors for the ATLAS and CMS experiments at the High-Luminosity LHC
This work discusses the design and the main results relevant to the characterization of analog front-end processors in view of their operation in the pixel detector readout chips of ATLAS and CMS at the High-Luminosity LHC. The front-end channels presented in this paper are part of RD53A, a large scale demonstrator designed in a 65 nm CMOS technology by the RD53 collaboration.The collaboration is now developing the full-sized readout chips for the actual experiments. Some details on the improvements implemented in the analog front-ends are provided in the paper.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Achieving Health Security and Threat Reduction through Sharing Sequence Data
With the rapid development and broad applications of next-generation sequencing platforms and bioinformatic analytical tools, genomics has become a popular area for biosurveillance and international scientific collaboration. Governments from countries including the United States (US), Canada, Germany, and the United Kingdom have leveraged these advancements to support international cooperative programs that aim to reduce biological threats and build scientific capacity worldwide. A recent conference panel addressed the impacts of the enhancement of genomic sequencing capabilities through three major US bioengagement programs on international scientific engagement and biosecurity risk reduction. Here, the panel contrasted the risks and benefits of supporting the enhancement of genomic sequencing capabilities through international scientific engagement to achieve biological threat reduction and global health security. The lower costs and new bioinformatic tools available have led to the greater application of sequencing to biosurveillance. Strengthening sequencing capabilities globally for the diagnosis and detection of infectious diseases through mutual collaborations has a high return on investment for increasing global health security. International collaborations based on genomics and shared sequence data can build and leverage scientific networks and improve the timeliness and accuracy of disease surveillance reporting needed to identify and mitigate infectious disease outbreaks and comply with international norms. Further efforts to promote scientific transparency within international collaboration will improve trust, reduce threats, and promote global health security.
60 APPLIED LIFE SCIENCES↗
40 Years of SCES at Los Alamos
Reports of unconventional superconductivity in UBe 13 in 1983 and soon thereafter of the possible coexistence of bulk superconductivity and spin fluctuations in UPt 3 marked the beginning of a 40-year adventure in the study of strongly correlated quantum materials and phenomena at Los Alamos. The subsequent discovery and exploration of heavy-fermion magnetism, cuprates, Kondo insulators, Ce- and Pu-115 superconductors and, more broadly, quantum states of narrow-band systems provided challenges for the next 30 years. Progress was not made in a vacuum but benfitted from significant advances in the Americas, Asia and Europe as well as from essential collaborations, visitors and Los Alamos students and postdocs, many subsequently setting their own course in SCES. As often the case, serendipity played a role in shaping this history.
36 MATERIALS SCIENCE↗