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DOE OSTI2015

Final technical report for: Insertional Mutagenesis of Brachypodium distachyon DE-AI02-07ER64452

Several bioenergy grasses are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of grass biology (e.g. identification of the genes that control cell wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these species. The use of an appropriate model system is an efficient way to gain this knowledge. Brachypodium distachyon is a small annual grass with all the attributes needed to be a modern model organism including simple growth requirements, fast generation time, small stature, small genome size and self-fertility. These attributes led to the recommendation in the DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda” report to propose developing and using B. distachyon as a model for energy crops to accelerate their domestication. Strategic investments (e.g. genome sequencing) in B. distachyon by the DOE are now bearing fruit and B. distachyon is being used as a model grass by hundreds of laboratories worldwide. Sequence indexed insertional mutants are an extremely powerful tool for both forward and reverse genetics. They allow researchers to order mutants in any gene tagged in the collection by simply emailing a request. The goal of this project was to create a collection of sequence indexed insertional mutants (T-DNA lines) for the model grass Brachypodium distachyon in order to facilitate research by the scientific community. During the course of this grant we created a collection of 23,649 B. distachyon T-DNA lines and identified 26,112 unique insertion sites. The collection can be queried through the project website (http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/) and through the Phytozome genome browser (http://phytozome.jgi.doe.gov/pz/portal.html). The collection has been heavily utilized by the research community and, as of October 23, 2015, 223 orders for 12,069 seeds packets have been filled. In addition to creating this resource, we also optimized methods for transformation and sequencing DNA flanking insertion sites.

09 BIOMASS FUELS↗

DOE OSTI2017

FY2017 Report on NISC Measurements and Detector Simulations

FY17 work focused on automation, both of the measurement analysis and comparison of simulations. The experimental apparatus was relocated and weeks of continuous measurements of the spontaneous fission source 252 Cf was performed. Programs were developed to automate the conversion of measurements into ROOT data framework files with a simple terminal input. The complete analysis of the measurement (which includes energy calibration and the identification of correlated counts) can now be completed with a documented process which involves one simple execution line as well. Finally, the hurdles of slow MCNP simulations resulting in low simulation statistics have been overcome with the generation of multi-run suites which make use of the highperformance computing resources at LANL. Preliminary comparisons of measurements and simulations have been performed and will be the focus of FY18 work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS1975

Confirmation of interstellar N2H/+/

The proposed identification of the triplet of interstellar lines recently discovered at 93.174 GHz with the molecular ion N2H(+) is confirmed by resolving the predicted hyperfine structure of the inner nitrogen nucleus in the narrow-line molecular source OMC-2 in the Orion Nebula. The hyperfine constants of N2H(+) are derived from the observational data, and the rest center frequency of the J = 1-0 rotational transition is determined. It is noted that the full width at half-maximum of the weakest line (F sub 1 = 0-1) is only 230 kHz (0.74 km/sec in radial velocity), making it the narrowest molecular emission line (excluding maser point sources) thus far observed in the direction of a H II region or IR source.

Thaddeus, P.↗

NASA NTRS1993

Detection of high-energy gamma rays from quasar PKS 0528 + 134 by EGRET on the Compton Gamma Ray Observatory

The first several pointing directions of the Compton Gamma Ray Observatory, launched on 1991 April 5, were toward the Galactic anticenter. In addition to the known gamma-ray sources, Crab and Geminga, high-energy gamma-ray emission was observed from the quasar PKS 0528 + 134 by the Energetic Gamma Ray Experiment Telescope (EGRET). A redshift measurement, reported here, of 2.07 confirms the identification of this object as a quasar. The differential photon spectrum is well represented by a power law with an exponent of 2.56 +/- 0.09 and a photon intensity above 100 MeV of (8.4 +/- 1.0) x 10 exp -7 photons sq cm/s. There is evidence for time variability on a time scale of a few days.

