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DOE OSTI2022

Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron

Abstract New variants of SARS-CoV-2 show remarkable heterogeneity in their relative fitness over both time and space. In this paper we extend the tools available for estimating the selection strength for new SARS-CoV-2 variants to a hierarchical, mixed-effects, renewal equation model. This formulation allows us to estimate selection effects at the global level while incorporating both measured and unmeasured heterogeneity among countries. Applying this model to the spread of Omicron in forty countries, we find evidence for very strong but very heterogeneous selection effects. To test whether this heterogeneity is explained by differences in the immune landscape, we considered several measures of vaccination rates and recent population-level infection as covariates, finding moderately strong, statistically significant effects. We also found a significant positive correlation between the selection advantage of Delta and Omicron at the country level, suggesting that other region-specific explanatory variables of fitness differences do exist. Our method is implemented in the Stan programming language, can be run on standard consumer-grade computing resources, and will be straightforward to apply to future variants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Signatures of Thermal and Electrical Crosstalk in a Microwave Multiplexed Hard X-ray Transition Edge Sensor Array

We investigate the crosstalk between Transition-Edge Sensor (TES) pixels in a 24-pixel hard X-ray spectrometer array fabricated at the Advanced Photon Source, Argonne National Laboratory. Analysis shows thermal cross talk, possibly associated with insufficient thermalization, and rare but larger in magnitude electrical crosstalk between specific perpetrator-victim pixel combinations, potentially due to defects in the bias wiring or microwave multiplexing circuit. We use a method based on group-triggering and averaging to isolate the crosstalk response despite only having access to X-ray photon illumination uniform across the entire array. This allows us to identify thermal and electrical crosstalk between pixel pairs in repeated measurements to the level of 1 part in 1000 or better. In the array under study, the magnitude of observed crosstalk is small but comparable to the resolving power of this pixel design (E/Delta E similar to\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$E/\Delta {}E \sim$$\end{document} 1000 at 20 keV) and so potentially responsible for a degradation in energy resolution of the array at high incident photon rates. Having proven the methods to identify and quantify crosstalk in our setup, we can now consider mitigations.

Triamkitsawat, Panthita↗

DOE OSTI2026

AmeriFlux FLUXNET-1F US-HRC Humnoke Farm Rice Field – Field C

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-HRC Humnoke Farm Rice Field – Field C. This is the FLUXNET version of the carbon flux data for the site US-HRC Humnoke Farm Rice Field – Field C produced by applying the standard ONEFlux (1F) software. Site Description - Conventional flood irrigation method on a rice field under continuous rice operation for 50 years

Reba, Michele L. [USDA, ARS, DELTA WATER MANAGEMEN↗

DOE OSTI2020

Hetero-site Double Core Ionization Energies with Sub-electronvolt Accuracy from Delta-Coupled-Cluster Calculations

Benchmark scalar-relativistic delta-coupled-cluster calculations of hetero-site double core ionization energies of small molecules containing second-row elements are reported. The present study has focused on the high-spin triplet components of two-site double core-ionized states, which are single reference in character and consistent with the use of standard coupledcluster methods. Contributions to computed double core ionization energies from electron-correlation and basis-set effects as well as corrections to the core-valence separation approximation have been analyzed. Furthermore, on the basis of systematic convergence of computational results with respect to these effects, delta-coupled-cluster calculations have been shown to be capable of providing accurate double core ionization energies with remaining errors estimated to be below 0.3 eV, and thus they are recommended for use to facilitate experimental studies of two-site double core-ionized states that are involved in X-ray pump/X-ray probe studies of electronic and molecular dynamics following inner shell ionization or excitation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Measurement of Dielectric Loss in Silicon Nitride at Centimeter and Millimeter Wavelengths

