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At least 1,045 records · Page 58

Sequencing and analysis of 131 SARS-CoV-2 isolates in previously sampled and unsampled regions of Jordan from 2020 to 2023

The Hashemite Kingdom of Jordan remains an understudied country for next generation sequencing analysis of SARS-CoV-2 genomes collected during the 2019 pandemic. Here we provide 131 additional reference genomes collected between 2020–2023 from SARS-CoV-2-positive patients across Jordan. Phylogenetic analysis supports existing pandemic narratives of changing clade dominance over time and adds genomes in novel Jordanian locations and timepoints to make Jordan SARS-CoV-2 databases more comprehensive. Samples from the less-sequenced cities of Ajloun, Jaresh, Karak, and Madaba identified previously unreported lineages while Amman, Irbid, and Zarqa have existing sequencing efforts bolstered. Despite many incomplete patient records and a relatively small sample size, we observe interesting symptom patterns that support existing global and Jordanian pandemic narratives. We note how in-country COVID-19 pandemic genomic studies showcase Jordan’s efforts to expand next generation sequencing capabilities, especially through the leveraging of EDGE COVID-19, a bioinformatics platform for performing rapid, batched analysis of SARS-CoV-2 sequencing that streamlines sample processing prepared from a network of hospital locations.

60 APPLIED LIFE SCIENCES↗

GeoThermalCloud framework for fusion of big data and multi-physics models in Nevada and Southwest New Mexico

Our GeoThermalCloud framework is designed to process geothermal datasets using a novel toolbox for unsupervised and physics-informed machine learning called SmartTensors. More information about GeoThermalCloud can be found at the GeoThermalCloud GitHub Repository. More information about SmartTensors can be found at the SmartTensors Github Repository and the SmartTensors page at LANL.gov. Links to these pages are included in this submission. GeoThermalCloud.jl is a repository containing all the data and codes required to demonstrate applications of machine learning methods for geothermal exploration. GeoThermalCloud.jl includes: - site data - simulation scripts - jupyter notebooks - intermediate results - code outputs - summary figures - readme markdown files GeoThermalCloud.jl showcases the machine learning analyses performed for the following geothermal sites: - Brady: geothermal exploration of the Brady geothermal site, Nevada - SWNM: geothermal exploration of the Southwest New Mexico (SWNM) region - GreatBasin: geothermal exploration of the Great Basin region, Nevada Reports, research papers, and presentations summarizing these machine learning analyses are also available and will be posted soon.

15 GEOTHERMAL ENERGY↗

CalderaCast Example Output

A sample output file generated by CalderaCast, showcasing typical results and data structure. This example helps users understand expected outputs from the tool.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Subsurface Characterization of Hydraulic Fracture Test Site-2 (HFTS-2), Delaware Basin

Hydraulic Fracturing Test Site-2 (HFTS-2) is a field-based research experiment performed in the Wolfcamp Formation of the Permian (Delaware) Basin. This paper focuses on integration, advanced geological characterization, and 3D subsurface modeling of the comprehensive HFTS-2 dataset. The study showcases a multidisciplinary reservoir characterization approach that incorporates geology, petrophysics, geochemistry, geomechanics, microseismic, and subsurface engineering analysis. Subsurface characterization of organic-rich mudstone formations requires understanding complex hydraulic fracture network growth in relation to inherent lithology, geomechanical properties, and interaction with pre-existing natural fractures. This paper presents a characterization workflow incorporating pre- and post-stimulation subsurface data, unique to the HFTS-2 dataset. The study integrated: (1) rock properties from logs, cores, and thin sections; (2) natural and hydraulic fracture descriptions from cores and image logs; (3) local and regional stresses; (4) geomechanics; (5) microseismic; (6) fiber optic (FO) and bottomhole pressure gauge (BHPG) response; and (7) produced fluids analysis. During a stimulation treatment, creation of the stimulated rock volume (SRV) is influenced by several subsurface factors. Key contributing factors include structural context, stress conditions, lithology, facies architecture, pre-existing natural fractures, and geomechanical properties. The HFTS-2 subsurface data integration indicates that the SRV is comprised of a complex juxtaposition of hydraulic fracture swarms, as evidenced by image logs analysis, core description, and microseismic monitoring. The HFTS-2 microseismic event density was used to generate 3D heat maps that serve as a representative SRV footprint, corroborated by secondary datasets. These maps were further integrated with petrophysical and geomechanical characteristics, as well as responses from FO and BHPG, to estimate the lateral and vertical dimensions of the effective fractures. The geological characterization for the HFTS-2 dataset combined with 3D modeling for petrophysical and geomechanical properties provides a strong foundation for subsurface simulation and optimization studies. Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/1-21URTC/D011S005R001/2477501/urtec-2021-5243-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5243 The workflow improved our understanding of HFTS-2 hydraulic fracture propagation and characteristics in relation to offset pressure depletion and interaction with pre-existing natural fractures. Analysis showed that fracture geometry varies by stage and by well, and a complex fracture network is generated with varying fracture density. The multidisciplinary workflow presented herein for integration and characterization serves as a foundation to evaluate completion efficiency and estimate areal and vertical stimulation and depletion extent for the project. Furthermore, the workflow and learnings can also be transferred to other unconventional plays.