Hunter, S. D.↗

DOE OSTI2017

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

Here, we present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution (HOD), the conditional luminosity function (CLF), abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos, or to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. Here, the package has an optimized toolkit to make mock observations on a synthetic galaxy population, including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others, allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Advanced Sensor Deployment for Distribution System State Estimation and Fault Identification

Distribution systems are currently facing steep operational challenges as a result of the rapidly increasing integration of renewables and other distributed energy resources (DERs) at both the primary and secondary circuit levels. Distribution utilities and system operators have traditionally had some visibility of their primary circuits using low-frequency supervisory control and data acquisition systems, and they have had very poor if not zero visibility of the secondary circuits where the presence of DERs is constantly increasing. Therefore, this paper presents simulation studies to demonstrate the benefits of an advanced, high-fidelity sensor technology, called as the Meta-Alert System (MAS), developed by Electrical Grid Monitoring, Ltd. (EGM), on the distribution grid. First, a reliable model of the EGM sensors is developed, and then two use cases, distribution system state estimation (DSSE) and fault identification are simulated to evaluate the performance of the MAS technology. Simulation results on the Electric Power Research Institute J1 feeder demonstrate that the MAS can effectively participate in system-level DSSE programs and can detect and locate faults faster than traditional distribution protection schemes.

distribution system↗

DOE OSTI2016

CHANDRA ACIS SURVEY OF X-RAY POINT SOURCES: THE SOURCE CATALOG

The Chandra archival data is a valuable resource for various studies on different X-ray astronomy topics. In this paper, we utilize this wealth of information and present a uniformly processed data set, which can be used to address a wide range of scientific questions. The data analysis procedures are applied to 10,029 Advanced CCD Imaging Spectrometer observations, which produces 363,530 source detections belonging to 217,828 distinct X-ray sources. This number is twice the size of the Chandra Source Catalog (Version 1.1). The catalogs in this paper provide abundant estimates of the detected X-ray source properties, including source positions, counts, colors, fluxes, luminosities, variability statistics, etc. Cross-correlation of these objects with galaxies shows that 17,828 sources are located within the D {sub 25} isophotes of 1110 galaxies, and 7504 sources are located between the D {sub 25} and 2 D {sub 25} isophotes of 910 galaxies. Contamination analysis with the log N –log S relation indicates that 51.3% of objects within 2 D {sub 25} isophotes are truly relevant to galaxies, and the “net” source fraction increases to 58.9%, 67.3%, and 69.1% for sources with luminosities above 10{sup 37}, 10{sup 38}, and 10{sup 39} erg s{sup −1}, respectively. Among the possible scientific uses of this catalog, we discuss the possibility of studying intra-observation variability, inter-observation variability, and supersoft sources (SSSs). About 17,092 detected sources above 10 counts are classified as variable in individual observation with the Kolmogorov–Smirnov (K–S) criterion ( P {sub K–S} < 0.01). There are 99,647 sources observed more than once and 11,843 sources observed 10 times or more, offering us a wealth of data with which to explore the long-term variability. There are 1638 individual objects (∼2350 detections) classified as SSSs. As a quite interesting subclass, detailed studies on X-ray spectra and optical spectroscopic follow-up are needed to categorize these SSSs and pinpoint their properties. In addition, this survey can enable a wide range of statistical studies, such as X-ray activity in different types of stars, X-ray luminosity functions in different types of galaxies, and multi-wavelength identification and classification of different X-ray populations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A study of examiner accuracy in cartridge case comparisons. Part 1: Examiner error rates

