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At least 37 records · Page 2

The Dark Energy Survey supernova program: cosmological biases from supernova photometric classification

ABSTRACT Cosmological analyses of samples of photometrically identified type Ia supernovae (SNe Ia) depend on understanding the effects of ‘contamination’ from core-collapse and peculiar SN Ia events. We employ a rigorous analysis using the photometric classifier SuperNNova on state-of-the-art simulations of SN samples to determine cosmological biases due to such ‘non-Ia’ contamination in the Dark Energy Survey (DES) 5-yr SN sample. Depending on the non-Ia SN models used in the SuperNNova training and testing samples, contamination ranges from 0.8 to 3.5 per cent, with a classification efficiency of 97.7–99.5 per cent. Using the Bayesian Estimation Applied to Multiple Species (BEAMS) framework and its extension BBC (‘BEAMS with Bias Correction’), we produce a redshift-binned Hubble diagram marginalized over contamination and corrected for selection effects, and use it to constrain the dark energy equation-of-state, w. Assuming a flat universe with Gaussian ΩM prior of 0.311 ± 0.010, we show that biases on w are <0.008 when using SuperNNova, with systematic uncertainties associated with contamination around 10 per cent of the statistical uncertainty on w for the DES-SN sample. An alternative approach of discarding contaminants using outlier rejection techniques (e.g. Chauvenet’s criterion) in place of SuperNNova leads to biases on w that are larger but still modest (0.015–0.03). Finally, we measure biases due to contamination on w0 and wa (assuming a flat universe), and find these to be <0.009 in w0 and <0.108 in wa, 5 to 10 times smaller than the statistical uncertainties for the DES-SN sample.

79 ASTRONOMY AND ASTROPHYSICS↗

Novel data analysis method for obtaining better performance from a complex 3D-printed collimator

Additively manufactured scattered beam collimators are increasingly being employed to boost the sample to cell peak signal ratio in high pressure neutron diffraction studies because of manufacturing versatility and performance improvements. We study how the measured diffraction pattern is affected by the presence of a collimator downstream of the sample, and develop a novel protocol that provides more effective background rejection. This protocol takes into account critical performance-determinants that were identified in this study, namely: (i) effectively identifying the collimator pattern on the detector; (ii) understanding the dependence of this pattern on sample and cell composition; and (iii) accurately identifying and differentiating the different regions of the pattern on the detector based on the dependency of the cell or sample and finally (iv) resolving the intensities at regions of the detector where neutrons scattered from the sample are preferentially represented, in order to boost the sample to cell peak signal ratio. Application of this novel analysis protocol is shown to increase the collimator performance over the traditional method.

3D printing↗

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗

Methodology to Generate the Decay Gamma Source for a Second Target Station Target Wedge

This report details the specifics of applying the Position-Averaged Method methodology for the calculation of the rotating lasagna-style target wedge activation and the resulting decay gamma source terms. The methodology uses MCNP® Code Version 6.2.0 with the RNUCS patch coupled with CINDER2008 from the AARE V1.0 package. The process begins with model preparations that include ensuring impurities are included in the materials in the regions of interest along with segmentation of the geometry in order to capture the decay gamma source gradients. This report also details the physics models and other MCNP®, CINDER2008, and ADVANTG 3.2.0 related options used to calculate the decay gamma source terms. ADVANTG 3.2.0 is used to generate a weight window set to aid in convergence of the neutron fluxes in the initial MCNP® protons-on-target particle transport calculation to calculate the neutron fluxes and spallation products in the regions of interest. The neutron fluxes and spallation products are then used in the CINDER2008 transmutation calculation, and the decay gamma sources are generated by the AARE_GAMMA_SOURCE_SCRIPT as a part of the AARE V1.0 package. These decay gamma sources include the energy distributions as well as the necessary distributions to sample the location of the source using the cell rejection method. The gamma sources that are produced using the methodology may be used for a wide variety of analysis involving the target wedge. This report includes the material specifications, physics options, proton source term description, geometrical configuration, and post-processing details.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer

Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.

