Results for “identity” — Page 9

DOE OSTI2020

Influence of Proton Activity Gaps between Electrodes on Open-Circuit Potential of H 2 /H 2 and H 2 /Air Cells

Polymer -electrolyte-fuel-cell open-circuit voltages (OCVs) are exactly defined by equation (1), where cathode and anode proton activities [(aH+)cathode and (aH+)anode, respectively] usually are identical, so the third term in the right-hand side of equation (2) is ignored. OCV=E0+RT/2F*ln(a1/2 O2*(a2 H+)cathode/aH2O)-RT/2F*ln((a2 H+)anode/aH2) (1) =E0+RT/2F*ln(a1/2 O2*aH2/aH2O)+RT/2F*ln((a2 H+)cathode/(a2 H+)anode) (2) Water vapor pressure is a colligative property that fundamentally correlates to electrolyte concentrations in aqueous solutions. Proton activity is a function of acid concentration, such as pH, when electrolytes are acids. In polymer-electrolyte membranes, water vapor pressure and acid concentration are understood as relative humidity (RH) and water uptake (λ), respectively, where λ represents number of water molecules per sulfonic acid molecule. Several investigations have reported the relationship between RH and λ, meaning that proton activities and associated water uptakes are intimately related to RH. In actual fuel cell operation, cathode RH is determined by ambient-atmosphere and/or humidifier RH(s), and anode RH depends on hydrogen-circulator RH. Therefore, RH is not always identical at both electrodes, and the difference between electrode RHs is considerable during dry operation of polymer electrolyte fuel cells. Therefore, the third term in the right-hand side of equation (2) may be significant for dry operation. We measured OCVs when hydrogen was supplied to both electrodes at 80°C. One electrode (A) was fixed at 30% RH, while RH at the other electrode (B) was varied (0, 5, 10, 20, and 30%). Measured OCVs varied from 0 to 75 mV. For fuel cell tests, electrode A was supplied with hydrogen at 30% RH; electrode B, oxygen at 0, 5, 10, 20, and 30% RH. OCVs deviated from that measured when RH at electrode B was 30%, increasing from 0 to 60 mV with decreasing RH at electrode B. Results are also shown in Figure 1. Proton activities of both electrodes were thermodynamically calculated. The Gibbs–Duhem relation was applied to obtain molar Gibbs free energies of water and sulfonic acid, and proton activity coefficient was calculated using the Gibbs free energy of sulfonic acid and the relationship between RH and λ1–4, assuming that protons and sulfonic anions show identical ionic-activity coefficients. OCVs were estimated using the third term in the right-hand side of equation (2). Results are shown in Figure 1. Fuel-cell current–voltage performance was poor when RHs at the anode and cathode were 30 and 20%, respectively. To determine kinetic current, we measured the oxygen-reduction reaction (ORR) using a rotating-disk electrode (RDE) in concentrated-acid aqueous solutions, which modeled catalyst-layer ionomers. Kinetic currents decreased with acid concentrations. References T. A. Zawodzinski, Jr., C. Derouin, S. Radzinski, R. J. Sherman, V. T. Smith, T. E. Springer and S. Gottesfeld , J. Electrochem. Soc., 140,1041 (1993) P. K. Das and A. Z. Weber, Proceedings of the ASME 2013 11th Fuel Cell Science, Engineering and Technology Conference, Fuel Cell 18010 (2013) V. A. Sethuraman, J. W. Weidner, A. T. Haug, S. Motupally,b and L. V. Protsailo, J. Electrochem. Soc., 155, B50 (2008) A. Kusoglu and A. Z. Weber, Chem. Rev., 117, 987 (2017) Figure 1