This report describes a study undertaken to estimate examiner (not laboratory) error rates for false Identifications and false Eliminations when comparing an unknown to a collection of three known cartridge cases. Volunteer active examiners with Association of Firearm and Toolmark Examiners (AFTE) membership or working in laboratories that participate in the Association of Crime Laboratory Directors (ASCLD) were provided with 15 sets of three known and one questioned cartridge cases fired from a collection of 25 new Ruger SR9 handguns. Remington 9-mm Luger (manufacturer designation L9MM3) ammunition was used and comparison sets were made up of cartridge cases fired within 100 cartridges of each other for each gun. Examiners were provided with a background survey, an answer sheet allowing for the AFTE Range of Conclusions, and return shipping materials. In addition to determining whether the known and questioned cartridge cases were fired with the same handgun, examiners were also asked to assess how many of the three knowns in each set were suitable for comparison, providing an estimated rate of how often each firearm used in the study produces useable, quality marks. The participating examiners were provided with both same-source and different-source comparison sets allowing the study to assess both error rates. Responses were received from 218 participating examiners. The overall rate of false Eliminations was estimated as 0.367% from comparisons known to be from the same firearm but reported as Eliminations. The overall rate of false Identifications was estimated as 1.01% from comparisons known to be from different firearms but reported as Identifications. The rates are not uniform across the sample population with a few examiners providing most of the false Identification responses. Rates of poor-quality mark production varied across the 25 sample handguns; those rates were 2.3% (±1.4%). Both false Elimination and false Identification rates are comparable to or lower than the rate of production of poor-quality marks by the firearms used in this study.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2019

Development and refinement of an in situ ‘molecular microscope’ utilizing ultrahigh resolution mass spectrometry

The ability to elucidate complex metabolic behavior of living organisms in situ and with cellular resolution is a bioanalytical grand challenge that is yet to be realized. Mass spectrometry imaging (MSI) using laser ablation electrospray ionization mass spectrometry (LAESI) has recently been demonstrated, and holds promise for direct spatially resolved molecular profiling in a variety of living systems of DOE relevance (e.g., plant leaf, stem, and root tissue). The LAESI MSI approach has revealed cell-to-cell heterogeneity of metabolites within living plant tissue, in a multiplexed fashion and without the need for labeling. Cellular resolution by in situ, ambient pressure MSI methods are far from routine, however, and have inadequate spatial resolution for many biological questions of interest. We propose to develop next-generation LAESI approaches, using advanced fiber optics and transmission-based geometries, in efforts to attain dynamic bioanalysis of living systems at better than 20 µm lateral resolution. In parallel with LAESI innovations, attendant increases in sensitivity and dynamic range of the mass spectrometer system will also be necessary for detection of the limited amount of material being ionized. To respond to this need, a new, high magnetic field (21 Tesla) Fourier Transform Ion Cyclotron Resonance (FTICR) MS at the EMSL/PNNL will be coupled with the newly developed LAESI source. This mass spectrometer, currently being assembled, will be one of only two such systems in the world, and the only one in a DOE laboratory or user facility. Fundamentally, all key figures of merits of FTICR MS performance improve with increased magnetic field strength, providing the ability to achieve unparalleled molecular specificity (near unequivocal molecular constituent identification) at the highest possible mass resolving power and sensitivity. The work proposed here will greatly increase the utility of this FTICR MS instrument, providing unique capabilities to support BER-relevant science. The research plan is comprised of three tasks, two of which are directed by the academic leads (University of Missouri and George Washington University), and one of which will be performed in conjunction with the BER user facility at EMSL/PNNL. In task 1, advancements of the LAESI technology will be achieved, with oversight and leadership of Professor Akos Vertes of George Washington University. In task 2, incorporation of this ion source with EMSL’s new 21T FTICR MS system will be undertaken, supplemented by global omics measurements and calibrated against more conventional MSI platforms also available at EMSL (Drs. Pasa-Tolic, Anderton, and Koppenaal team). In the final task, the resultant innovations and advancements will be tested and validated by addressing important BER relevant science questions on model systems of interest under the direction of Professor Gary Stacey of the University of Missouri. This research follows on key recommendations of the recent BER “Research in Sustainable Bioenergy” report that, for example, stressed that “The design of sustainable biofuel systems requires knowledge about key plant-microbe-environment interactions that provide a range of ecosystem services.” This task will focus on validation of the instrumentation developed through this proposal, advertising this capability to the community through demonstration and, finally, discovering new biology relevant to the BER mission. This final objective will make use of Setaria viridis, a model C4 grass species, as well as switchgrass and sorghum, two promising biofuel crops. Specifically, we will demonstrate applicability to plant-microbe rhizosphere interactions focusing on the biological nitrogen fixation by monitoring metabolic changes in real-time with nutrient, growth condition, and other perturbations.