58 GEOSCIENCES↗

Engineering solar cells based on correlative X-ray microscopy

In situ and operando measurement techniques combined with nanoscale resolution have proven invaluable in multiple fields of study. We argue that evaluating device performance as well as material behavior by correlative X-ray microscopy with <100 nm resolution can radically change the approach for optimizing absorbers, interfaces and full devices in solar cell research. Here, we thoroughly discuss the measurement technique of X-ray beam induced current and point out fundamental differences between measurements of wafer-based silicon and thin-film solar cells. Based on reports of the last years, we showcase the potential that X-ray microscopy measurements have in combination with in situ and operando approaches throughout the solar cell lifecycle: from the growth of individual layers to the performance under operating conditions and degradation mechanisms. Enabled by new developments in synchrotron beamlines, the combination of high spatial resolution with high brilliance and a safe working distance allows for the insertion of measurement equipment that can pave the way for a new class of experiments. When applied to photovoltaics research, we highlight today’s opportunities and challenges in the field of nanoscale X-ray microscopy, and give an outlook on future developments.

36 MATERIALS SCIENCE↗

Nanostructured cerium oxide: preparation, characterization, and application in energy and environmental catalysis

Nanostructured cerium oxide (CeO 2 ) with outstanding physical and chemical properties has attracted extensive interests over the past few decades in environment and energy-related applications. With controllable synthesis of nanostructured CeO 2 , much more features were technologically brought out from defect chemistry to structure-derived effects. This paper highlights recent progress on the synthesis and characterization of nanostructured ceria-based materials as well as the traditional and new applications. Specifically, several typical applications based on the desired ceria nanostructures are focused to showcase the importance of nanostructure-derived effects. Moreover, some challenges and perspectives on the nanostructured ceria are presented, such as defects controlling and retainment, scale-up fabrication, and monolithic devices. Hopefully, this paper can provide an improved understanding of nanostructured CeO 2 and offer new opportunities to promote the further research and applications in the future.

36 MATERIALS SCIENCE↗

Impact of COVID-19 on materials science research innovation and related pandemic response

The scope of impact that the coronavirus SARS-CoV-2 has had and continues to have on life, society, and the world as we know it will be debated for years to come. One thing is for certain, scientists, engineers, clinicians, and researchers around the globe rallied to heed the call for innovation, particularly in the field of materials science. Here, we feature six articles, two of which showcase primary consumable materials research and development, along with four review articles highlighting materials innovation over the last 18 months in diagnostics, prevention, and treatment of SARS-CoV-2 infection.

36 MATERIALS SCIENCE↗

Interface potentials inside solid-state batteries: Origins and implications

Interface resistance has become a significant bottleneck for solid-state batteries (SSBs). Most studies of interface resistance have focused on extrinsic mechanisms such as interface reactions and imperfect contact between electrodes and solid electrolytes. Interface potentials are an important intrinsic mechanism that is often ignored. Here, we highlight Kelvin probe force microscopy (KPFM) as a tool to image the local potential at interfaces inside SSBs, examining the existing literature and discussing challenges in interpretation. Drawing analogies with electron transport in metal/semiconductor interfaces, we showcase a formalism that predicts intrinsic ionic resistance based on the properties of the contacting phases, and we emphasize that future battery designs should start from material pairs with low intrinsic resistance. Here, we conclude by outlining future directions in the study of interface potentials through both theory and experiment.