Yoshida, Toshihiko↗

DOE OSTI2026

CHESS 2025: Field-collected vegetation attributes and site photos

This dataset represents field observations of vegetation samples collected as part of the Colorado Headwaters Ecological Spectroscopy Study (CHESS) during June and July of 2025. Samples were collected in the field using tablet computers and digital forms, with target data differing by sample type (individual trees, individual shrubs, or 1-meter square plots of meadow and subshrub vegetation). Field samples were collected within 72 hours of airborne data collection using the National Ecological Observatory Network’s Aerial Observation Platform (NEON AOP). The NEON AOP collected waveform LiDAR (Light Detection and Ranging) and imaging spectrometer data in 426 spectral bands from the visible to shortwave infrared. Remote sensing data for the project is available on ESS-DIVE (DOI and citation to be added upon publication). Field data collected included canopy height and per-species horizontal proportional cover for meadow plots, species identity and height information for shrubs, as well as species identity, height, diameter at breast height, and health assessment information for trees. Photos of the focal site and surrounding landscape were taken for all sampling sites and are included in this archive. Green leaves or needles were collected for plant trait and foliar chemistry analysis. This data is archived separately (DOI and citation to be added upon publication). High-precision geospatial data for each sample (crown perimeter polygons for trees and shrubs, plot boundaries for meadow plots) is available here (Henderson et al., 2026). Field and remote sensing protocols largely followed those of a previous field and airborne imaging campaign performed in 2018 (described in Chadwick et al. 2020). Field data from the 2018 campaign can be found here (Chadwick et al., 2020 doi:10.15485/1618130). Because different field measurements were taken for meadow, shrub, and tree sites, data from these three sample types are archived as separate tables (chess_meadow_site_cleaned.csv, chess_shrub_site_cleaned.csv, chess_tree_site_cleaned.csv). Meadow proportional cover data is stored in a separate table (chess_meadow_cover_cleaned.csv). Taxonomy was treated identically between sample types, and the dataset shares a common set of voucher specimens (chess_voucher_IDs_cleaned.csv), as well as a single species list (chess_species_list_cleaned.csv). All taxonomic determinations were performed to the species level, and adhere to the Global Biodiversity Information Facility (GBIF) backbone taxonomy as of January 10th, 2026 (GBIF Secretariat 2023). CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

DOE OSTI2022

Nb3Sn Coating of Twin Axis Cavity for SRF Applications

The twin axis cavity with two identical accelerating beams has been proposed for Energy recovery linac (ERL) applications. Nb3Sn is a superconducting material with a higher critical temperature and a higher critical field as compared to Nb, which promises a lower operating cost due to higher quality factors. Two niobium twin axis cavities fabricated at JLab and were proposed to be coated with Nb3Sn. Due to their more complex geometry, the typical coating process used for basic elliptical cavities needs to be improved to coat these cavities. This devel-opment advances the current coating system at JLab for coating complex cavities. Two twin axis cavities were coated recently for the first time. This contribution dis-cusses initial results from coating of twin axis cavities, RF testing and witness sample analysis with an overview of the current challenges towards high performance Nb3Sn coated twin axis cavities.

Tiskumara, J.↗

DOE OSTI2025

Geometry-driven modeling of electron localization in InAs/GaAs double quantum dots

The coupled electronic states in two-dimensional (2D) and three-dimensional (3D) double quantum dot (DQD) systems are investigated using a phenomenological model applied to InAs/GaAs heterostructures. The single-band k • p effective potential approach previously proposed by our group is employed to numerically calculate the energy spectrum and spatial localization of a single electron, serving as an indicator of the coupling strength within the binary system. For identical quantum dots (QDs) in a DQD, the electronic states exhibit ideal coherence. We systematically vary the DQD geometry and the strength of the confinement potential (via an applied electric field) to examine the effects of symmetry breaking and the sensitivity of electron localization in both identical and nearly identical DQDs. Our results show that coherence in DQDs is highly sensitive to these subtle variations. This sensitivity can be harnessed to detect changes in the surrounding environment, such as fluctuations in chemical or electrical properties that affect the DQD system.

electron localization↗

DOE OSTI2021

The Cosmological Bootstrap: Spinning correlators from symmetries and factorization

We extend the cosmological bootstrap to correlators involving massless spinning particles, focusing on spin-1 and spin-2. In de Sitter space, these correlators are constrained both by symmetries and by locality. In particular, the de Sitter isometries become conformal symmetries on the future boundary of the spacetime, which are reflected in a set of Ward identities that the boundary correlators must satisfy. We solve these Ward identities by acting with weight-shifting operators on scalar seed solutions. Using this weight-shifting approach, we derive three- and four-point correlators of massless spin-1 and spin-2 fields with conformally coupled scalars. Four-point functions arising from tree-level exchange are singular in particular kinematic configurations, and the coefficients of these singularities satisfy certain factorization properties. We show that in many cases these factorization limits fix the structure of the correlators uniquely, without having to solve the conformal Ward identities. The additional constraint of locality for massless spinning particles manifests itself as current conservation on the boundary. We find that the four-point functions only satisfy current conservation if the s, t, and u-channels are related to each other, leading to nontrivial constraints on the couplings between the conserved currents and other operators in the theory. For spin-1 currents this implies charge conservation, while for spin-2 currents we recover the equivalence principle from a purely boundary perspective. For multiple spin-1 fields, we recover the structure of Yang--Mills theory. Finally, we apply our methods to slow-roll inflation and derive a few phenomenologically relevant scalar-tensor three-point functions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Confidence Assessment for Automatic Target Recognition

