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DOE OSTI2024

Chemical screening by time-resolved X-ray scattering to discover allosteric probes

Abstract Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis ( k VR ), capture structure–activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF–aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF–aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a longread sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Observations Regarding Commonly Available Materials for Face Shield Emulated-Personal Protective Equipment

The Center for Disease Control has recommended that to reduce potential exposure to COVID-19 the public should wear cloth face coverings in public settings where other social distancing measures are difficult to maintain. These face coverings and other Emulated-Personal Protective Equipment (E-PPE) can be made by using Commonly Available Materials (CAMs). As E-PPE recommendations continue to flood the media, a Sandia COVID-19 LDRD effort, the Sandia E-PiPEline Team, systematically evaluated E-PPE design options considering their effectiveness, durability, build difficulty, build cost, and comfort. Using qualitative and semi-quantitative evaluation tools, results of the investigation are presented here to provide guidelines for home and office construction of E-PPE.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Observations Regarding Commonly Available Materials for Face Covering Emulated-Personal Protective Equipment

36 MATERIALS SCIENCE↗

DOE OSTI2024

The Simons Observatory: Combining cross-spectral foreground cleaning with multitracer B -mode delensing for improved constraints on inflation

The Simons Observatory (SO), due to start full science operations in early 2025, aims to set tight constraints on inflationary physics by inferring the tensor-to-scalar ratio r from measurements of cosmic microwave background (CMB) polarization B-modes. Its nominal design including three small-aperture telescopes (SATs) targets a precision σ⁡(r = 0) ≤ 0.003 without delensing. Achieving this goal and further reducing uncertainties requires a thorough understanding and mitigation of other large-scale B-mode sources such as Galactic foregrounds and weak gravitational lensing. We present an analysis pipeline aiming to estimate r by including delensing within a cross-spectral likelihood, and demonstrate it for the first time on SO-like simulations accounting for various levels of foreground complexity, inhomogeneous noise and partial sky coverage. As introduced in an earlier SO delensing paper, lensing B-modes are synthesized using internal CMB lensing reconstructions as well as Planck-like cosmic infrared background maps and LSST-like galaxy density maps. We then extend SO’s power-spectrum-based foreground-cleaning algorithm to include all auto- and cross-spectra between the lensing template and the SAT B-modes in the likelihood function. This allows us to constrain r and the parameters of our foreground model simultaneously. Within this framework, we demonstrate the equivalence of map-based and cross-spectral delensing and use it to motivate an optimized pixel-weighting scheme for power spectrum estimation. We start by validating our pipeline in the simplistic case of uniform foreground spectral energy distributions. In the absence of primordial B-modes, we find that the 1⁢σ statistical uncertainty on r, σ⁡(r), decreases by 37% as a result of delensing. Tensor modes at the level of r = 0.01 are successfully detected by our pipeline. Even when using more realistic foreground models including spatial variations in the dust and synchrotron spectral properties, we obtain unbiased estimates of r both with and without delensing by employing the moment-expansion method. In this case, uncertainties are increased due to the higher number of model parameters, and delensing-related improvements range between 27% and 31%. These results constitute the first realistic assessment of the delensing performance at SO’s nominal sensitivity level.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2011

All-Sky Search for Periodic Gravitational Waves in the Full S5 LIGO Data

We report on an all-sky search for periodic gravitational waves in the frequency band 50-800 Hz and with the frequency time derivative in the range of 0 through -6 x 10(exp -9) Hz/s. Such a signal could be produced by a nearby spinning and slightly non-axisymmetric isolated neutron star in our galaxy. After recent improvements in the search program that yielded a 10x increase in computational efficiency, we have searched in two years of data. collected during LIGO's fifth science run and have obtained the most sensitive all-sky upper limits on gravitational wave strain to date. Near 150 Hz our upper limit on worst-case linearly polarized strain amplitude h(sub 0) is 1 x 10(exp -24), while at the high end of our frequency ra.nge we achieve a worst-case upper limit of 3.8 x 10(exp -24) for all polarizations and sky locations. These results constitute a factor of two improvement upop. previously published data. A new detection pipeline utilizing a Loosely Coherent algorithm was able to follow up weaker outliers, increasing the volume of space where signals can be detected by a factor of 10, but has not revealed any gravitational wave signals. The pipeline has been tested for robustness with respect to deviations from the model of an isolated neutron star, such as caused by a low-mass or long.period binary companion.

