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At least 1,063 records · Page 59

A Review of the Intrinsic Heavy Quark Content of the Nucleon

We present a review of the state of the art of our understanding of the intrinsic charm and bottom content of the nucleon. We discuss theoretical calculations, constraints from global analyses, and collider observables sensitive to the intrinsic heavy quark distributions. A particular emphasis is put on the potential of a high energy and high luminosity fixed target experiment using the LHC beams (AFTER@LHC) to search for intrinsic charm.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Effect of Deposition Conditions on Phase Content and Mechanical Properties of Yttria-Stabilized Zirconia Thin Films Deposited by Sol-Gel/Dip-Coating

The effect of yttria concentration (0-33.4 mol%), extraction rates (0.17, 0.33, 0.50, and 0.67 mm s -1 ), and the number of layers (up to four) on the phase content, surface defects, thickness, hardness, adhesion strength, and wear rate of yttria-stabilized zirconia coatings produced by sol-gel/dip-coating were studied for its use on thermolabile substrates. At 700°C, a metastable tetragonal phase ($\mathcal{t''}$) was obtained even with 33.4 mol% yttria when heat treated for 24 hours; however, a fully cubic structure was attained by extending the heat treatment up to 48 hours as confirmed by Raman spectroscopy. Furthermore, it was necessary to use withdrawal speeds of at least 0.67 mm s -1 to produce defect-free coatings. Although the coatings were produced at low temperature, they showed 41% lower wear rate than steel and an adhesion strength of 30 MPa. Our work stresses the importance of the heat treatment history on the stabilization of the cubic phase in sol-gel YSZ coatings.

36 MATERIALS SCIENCE↗

Accessible Content Optimization for Research Needs (ACORN)

ACORN employs a set of automated processes for informing and/or enforcing defined content schemas to create standardized and highly structured data. Because of its standardized data source, ACORN easily applies computer automation to generate communication assets such as PDFs, Powerpoint presentations, and web pages. Built using the memory-safe Rust programming language, ACORN is portable and accessible for use on any Windows, Mac, or Linux machine.

Wohlgemuth, JasonHoward [Oak Ridge National Labora↗

On the Relationship between Regional Ocean Heat Content and Sea Surface Height

Abstract An accurate diagnosis of ocean heat content (OHC) is essential for interpreting climate variability and change, as evidenced for example by the broad range of hypotheses that exists for explaining the recent hiatus in global mean surface warming. Potential insights are explored here by examining relationships between OHC and sea surface height (SSH) in observations and two recently available large ensembles of climate model simulations from the mid-twentieth century to 2100. It is found that in decadal-length observations and a model control simulation with constant forcing, strong ties between OHC and SSH exist, with little temporal or spatial complexity. Agreement is particularly strong on monthly to interannual time scales. In contrast, in forced transient warming simulations, important dependencies in the relationship exist as a function of region and time scale. Near Antarctica, low-frequency SSH variability is driven mainly by changes in the circumpolar current associated with intensified surface winds, leading to correlations between OHC and SSH that are weak and sometimes negative. In subtropical regions, and near other coastal boundaries, negative correlations are also evident on long time scales and are associated with the accumulated effects of changes in the water cycle and ocean dynamics that underlie complexity in the OHC relationship to SSH. Low-frequency variability in observations is found to exhibit similar negative correlations. Combined with altimeter data, these results provide evidence that SSH increases in the Indian and western Pacific Oceans during the hiatus are suggestive of substantial OHC increases. Methods for developing the applicability of altimetry as a constraint on OHC more generally are also discussed.

54 ENVIRONMENTAL SCIENCES↗

Evolution of Ocean Heat Content Related to ENSO

As the strongest interannual perturbation to the climate system, El Niño–Southern Oscillation (ENSO) dominates the year-to-year variability of the ocean energy budget. Here we combine ocean observations, reanalyses, and surface flux data with Earth system model simulations to obtain estimates of the different terms affecting the redistribution of energy in the Earth system during ENSO events, including exchanges between ocean and atmosphere and among different ocean basins, and lateral and vertical rearrangements. This comprehensive inventory allows better understanding of the regional and global evolution of ocean heat related to ENSO and provides observational metrics to benchmark performance of climate models. Results confirm that there is a strong negative ocean heat content tendency (OHCT) in the tropical Pacific Ocean during El Niño, mainly through enhanced air–sea heat fluxes Q into the atmosphere driven by high sea surface temperatures. In addition to this diabatic component, there is an adiabatic redistribution of heat both laterally and vertically (0–100 and 100–300 m) in the tropical Pacific and Indian oceans that dominates the local OHCT. Heat is also transported and discharged from 20°S–5°N into off-equatorial regions within 5°–20°N during and after El Niño. OHCT and Q changes outside the tropical Pacific Ocean indicate the ENSO-driven atmospheric teleconnections and changes of ocean heat transport (i.e., Indonesian Throughflow). The tropical Atlantic and Indian Oceans warm during El Niño, partly offsetting the tropical Pacific cooling for the tropical oceans as a whole. While there are distinct regional OHCT changes, many compensate each other, resulting in a weak but robust net global ocean cooling during and after El Niño.

