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At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The IMG/M data management and analysis system v.7: content updates and new features

The Integrated Microbial Genomes & Microbiomes system at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. Here, we also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗
DOE OSTI2024

Correction to ‘Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9’

In the originally published online version of this manuscript, there were two co-authors missing from the author list: Tanja Woyke (https://orcid.org/0000-0002-9485-5637) and Emiley Eloe-Fadrosh (https://orcid.org/0000-0002-8162-1276). The author list should read: ‘Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A. Nicolopoulos, Alessandro Favognano, Tanja Woyke, Emiley A. Eloe-Fardosh, I-Min A. Chen, Nikos C. Kyrpides and T.B.K. Reddy’. This emendation is outlined only in this correction notice to preserve the version of record.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Correction to ‘Genomes OnLine Database (GOLD) v.8: overview and updates’

In the originally published online version of this manuscript, there were two co-authors missing from the author list: Tanja Woyke (https://orcid.org/0000-0002-9485-5637) and Emiley Eloe-Fadrosh (https://orcid.org/0000-0002-8162-1276). The list should now read: ‘Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Jagadish Chandrabose Sundaramurthi, Janey Lee, Mahathi Kandimalla, Tanja Woyke, Emiley A. Eloe-Fardosh, I-Min A. Chen, Nikos C. Kyrpides and T.B.K. Reddy’. The emendation is outlined only in this correction notice to preserve the version of record.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Responses of the Plant Cell Wall to Sub-Zero Temperatures: A Brief Update

Our general understanding of plant responses to sub-zero temperatures focuses on mechanisms that mitigate stress to the plasma membrane. The plant cell wall receives comparatively less attention, and questions surrounding its role in mitigating freezing injury remain unresolved. Despite recent molecular discoveries that provide insight into acclimation responses, the goal of reducing freezing injury in herbaceous and woody crops remains elusive. This is likely due to the complexity associated with adaptations to low temperatures. Understanding how leaf cell walls of herbaceous annuals promote tissue tolerance to ice does not necessarily lead to understanding how meristematic tissues are protected from freezing by tissue-level barriers formed by cell walls in overwintering tree buds. In this mini-review, we provide an overview of biological ice nucleation and explain how plants control the spatiotemporal location of ice formation. We discuss how sugars and pectin side chains alleviate adhesive injury that develops at sub-zero temperatures between the matrix polysaccharides and ice. The importance of site-specific cell-wall elasticity to promote tissue expansion for ice accommodation and control of porosity to impede ice growth and promote supercooling will be presented. How specific cold-induced proteins modify plant cell walls to mitigate freezing injury will also be discussed. The opinions presented in this report emphasize the importance of a plant’s developmental physiology when characterizing mechanisms of freezing survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Updated systematics of intermediate-energy single-nucleon removal cross sections

The body of experimental measurements of intermediate-energy reactions that remove a single nucleon from a secondary beam of neutron- or proton-rich nuclei continues to grow. These data have been analyzed consistently using an approximate, eikonal-model treatment of the reaction dynamics combined with appropriate shell-model descriptions of the projectile initial state, the bound final states spectrum of the reaction residue, and single-particle removal strengths computed from their wave-function overlaps. Here, the systematics of the ratio R s of the measured inclusive cross section to all bound final states and the calculated cross section to bound shell-model states—in different regions of the nuclear chart and involving both very weakly bound and strongly bound valence nucleons—is important in relating the empirically deduced orbital occupancies to those from the best available shell-model predictions. Importantly, several new higher-energy measurements, for which the sudden-approximation aspect of the dynamical description is placed on an even stronger footing, now supplement the previously analyzed measurements. These additional data sets are discussed. Their R s values are shown to conform to and reinforce the earlier-observed systematics, with no indication that the approximately linear reduction in R s with increasing nucleon separation energy is a consequence of a breakdown of the sudden approximation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Updated analysis of the Er 170 ( p , t ) Er 168 reaction data

More than 200 states up to 4.1 MeV excitation have been populated in 168 Er with the 170 Er ( p , t ) reaction at 25 MeV incident energy. About 80 of these states, with 0 + and 2 + assignments, were reported in a previous publication [D. Bucurescu et al., Phys. Rev. C 73, 064309 (2006)]. Here, the present work considerably enriches the knowledge of this nucleus. A multistep coupled-channels analysis of the angular distributions is now presented for all the states observed in this experiment. Spin and parity values between 0 + and 7 - are newly assigned for more than 100 states. For the states already reported in the ENSDF database with J π values there is a good agreement with our values. The 168 Er nucleus remains one of the best experimentally known nuclei for states with low and medium spins below 4 MeV excitation energy, representing a challenge for future microscopic structure model calculations aiming to disentangle the contributions of different excitation degrees of freedom.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Updated constraints on asteroid-mass primordial black holes as dark matter