This work presents a suite of measurement techniques for characterizing the dielectric loss tangent across a wide frequency range from similar to 1 GHz to 150 GHz using the same test chip. In the first method, we fit data from a microwave resonator at different temperatures to a model that captures the two-level system (TLS) response to extract and characterize both the real and imaginary components of the dielectric loss. The inverse of the internal quality factor is a second measure of the overall loss of the resonator, where TLS loss through the dielectric material is typically the dominant source. The third technique is a differential optical measurement at 150 GHz. The same antenna feeds two microstrip lines with different lengths that terminate in two microwave kinetic inductance detectors (MKIDs). The difference in the detector response is used to estimate the loss per unit length of the microstrip line. Our results suggest a larger loss for SiNx at 150 GHz of tan delta similar to 4 x 10(-3) compared to 2.0 x 10(-3) and greater than or similar to 1 x 10(-3) measured at similar to 1 GHz using the other two methods. These measurement techniques can be applied to other dielectrics by adjusting the microstrip lengths to provide enough optical efficiency contrast and other mm/sub-mm frequency ranges by tuning the antenna and feedhorn accordingly.

Dielectrics loss↗

DOE OSTI2024

Delta-Rice: A HDF5 Compression Plugin optimized for Digitized Detector Data

Delta-Rice is an HDF5 (The HDF Group et al., 2020) filter plugin that was developed to compress digitized detector signals recorded by the Nab experiment (Fry et al., 2019), a fundamental neutron physics experiment. This is a two-step process where incoming data is passed through a pre-processing filter and then compressed with Rice coding. A routine for determining the optimal pre-processing filter for a dataset is provided along with an example GPU deployment. When applied to data collected by the Nab data acquisition system, this method produced output files 29% their initial size, and was able to do so with an average read/write throughput in excess of 2 GB/s on a single CPU. Compared to the widely used Gzip compression routine, Delta-Rice reduces the file size by 33% more with over an order of magnitude increase in read/write throughput. Delta-Rice is available on CPU to users through the HDF5 library.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Nucleon-Pion Spectroscopy from Sparsened Correlators

Neutrino oscillation experiments require accurate reconstructions of neutrino energies, which depend in part on a theoretical understanding of the axial $N\rightarrow\Delta$ transition form factors. A lattice QCD study of this transition will require construction of all hadronic states with energies up to $m_\Delta$, which at the physical point includes $N\pi$ and $N\pi\pi$. Building interpolating operators from sparse grids at the source and sink is a versatile method that allows construction of a wide range of diagram topologies and has successfully been used in other multi-hadron calculations. We will discuss application of this method to nucleon-pion systems and present preliminary results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Investigation of microorganisms in cannabis after heating in a commercial vaporizer

There are concerns about microorganisms present on cannabis materials used in clinical settings by individuals whose health status is already compromised and are likely more susceptible to opportunistic infections from microbial populations present on the materials. Most concerning is administration by inhalation where cannabis plant material is heated in a vaporizer, aerosolized, and inhaled to receive the bioactive ingredients. Heating to high temperatures is known to kill microorganisms including bacteria and fungi; however, microbial death is dependent upon exposure time and temperature. It is unknown whether the heating of cannabis at temperatures and times designated by a commercial vaporizer utilized in clinical settings will significantly decrease the microbial loads in cannabis plant material. To assess this question, bulk cannabis plant material supplied by National Institute on Drug Abuse (NIDA) was used to assess the impact of heating by a commercial vaporizer. Initial method development studies using a cannabis placebo spiked with Escherichia coli were performed to optimize culture and recovery parameters. Subsequent studies were carried out using the cannabis placebo, low delta-9 tetrahydrocannabinol (THC) potency and high THC potency cannabis materials exposed to either no heat or heating for 30 or 70 seconds at 190°C. Phosphate-buffered saline was added to the samples and the samples agitated to suspend the microorganism. Microbial growth after no heat or heating was evaluated by plating on growth media and determining the total aerobic microbial counts and total yeast and mold counts. Overall, while there were trends of reductions in microbial counts with heating, these reductions were not statistically significant, indicating that heating using standard vaporization parameters of 70 seconds at 190°C may not eliminate the existing microbial bioburden, including any opportunistic pathogens. When cultured organisms were identified by DNA sequence analyses, several fungal and bacterial taxa were detected in the different products that have been associated with opportunistic infections or allergic reactions including Enterobacteriaceae, Staphylococcus, Pseudomonas, and Aspergillus.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A novel approach to partitioning evapotranspiration into evaporation and transpiration in flooded ecosystems