54 ENVIRONMENTAL SCIENCES↗

Budgets for Decadal Variability in Pacific Ocean Heat Content

A slowdown in the rate of surface warming in the early 2000s led to renewed interest in the redistribution of ocean heat content (OHC) and its relationship with internal climate variability. In this work we use the Community Earth System Model version 1 to study the relationship between OHC and the interdecadal Pacific oscillation (IPO), a major mode of decadal sea surface temperature variability in the Pacific Ocean. By comparing the relative contributions of surface heat flux and ocean dynamics to changes in OHC for different phases of the IPO, we try to identify the underlying physical processes involved. Our results suggest that during IPO phase transitions, changes of 0–300-m OHC across the northern extratropical Pacific are positively contributed by both surface heat flux and oceanic heat transport. By contrast, oceanic heat transport appears to drive the OHC changes in equatorial Pacific whereas surface heat flux acts as a damping term. During a positive IPO phase, weakened wind-driven circulation acts to increase the OHC in the equatorial Pacific while the enhanced evaporation acts to damp OHC anomalies. In the Kuroshio–Oyashio Extension region, a dipole anomaly of zonal heat advection amplifies an OHC dipole anomaly that moves eastward, while strong turbulent heat fluxes act to dampen this OHC anomaly. In the northern subtropical Pacific, both the wind-driven evaporation change and the change of zonal heat advection along Kuroshio Extension contribute to the OHC change during phase transition. For the northern subpolar Pacific, both surface heat flux and enhanced meridional advection contribute to the positive OHC anomalies during the positive IPO phase.

54 ENVIRONMENTAL SCIENCES↗

Distinctive Pattern of Global Warming in Ocean Heat Content

Abstract Huge heat anomalies in the atmosphere and ocean in recent years are not yet explained. Strong characteristic patterns in temperatures for upper layers of the ocean occurred from 2000 to 2023 in the presence of global warming from increasing atmospheric greenhouse gases. Here, we show that the deep tropics are warming, although sharply modulated by El Niño–Southern Oscillation events, with strong heating in the extratropics near 40°N and 40°–45°S but little heating near 20°N and 25°–30°S. The heating is most clearly manifested in zonal-mean ocean heat content and is evident in sea surface temperatures. The strongest heating is in the Southern Hemisphere, where aerosol effects are small. Estimates are made of the contributions to heating of top-of-atmosphere (TOA) radiation, atmospheric energy transports, surface fluxes of energy, and redistribution of energy by surface winds and ocean currents. The patterns of change are not directly related to TOA radiation but are evident in net surface energy fluxes and inferred ocean heat transports, underscoring their coupled origin. Changes in the atmospheric circulation through a poleward shift in ocean jet streams and storm tracks are reflected in surface wind-driven ocean Ekman transports. As well as human-induced climate change, internal natural variability is likely in play. Hence, the atmosphere and ocean currents are systematically redistributing heat from global warming, profoundly affecting local climates. Significance Statement As the climate changes, it has been difficult to discern meaningful patterns. Distinctive patterns of change have occurred in the ocean when examined as zonal averages around latitude bands. Most excess heat from global warming resides in the ocean and, since 2005, has become focused into bands near 40°N and 40°S, with little net warming in the subtropics. The strongest warming is in the Southern Hemisphere, although sea surface temperatures have increased more in the Northern Hemisphere. Changes in the atmospheric circulation through a poleward shift in the jet stream and storm tracks are primarily responsible along with corresponding changes in ocean currents. These changes are linked through surface exchanges of energy via heat, moisture, and wind stress.

Trenberth, Kevin E. [National Center for Atmospher↗

A Technique for Estimating Liquid Droplet Diameter and Liquid Water Content in Stratocumulus Clouds Using Radar and Lidar Measurements

This paper describes a technique for estimating the liquid water content (LWC) and a characteristic particle diameter in stratocumulus clouds using radar and lidar observations. The uncertainty in LWC estimate from radar and lidar measurements is significantly reduced once the characteristic particle diameter is known. The technique is independent of the drop size distribution. It is applicable for a broad range of W-band reflectivity Z between -30 and 0 dBZ and all values of lidar backscatter β observations. No partitioning of cloud or drizzle is required on the basis of an arbitrary threshold of Z as in prior studies. A method for estimating droplet diameter and LWC was derived from the electromagnetic simulations of radar and lidar observations. In situ stratocumulus cloud and drizzle probe spectra were input to the electromagnetic simulation. The retrieved droplet diameter and LWC were validated using in situ measurements from the southeastern Pacific Ocean. The retrieval method was applied to radar and lidar measurements from the northeastern Pacific. Uncertainty in the retrieved droplet diameter and LWC that are due to the measurement errors in radar and lidar backscatter measurements are 7% and 14%, respectively. The retrieved LWC was validated using the concurrent G-band radiometer estimates of the liquid water path.

