Results for “background selection”

DOE OSTI2023

Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History

Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data

Abstract The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Soni, Vivak (ORCID:0000000294969562)↗

DOE OSTI2026

Wasserstein normalized autoencoder for anomaly detection

A novel anomaly detection algorithm is presented. The Wasserstein normalized autoencoder (WNAE) is a normalized probabilistic model that minimizes the Wasserstein distance between the learned probability distribution—a Boltzmann distribution where the energy is the reconstruction error of the autoencoder (AE)—and the distribution of the training data. This algorithm has been developed and applied to the identification of semivisible jets—conical sprays of visible standard model (SM) particles and invisible dark matter states—with the CMS experiment at the CERN LHC. Trained on jets of particles from simulated SM processes, the WNAE is shown to learn the probability distribution of the input data in a fully unsupervised fashion, such that it effectively identifies new physics jets as anomalies. The model exhibits stable, convergent training and recovers strong classification performance for a wide range of signals against the selected background process, for which a standard AE fails because of outlier reconstruction. In addition, the model improves upon standard normalized autoencoders while remaining fully agnostic to the signal. The WNAE directly tackles the problem of outlier reconstruction, a common failure mode of autoencoders in anomaly detection tasks.

Hayrapetyan, Aram [Yerevan Phys. Inst.]↗

DOE OSTI2026

Search for Long-Lived Particles with Muon Detector Shower Signature in the CMS Run-3 data

Many beyond standard model theories predict the existence of long-lived particles (LLPs). These LLPs can have sizable lifetimes and decay several meters from their production vertex. In this poster/talk, we present the analysis strategy for searching for LLPs using the Compact Muon Solenoid (CMS) Experiment. The proton-proton collision data used in this analysis were collected from 2022 to 2024 at a center-of-mass energy of 13.6 TeV, corresponding to an integrated luminosity of 170 fb^-1. The LLP decays are reconstructed as a high-multiplicity cluster of detector hits in the cathode strip chambers (CSC) of the muon system endcap. This signature is referred to as the Muon Detector Showers (MDS). This search requires events to contain at least one MDS cluster. The analysis focuses on LLP hadronic decays and LLP masses up to a few tens of GeV. We present the signal properties in MonteCarlo simulation, event selection, background modeling, and evaluation of the expected sensitivity. The results are interpreted under the Twin Higgs model benchmark.

Agyemang-Duah, Andrews [Grambling State U.]↗

DOE OSTI2026

Using AI to Reproduce Neutrino Cross Section Analysis - Prototyping the Neutrino Discovery Platform

The Neutrino Discovery Platform (NDP) aims to accelerate DUNE-era science by making the neutrino program's existing datasets analyzable through fast, reproducible, and auditable workflows. We report a working version of two of its layers, data curation and agentic orchestration, built and tested end to end on MINERvA open data. The guiding lesson throughout is that a cross section is a measurement, and not just a plotted shape, only if it carries a defensible systematic-uncertainty budget, a trustworthy unfolding, and a reproducible record. Using a single medium-energy playlist pair from the MINERvA open-data release (about $2.05\times10^{17}$ protons on target of data), we first reproduced the shapes of two published charged-current inclusive $\nu_\mu$ measurements through a complete extraction ladder: selection, background subtraction, D'Agostini unfolding, efficiency correction, and flux normalization. These shape-level reproductions ran and tracked the published results, but they lacked the systematic-uncertainty machinery that defines a MINERvA cross section. To supply it, we vendored and built the MINERvA Analysis Toolkit and developed a many-universe systematic-uncertainty tool that produces a portable covariance artifact, a parallel event-loop runner, and a per-run auditability harness. Validated against a published covariance release, the toolchain reproduces the released statistical, flux, and muon-energy-scale terms and shows that they account for roughly 63\% of the total variance, with the remainder unreleased. Using this same infrastructure, we then performed a measurement of our own design, the hadronic recoil-energy distribution of low-energy ($E_\nu<2.5$~GeV) charged-current inclusive events, and found data/simulation shape agreement of $\chi^2/\mathrm{ndf}=1.26$. Together these results show that the platform supports original physics and not only reproductions.

