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At least 919 records · Page 51

Metabolic skinflint or spendthrift? Insights into ground sloth integument and thermophysiology revealed by biophysical modeling and clumped isotope paleothermometry

Abstract Remains of megatheres have been known since the 18th -century and were among the first megafaunal vertebrates to be studied. While several examples of preserved integument show a thick coverage of fur for smaller ground sloths living in cold climates such as Mylodon and Nothrotheriops , comparatively very little is known about megathere skin. Assuming a typical placental mammal metabolism, it was previously hypothesized that megatheres would have had little-to-no fur as they achieved giant body sizes. Here the “hairless model of integument” is tested using geochemical analyses to estimate body temperature to generate novel models of ground sloth metabolism, fur coverage, and paleoclimate with Niche Mapper software. The simulations assuming metabolic activity akin to those of modern xenarthrans suggest that sparse fur coverage would have resulted in cold stress across most latitudinal ranges inhabited by extinct ground sloths. Specifically, Eremotherium predominantly required dense 10 mm fur with implications for seasonal changes of coat depth in northernmost latitudes and sparse fur in the tropics; Megatherium required dense 30 mm fur year-round in its exclusive range of cooler, drier climates; Mylodon and Nothrotheriops required dense 10–50 mm fur to avoid thermal stress, matching the integument remains of both genera, and further implying the use of behavioral thermoregulation. Moreover, clumped isotope paleothermometry data from the preserved teeth of four genera of ground sloth yielded reconstructed body temperatures lower than those previously reported for large terrestrial mammals (29 ± 2°–32 ± 3° C). This combination of low metabolisms and thick fur allowed ground sloths to inhabit various environments.

Deak, Michael D.↗

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗

Transport Barriers in Symplectic Maps

Chaotic transport is a subject of paramount importance in a variety of problems in plasma physics, specially those related to anomalous transport and turbulence. On the other hand, a great deal of information on chaotic transport can be obtained from simple dynamical systems like two-dimensional area-preserving (symplectic) maps, where powerful mathematical results like KAM theory are available. In this work we review recent works on transport barriers in area-preserving maps, focusing on systems which do not obey the so-called twist property. For such systems KAM theory no longer holds everywhere and novel dynamical features show up as nonresistive reconnection, shearless curves and shearless bifurcations. After presenting some general features using a standard nontwist mapping, we consider magnetic field line maps for magnetically confined plasmas in tokamaks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

dCache: The Storage System of Choice for Data-Intensive Applications

The ever-increasing volumes of data produced by modern scientific facilities like EuXFEL and LHC put significant stress on data management infrastructure operated by laboratories and research centers. The challenges to be addressed span the entire data life cycle, from ingest and efficient data analysis to long-term preservation, typically involving large tape libraries. dCache, a storage system developed in collaboration between the Deutsches Elektronen-Synchrotron (DESY), Fermi National Accelerator Laboratory, and Nordic e-Infrastructure Collaboration (NeIC), is designed to manage a large number of disk servers and to facilitate transparent data migration to and from archival storage. Its multifaceted approach offers a unified method to support a variety of scientific use cases with the same storage infrastructure, including high-throughput data ingest, data sharing over wide area networks, efficient access from HPC clusters, and long-term data preservation on tertiary storage. Initially developed for high energy physics (HEP) experiments, dCache is now used by various scientific communities, including astrophysics, biomedical research, and life sciences, each having specific requirements. This paper presents architecture, deployment strategies, performance and scalability enhancements, and recent advancements in dCache addressing the needs of scientific communities. Finally, we touch on the development and release process, ensuring the software’s high quality.