54 ENVIRONMENTAL SCIENCES↗

Information Content of a Synergy of Ground-Based and Space-Based Infrared Sounders. Part I: Clear-Sky Environments

Abstract Profiles of atmospheric temperature and water vapor from remotely sensed platforms provide critical observations within the temporal and spatial gaps of the radiosonde network. The 2017 National Academies of Science Decadal Survey highlighted that observations of the planetary boundary layer (PBL) from the current space-based observing system are not of the necessary accuracy or resolution for monitoring and predicting high-impact weather phenomena. One possible solution to improving observations of the PBL is supplementing the existing space-based observing system with a network of ground-based profilers. A synthetic information content study is developed utilizing profiles from the Atmospheric Radiation Measurement (ARM) program sites at the Southern Great Plains (SGP), east North Atlantic (ENA), and North Slope of Alaska (NSA) to assess the benefits, in terms of degrees of freedom (DOF), vertical resolution, and uncertainties, of a synergy between the ground-based Atmospheric Emitted Radiance Interferometer (AERI) with space-based hyperspectral infrared (IR) sounders. A combination of AERI with any of the three polar-orbiting IR sounders: the Atmospheric Infrared Sounder (AIRS), the Cross-track Infrared Sounder (CrIS), or the Infrared Atmospheric Sounding Interferometer (IASI), results in a DOF increase of 30%–40% in the surface-to-700-hPa layer compared to the space-based instrument alone. Introducing AERI measurements to the observing system also results in significant improvements to vertical resolution and uncertainties in the bottom 1000 m of the atmosphere compared to CrIS measurements alone. A synergy of CrIS and AERI exceeds the 1-km-vertical-resolution goal set by the Decadal Survey in the lowest 1000 m.

54 ENVIRONMENTAL SCIENCES↗

Estimating Ice Water Content for Winter Storms from Millimeter-Wavelength Radar Measurements Using a Synthesis of Polarimetric and Dual-Frequency Radar Observations

The potential of millimeter-wavelength radar-based ice water content (IWC) estimation is demonstrated using a Ka-band Scanning Polarimetric Radar (KASPR) for the U.S. northeast coast winter storms. Two IWC relations for Ka-band polarimetric radar measurements are proposed: one that uses a combination of the radar reflectivity Z and the estimated total number concentration of snow particles N t and the other based on the joint use of Z, specific differential phase K DP , and the degree of riming f rim . A key element of the algorithms is to obtain the “Rayleigh-equivalent” value of Z measured at the Ka band, i.e., the corresponding Z at a longer radar wavelength for which Rayleigh scattering takes place. This is achieved via polarimetric retrieval of the mean volume diameter D m and incorporating the relationship between the dual-wavelength ratio DWR S/Ka and D m . Those techniques allow for retrievals from single millimeter-wavelength radar measurements and do not necessarily require the dual-wavelength ratio (DWR) measurements, if the DWR–D m relation and Rayleigh assumption for Ka-band K DP are valid. Comparison between the quasivertical profile product obtained from KASPR and the columnar vertical profile product generated from the nearby WSR-88D S-band radar measurements demonstrates that the DWR S/Ka can be estimated from the two close radars without the need for collocated radar beams and synchronized antenna scanning and can be used for determining the Rayleigh-equivalent value of Z. As a result, the performance of the suggested techniques is evaluated for seven winter storms using surface disdrometer and snow accumulation measurements.

Cloud retrieval↗

A study of the viability of exploiting memory content similarity to improve resilience to memory errors

Building the next-generation of extreme-scale distributed systems will require overcoming several challenges related to system resilience. As the number of processors in these systems grow, the failure rate increases proportionally. One of the most common sources of failure in large-scale systems is memory. In this paper, we propose a novel runtime for transparently exploiting memory content similarity to improve system resilience by reducing the rate at which memory errors lead to node failure. We evaluate the viability of this approach by examining memory snapshots collected from eight high-performance computing (HPC) applications and two important HPC operating systems. Based on the characteristics of the similarity uncovered, we conclude that our proposed approach shows promise for addressing system resilience in large-scale systems.

97 MATHEMATICS AND COMPUTING↗

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes

Background: The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads. Results: The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes. Conclusions: Application of these procedures, based solely on k-mer abundances in short read data sets, allows aspects of genome structure to be resolved that are not apparent from conventional short read assemblies. This knowledge of the repetitive content of genomes provides insights into genome evolution and diversity.