Abadie, J.↗

DOE OSTI2021

Deep learning for Alzheimer's disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation

Abnormal tau inclusions are hallmarks of Alzheimer's disease and predictors of clinical decline. Several tau PET tracers are available for neurodegenerative disease research, opening avenues for molecular diagnosis in vivo. However, few have been approved for clinical use. Understanding the neurobiological basis of PET signal validation remains problematic because it requires a large-scale, voxel-to-voxel correlation between PET and (immuno) histological signals. Large dimensionality of whole human brains, tissue deformation impacting co-registration, and computing requirements to process terabytes of information preclude proper validation. We developed a computational pipeline to identify and segment particles of interest in billion-pixel digital pathology images to generate quantitative, 3D density maps. The proposed convolutional neural network for immunohistochemistry samples, IHCNet, is at the pipeline's core. We have successfully processed and immunostained over 500 slides from two whole human brains with three phospho-tau antibodies (AT100, AT8, and MC1), spanning several terabytes of images. Our artificial neural network estimated tau inclusion from brain images, which performs with ROC AUC of 0.87, 0.85, and 0.91 for AT100, AT8, and MC1, respectively. Introspection studies further assessed the ability of our trained model to learn tau-related features. We present an end-to-end pipeline to create terabytes-large 3D tau inclusion density maps co-registered to MRI as a means to facilitate validation of PET tracers.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Geologic hydrogen: a review of resource potential, subsurface dynamics, exploration, production, transportation, and research opportunities

Hydrogen is a versatile resource with critical roles in decarbonization, industrial manufacturing, and energy integration. However, most hydrogen today is produced from fossil fuels, resulting in high emissions and energy consumption. Although low-carbon hydrogen production methods, such as steam methane reforming with carbon capture and renewable-powered electrolysis, are advancing, their high costs hinder large-scale deployment. Identifying alternative pathways for producing low-cost, low-emission hydrogen is therefore essential. Geologic hydrogen, referring to natural and stimulated hydrogen generated in the Earth's subsurface, has attracted growing attention as a potential source of sustainable, economically viable, and environmentally favorable hydrogen. This paper provides a comprehensive review of geologic hydrogen, covering its resource potential, origins, migration and trapping mechanisms, exploration techniques, production strategies, and pipeline transportation. It also identifies key knowledge gaps and proposes a roadmap for future research. The review indicates that geologic hydrogen has vast resource potential and can leverage existing subsurface technologies and geophysical exploration methods. However, major challenges persist, including uncertain hydrogen generation rates, limited understanding and control of serpentinization processes, costly transportation infrastructure, the lack of validated techno-economic analysis, and potential social and environmental issues. As the field is still in its early stages, progress will require interdisciplinary collaboration spanning geoscience, engineering, economics, environmental science, and policy and regulation.

42 ENGINEERING↗

DOE OSTI2013

THE HERSCHEL AND JCMT GOULD BELT SURVEYS: CONSTRAINING DUST PROPERTIES IN THE PERSEUS B1 CLUMP WITH PACS, SPIRE, AND SCUBA-2

We present Herschel observations from the Herschel Gould Belt Survey and SCUBA-2 science verification observations from the JCMT Gould Belt Survey of the B1 clump in the Perseus molecular cloud. We determined the dust emissivity index using four different techniques to combine the Herschel PACS+SPIRE data at 160-500 {mu}m with the SCUBA-2 data at 450 {mu}m and 850 {mu}m. Of our four techniques, we found that the most robust method was filtering out the large-scale emission in the Herschel bands to match the spatial scales recovered by the SCUBA-2 reduction pipeline. Using this method, we find {beta} Almost-Equal-To 2 toward the filament region and moderately dense material and lower {beta} values ({beta} {approx}> 1.6) toward the dense protostellar cores, possibly due to dust grain growth. We find that {beta} and temperature are more robust with the inclusion of the SCUBA-2 data, improving estimates from Herschel data alone by factors of {approx}2 for {beta} and by {approx}40% for temperature. Furthermore, we find core mass differences of {approx}< 30% compared to Herschel-only estimates with an adopted {beta} = 2, highlighting the necessity of long-wavelength submillimeter data for deriving accurate masses of prestellar and protostellar cores.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

Automated Mechanical Ventilator Waveform Analysis of Patient-Ventilator Asynchrony

Poster for conference. A pipeline combining wireless ventilator data acquisition and rule-based signal analysis algorithms informed by the principles of bedside ventilator waveform analysis allows for accurate, automated, quantitative breath-by-breath analysis of patient-ventilator interactions.