Breaux, Auto [Tulane U. (main)]↗

DOE OSTI2026

Toward the Neutrino Discovery Platform: An Auditable, Uncertainty-Bearing Toolchain for MINERvA Open-Data Cross-Section Analysis

The Neutrino Discovery Platform (NDP) aims to accelerate DUNE-era science by making the neutrino program's existing datasets analyzable through fast, reproducible, and auditable workflows. We report a working version of two of its layers, data curation and agentic orchestration, built and tested end to end on MINERvA open data. The guiding lesson throughout is that a cross section is a measurement, and not just a plotted shape, only if it carries a defensible systematic-uncertainty budget, a trustworthy unfolding, and a reproducible record. Using a single medium-energy playlist pair from the MINERvA open-data release (about $2.05\times10^{17}$ protons on target of data), we first reproduced the shapes of two published charged-current inclusive $\nu_\mu$ measurements through a complete extraction ladder: selection, background subtraction, D'Agostini unfolding, efficiency correction, and flux normalization. These shape-level reproductions ran and tracked the published results, but they lacked the systematic-uncertainty machinery that defines a MINERvA cross section. To supply it, we vendored and built the MINERvA Analysis Toolkit and developed a many-universe systematic-uncertainty tool that produces a portable covariance artifact, a parallel event-loop runner, and a per-run auditability harness. Validated against a published covariance release, the toolchain reproduces the released statistical, flux, and muon-energy-scale terms and shows that they account for roughly 63\% of the total variance, with the remainder unreleased. Using this same infrastructure, we then performed a measurement of our own design, the hadronic recoil-energy distribution of low-energy ($E_\nu<2.5$~GeV) charged-current inclusive events, and found data/simulation shape agreement of $\chi^2/\mathrm{ndf}=1.26$. Together these results show that the platform supports original physics and not only reproductions.

Breaux, Auto [Tulane U. (main)]↗

DOE OSTI2026

Background cancellation for frequency-selective quantum sensing

A key challenge in quantum sensing is the detection of weak time dependent signals, particularly those that arise as specific frequency perturbations over a background field. Conventional methods usually demand complex dynamical control of the quantum sensor and heavy classical post-processing. We propose a quantum sensor that leverages time independent interactions and entanglement to function as a passive, tunable, thresholded frequency filter. By encoding the frequency selectivity and thresholding behavior directly into the dynamics, the sensor is responsive only to a target frequency of choice whose amplitude is above a threshold. This approach circumvents the need for complex control schemes and reduces the post-processing overhead.

Puig, Ricard [Los Alamos; Ecole Polytechnique, Lau↗

DOE OSTI2023

Survey of the mechanical and physical behaviors of yttria-stabilized zirconia from multiple dental laboratories

Background: When selecting zirconia for a dental restoration, laboratory prescriptions often refer to high strength and high translucency. In this survey, zirconia specimens were ordered from various dental laboratories for posterior (high strength) and anterior (high translucency) clinical indications. The specimens were then tested and evaluated for their mechanical and physical behaviors. Methods: In a double-blinded manner, 9 laboratories provided 32 specimens from 17 different zirconia blanks, which were tested in the American Dental Association laboratory. Flexural strength tests were performed on standard specimens, and fracture surfaces were examined using both optical and scanning electron microscopy. Chemical composition, Vickers hardness, and absolute transmittance measurements were also performed. Results: A large scatter in the strength values was observed. The zirconia intended for posterior applications displayed strengths (SD) from 195 through 783 MPa (490 [183] MPa), which overlapped greatly with the strengths (SD) of the zirconia intended for anterior applications, 320 through 768 MPa (581 [136] MPa). However, when the strength values were recalculated on the basis of yttria content, the strengths (SD) were 584 (158) MPa for 3 mol% yttria and 373 (104) MPa for 5 mol% yttria. Conclusions: When a prescription was given to dental laboratories to request zirconia on the basis of clinical requirements, there was a large scatter and no consistency in the resulting strength values partly because of mixed use of 3 mol% and 5 mol% yttria zirconia. The 3 mol% materials had much higher strength when the strength values were grouped according to yttria content. Strength was also highly dependent on processing and finishing at the dental laboratories.

3 mol% yttria-tetragonal zirconia polycrystal (3Y-↗

DOE OSTI2025

Hydrodynamic modeling of plasma channel systems for laser plasma accelerators

Structured plasma channels are an essential technology for driving high-gradient, plasma-based acceleration and control of electron and positron beams for advanced concepts accelerators. Laser and gas technologies can permit the generation of long plasma columns known as hydrodynamic, optically-field-ionized (HOFI) channels, which feature low on-axis densities and steep walls. By carefully selecting the background gas and laser properties, one can generate narrow, tunable plasma channels for guiding high intensity laser pulses. Here, we present on the development of simulations of HOFI channels using the FLASH code, a publicly available radiation hydrodynamics code. We explore sensitivities of the channel evolution to laser profile, intensity, and background gas conditions, and identify relevant scalings with laser intensity through a range of practical channel delays.