59 BASIC BIOLOGICAL SCIENCES↗

Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins

Background: Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c-type cytochromes, which are crucial for their respiratory versatility. In our previous study of the Shewanella loihica PV-4 strain, we found that the disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), but it is different in Shewanella oneidensis MR-1. Hence, the function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, are investigated in S. oneidensis MR-1. Result: In the present study, deletion of either hemH1 or hemH2 in S. oneidensis MR-1 did not lead to overproduction of extracellular protoporphyrin IX (PPIX) as previously described in the hemH1 mutants of S. loihica PV-4. Moreover, supplement of exogenous hemins made it possible to generate the hemH1 and hemH2 double mutant in MR-1, but not in PV-4. Under aerobic condition, exogenous hemins were required for the growth of MR-1ΔhemH1ΔhemH2, which also overproduced extracellular PPIX. These results suggest that heme is essential for aerobic growth of Shewanella species and MR-1 could also uptake hemin for biosynthesis of essential cytochrome(s) and respiration. Besides, the exogenous hemin mediated CymA cytochrome maturation and the cellular KatB catalase activity. Both hemH paralogues were transcribed in wild-type MR-1, and the hemH2 transcription was remarkably up-regulated in MR-1ΔhemH1 mutant to compensate for the loss of hemH1. The periplasmic glutathione peroxidase gene pgpD, located in the same operon with hemH2, and a large gene cluster coding for iron, heme (hemin) uptake systems are absent in the PV-4 genome. Conclusion: Our results indicate that the genetic divergence in gene content and gene expression between these Shewanella species, accounting for the phenotypic difference described here, might be due to their speciation and adaptation to the specific habitats (iron-rich deep-sea vent versus iron-poor freshwater) in which they evolved and the generated mutants could potentially be utilized for commercial production of PPIX.

59 BASIC BIOLOGICAL SCIENCES↗

Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis

One-carbon (C1) metabolism is important for synthesizing a range of biologically important compounds that are essential for life. In plants, the C1 pathway is crucial for the synthesis of a large number of secondary metabolites, including lignin. Tetrahydrofolate and its derivatives, collectively referred to as folates, are crucial co-factors for C1 metabolic pathway enzymes. Given the link between the C1 and phenylpropanoid pathways, we evaluated whether folylpolyglutamate synthetase (FPGS), an enzyme that catalyzes the addition of a glutamate tail to folates to form folylpolyglutamates, can be a viable target for reducing cell wall recalcitrance in plants. Consistent with its role in lignocellulosic formation, FPGS1 was preferentially expressed in vascular tissues. Total lignin was low in fpgs1 plants leading to higher saccharification efficiency of the mutant. The decrease in total lignin in fpgs1 was mainly due to lower guaiacyl (G) lignin levels. Glycome profiling revealed subtle alterations in the cell walls of fpgs1. Further analyses of hemicellulosic polysaccharides by NMR showed that the degree of methylation of 4-O-methyl glucuronoxylan was reduced in the fpgs1 mutant. Microarray analysis and real-time qRT-PCR revealed that transcripts of a number of genes in the C1 and lignin pathways had altered expression in fpgs1 mutants. Consistent with the transcript changes of C1-related genes, a significant reduction in S-adenosyl-l-methionine content was detected in the fpgs1 mutant. The modified expression of the various methyltransferases and lignin-related genes indicate possible feedback regulation of C1 pathway-mediated lignin biosynthesis. In conclusion, our observations provide genetic and biochemical support for the importance of folylpolyglutamates in the lignocellulosic pathway and reinforces previous observations that targeting a single FPGS isoform for down-regulation leads to reduced lignin in plants. Because fpgs1 mutants had no dramatic defects in above ground biomass, selective down-regulation of individual components of C1 metabolism is an approach that should be explored further for the improvement of lignocellulosic feedstocks.

59 BASIC BIOLOGICAL SCIENCES↗

Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities

Viruses play important roles in the ocean’s biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts. We analysed 58 viral communities associated with size-fractionated free-living (0.2–0.8 μm) and particle-attached (0.8–20 μm) cellular metagenomes from bathypelagic (2150–4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses. These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Adapting C4 Photosynthesis to Atmospheric Change and Increasing Productivity by Elevating Rubisco Content in Sorghum and Sugarcane

This repository includes data sets and R scripts that were used to perform analysis and produce figures for the following publication: Salesse-Smith, C. E. et al. “Adapting C4 photosynthesis to atmospheric change and increasing productivity by elevating Rubisco content in sorghum and sugarcane.” Proceedings of the National Academy of Sciences 122, e2419943122 (2025) doi:10.1073/pnas.2419943122.

Biomass Analytics↗