09 BIOMASS FUELS↗

DOE OSTI2015

Excitation of XPS spectra from nanoscaled particles by local generation of x-rays

In preliminary work, the authors have shown that use of an aluminum substrate to support a distribution of copper particles enables their characteristic photoelectrons to be observed within the Auger electron spectrum generated by an incident electron beam. This observation raises the possibility of the use of chemical shifts and the corresponding Auger parameter to identify the chemical states present on the surface of individual submicrometer particles within a mixture. In this context, the technique has an advantage in that, unlike conventional Auger electron spectroscopy, the electron beam does not dwell on the particle but on the substrate adjacent to it. Given the importance, for both medical and toxicological reasons, of the surface composition of such particles, the authors have continued to explore the potential of this development. In this contribution, the authors show that proximal excitation of x-rays is equally successful with magnesium substrates. In some regions of the x-ray photoelectron spectrum, the much larger Auger peaks generated by the electron beam can cause inconvenient clustering of Auger and photoelectron peaks. As in conventional x-ray photoelectron spectroscopy, the ability to switch between Al and Mg sources is useful in such situations. In this context, the authors have extended the studies to iron particles where the authors show that use of Al or Mg substrates, as necessary, can make a contribution to clear identification of individual components in the Fe 2p peaks. For this development in electron spectroscopy to achieve its full potential, it is necessary to optimize the beam conditions used to generate the local x-ray to give good selectivity of a given particle. Measurements made in support of this will be given. Of greater concern is a possible problem of local heating associated with x-ray generation. The authors continue to explore this problem and report some progress in minimizing heating of the particle while maintaining the particle selectivity that is central to this exciting development.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2011

Soft Landing of Complex Molecules on Surfaces

Mass spectrometry is a versatile technique for identification and structural characterization of large molecules. The advent of soft ionization techniques such as electrospray (ESI) (1-2) has enabled ionization of a wide variety of complex molecules without significant \fragmentation while non-thermal ion sources such as laser vaporization (3-4) and magnetron sputtering (5-6) have provided access to materials that cannot, currently, be produced through conventional techniques. Most mass spectrometry studies rely on ionization of a molecule of interest or a complex mixture followed by mass analysis. Alternatively, mass spectrometry may be used as a preparatory technique, in which mass-selected ions are deposited onto solid supports or into liquid materials (7-18). Preparatory mass spectrometry offers several unique advantages for deposition of complex molecules on substrates including the ability to generate high-purity uniform films (19-20), unprecedented selectivity and specificity of preparation of deposited species (11, 21-22), the ability to focus and pattern an ion beam (23-24), and flexibility in both ion formation (1, 3, 25-26) and mass selection (27-32) processes. This review will highlight applications of mass-selected deposition of complex molecules for selective immobilization of biological molecules and catalytically active complexes on substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Implementation of ISO 15118-202 messages within Everest EV Charging Open Source Framework [SWR-25-56]