DCache↗

Topographic hydro-conditioning to resolve surface depression storage and ponding in a fully distributed hydrologic model

Land surface depressions play a central role in the transformation of rainfall to ponding, infiltration and runoff, yet digital elevation models (DEMs) used by spatially distributed hydrologic models that resolve land surface processes rarely capture land surface depressions at spatial scales relevant to this transformation. Methods to generate DEMs through processing of remote sensing data, such as optical and light detection and ranging (LiDAR) have favored surfaces without depressions to avoid adverse slopes that are problematic for many hydrologic routing methods. Here, in this study, we present a new topographic conditioning workflow, Depression-Preserved DEM Processing (D2P) algorithm, which is designed to preserve physically meaningful surface depressions for depression-integrated and efficient hydrologic modeling. D2P includes several features: (1) an adaptive screening interval for delineation of depressions, (2) the ability to filter out anthropogenic land surface features (e.g., bridges), (3) the ability to blend river smoothing (e.g., a general downslope profile) and depression resolving functionality. From a case study in the Goodwin Creek Experimental Watershed, D2P successfully resolved 86% of the ponds at a DEM resolution of 10 m. Topographic conditioning was achieved with minimum impact as D2P reduced the number of modified cells from the original DEM by 51% compared to a conventional algorithm. Furthermore, hydrologic simulation using a D2P processed DEM resulted in a more robust characterization on surface water dynamics based on higher surface water storage as well as an attenuated and delayed peak streamflow.

54 ENVIRONMENTAL SCIENCES↗

Impact of storage and blending of algae and forest product residue on fuel blendstock production

Seasonal impacts on the production of algae biomass require blending with other feedstocks such as wood to maintain consistent annual conversion capacity. Idaho National Laboratory (INL) has developed a long-term storage strategy for algae biomass using ensiling, or anaerobic wet storage, that was tested for blends of algae and wood to stabilize the feedstock supply for processing to fuels. Additionally, blending biomass (algae and wood) leverages existing biomass storage approaches commonly used by the feed and forage industry. Earlier research also has demonstrated positive results that indicate ensiling is more effective and economical in normalizing biomass feedstock supply prior to conversions such as HTL (hydrothermal liquefaction) than preserving biomass by drying. By assessing impacts beginning with upstream logistic operations and proceeding through each conversion step, this work focuses on conversion of ensiled and blended biomass to fungible liquid transportation fuel blendstocks. This is accomplished by conversion of the blended biomass (62% Chlorella sp. blended with 38% loblolly pine forest product residues [FPR]) to bio-crude through HTL and subsequent upgrading through HT (hydrotreating) with a commercial refinery catalyst analogous to a refinery process to produce hydrocarbon fuel. In this work, results indicate that carbon retention and quality are preserved in both the bio-crude and upgraded fuel from the ensiled blend, indicating the potential of this approach for managing seasonal variations in algae biomass productivity.

09 BIOMASS FUELS↗

Transient Multiphysics Simulations with Pin Power Reconstruction in the Griffin Reactor Physics Code

This work introduces the pin power reconstruction capability available in the Griffin reactor physics code. This capability is implemented in an unstructured mesh framework, and the methods introduced are applied to the 2D SIMBA reactor core, which has assemblies and pins arranged in a hexagonal lattice. Since this reactor has a non-Cartesian geometry and also operates in the thermal spectrum, a general approach to pin power reconstruction is adopted, where SPH-based equivalence is leveraged to preserve assembly-wise reaction rates, while computing full-core form functions to preserve pin-wise fission production rates within the fuel pins of the reactor core. In a 2D microreactor benchmark problem, this pin power reconstruction approach was shown to reproduce pin powers compared to the Serpent2 Monte Carlo code for fixed temperature conditions and control drum rotation angles, yielding a core-wide RMS error level of 0.6\% and a maximum absolute pin error of 2.3\%. In addition, a tabulated library of multigroup cross sections, SPH factors, and form functions was generated to demonstrate the applicability of pin power reconstruction to a thermal feedback problem. Finally, a control drum transient was successfully simulated, showcasing the application of pin power reconstruction in a transient multiphysics feedback problem.