25 ENERGY STORAGE↗

Chemical and architectural intricacy from nanoscale tetrahedra and their analogues

The tetrahedron, as the simplest platonic shape, is a profound building block with the potential to create intricate superstructures. Noteworthy designs utilizing tetrahedral building blocks include the Sierpiński tetrahedron (the most fundamental three-dimensional fractal), a one-dimensional helical structure known as the tetrahelix, and various crystalline and quasicrystalline packings. Historically, the practicality of tetrahedral superstructures has been evident, providing stable, well-defined frameworks for various constructions, including truss bridges, tower cranes, and electricity transmission line pylons. In the field of self-assembled nanocrystal superlattices, tetrahedral nanocrystals, as building blocks, occupy a unique place among all the possible nanoscale particles. Mathematical models, simulation work, and experimental studies using nanocrystals in the laboratory have suggested that self-assembled structures derived from nanoscale tetrahedral building blocks are notably intricate, giving rise to new horizons of high-entropy nanocrystal superlattices. An important implication from previous works is that such tetrahedral nanocrystal superlattices form through highly delicate interparticle interactions, emphasizing the importance of the fine features of these nanocrystals. In this article, we summarize the advances in superlattices assembled from tetrahedral nanocrystals. Here, we first define the tetrahedron and tetrahedron analogues based on Conway’s transformation and graph theory, underscoring their relevance to the crystallization process producing tetrahedral nanocrystals. Then, we showcase previous reports on the synthesis of tetrahedral nanocrystals and the resulting nanocrystal superstructures. Finally, we conclude by offering insights and perspective into the chemical and architectural intricacy that could emerge from tetrahedral nanocrystals.

Nanostructure↗

A brief review on strain engineering of ferroelectric K x Na 1- x NbO 3 epitaxial thin films: Insights from phase-field simulations

Strains play a pivotal role in determining the phase equilibrium, domain configuration, and functional properties of the low-dimensional ferroelectrics. There is growing interest in the strain engineering of ferroelectric K x Na 1- x NbO 3 (KNN) epitaxial thin films, which exhibit excellent physical properties and promise as eco-friendly alternatives to lead-based ferroelectrics for microdevice applications. Further, advances have been made in understanding the phase equilibria and transitions, domains and domain walls, and their relations to the physical properties of KNN epitaxial thin films using a combination of experiments and theoretical modeling, particularly phase-field simulations. Here, we review recent progress in these aspects and showcase the phase-field method for establishing strain phase diagrams, elucidating the domain and domain wall structures at equilibrium, and predicting the structure–property relationships in ferroelectric KNN thin films. We also discuss challenges and opportunities to further advance our understanding of KNN thin films and potentially unlock new functionalities by leveraging phase-field simulations.

36 MATERIALS SCIENCE↗

Multilevel Monte Carlo Estimators For Derivative-Free Optimization Under Uncertainty

Optimization is a key tool for scientific and engineering applications; however, in the presence of models affected by uncertainty, the optimization formulation needs to be extended to consider statistics of the quantity of interest. Optimization under uncertainty (OUU) deals with this endeavor and requires uncertainty quantification analyses at several design locations; i.e., its overall computational cost is proportional to the cost of performing a forward uncertainty analysis at each design location. An OUU workflow has two main components: an inner loop strategy for the computation of statistics of the quantity of interest, and an outer loop optimization strategy tasked with finding the optimal design, given a merit function based on the inner loop statistics. Here, in this work, we propose to alleviate the cost of the inner loop uncertainty analysis by leveraging the so-called multilevel Monte Carlo (MLMC) method, which is able to allocate resources over multiple models with varying accuracy and cost. The resource allocation problem in MLMC is formulated by minimizing the computational cost given a target variance for the estimator. We consider MLMC estimators for statistics usually employed in OUU workflows and solve the corresponding allocation problem. For the outer loop, we consider a derivative-free optimization strategy implemented in the SNOWPAC library; our novel strategy is implemented and released in the Dakota software toolkit. We discuss several numerical test cases to showcase the features and performance of our approach with respect to its Monte Carlo single fidelity counterpart.