Accelerators↗

DOE OSTI2025

Using Neural Networks for Low Energy Reconstruction and Neutron Identification in the MicroBooNE LArTPC

Identifying and reconstructing final-state neutrons from neutrino interactions in Liquid Argon Time Projection Chambers (LArTPCs) will enhance future oscillation measurements by recovering missing energy and improving neutrino interaction channel identification. However, neutrons are challenging to reconstruct as the majority leave only small, isolated charge signatures known as blips. Here we present initial efforts to identify neutrons in the MicroBooNE LArTPC with low energy protons from neutron-argon inelastic interactions that present as blips below the traditional tracking threshold in the TPC. Unlike for tracks, there is no algorithmic method to determine direction for blips since they span only a few wires. Therefore, we developed and trained a Recurrent Neural Network (RNN) to reconstruct the directionality of proton-induced blips, allowing us to separate signal from background by selecting blips that point back to the neutrino vertex. The model achieves a preliminary average angular resolution of 17 degrees when tested on a simulated sample of protons over 6 MeV in kinetic energy. This novel tool will enhance neutron detection in LArTPCs and expand a broad range of other low-energy physics searches such as for solar and supernova neutrinos.

Silva, Liani Isabel [Unlisted, US]↗

DOE OSTI2024

Search for Heavy Neutral Leptons at the MINER$\nu$A detector

Heavy Neutral Leptons (HNL) are particles hypothesised to provide a mass generation mechanism for the active (observed) neutrino species, which are known to have nonzero mass from the definitive observation of neutrino oscillations. HNL are eigenstates of mass of the order $\mathcal{O}(0.1 − 1\,\,\mathrm{GeV}/c^{2})$, which mix into the active flavour eigenstates through the extended leptonic mixing matrix. Apart from neutrino mass, they could provide a natural dark matter candidate and a mechanism for matter-antimatter asymmetry in the early Universe, giving rise to today’s matter-dominated cosmos. Searches for HNL typically attempt to either confirm the existence of HNL through an excess in data that is most compatible with an HNL hypothesis, or by setting limits on the HNL parameter space $\left(M_{N4}, \left|U_{\alpha 4}\right|^{2}\right)$ in the case of statistically insignificant excess. Such searches are intensifying as part of a global research programme at both colliders and accelerator / atmospheric neutrino experiments. One such setting is the MINER$\nu$A experiment, located in the NuMI beamline at Fermilab. MINER$\nu$A has collected a large amount of data over seven years of operation to measure the cross-sections of neutrino-nucleus interactions necessary to drive systematic uncertainties down, in order for neutrino oscillation experiments to achieve sensitivity to CP violation in the neutrino sector. With the high-energy, high-intensity NuMI beam, and with good timing, position, and angular resolution leading to sensitivity to HNL decays, MINER$\nu$A is fertile ground for an HNL search, which is performed in this thesis. Specifically, a novel, experiment-agnostic and general simulation of HNL production and decay is presented and deployed; this simulation has been incorporated in the ubiquitous GENIE neutrino event generator for use with neutrino experiments in the future. The event selection and background characterisation is discussed in detail, including the primary background coming from charged-current coherent and diffractive pion production from neutrino-nucleus interactions, and constraints on the background using control regions from MINER$\nu$A data are derived. Finally, by means of a fake-data study given a background of $\mathcal{O}(500)$ events, the discovery potential and limit-setting capacity of MINER$\nu$A is demonstrated, and ways to improve this capacity are expounded upon.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Frequency-Selectable Laser Source for Cosmic Microwave Background Experiments

Cosmic Microwave Background (CMB) experiments measure remnant radiation from the early universe and use that data to determine fundamental properties of the universe. We can constrain key parameters, such as \textit{r}, the cosmic tensor-to-scalar ratio, and $N_\text{eff}$, the effective number of relativistic species, by analyzing the CMB power spectra. Improving our measurements of the CMB requires improving our instrument systematics, one of the most important of which is detector bandpass. Current experiments use a Fourier Transform Spectrometer (FTS) to measure bandpass. However, the FTS is systematics limited, and cannot achieve the accuracy needed to make improved CMB measurements. For this reason, we are developing a new instrument, the Frequency-Selectable Laser Source (FLS) to decrease the uncertainty in bandpass by an order of magnitude. In this paper, we describe work completed to support the version 2 upgrade to the FLS. Using ray-tracing software, we modeled the FLS optics to set physical tolerances for the new design. We also discuss the laser calibration, and future work to be completed in further development of the FLS upgrade.