97 - MATHEMATICS AND COMPUTING↗

Entanglement Enabled Intensity Interferometry of different wavelengths of light

Highlights: • We use quantum entanglement to erase the color of photons for a new imaging method. • Can achieve higher resolution imaging by accessing hidden phase information. • We detail practical experimental designs to implement our theoretical protocols. We propose methods to perform intensity interferometry of photons having two different wavelengths. Distinguishable particles typically cannot interfere with each other, but we overcome that obstacle by processing the particles via entanglement and projection so that they lead to the same final state at the detection apparatus. Specifically, we discuss how quasi-phase-matched nonlinear crystals can be used to convert a quantum superposition of light of different wavelengths onto a common wavelength, while preserving the phase information essential for their meaningful interference. We thereby gain access to a host of new observables, which can probe subtle frequency correlations and entanglement. Further, we generalize the van Cittert–Zernike formula for the intensity interferometry of extended sources, demonstrate how our proposal supports enhanced resolution of sources with different spectral character, and suggest potential applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Electron–phonon interaction in Kondo lattice systems

Highlights: • Rigorous study of ground state properties of the Kondo lattice model with an electron–phonon. • The ground state is proved to be unique. • The total spin of the ground state is determined according to the lattice structure. • Novel applications of order preserving operator inequalities. We study ground state properties of the Kondo lattice model with an electron–phonon interaction. The ground state is proved to be unique; in addition, the total spin of the ground state is determined according to the lattice structure. To prove the assertions, an extension of the method of spin reflection positivity is given in terms of order preserving operator inequalities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Selective recovery of native copper from basalt tailings using alkaline glycinate solution

Mafic and ultramafic rocks present an intriguing pathway for CO 2 capture through strategic enhancements to the natural silicate weathering cycle. Simultaneously, these rock types are often hosts to appreciable amounts of metals critical to U.S. energy independence, particularly in the context of alkaline mine tailings from historical metal mining. The research and scientific prerogative, then, is to identify promising mafic and ultramafic feedstocks and conduct exploratory studies to effectively recover these critical minerals while preserving the potential for mineral carbonation. The Keweenaw Peninsula of Michigan hosts the largest native Cu reservoir within basalt in the world and experienced a rich history of Cu production spanning from pre-historic times to the mid-1900s. Today, much of the Cu mining legacy remains as mine waste tailings. In this study, we examined the Cu extractability from Keweenaw Basalt tailings using a sodium glycinate solution, in comparison with acid and sodium hydroxide leaching. Experimental results showed an 85 % Cu extraction rate using sodium glycinate as the extraction solution with negligible release of other cations from the basalt. The kinetic and extraction mechanisms of Cu selective recovery using glycinate solution were discussed using time-resolved experimental data and kinetic geochemical modeling. Theoretical estimation of carbon mineralization potential of all the existing basalt waste tailings (∼500 million tons) can reach 85.5 MMT CO 2 . A total of 0.786 MMT Cu can be recovered with sodium glycinate, with a value of 7.7 billion USD. In conclusion, this novel application of alkaline glycinate for selective Cu recovery from basalt mine tailings demonstrates the viability of selective metal recovery using a non-hazardous chemical while preserving CO 2 capture potential and presents a potential pathway toward reducing energy-related emissions and providing an unconventional domestic source of critical minerals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Germplasm cryopreservation of macroalgae for aquaculture breeding and natural resource conservation: A review

The expansion of the global macroalgal aquaculture and climate change creates the need for germplasm preservation of valuable aquaculture strains and maintenance of natural biodiversity. Compared to the large number of studies in fish and shellfish species, relative few studies have been conducted on the macroalgal germplasm cryopreservation. The first cryopreservation of macroalgae to –75 °C was reported on Neopyropia tenera (formerly called Porphyra tenera) in 1964. To date, a total of 34 studies reported germplasm cryopreservation in 33 species, including Chlorophyta (7 species), Ochrophyta (14 species), and Rhodophyta (12 species). Here, the goal of this review was to summarize the published studies on macroalgal germplasm cryopreservation, compare the reported protocols for the cryopreservation process, and identify the factors affecting post-thaw viability. Overall, macroalgal germplasm cryopreservation included haploid or diploid thalli, spores, and gametes. Cryotubes (1.5-ml or 2-ml) have been widely used to package germplasm samples for cooling and storage in most studies, and the 0.5-ml straws and 5-ml cryotubes have been used in several studies. Two approaches (programmable controlled cooling and vitrification) were employed for macroalgal germplasm cryopreservation. A two-step programmable controlled cooling (e.g., from initial culture temperature to a frozen temperature, such as –40 °C, and then directly plunging into liquid nitrogen at –196 °C) was determined to be an effective cooling strategy. Vitrification, a super rapid cooling for a sample to form non-crystalline amorphous solid, was applied on macroalgal germplasm cryopreservation with sample encapsulation and dehydration. Survival of post-thaw samples varied significantly in different studies. Based on research updates, recommendations are made for future research. It is expected that this review can serve as a foundation for future germplasm banking of macroalgae for aquaculture and biodiversity preservation.