42 ENGINEERING↗

DOE OSTI2014

Transportation Design and Products Specification (SECARB Phase III Work Product 6.2.2.a)

The SECARB Anthropogenic Test at the Citronelle oil field in Mobile County, Alabama is the largest fully integrated coal-fired carbon capture, transportation and storage project in the United States. Constructed and funded by Southern Company and Mitsubishi Heavy Industries, the CO 2 capture facility at Alabama Power’s 2,657-megawatt Plant Barry captures up to 500 metric tons of CO 2 per day, the equivalent emissions from 25 MW of the plant’s power generation. Captured CO 2 is transported to the mature Citronelle oil field atop a 16,380 acre (66.3 km2 of surface area), geologic salt dome. Citronelle oil field is operated by Denbury Onshore, LLC. The CO 2 is injected through ten perforated intervals in the injection well casing at depths ranging from 9,436 ft to 9,800 ft into the porous and permeable sandstones of the Paluxy Formation. This report describes the transportation design and product specifications for captured CO 2 transported from the capture facility to the underground storage reservoir. CO 2 is transported through approximately 12 miles of pipeline from Plant Barry’s capture facility and is injected into the saline aquifer sandstones of the Paluxy formation at Citronelle oil field. The following outlines the details and characteristics of each point of transportation and the quality of CO 2 being transported.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2019

Research Technology Laboratory (RTL) Disposition Program Final Status Survey Report

As part of the Battelle Facility Restoration Program (Smoter and Biebesheimer 2017), the Research Technology Laboratory (RTL) Complex was remediated through demolition and surveyed to show it meets the radiological release criteria for unrestricted use under the clearance process (DOE 2011). The restoration program has directed the implementation of the Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM) methodology (NRC 2011) to verify the suitability of the site to be released for unrestricted use under the clearance process in U.S. Department of Energy (DOE) Order 458.1 (Biebesheimer 2018a; DOE 2011). The use of MARSSIM is accepted by federal and state agencies, including DOE. This report documents how the MARSSIM process was used to assure any residual radioactivity is within acceptable levels and as low as reasonably achievable. Past land use for the RTL Complex property included agricultural, residential, and industrial activity. The historical site assessment (HSA) (Lindenmeier et al. 2015; Biebesheimer 2018b) identified use of radionuclides in past RTL Complex research and development activities from commissioning in 1966 until it was vacated in 2017. Based on the information provided in the HSA, the RTL Complex was delineated into six survey units. The 520 building footprint, tank vault and 530 building footprint, other building footprints, and pipeline survey units included excavated areas. The paved areas and open areas survey units were unexcavated areas. Survey units were all determined to be Class 3, with low probability of containing residual radioactivity, after demolition of the structures within the RTL Complex. The Research Technology Laboratory (RTL) Disposition Program: Final Status Survey Plan (Bunn et al. 2018) was designed and conducted to provide quantitative data regarding the residual radioactivity present in each survey unit. Authorized radiological release limits were developed and approved by the DOE Office of Science in December 2016 (DOE 2017). Fourteen random sample locations were identified within each survey unit. Forty-four specific judgmental sample locations were selected across the site based on information in the HSA. The number of sample locations within a survey unit ranged from 15 to 28, for a total of 127 random and judgmental sample locations identified across the RTL Complex. Sampling for the final status survey occurred over 12 days between November 11 and December 7, 2018. Laboratory results were independently validated by Analytical Quality Associates prior to evaluation. All of the over 880 residual radioactivity measurements were less than the release limits and action levels established through the RTL Disposition Program. A sum of fractions calculation for each survey unit resulted in values that were less than unity. Based on the results presented in this report, the restoration program recommends that the RTL Complex be released for unrestricted use.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

A novel statistical methodology for quantifying the spatial arrangements of axons in peripheral nerves

A thorough understanding of the neuroanatomy of peripheral nerves is required for a better insight into their function and the development of neuromodulation tools and strategies. In biophysical modeling, it is commonly assumed that the complex spatial arrangement of myelinated and unmyelinated axons in peripheral nerves is random, however, in reality the axonal organization is inhomogeneous and anisotropic. Present quantitative neuroanatomy methods analyze peripheral nerves in terms of the number of axons and the morphometric characteristics of the axons, such as area and diameter. In this study, we employed spatial statistics and point process models to describe the spatial arrangement of axons and Sinkhorn distances to compute the similarities between these arrangements (in terms of first- and second-order statistics) in various vagus and pelvic nerve cross-sections. We utilized high-resolution transmission electron microscopy (TEM) images that have been segmented using a custom-built high-throughput deep learning system based on a highly modified U-Net architecture. Our findings show a novel and innovative approach to quantifying similarities between spatial point patterns using metrics derived from the solution to the optimal transport problem. We also present a generalizable pipeline for quantitative analysis of peripheral nerve architecture. Our data demonstrate differences between male- and female-originating samples and similarities between the pelvic and abdominal vagus nerves.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2001