Rosen-Turits, Gabriel M. [Fermilab]↗

DOE OSTI2023

Perspectives for measuring NuMI n-Ar cross-section @ ICARUS and cosmic background constraints in the nm inclusive selection

Explore the source record for details and available documents.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Masses of Sunyaev-Zel’dovich galaxy clusters detected by the Atacama Cosmology Telescope: Stacked lensing measurements with Subaru HSC year 3 data

We present a stacked lensing analysis of 96 galaxy clusters selected by the thermal Sunyaev-Zel’dovich (SZ) effect in maps of the cosmic microwave background (CMB). We select foreground galaxy clusters with a 5 σ -level SZ threshold in CMB observations from the Atacama Cosmology Telescope, while we define background source galaxies for the lensing analysis with secure photometric redshift cuts in Year 3 data of the Subaru Hyper Suprime Cam survey. We detect the stacked lensing signal in the range of 0.1 < R [ h - 1 Mpc ] < 100 in each of three cluster redshift bins, 0.092 < z ≤ 0.445 , 0.445 < z ≤ 0.695 , and 0.695 < z ≤ 1.180 , with 32 galaxy clusters in each bin. The cumulative signal-to-noise ratios of the lensing signal are 14.6, 12.0, and 6.6, respectively. Using a halo-based forward model, we then constrain statistical relationships between the mass inferred from the SZ observation (i.e. SZ mass) and the total mass derived from our stacked lensing measurements. At the average SZ mass in the cluster sample ( 2.1 - 2.4 × 10 14 h - 1 M ⊙ ), our likelihood analysis shows that the average total mass differs from the SZ counterpart by a factor of 1.3 ± 0.2 , 1.6 ± 0.2 , and 1.6 ± 0.3 (68%) in the aforementioned redshift ranges, respectively. Our limits are consistent with previous lensing measurements, and we find that the cluster modeling choices can introduce a 1 σ -level difference in our parameter inferences.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

RAIS Generic Soil Background Values

The RAIS offers two approaches to background screening: generic and site-specific. The Generic Background Values tool (https://rais.ornl.gov/tools/bg_search.php) contains generic soil background values for selected metals. These values can be applied to any area across the U.S. Users can compare these values against local background data or supplement an existing background value dataset. Results can be downloaded in .xlsx format.

Dolislager, Fred [Oak Ridge National Laboratory (O↗

DOE OSTI2023

Tools for estimating fake/non-prompt lepton backgrounds with the ATLAS detector at the LHC

Measurements and searches performed with the ATLAS detector at the CERN LHC often involve signatures with one or more prompt leptons. Such analyses are subject to 'fake/non-prompt' lepton backgrounds, where either a hadron or a lepton from a hadron decay or an electron from a photon conversion satisfies the prompt-lepton selection criteria. These backgrounds often arise within a hadronic jet because of particle decays in the showering process, particle misidentification or particle interactions with the detector material. As it is challenging to model these processes with high accuracy in simulation, their estimation typically uses data-driven methods. Three methods for carrying out this estimation are described, along with their implementation in ATLAS and their performance.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Frequency-Selectable Laser Source (FLS) for Cosmic Microwave Background Experiments

Cosmic Microwave Background (CMB) experiments measure remnant radiation from the early universe and use that data to determine fundamental properties of the universe. We can constrain key parameters, such as \textit{r}, the cosmic tensor-to-scalar ratio, and $N_\text{eff}$, the effective number of relativistic species, by analyzing the CMB power spectra. Improving our measurements of the CMB requires improving our instrument systematics, one of the most important of which is detector bandpass. Current experiments use a Fourier Transform Spectrometer (FTS) to measure bandpass. However, the FTS is systematics limited, and cannot achieve the accuracy needed to make improved CMB measurements. For this reason, we are developing a new instrument, the Frequency-Selectable Laser Source (FLS) to decrease the uncertainty in bandpass by an order of magnitude. In this paper, we describe work completed to support the version 2 upgrade to the FLS. Using ray-tracing software, we modeled the FLS optics to set physical tolerances for the new design. We also discuss the laser calibration, and future work to be completed in further development of the FLS upgrade.