Confidence assessment is critical for effective automatic target recognition (ATR). Productive use and interpretation of ATR results by analysts or downstream algorithms requires not only algorithmic declarations of target presence and identity, but also algorithmic assessment of the certainty of those declarations in comparison to the certainties of alternative target-identity possibilities. Unfortunately, despite its importance, confidence assessment is an understudied, underdeveloped, and often-neglected function of ATR systems. This lack of regard stems not only from the difficulty of accurate algorithmic determination of target-identity certainty, but also from a general lack of understanding and careful consideration about what confidence should actually represent. We present a framework for confidence assessment that establishes a clear definition of confidence and provides a straightforward theoretical basis for its calculation. This framework is grounded in a hypothesis-theoretic consideration of ATR and it springs from from a handful of axiomatic principles concerning the nature and meaning of confidence in this context. This framework establishes a rigorous mathematical definition of confidence and it provides equations relating confidence to other information that is almost always provided by ATRs. We present an approach for computing confidence within this framework, using an advance process of ATR characterization followed by a simple computation at the time of ATR execution. We discuss practical difficulties with our approach, and we suggest methods for effective mitigation of these difficulties in implemented systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Characterization of Peripheral Neurophotonic Systems for High-Performance Human-Computer Interfaces (CRADA Final Report)

As part of the Cyclotron Road program, Morphosis Inc. sought to investigate a non-invasive neuromuscular sensing approach for use as an intuitive and secure human–computer interface. These highly miniaturized, wearable neural interfaces were completely non-invasive and maintained stable, high-bandwidth, long-term access to a user’s actions, intent, and identity, while offering an exceptionally high signal-to-noise ratio compared to contemporary neural recording technologies. The widespread adoption of neural interfaces had the potential to reshape how people interact with technology, with profound societal impacts. Millions worldwide suffered from movement and/or speech disabilities, and these tools had the potential to democratize access to technology to enhance autonomy and quality of life. More broadly, interfaces capable of accurately conveying intentions and safeguarding identities could serve as a cornerstone for privacy, trust, and personal authenticity in digital environments. The use of thought-driven control of digitally enabled devices and governance of digital identities had the potential to revolutionize relationships with technology, transforming how people learn, communicate, and interact with the world.

42 ENGINEERING↗

DOE OSTI2024

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2024

KBase Narrative - Lachnospiraceae sp. C1.1 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2021

Identification of an Attenuated Substrain of Francisella tularensis SCHU S4 by Phenotypic and Genotypic Analyses

Pneumonic tularemia is a highly debilitating and potentially fatal disease caused by inhalation of Francisella tularensis. Most of our current understanding of its pathogenesis is based on the highly virulent F. tularensis subsp. tularensis strain SCHU S4. However, multiple sources of SCHU S4 have been maintained and propagated independently over the years, potentially generating genetic variants with altered virulence. In this study, the virulence of four SCHU S4 stocks (NR-10492, NR-28534, NR-643 from BEI Resources and FTS-635 from Battelle Memorial Institute) along with another virulent subsp. tularensis strain, MA00-2987, were assessed in parallel. In the Fischer 344 rat model of pneumonic tularemia, NR-643 and FTS-635 were found to be highly attenuated compared to NR-10492, NR-28534, and MA00-2987. In the NZW rabbit model of pneumonic tularemia, NR-643 caused morbidity but not mortality even at a dose equivalent to 500x the LD 50 for NR-10492. Genetic analyses revealed that NR-10492 and NR-28534 were identical to each other, and nearly identical to the reference SCHU S4 sequence. NR-643 and FTS-635 were identical to each other but were found to have nine regions of difference in the genomic sequence when compared to the published reference SCHU S4 sequence. Given the genetic differences and decreased virulence, NR-643/FTS-635 should be clearly designated as a separate SCHU S4 substrain and no longer utilized in efficacy studies to evaluate potential vaccines and therapeutics against tularemia. View Full-Text