97 MATHEMATICS AND COMPUTING↗

Peripheral Blood Transcript Signatures after Internal 131 I-mIBG Therapy in Relapsed and Refractory Neuroblastoma Patients Identifies Early and Late Biomarkers of Internal 131 I Exposures

131 I-metaiodobenzylguanidine ( 131 I-mIBG) is a targeted radiation therapy developed for the treatment of advanced neuroblastoma. We have previously shown that this patient cohort can be used to predict absorbed dose associated with early 131 I exposure, 72 h after treatment. We now expand these studies to identify gene expression differences associated with 131 I-mIBG exposure 15 days after treatment. Total RNA from peripheral blood lymphocytes was isolated from 288 whole blood samples representing 59 relapsed or refractory neuroblastoma patients before and after 131 I-mIBG treatment. We found that several transcripts predictive of early exposure returned to baseline levels by day 15, however, selected transcripts did not return to baseline. At 72 h, all 17 selected pathway-specific transcripts were differentially expressed. Transcripts CDKN1A (P < 0.000001), FDXR (P < 0.000001), DDB2 (P < 0.000001), and BBC3 (P < 0.000001) showed the highest up-regulation at 72 h after 131 I-mIBG exposure, with mean log2 fold changes of 2.55, 2.93, 1.86 and 1.85, respectively. At day 15 after 131I-mIBG, 11 of the 17 selected transcripts were differentially expressed, with XPC, STAT5B, PRKDC, MDM2, POLH, IGF1R, and SGK1 displaying significant up-regulation at 72 h and significant down-regulation at day 15. Interestingly, transcripts FDXR (P = 0.01), DDB2 (P = 0.03), BCL2 (P = 0.003), and SESN1 (P < 0.0003) maintained differential expression 15 days after 131 I-mIBG treatment. These results suggest that transcript levels for DNA repair, apoptosis, and ionizing radiation-induced cellular stress are still changing by 15 days after 131 I-mIBG treatment. Our studies showcase the use of biodosimetry gene expression panels as predictive biomarkers following early (72 h) and late (15 days) internal 131 I exposure. Our findings also demonstrate the utility of our transcript panel to differentiate exposed from non-exposed individuals up to 15 days after exposure from internal 131 I.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Along-Trajectory Acoustic Signal Variations Observed During the Hypersonic Re-Entry of the OSIRIS-REx Sample Return Capsule

The re-entry of the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) sample return capsule (SRC) on 24 September 2023 presented a rare opportunity to study atmospheric entry dynamics through a dense network of ground-based infrasound sensors. As the first interplanetary capsule to re-enter over the United States since Stardust in 2006, this event allowed for unprecedented observations of infrasound signals generated during hypersonic descent. We deployed 39 single-sensor stations across Nevada and Utah, strategically distributed to capture signals from distinct trajectory points. Infrasound data were analyzed to examine how signal amplitude and period vary with altitude and propagation path for a nonablating hypersonic object with well-defined physical and aerodynamic properties. Raytracing simulations incorporated atmospheric specifications from the ground-2-space model to estimate source altitudes for observed signals. Results confirmed ballistic arrivals at all stations, with source altitudes ranging from 44 to 62 km along the trajectory. Signal period and amplitude exhibited strong dependence on source altitude, with higher altitudes corresponding to lower amplitudes, longer periods, and reduced high-frequency content. Regression analysis demonstrated strong correlations between signal characteristics and both altitude and propagation geometry. Our results suggest, when attenuation is considered, the amplitude is primarily determined by the source, with the propagation path playing a secondary role over the distances examined. These findings emphasize the utility of controlled SRC re-entries for advancing our understanding of natural meteoroid dynamics, refining atmospheric entry models, and improving methodologies for planetary defense. The OSIRIS-REx SRC campaign represents the most comprehensive infrasound study of a hypersonic re-entry to date, showcasing the potential of coordinated geophysical observational networks for high-energy atmospheric phenomena, including space debris re-entries.