Microlensing of stars places significant constraints on subplanetary-mass compact objects, including primordial black holes, as dark matter candidates. As the lens’ Einstein radius in the source plane becomes comparable to the size of the light source, however, source amplification is strongly suppressed, making it challenging to constrain lenses with a mass at or below 10 –10 solar masses, i.e., asteroid-mass objects. Current constraints, using Subaru Hyper Suprime Cam (HSC) observations of M31, assume a fixed source size of one solar radius. However, the actual stars in M31 bright enough to be used for microlensing are typically much larger. We correct the HSC constraints by constructing a source size distribution based on the M31 PHAT survey and on a synthetic stellar catalog and by correspondingly weighting the finite-size source effects. In this work, we find that the actual HSC constraints are weaker by up to almost 3 orders of magnitude in some cases, broadening the range of masses for which primordial black holes can be the totality of the cosmological dark matter by almost 1 order of magnitude.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Updated MiniBooNE neutrino oscillation results with increased data and new background studies

The MiniBooNE experiment at Fermilab reports a total excess of $638.0 \pm 132.8$ electron-like events ($4.8 \sigma$) from a data sample corresponding to $18.75 \times 10^{20}$ protons-on-target in neutrino mode, which is a 46% increase in the data sample with respect to previously published results, and $11.27 \times 10^{20}$ protons-on-target in antineutrino mode. The additional statistics allow several studies to address questions on the source of the excess. First, we provide two-dimensional plots in visible energy and cosine of the angle of the outgoing lepton, which can provide valuable input to models for the event excess. Second, we test whether the excess may arise from photons that enter the detector from external events or photons exiting the detector from $\pi^0$ decays in two model independent ways. Beam timing information shows that almost all of the excess is in time with neutrinos that interact in the detector. The radius distribution shows that the excess is distributed throughout the volume, while tighter cuts on the fiducal volume increase the significance of the excess. We conclude that models of the event excess based on entering and exiting photons are disfavored.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Update of Euclidean windows of the hadronic vacuum polarization

We compute the standard Euclidean window of the hadronic vacuum polarization using multiple independent blinded analyses. We improve the continuum and infinite-volume extrapolations of the dominant quark-connected light-quark isospin-symmetric contribution and address additional subleading systematic effects from sea-charm quarks and residual chiral-symmetry breaking from first principles. We find 𝑎$^{W}_{μ}$ = 235.56⁢(65)⁢(50) × 10 −10 , which is in 3.8⁢𝜎 tension with the recently published dispersive result of 𝑎$^{W}_{μ}$ =229.4⁢(1.4) × 10 −10 [G. Colangelo, A. X. El-Khadra, M. Hoferichter, A. Keshavarzi, C. Lehner, P. Stoffer, and T. Teubner, Phys. Lett. B 833, 137313 (2022)] and in agreement with other recent lattice determinations. We also provide a result for the standard short-distance window. The results reported here are unchanged compared to our presentation at the Edinburgh workshop of the g-2 Theory Initiative in 2022 [C. Lehner, Talk Presented at the 5th Plenary Meeting of the g-2 Theory Initiative in Edinburgh (2022)].

Lattice QCD↗
DOE OSTI2024

Updated measurements of the M1 transition ψ ( 3686 ) → γ η c ( 2 S ) with η c ( 2 S ) → K K ¯ π

Based on a data sample of ( 2712.4 ± 14.3 ) × 10 6 ψ ( 3686 ) events collected with the BESIII detector at the BEPCII collider, the M1 transition ψ ( 3686 ) → γ η c ( 2 S ) with η c ( 2 S ) → K K ¯ π is studied, where K K ¯ π is K + K − π 0 or K S 0 K ± π ∓ . The mass and width of the η c ( 2 S ) are measured to be ( 3637.8 ± 0.8 ( stat ) ± 0.2 ( syst ) ) MeV / c 2 and ( 10.5 ± 1.7 ( stat ) ± 3.5 ( syst ) ) MeV , respectively. The product branching fraction B ( ψ ( 3686 ) → γ η c ( 2 S ) ) × B ( η c ( 2 S ) → K K ¯ π ) is determined to be ( 0.97 ± 0.06 ( stat ) ± 0.09 ( syst ) ) × 10 − 5 . Using B ( η c ( 2 S ) → K K ¯ π ) = ( 1.8 6 − 0.49 + 0.68 ) % , we obtain the branching fraction of the radiative transition to be B ( ψ ( 3686 ) → γ η c ( 2 S ) ) = ( 5.2 ± 0.3 ( stat ) ± 0.5 ( syst ) − 1.4 + 1.9 ( extr ) ) × 10 − 4 , where the third uncertainty is due to the quoted B ( η c ( 2 S ) → K K ¯ π ) . Published by the American Physical Society 2024

Astronomy & Astrophysics↗