Using XML and Java Technologies for Astronomical Instrument Control

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center, under the Instrument Remote Control (IRC) project, is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is that the software is driven by an instrument description, written using the Instrument Markup Language (IML), a dialect of XML. IML is used to describe the command sets and command formats of the instrument, communication mechanisms, format of the data coming from the instrument, and characteristics of the graphical user interface to control and monitor the instrument. The IRC framework allows the users to define a data analysis pipeline which converts data coming out of the instrument. The data can be used in visualizations in order for the user to assess the data in real-time, if necessary. The data analysis pipeline algorithms can be supplied by the user in a variety of forms or programming languages. Although the current integration effort is targeted for the High-resolution Airborne Wideband Camera (HAWC) and the Submillimeter and Far Infrared Experiment (SAFIRE), first-light instruments of the Stratospheric Observatory for Infrared Astronomy (SOFIA), the framework is designed to be generic and extensible so that it can be applied to any instrument. Plans are underway to test the framework with other types of instruments, such as remote sensing earth science instruments.

Ames, Troy↗

NASA NTRSDate not supplied

Distributed Lunar Data Platform with Advanced Machine Learning Capabilities in Support of Lunar Science and Exploration

The United States 2020 Space Policy directive declares that NASA, in cooperation with private industry, will “extend human economic activity into deep space by establishing a permanent human presence on the Moon”. This goal will require advanced data management, as well as analysis, modeling and representation of lunar information in order to prepare for Artemis human missions, lunar science investigations and exploration. To meet this requirement, we conceptualize and present an implementation strategy for a distributed platform for lunar data retrieval, inferencing and analysis, which will be based on federated learning and the NASA Celestial Mapping System (CMS). In addition to demonstrating the imperative of enabling lunar-borne data to remain in-situ but still accessible, this presentation will also include examples of how third parties could contribute both datasets and new functionality into this platform using an AI-based data import pipeline and a plug-in architecture respectively.

Artificial Intelligence↗

DOE OSTI2016

Independent Review of Elemental Phosphorus Remediation at the Eastern Michaud Flats FMC Operable Unit near Pocatello, Idaho

If, despite risks to workers and these potential impacts, stakeholders decide that P4 wastes need to be excavated and treated, the Review Team determined that a number of the ETTs examined warrant further consideration for the treatment of P4 waste that has been characterized (for example, P4 waste present in the historical ponds). Nevertheless, concerns about the health and safety of site investigation workers using then-available investigation approaches prevented the collection of subsurface samples containing P4 from large areas of the site (e.g., the railroad swale, the vadose zone beneath the Furnace Building, and the abandoned railcars), As a result, the contaminant CSM in those particular areas was not refined enough to allow the Review Team to draw conclusions about using some of the ETTs to treat P4 waste in those areas. The readiness of an ETT for implementation varies depending on many factors, including stakeholder input, permitting, and remedial action construction requirements. Technologies that could be ready for use in the near term (within 1 year) include the following: mechanical excavation, containment technologies, off-site incineration, and drying and mechanical mixing under a tent structure. Technologies that could be ready for use in the mid-term (1 to 2 years) include cutter suction dredging, thermal-hydraulic dredging, and underground pipeline cleaning technologies. Technologies requiring a longer lead time (2 to 5 years) include on-site incineration, a land disposal restriction waste treatment system, an Albright & Wilson batch mud still, post-treatment on-site disposal, and post-treatment off-site disposal.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

PNNL Superfund Research Program Analytics (srpAnalytics Data Release v.1.0)

The OSU/PNNL superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. The PNNL Superfund have implemented a dose-response modelling pipeline to calculate benchmark dose parameters that enable the comparison of potency across chemicals and phenotypes. Our portal provides public access to this dataset and an interactive web site designed to enable exploration and re-use of this data by the scientific community at http://srp.pnnl.gov.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of Lserine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

59 BASIC BIOLOGICAL SCIENCES↗