59 BASIC BIOLOGICAL SCIENCES↗

Selective adsorption removal of carbonyl molecular foulants from real fast pyrolysis bio-oils

A novel sorbent-based separation process has been developed to selectively remove target molecules from the real fast pyrolysis (FP) pine bio-oils. Specifically, zeolitic molecular sieves and functionalized polymeric resins were found to effectively reduce carbonyl content and carboxylic acid number of a real pine fast pyrolysis bio-oils, therefore enhance bio-oil stability and preserve down-stream catalyst. Our results provide the first-time evidence on the potential effectiveness of sorption technology strategy for dealing with real FP bio-oils, reducing the carbonyl-rich FP oils from 7.5 mmolg-1 down to 4 mmolg-1 at 40 ?, which has potential to enable bio-oil stabilization and enhance operation stability for down-stream upgrading/hydrotreating processes.

Church, Aimee L.↗

Alkali-facilitated deep eutectic solvent for effective bamboo saccharification

In this report, a Na 2 S promoted deep eutectic solvent (DES) was established to reduce the natural recalcitrance of moso bamboo (MB) and improve the subsequent enzymatic saccharification. It was found that the addition of Na 2 S (Choline chloride/Ethylene glycol/Na 2 S) dramatically promoted the deconstructions of lignin with highest removal of 74.67 %, but at the same time preserved glucan and hemicellulose to the maximum extent. With the fractionation, the enzymatic saccharification yield of pretreated MB can reach 100 % under the pretreatment condition of 140 °C, and lignin could be readily recovered with a high yield of 81.47 %. The proposed DES is superior to normal alkaline DES in terms of the higher lignin removal and recovery yield, carbohydrate preservation and enzymatic digestibility, which indicated Na 2 S as a novel and powerful reinforcer enhancing the DES fractionation efficiency.

09 BIOMASS FUELS↗

Hybrid geological modeling: Combining machine learning and multiple-point statistics

Accurately modeling and constructing a geologically realistic subsurface model remains an outstanding problem as the morphology controls the flow behaviors. Particularly, one of the pattern-based methods, namely cross-correlation based simulation, has been proved to be an effective way to reconstruct a realistic model, at both small and large scales. However, conditioning to point data in the large-scale problems is still a crucial issue in these algorithms, since there is always a trade-off between the quality of the realizations and the degree of point data reproduction. Specifically, it is not practical to build a training image (TI) which includes all the possibilities and variabilities. Therefore, finding a pattern that can represent the point data and, at the same time, preserving the connectivities is difficult. This leads to producing highly-connected realizations with a significant mismatch or poor models with a reasonable degree of point data reproduction. To accurately reproduce the densely distributed hard data, pixel-based methods can also produce some unrealistic artifacts around the hard data. In this paper, to overcome this challenge, however, we use pattern-based methods as they often produce more disconnected geobodies when dealing with dense hard data, and proposed a hybrid algorithm using the pattern-based methods and convolutional neural network (CNN). The trained CNN model is utilized to improve the quality of conditioning to point data for the original realizations generated by the pattern-based algorithm. As such, the mismatch locations are identified, and the same regions are used in the training of CNN to mimic the procedure through which a missing region can be filled. To evaluate the performance of the proposed hybrid algorithm, it is tested on cases with different dimensions and different numbers of facies. Then, the newly improved realizations are compared with the initial realizations generated by the pattern-based algorithm. The comparison is also conducted by the flow simulation test. And it indicates that the proposed hybrid algorithm can better reproduce the point data, while the connectivities are better preserved.