This software implements the messages defined in the ISO 15118-202 standard within the Everest EV Charging open source framework. The protocol and messages defined in the ISO 15118-202 standard enable the exchange of additional information which is not available for exchange within the currently deployed EV/EVSE communications protocols. This information includes co-identification parameters, error message exchange and more. This fork of the everest-core repository adds a prototype of the Extensible Supply Equipment Communication Controller (SECC) Discovery Protocol (ESDP) implemented based on a draft of the ISO 15118-202 standard. This is achieved through additions and modifications to the EvseV2G module. The implementation provides a demonstration of the ESDP messages, encoding and decoding but does not include a full integration within the Everest framework. Much of the information being sent over ESDP in this implementation is set statically for the sake of demonstrating the protocol itself. This fork of the ext-switchev-iso15118 repository adds a prototype of the Extensible Supply Equipment Communication Controller (SECC) Discovery Protocol (ESDP) implemented based on a draft of the ISO 15118-202 standard. The implementation provides a demonstration of the ESDP messages, encoding and decoding but does not include a full integration within the Everest framework. Much of the information being sent over ESDP in this implementation is set statically for the sake of demonstrating the protocol itself. This fork adds the ESDP features for only the EVCC controller because that is the only portion that is utilized in the everest Software-in-the-Loop.

Watt, Ed [National Renewable Energy Laboratory (NR↗

DOE OSTI2023

Knowledge-Informed Uncertainty-Aware Machine Learning for Time Series Forecasting of Dynamical Engineered Systems

The high complexity and multiscale nature of many engineered systems—such as those in nuclear power plants—make representing and forecasting their dynamic behavior challenging. Physics-based models can be overly complex and computationally intractable, whereas machine learning (ML) tools are often data-hungry and prone to unphysical solutions. This study proposes a knowledge-informed ML-aided hybrid residual modeling approach that offers accurate and efficient time series forecasting for the operation of dynamical engineered systems. Hybrid residual modeling entails a baseline solution from domain knowledge and known physics expressions about the system dynamics integrated with an ML model to capture undiscovered information from the mismatch (i.e., residuals) between true states from measurements and baseline-predicted outputs. This study further quantifies the ML model uncertainty to provide trustworthy solutions. Real-time operational data from thermal-hydraulic flow loops of the cryogenic moderator system in Oak Ridge National Laboratory’s Spallation Neutron Source facility were used to demonstrate the potential of knowledge-informed uncertainty-aware ML in real-world applications. The state variables of the cryogenic helium loop were modeled with (1) first principles–based system identification (sysID), (2) long short-term memory (LSTM) neural network, and (3) hybrid sysID (baseline) + LSTM (residual). The superior predictive capability of the sysID+LSTM model versus stand-alone sysID and LSTM is confirmed by average performance metrics and individual data points across different prediction horizons. By creating a robust representation of the underlying physical system, the widely applicable hybrid residual modeling approach will enable the future development of digital twins for performance prediction, prognostics, and operation control.

Zhao, Xingang↗

DOE OSTI2020

Time Series Dimension Reduction for Surrogate Models of Port Scanning Cyber Emulations

Surrogate model development is a key resource in the scientific modeling community for providing computational expedience when simulating complex systems without loss of great fidelity. The initial step to development of a surrogate model is identification of the primary governing components of the system. Principal component analysis (PCA) is a widely used data science technique that provides inspection of such driving factors, when the objective for modeling is to capture the greatest sources of variance inherent to a dataset. Although an efficient linear dimension reduction tool, PCA makes the fundamental assumption that the data is continuous and normally distributed. Thus, it provides ideal performance when these conditions are met. In the case for which cyber emulations provide realizations of a port scanning scenario, the data to be modeled follows a discrete time series function comprised of monotonically increasing piece-wise constant steps. The sources of variance are related to the timing and magnitude of these steps. Therefore, we consider using XPCA, an extension to PCA for continuous and discrete random variates. This report provides the documentation of the trade-offs between the PCA and XPCA linear dimension reduction algorithms, for the intended purpose to identify key components of greatest variance in our time series data. These components will ultimately provide the basis for future surrogate models of port scanning cyber emulations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

High-Energy X-ray Diffraction Microscopy for Nuclear Forensics FY2022 Project Report