Rosen-Turits, Gabriel M.↗

DOE OSTI2026

Measuring the neutrino-oxygen neutral current quasielastic cross section using the accelerator neutrino neutron interaction experiment

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a 26-ton gadolinium-doped water Cherenkov detector located on-axis to Fermilab’s Booster Neutrino Beam (BNB). ANNIE is uniquely positioned to perform high-statistics measurements of neutrino-nucleus interactions in water, benefiting from a large neutrino flux due to a short (100-meter) baseline. A central focus of ANNIE’s physics program is the measurement of both charged current (CC) and neutral current (NC) cross sections on water, including neutral current quasielastic (NCQE) and CC-inclusive channels. The NCQE measurement is particularly critical for constraining uncertainties in rare-event searches such as the Diffuse Supernova Neutrino Background (DSNB), where atmospheric $\nu$NCQE interactions constitute a significant and poorly constrained background. This dissertation presents a measurement of the flux-averaged neutrino-oxygen neutral current quasielastic ($\nu$NCQE) cross section using $2.573 \times 10^{20}$~POT of BNB exposure from the 2022 and 2023 beam years. The $\nu$NCQE interaction is identified through the primary $\gamma$-rays produced by nuclear de-excitation of the residual $^{15}$N$^*$ or $^{15}$O$^*$ nucleus following nucleon knockout from $^{16}$O. A dedicated Monte Carlo (MC) re-tuning campaign was conducted using an americium-beryllium (AmBe) calibration source, Michel electrons from stopped muons, and throughgoing dirt muons originating upstream of the detector. This multi-sample approach provided a wide-ranging $\mathcal{O}(\text{MeV})$--$\mathcal{O}(\text{GeV})$ dataset for tuning the simulated detector response, which was subsequently validated against AmBe neutron and Michel electron data for use in the $\nu$NCQE analysis. A dedicated laser calibration campaign was carried out to reduce timing uncertainties across the PMT system, enabling reconstruction of the BNB bunch substructure with sufficient resolution to serve as a background rejection tool. By selecting events in-time with individual neutrino bunches, beam-correlated $\nu$NCQE events are separated from diffuse and accelerator-induced backgrounds, notably skyshine neutrons and externally-originating events, that would otherwise dominate traditional charge-based selections within a small-scale, surface-level, short-baseline detector. A data-driven estimation of the skyshine neutron and external background rates was performed and incorporated into the systematic uncertainty budget. The flux-averaged $\nu$NCQE cross section on oxygen is measured to be $1.57 \pm 0.06\,(\text{stat.})$ $^{+0.91}_{-0.67}\,(\text{syst.})$ $\times 10^{-38}\ \text{cm}^{2}$. A full systematic budget is constructed by propagating uncertainties in the secondary hadronic interaction modeling, background cross section normalizations, detector response, neutrino flux, and the primary $\gamma$-ray emission probabilities from oxygen nuclear de-excitation. An idealized de-excitation model, constructed from existing measurements in the literature is developed to benchmark the predictions of the \textsc{GENIE} event generator. A comparison reveals that \textsc{GENIE} systematically overpredicts the primary $\gamma$-ray emission probability from oxygen de-excitation by a factor of $1.49\times$ for $E_\gamma > 6$~MeV and $3.07\times$ in the $3$--$6$~MeV band. This comparison motivates the dominant systematic uncertainty in this analysis, where a conservative uncertainty of $^{+39.9\%}_{-0\%}$ on the primary $\gamma$-ray signal prediction is assigned. The ANNIE result is consistent with and complementary to existing flux-averaged $\nu$NCQE cross section measurements from T2K and Super-Kamiokande, providing an independent measurement with a different detector, neutrino beam, and analysis methodology. Looking ahead, an upgrade to the ANNIE DAQ infrastructure enabling continuous extended readout will allow a complementary $\nu$NCQE neutron multiplicity measurement, directly relevant to constraining the NCQE background in DSNB searches, competitive with the recent T2K measurement at SK-Gd. The planned Super-SANDI upgrade, deploying a large Water-based Liquid Scintillator (WbLS) volume, will further extend ANNIE's reach to hadronic final states and exclusive NC channels, and enable joint measurements with liquid argon detectors sharing the BNB beamline ahead of DUNE and Hyper-Kamiokande.

Doran, Steven [Iowa State U.]↗