58 GEOSCIENCES↗

Effect of moderate temperatures on compressive strength of ultra-high-performance concrete: A microstructural analysis

Highlights: • All coarse aggregates and steel fibres were surrounded by the binder. • X-ray diffraction is useful for explaining the increase in compressive strength with increasing temperature. • Rosenhahnite and/or quartz Dauphiné-twinned phases improved the compressive strength. • Polypropylene fibres prevented spalling and preserved the compressive strength. • Concrete with steel and polypropylene fibres did not exhibit spalling at 300 °C. Concrete with two types of steel fibres and a polypropylene fibre prevented spalling and preserved the compressive strength at 300 °C, which makes these concretes suitable for long-term applications up to 300 °C, such as for steam collectors or thermal energy storage systems. The compressive strength behaviour of three types of ultra-high-performance fibre-reinforced concrete manufactured with the same matrix was investigated. For this purpose, a complete characterisation of all the raw materials and the three types of fibres used was performed. The morphology of all concrete mixtures at room temperature was analysed using scanning electron microscopy–energy-dispersive X-ray spectroscopy. From the results, it was ascertained that the steel fibres and coarse siliceous aggregates were not in contact (being separated by ≥3.41 μm) and were surrounded by the binder (of ≥1 μm in thickness) for all the mixtures studied. Rosenhahnite and/or quartz Dauphiné-twinned phases improved the compressive strength (as determined by X-ray diffraction).

36 MATERIALS SCIENCE↗

Argon broad ion beam sectioning and high resolution scanning electron microscopy imaging of hydrated alite

Highlights: • The native fibrous outer and dense inner C-S-H structure are preserved by using low energy argon broad ion beam sectioning. • Possible artefacts of the preparation and imaging of hydrated alite are shown and discussed. • An approach for a semi automated pore analysis of the obtained high resolution images is demonstrated. Scanning electron microscopy (SEM) imaging is able to visualize micro- to nano-structures of cement and concrete. A prerequisite is that the sample preparation preserves the native structure of the specimen. In this study, argon broad ion beam (BIB) sectioning is compared to state-of-the-art sample preparation (resin embedding, polishing) for hydrated alite. Additionally, it is investigated if during BIB, sample cooling is beneficial to avoid deterioration of cement hydrates. The aim is to quantitatively measure pore size distributions in hardened alite pastes. Therefore, not only optimized sample preparation but also optimized imaging conditions are investigated. Finally, it is demonstrated that by image analysis pores down to a diameter of 5 nm in hydrated alite pastes can be quantitatively analysed.

36 MATERIALS SCIENCE↗

Spatially resolved X-ray imaging and molecular characterisation of sulfur and iron in organic- and sulfur-rich hydrocarbon source mudstones

Sulfurisation of organic matter (OM) is a prominent preservation mechanism, however iron sulfide precipitation, particularly pyrite (FeS2), can counteract this mechanism. There is a dearth of high-resolution, spatially-resolved spectroscopic (redox) information on sulfur and iron inventories within organic-rich rocks that would improve our understanding of prevailing environmental conditions during deposition. Here, state-of-the-art synchrotron-based X-ray absorption and fluorescence analyses of key organic- and sulfur-rich mudstones demonstrate the potential of these techniques to non-destructively map and produce detailed spectroscopic information. Detailed high-resolution analyses (μm- to mm-scale) reveal the presence of widespread sulfurised OM in the Blackstone Band of the Kimmeridge Clay Formation, in line with a persistence of euxinia over a long temporal span and low reactive iron input, facilitating the preservation of OM through sulfurisation. In contrast, the presence of sulfurised OM was transitional in the Monterey Formation, consistent with fluctuating water column redox conditions, and is less significant in the Whitby Mudstone Formation, likely due to the high reactive iron concentrations outcompeting sulfurised OM formation. Analyses of sulfur species using model compounds further indicate that the Whitby Formation is strongly enriched in inorganic reduced sulfur minerals, while both the Kimmeridge Clay and Monterey Formations are dominated by organic sulfur species. These synchrotron-based observations improve our understanding of environmental conditions during the time of deposition of these mudstones and thus show great promise in the study of organic-rich sediments, especially in allowing their depositional settings to be more accurately reconstructed.

Kimmeridge Clay Formation↗