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Integration of Complete Plasmids Containing Bont Genes into Chromosomes of Clostridium parabotulinum , Clostridium sporogenes , and Clostridium argentinense

At least 40 toxin subtypes of botulinum neurotoxins (BoNTs), a heterogenous group of bacterial proteins, are produced by seven different clostridial species. A key factor that drives the diversity of neurotoxigenic clostridia is the association of bont gene clusters with various genomic locations including plasmids, phages and the chromosome. Analysis of Clostridium sporogenes BoNT/B1 strain CDC 1632, C. argentinense BoNT/G strain CDC 2741, and Clostridium parabotulinum BoNT/B1 strain DFPST0006 genomes revealed bont gene clusters within plasmid-like sequences within the chromosome or nested in large contigs, with no evidence of extrachromosomal elements. A nucleotide sequence (255,474 bp) identified in CDC 1632 shared 99.5% identity (88% coverage) with bont/B1-containing plasmid pNPD7 of C. sporogenes CDC 67071; CDC 2741 contig AYSO01000020 (1.1 MB) contained a ~140 kb region which shared 99.99% identity (100% coverage) with plasmid pRSJ17_1 of C. argentinense BoNT/G strain 89G; and DFPST0006 contig JACBDK0100002 (573 kb) contained a region that shared 100% identity (99%) coverage with the bont/B1-containing plasmid pCLD of C. parabotulinum Okra. This is the first report of full-length plasmid DNA-carrying complete neurotoxin gene clusters integrated in three distinct neurotoxigenic species: C. parabotulinum, C. sporogenes and C. argentinense.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Description of Pegethrix niliensis sp. nov., a Novel Cyanobacterium from the Nile River Basin, Egypt: A Polyphasic Analysis and Comparative Study of Related Genera in the Oculatellales Order

In this paper, we examine the filamentous cyanobacterial strain NILCB16 and describe it as a new species within the genus Pegethrix. The original population was sampled from a mat growing in an irrigation canal in the Nile River, Egypt. Initially classified under Plectonema or Planktolyngbya, the strain is a potential producer of the toxins microcystin and β-N-Methylamino-L-Alanine (BMAA). Additionally, we reviewed the taxonomic relationships between the Oculatellales genera. To describe the new species, we conducted a polyphasic study, encompassing 16S rRNA gene phylogenetic analyses performed using both Maximum Likelihood and Bayesian methods, sequence identity (p-distance) analysis, 16S-23S ITS secondary structures, and morphological and habitat comparisons. The phylogenetic analysis revealed that strain NILCB16 clustered within the Pegethrix clade with strong phylogenetic support, but in a distinct position from other species in the genus. The strain shared a maximum 16S rRNA gene identity of 97.3% with P. qiandaoensis and 96.1% with the type species, P. bostrychoides. Morphologically, NILCB16 can be differentiated from other species in the genus by its lack of false branching. Our phylogenetic analyses also show that Pegethrix, Cartusia, Elainella, and Maricoleus are clustered with strong phylogenetic support. They exhibit high 16S rRNA gene identity and are morphologically indistinguishable, suggesting they could potentially be merged into a single genus in the future.

Hentschke, Guilherme Scotta (ORCID:000000034396024↗

DOE OSTI2023

Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning

In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150–200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Pitting Propagation Behavior on Low Alloy AISI 4130 (UNS G41300) Steel Exposed to Various Alkali and Alkaline Earth Metal Chlorides

Pit propagation studies were conducted to elucidate whether alkali and alkali earth metal cations such as Na+ and Rb+ present in the form of metal chloride salts such as RbCl affect pitting behavior in distinctly different manner than NaCl. Pit propagation studies were conducted on a low alloy steel using one-dimensional (1-D) pit method over pit depths from 300-1000 µm. LSV and EIS of planar electrodes of 4130 in a range of Cl- solutions were conducted and revealed no detected differences in impedance, open circuit, corrosion potential (Ecorr), passive current density (ipass), and pitting potential (Epit) as a function of salt type. In the case of one-dimensional pits during fast downward scan rates, the saturation potential (Esat) varied as a function of cation identity when pit depths were shallow. Mass transported limited current density also differed with cations in shallow pits when various alkali metal and alkaline metal cations were present. The limiting current density was increased for RbCl relative to NaCl The pit surface potential (Esurf) of activated pit surfaces reached Ecorr prior to establishing a condition where the pit electrolyte surface concentration (Csurf) was less than the critical concentration for active acidified pitting (i.e. Csurf<Ccrit) in this marginally passivating steel. For various Esurf and pit current density (ipit) combinations at constant Csurf where Ccrit< Csurf < Csat, E-log(i) plots were constructed using the method of Tianshu to create IR ohmic voltage corrected Tafel plots for various fixed pit solution concentrations. Under these conditions, the influence of cation identity on charge transfer controlled kinetics indicated slight differences in Tafel behavior where RbCl was slightly more aggressive than NaCl for low alloy steel oxidation. Differences in metal cation identity exert no effect on passive or breakdown on planar electrodes and only effect pit propagation stage in shallow pits.