Reliable partitioning of micrometeorologically measured evapotranspiration (ET) into evaporation (E) and transpiration (T) would greatly enhance our understanding of the water cycle and its response to climate change related shifts in local-to-regional climate conditions and rising global levels of vapor pressure deficit (VPD). While some methods on ET partitioning have been developed, their underlying assumptions make them difficult to apply more generally, especially in sites with large contributions of E. Here, we report a novel ET partitioning method using artificial neural networks (ANNs) in combination with a range of environmental input variables to predict daytime E from nighttime ET measurements. The study uses eddy covariance data from four restored wetlands in the Sacramento-San Joaquin Delta, California, USA, as well as leaf-level T data for validation. The four wetlands vary in their vegetation make-up and structure, representing a range of ET conditions. The ANNs were built with increasing complexity by adding the input variable that resulted in the next highest average value of model testing R 2 across all sites. The order of variable inclusion (and importance) was: VPD > gap-filled sensible heat flux (H_gf) > air temperature (T air ) > friction velocity (u * ) > other variables. The model using VPD, H_gf, T air , and u * showed the best performance during validation with independent data and had a mean testing R 2 value of 0.853 (averaged across all sites, range from 0.728 to 0.910). In comparison to other methods, our ANN method generated T/ET partitioning results which were more consistent with CO 2 exchange data especially for more heterogeneous sites with large E contributions. Further, our method improves the understanding of T/ET partitioning. While it may be particularly suited to flooded ecosystems, it can also improve T/ET partitioning in other systems, increasing our knowledge of the global water cycle and ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

DUNE-PRISM – A New Method to Measure Neutrino Oscillations

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long baseline neutrino oscillation experiment designed to make precision measurements in a 1.2 2.4 MW neutrino beam, which is directed 1285 km from the Fermi National Accelerator Laboratory (Fermilab) to the Sandford Underground Research Facility (SURF) in South Dakota. Neutrinos are measured at two detector facilities: a near detector located at Fermilab close where the beam is produced and a far detector at SURF. The neutrino beam can be configured to be composed primarily of either muon or anti-muon neutrinos. DUNE measures the disappearance of muon and anti-muon neutrinos and appearance electron and anti-electron neutrinos in the neutrino beam. Measuring these neutrino flavour transitions provides DUNE with sensitivity to the neutrino mass ordering, $\delta_{CP}$, $\theta_{13}$, $\theta_{23}$ and the magnitude of $\Delta m^2_{23}$. The DUNE Precision Reaction Independent Spectrum Measurement (DUNE-PRISM) concept presents a novel way to perform a neutrino oscillation analysis, which has the potential to significantly reduce the impact of large systematic uncertainties in the neutrino interaction model. The PRISM method linearly combines measurements of off-axis neutrino interactions at the DUNE near detector to produce data-driven predictions of the oscillated neutrino event rate spectrum at the far detector. By building an oscillated far detector prediction directly from data, any unknown or poorly modelled neutrino interaction effects will be naturally incorporated into the measurement of the parameters of the neutrino oscillation model. This thesis presents the first complete neutrino oscillation analysis for DUNE using the PRISM method. Details of the methodology are fully explained and the prospects for further improvements to the techniques described are highlighted. The expected impact and relative importance of the neutrino flux, cross section and detector systematic uncertainties are described in detail. Finally, this thesis demonstrates that the PRISM method is capable of performing a measurement of the oscillation parameters that is robust against neutrino interaction modelling errors.

Hasnip, Ciaran↗

DOE OSTI2023

Real time monitoring of COVID-19 intervention effectiveness through contact tracing data

Communities worldwide have used vaccines and facemasks to mitigate the COVID-19 pandemic. When an individual opts to vaccinate or wear a mask, they may lower their own risk of becoming infected as well as the risk that they pose to others while infected. The first benefit–reducing susceptibility–has been established across multiple studies, while the second–reducing infectivity–is less well understood. Using a new statistical method, we estimate the efficacy of vaccines and facemasks at reducing both types of risks from contact tracing data collected in an urban setting. We find that vaccination reduced the risk of onward transmission by 40.7% [95% CI 25.8–53.2%] during the Delta wave and 31.0% [95% CI 19.4–40.9%] during the Omicron wave and that mask wearing reduced the risk of infection by 64.2% [95% CI 5.8–77.3%] during the Omicron wave. By harnessing commonly-collected contact tracing data, the approach can broadly provide timely and actionable estimates of intervention efficacy against a rapidly evolving pathogen.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Determining flow directions in river channel networks using planform morphology and topology