Morphological information on nuclear material has been identified using visible light and scanning electron microscopy. These identify qualitative differences in particle morphology. Three-dimensional imaging of materials through alternating scanning electron microscopy imaging and focused ion beam milling has also been used. Unfortunately, these techniques are time- and labor-intensive, with significant sample preparation required and lengthy analysis times. Further, the resulting 3D images are qualitative, require manual identification, and do not capture statistically-representative populations. High energy X-ray 3D imaging using a direct-beam or diffracted-beam (High-Energy Diffraction Microscopy) have been developed at the Advanced Photon Source and can produce quantitative information on grains (phase, location, etc.) and pores (size distribution, sphericity) in a material. These techniques require only minutes to characterize a sample volume and are non-destructive, thus suitable for a wide range of existing samples and for confirmatory analyses to be carried out using conventional microscopy techniques. In this first year of the project, all uranium oxide samples were synthesized and characterized using conventional analyses by the analytical chemistry laboratory. Conventional analysis methods included powder x-ray diffraction, scanning electron microscopy, impurity analysis via inductively coupled plasma mass spectrometry, and infrared spectroscopy. Impurity analysis shows a drop in boron content from UO 3 to the lowest U 3 O 8 calcination temperature, but otherwise no appreciable difference in any sample. Analysis of diffraction data shows a flip of peaks from UO 3 dominated for the 600 °C calcined sample to U 3 O 8 dominated at 700 °C and 800 °C. Analysis of scanning electron microscopy images shows that with increased calcination temperature the size distribution of particles seems to increase and broaden. Both of these last findings are in line with previously published data, though this work used significantly fewer particles to simply show similar trends instead of getting truly quantitative particle analysis. Infrared analysis similarly shows ingrowth of U 3 O 8 as calcination temperature is increased, along with depression of peaks associated with UO 3 and water. Samples were prepared for analysis at the Advanced Photon Source at beamline 1-ID. It is anticipated that analysis will occur in November of 2022. AI/ML techniques to de-noise data coming out of 1-ID during the analyses was also developed during this time using previously gathered data. Preliminary results using a self-supervision technique called Noise2Selfshow good de-noising of data. Once the uranium oxide samples are analyzed, real data will be used to test the de-noising and other AI/ML techniques that may be developed in the second year of the project.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

High-Energy X-ray Diffraction Microscopy for Nuclear Forensics (FY23 Project Report)

36 MATERIALS SCIENCE↗

NASA NTRS1985

Spectral identification/elimination of molecular species in spacecraft glow

Computer models of molecular electronic and vibrational emission intensities were developed. Known radiative emission rates (Einstein coefficients) permit the determination of relative excited state densities from spectral intensities. These codes were applied to the published spectra of glow above shuttle surface and to the Spacelab 1 results of Torr and Torr. The theoretical high-resolution spectra were convolved with the appropriate instrumental slit functions to allow accurate comparison with data. The published spacelab spectrum is complex but N2+ Meinel emission can be clearly identified in the ram spectrum. M2 First Positive emission does not correlate well with observed features, nor does the CN Red System. Spectral overlay comparisons are presented. The spectrum of glow above shuttle surfaces, in contrast to the ISO data, is not highly structured. Diatomic molecular emission was matched to the observed spectral shape. Source excitation mechanisms such as (oxygen atom)-(surface species) reaction product chemiluminescence, surface recombination, or resonance fluorescent re-emission will be discussed for each tentative assignment. These assignments are the necessary first analytical step toward mechanism identification. Different glow mechanisms will occur above surfaces under different orbital conditions.

Green, B. D.↗

NASA NTRS1988

Newly detected molecules in dense interstellar clouds

The last year or so has seen the identification of several new interstellar molecules, including C2S, C3S, C5H, C6H, and (probably) HC2CHO in the cold, dark cloud TMC-1, and the discovery of the first interstellar phosphorus-containing molecule, PN, in the Orion 'plateau' source. Further interesting results include the observations of (C-13))3H2 and C3HD, and the first detection of HCOOH (formic acid) in a (C-13)3H2 cold cloud.

Irvine, William M.↗