Demarest, Chalres↗

DOE OSTI2023

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Abstract. Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Bounds on spectral gaps of Hyperbolic spin surfaces

We describe a method for constraining Laplacian and Dirac spectra of two dimensional compact orientable hyperbolic spin manifolds and orbifolds. The key ingredient is an infinite family of identities satisfied by the spectra. These spectral identities follow from the consistency between 1) the spectral decomposition of functions on the spin bundle into irreducible representations of SL(2,R) and 2) associativity of pointwise multiplication of functions. Applying semidefinite programming methods to our identities produces rigorous upper bounds on the Laplacian spectral gap as well as on the Dirac spectral gap conditioned on the former. In several examples, our bounds are nearly sharp; a numerical algorithm based on the Selberg trace formula shows that the [0;3,3,5] orbifold, a particular surface with signature [1;3], and the Bolza surface nearly saturate the bounds at genus 0, 1 and 2 respectively. Under additional assumptions on the number of harmonic spinors carried by the spin-surface, we obtain more restrictive bounds on the Laplacian spectral gap. In particular, these bounds apply to hyperelliptic surfaces. We also determine the set of Laplacian spectral gaps attained by all compact orientable two-dimensional hyperbolic spin orbifolds. We show that this set is upper bounded by 12.13798; this bound is nearly saturated by the [0;3,3,5] orbifold, whose first non-zero Laplacian eigenvalue is λ^(0)_1 ≈ 12.13623.

Spectral theory↗

DOE OSTI2024

Factorized visual representations in the primate visual system and deep neural networks

Object classification has been proposed as a principal objective of the primate ventral visual stream and has been used as an optimization target for deep neural network models (DNNs) of the visual system. However, visual brain areas represent many different types of information, and optimizing for classification of object identity alone does not constrain how other information may be encoded in visual representations. Information about different scene parameters may be discarded altogether (‘invariance’), represented in non-interfering subspaces of population activity (‘factorization’) or encoded in an entangled fashion. In this work, we provide evidence that factorization is a normative principle of biological visual representations. In the monkey ventral visual hierarchy, we found that factorization of object pose and background information from object identity increased in higher-level regions and strongly contributed to improving object identity decoding performance. We then conducted a large-scale analysis of factorization of individual scene parameters – lighting, background, camera viewpoint, and object pose – in a diverse library of DNN models of the visual system. Models which best matched neural, fMRI, and behavioral data from both monkeys and humans across 12 datasets tended to be those which factorized scene parameters most strongly. Notably, invariance to these parameters was not as consistently associated with matches to neural and behavioral data, suggesting that maintaining non-class information in factorized activity subspaces is often preferred to dropping it altogether. Thus, we propose that factorization of visual scene information is a widely used strategy in brains and DNN models thereof.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

CMS Token Transition

Within the LHC community, a momentous transition has been occurring in authorization. For nearly 20 years, services within the Worldwide LHC Computing Grid (WLCG) have authorized based on mapping an identity, derived from an X.509 credential, or a group/role, derived from a VOMS extension issued by the experiment. A fundamental shift is occurring to capabilities: the credential, a bearer token, asserts the authorizations of the bearer, not the identity. By the HL-LHC era, the CMS experiment plans for the transition to tokens, based on the WLCG Common JSON Web Token profile, to be complete. Services in the technology architecture include the INDIGO Identity and Access Management server to issue tokens; a HashiCorp Vault server to store and refresh access tokens for users and jobs; a managed token bastion server to push credentials to the HTCondor CredMon service; and HTCondor to maintain valid tokens in long-running batch jobs. We will describe the transition plans of the experiment, current status, configuration of the central authorization server, lessons learned in commissioning token-based access with sites, and operational experience using tokens for both job submissions and file transfers.

43 PARTICLE ACCELERATORS↗