Abstract. The abundance of global, remotely sensed surface water observations has accelerated efforts toward characterizing and modeling how water moves across the Earth's surface through complex channel networks. In particular, deltas and braided river channel networks may contain thousands of links that route water, sediment, and nutrients across landscapes. In order to model flows through channel networks and characterize network structure, the direction of flow for each link within the network must be known. In this work, we propose a rapid, automatic, and objective method to identify flow directions for all links of a channel network using only remotely sensed imagery and knowledge of the network's inlet and outlet locations. We designed a suite of direction-predicting algorithms (DPAs), each of which exploits a particular morphologic characteristic of the channel network to provide a prediction of a link's flow direction. DPAs were chained together to create “recipes”, or algorithms that set all the flow directions of a channel network. Separate recipes were built for deltas and braided rivers and applied to seven delta and two braided river channel networks. Across all nine channel networks, the recipe-predicted flow directions agreed with expert judgement for 97 % of all tested links, and most disagreements were attributed to unusual channel network topologies that can easily be accounted for by pre-seeding critical links with known flow directions. Our results highlight the (non)universality of process–form relationships across deltas and braided rivers.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Redshift inference from the combination of galaxy colours and clustering in a hierarchical Bayesian model – Application to realistic N -body simulations

ABSTRACT Photometric galaxy surveys constitute a powerful cosmological probe but rely on the accurate characterization of their redshift distributions using only broad-band imaging, and can be very sensitive to incomplete or biased priors used for redshift calibration. A hierarchical Bayesian model has recently been developed to estimate those from the robust combination of prior information, photometry of single galaxies, and the information contained in the galaxy clustering against a well-characterized tracer population. In this work, we extend the method so that it can be applied to real data, developing some necessary new extensions to it, especially in the treatment of galaxy clustering information, and we test it on realistic simulations. After marginalizing over the mapping between the clustering estimator and the actual density distribution of the sample galaxies, and using prior information from a small patch of the survey, we find the incorporation of clustering information with photo-z’s tightens the redshift posteriors and overcomes biases in the prior that mimic those happening in spectroscopic samples. The method presented here uses all the information at hand to reduce prior biases and incompleteness. Even in cases where we artificially bias the spectroscopic sample to induce a shift in mean redshift of $\Delta \bar{z} \approx 0.05,$ the final biases in the posterior are $\Delta \bar{z} \lesssim 0.003.$ This robustness to flaws in the redshift prior or training samples would constitute a milestone for the control of redshift systematic uncertainties in future weak lensing analyses.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Data compression system using base values and methods thereof

In some embodiments, a memory controller in a processor includes a base value cache, a compressor, and a metadata cache. The compressor is coupled to the base value cache and the metadata cache. The compressor compresses a data block using at least a base value and delta values. The compressor determines whether the size of the data block exceeds a data block threshold value. Based on the determination of whether the size of the compressed data block generated by the compressor exceeds the data block threshold value, the memory controller transfers only a set of the compressed delta values to memory for storage. A decompressor located in the lower level cache of the processor decompresses the compressed data block using the base value stored in the base value cache, metadata stored in the metadata cache and the delta values stored in memory.