58 GEOSCIENCES↗

Offshore Geologic Carbon Storage Inventory Dashboard

The Offshore Geologic Carbon Storage Inventory Dashboard is an interactive dashboard. The dashboard showcases the Offshore Geologic Carbon Storage (GCS) Inventory. It is intended to be used for research and comparison purposes, see full disclaimer and credits.

Carbon Sequestration↗

Numerical Modelling of the Optical Stochastic Cooling Experiment at IOTA

A proof-of-principle optical-stochastic cooling (OSC) experiment is currently in its commissioning phase at the Fermilab’s IOTA ring. In support of this experiment, we recently implemented an OSC element in the ELEGANT tracking program. The model, based on a semi-analytic description of OSC [*], supports the simulation of a large number of macroparticles (10⁴-10⁶) over many turns (10⁶). This paper showcases the simulation capabilities to investigate the beam dynamics in the presence of cooling (or self-interacting radiation field in general) and quantify the impact of various sources of error (e.g. transverse and phase jitter), guide data analysis.

43 PARTICLE ACCELERATORS↗

Optimizing the sextupole configuration for simultaneous correction of third order resonances at the recycler ring

For the Recycler Ring at Fermilab, space charge tune shifts of almost 0.1 will have to be dealt with under the Proton Improvement Plan (PIP-II) framework. This will lead to the excitation of third order resonances. The minimization of Resonance Driving Terms (RDTs) allows to mitigate the harmful effect of these betatron resonances. Past work has shown that previously-installed sextupoles can compensate the RDTs of individual third order resonance lines, thus reducing particle losses in these operational regimes. Nevertheless, trying to compensate multiple resonances of the same order simultaneously with these existing sextupoles is limited due to current constraints in the magnets. The following study showcases the procedure to install additional sextupoles in order to aid the compensation of multiple resonances. This includes the optimization of the new sextupoles' locations in order to cancel out multiple RDTs while minimizing the currents needed. This is followed by a verification of their effectiveness by means of the RDT response matrix.

43 PARTICLE ACCELERATORS↗

ORBITAL ANGULAR MOMENTUM BEAMS RESEARCH USING A FREE-ELECTRON LASER OSCILLATOR

Orbital angular momentum (OAM) photon beams are excellent tools for non-contact optical manipulation of mat- ter in a broad photon energy range. A free-electron laser (FEL) oscillator is well-suited for studying OAM beams with various features including a wide spectral coverage, wavelength tunability, two-color lasing, polarization control, etc. Here, we report the first experimental demonstration of superposed OAM beams from an oscillator FEL. Lasing at around 458 nm, we have generated superposed OAM beams up to the fourth order as a superposition of two pure OAM modes with opposite helicities. These generated beams have a good beam quality, a high degree of circular polarization, and high power. Using external rf modulation with frequen- cies from 1 to 30 Hz, we also developed a pulsed mode operation of the OAM beams with a highly reproducible temporal structure. FEL operation showcased in this work can be extended to higher photon energies, e.g. using a future x-ray FEL oscillator. The operation of such an OAM FEL also paves the way for the generation of OAM gamma-ray beams via Compton scattering.

Liu, P.↗

LLM integration into EPICS

The utilization of large language models (LLMs) such as ChatGPT has seen a remarkable increase in various fields over the past few years. These models have demonstrated their versatility and capability in understanding and generating human-like text, making them invaluable tools in numerous applications. In this project, we explore the integration of a LLM into the Experimental Physics and Industrial Control System (EPICS). The primary focus of this integration is to employ the LLM for advanced image processing and spatial analysis on images obtained from the beamlines. By leveraging the capabilities of the LLM, we aim to enhance the accuracy and efficiency of image interpretation, enabling more precise data analysis and decision-making within the EPICS framework. This integration not only showcases the potential of LLMs in scientific and industrial applications but also sets the stage for future advancements in automated control systems.

Adams, Ethan↗