Seyedzadehdelcheh, SeyedMohammad↗

DOE OSTI2023

Data compression system using base values and methods thereof

Seyedzadehdelcheh, Seyed Mohammad↗

DOE OSTI2024

The geometry of the modular bootstrap

Abstract We explore the geometry behind the modular bootstrap and its image in the space of Taylor coefficients of the torus partition function. In the first part, we identify the geometry as an intersection of planes with the convex hull of moment curves onR + ⊗ℤ, with boundaries characterized by the total positivity of generalized Hankel matrices. We phrase the Hankel constraints as a semi-definite program, which has several advantages, such as the validity of bounds irrespective of spin truncation. We derive bounds on the gap, twist-gap, and the space of Taylor coefficients themselves. We find that if the gap is above$$ {\Delta }_{\textrm{gap}}^{\ast } $$ ∆ gap ∗ , where$$ \frac{c-1}{12}<{\Delta}_{\textrm{gap}}^{\ast }<\frac{c}{12} $$ c − 1 12 < Δ gap ∗ < c 12 , all coefficients become bounded on both sides and kinks develop in the space. In the second part, we propose an analytic method of imposing the integrality condition for the degeneracy number in the spinless bootstrap, which leads to a non-convex geometry. We find that even at very low derivative order this condition rules out regions otherwise allowed by bootstraps at high derivative order.

Physics↗

DOE OSTI2024

Generalized Analytical Estimation of Sensitivity Matrices in Unbalanced Distribution Networks

Fast and accurate estimation of sensitivity matrices is significant for the enhancement of distribution system modeling and automation. Analytical estimations have mainly focused on voltage magnitude sensitivity to active/reactive power injections for unbalanced networks with Wye-connected loads and neglecting DERs' smart inverter functionality. Hence, this paper enhances the scope of analytical estimation of sensitivity matrices for unbalanced networks with 1- Φ, 2- Φ, and 3- Φ Delta/Wye-connected loads, DERs with smart inverter functionality, and substation/line step-voltage regulators (SVR). A composite bus model comprising of DER, Delta- and Wye-connected load is proposed to represent a generic distribution bus, which can be simplified to load, PV, or voltage-controlled bus as required. Furthermore, the proposed matrix-based analytical method consolidates voltage magnitude and angle sensitivity to active/reactive power injection and tap-position of all SVRs into a single algorithm. Extensive case studies on IEEE and EPRI networks show the accuracy and wide scope of the proposed algorithm compared to the existing benchmark method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Fusion of 12 C+ 24 Mg far below the barrier: Evidence for the hindrance effect

Background: The phenomenon of fusion hindrance may have important consequences on the nuclear processes occurring in astrophysical scenarios, if it is a general behavior of heavy-ion fusion at extreme subbarrier energies, including reactions involving lighter systems, e.g., reactions in the carbon and oxygen burning stages of heavy stars. The hindrance is generally identified by the observation of a maximum of the S-factor vs energy. Whether there is an S-factor maximum at very low energies for systems with a positive fusion Q value is an experimentally challenging question. Purpose: Our aim has been to search for evidence of fusion hindrance in 12 C+ 24 Mg which is a medium-light m system with positive Q value for fusion, besides the heavier cases where hindrance is recognized to be a general phenomenon. 12 C+ 24 Mg is very close to the 16 O + 16 O and 12 C + 12 C systems that are important for the late evolution of heavy stars. Methods: The experiment has been performed in inverse kinematics using the 24 Mg beam from the XTU Tandem accelerator of LNL in the energy range 26-52 MeV with an intensity of 4-8 pnA. The targets were 12 C evaporations 50 mu g/cm 2 thick, isotopically enriched to 99.9%. The fusion-evaporation residues were detected at small angles by a E-Delta E-ToF detector telescope following an electrostatic beam deflector. Results: Previous measurements of fusion cross section for 12 C+ 24 Mg were limited to above-barrier energies. In the present experiment the excitation function has been extended down to similar or equal to 15 mu b and it appears that the S factor develops a clear maximum vs energy, indicating the presence of hindrance. This is the first convincing evidence of an S factor maximum in a medium-light system with a positive fusion Q value. These results have been fitted following a recently suggested method and a detailed analysis within the coupled-channels model that has been performed using a Woods-Saxon potential and including the ground state rotational band of 24 Mg. The coupled-channels calculations give a good account of the data near and above the barrier but overpredict the cross sections at very low energies. Conclusions: The hindrance phenomenon is clearly observed in 12 C+ 24 Mg, and its energy threshold is in reasonable agreement with the systematics observed for several medium-light systems. The fusion cross sections at the hindrance threshold show that the highest value (sigma(s) = 1.6 mb) is indeed found for this system. Therefore it may even be possible to extend the measurements further down in energy to better establish the position of the S-factor maximum.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