60 APPLIED LIFE SCIENCES↗

Cosmic Background Rejection of the ICARUS experiment at Fermilab

The Short Baseline Neutrino program at Fermilab aims to explore significant regions of parameter space, applicable to sterile neutrinos at the eV mass scale, as suggested by existing experimental anomalies. To this purpose it exploits Liquid Argon Time Projection Chamber detectors located along the Booster Neutrino Beamline to measure both νe appearance and νµ disappearance: the Short Baseline Neutrino Detector and the ICARUS-T600 detector at 110 and 600 m from the neutrino source, respectively. The ICARUS T-600 Far Detector, located at shallow depth, is surrounded by a Cosmic Ray Tagger system to mitigate the cosmic ray background. On average ~ 11 muon tracks are expected to cross the detector during the ~ 1 ms drift time. The cosmic ray tagger is composed of plastic scintillator bars, ensuring near 4π coverage of the detector aiming at tagging cosmic muons and thus reject 𝛾s produced by muon interactions in the surrounding materials that can generate an electromagnetic showers mimicking a νe signal. The system allows one to disentangle cosmic rays from particles originated in a neutrino interaction inside the detector by measuring their position and crossing time. A synchronization of the cosmic ray tagger with the ICARUS photon detection system with a nanosecond accuracy allows one to reject cosmic particles recorded during the beam spill and thus select an enriched sample of neutrino triggered events ahead of the event reconstruction. An overview of the cosmic ray tagger system as well as its role in the neutrino events identification and cosmic background rejection will be presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Integrated Metabolomics and Proteomics Analyses in the Local Milieu of Islet Allografts in Rejection versus Tolerance

An understanding of the immune mechanisms that lead to rejection versus tolerance of allogeneic pancreatic islet grafts is of paramount importance, as it facilitates the development of innovative methods to improve the transplant outcome. Here, we used our established intraocular islet transplant model to gain novel insight into changes in the local metabolome and proteome within the islet allograft’s immediate microenvironment in association with immune-mediated rejection or tolerance. We performed integrated metabolomics and proteomics analyses in aqueous humor samples representative of the graft’s microenvironment under each transplant outcome. The results showed that several free amino acids, small primary amines, and soluble proteins related to the Warburg effect were upregulated or downregulated in association with either outcome. In general, the observed shifts in the local metabolite and protein profiles in association with rejection were consistent with established pro-inflammatory metabolic pathways and those observed in association with tolerance were immune regulatory. Taken together, the current findings further support the potential of metabolic reprogramming of immune cells towards immune regulation through targeted pharmacological and dietary interventions against specific metabolic pathways that promote the Warburg effect to prevent the rejection of transplanted islets and promote their immune tolerance.

60 APPLIED LIFE SCIENCES↗

Seeing through noise in power laws

Despite widespread claims of power laws across the natural and social sciences, evidence in data is often equivocal. Modern data and statistical methods reject even classic power laws such as Pareto’s law of wealth and the Gutenberg–Richter law for earthquake magnitudes. We show that the maximum-likelihood estimators and Kolmogorov–Smirnov (K-S) statistics in widespread use are unexpectedly sensitive to ubiquitous errors in data such as measurement noise, quantization noise, heaping and censorship of small values. This sensitivity causes spurious rejection of power laws and biases parameter estimates even in arbitrarily large samples, which explains inconsistencies between theory and data. We show that logarithmic binning by powers of λ > 1 attenuates these errors in a manner analogous to noise averaging in normal statistics and that λ thereby tunes a trade-off between accuracy and precision in estimation. Binning also removes potentially misleading within-scale information while preserving information about the shape of a distribution over powers of λ, and we show that some amount of binning can improve sensitivity and specificity of K-S tests without any cost, while more extreme binning tunes a trade-off between sensitivity and specificity. We therefore advocate logarithmic binning as a simple essential step in power-law inference.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Seeing through noise in power laws

Despite widespread claims of power laws across the natural and social sciences, evidence in data is often equivocal. Modern data and statistical methods reject even classic power laws such as Pareto’s law of wealth and the Gutenberg–Richter law for earthquake magnitudes. We show that the maximum-likelihood estimators and Kolmogorov–Smirnov (K-S) statistics in widespread use are unexpectedly sensitive to ubiquitous errors in data such as measurement noise, quantization noise, heaping and censorship of small values. This sensitivity causes spurious rejection of power laws and biases parameter estimates even in arbitrarily large samples, which explains inconsistencies between theory and data. We show that logarithmic binning by powers of λ > 1 attenuates these errors in a manner analogous to noise averaging in normal statistics and that λ thereby tunes a trade-off between accuracy and precision in estimation. Binning also removes potentially misleading within-scale information while preserving information about the shape of a distribution over powers of λ, and we show that some amount of binning can improve sensitivity and specificity of K-S tests without any cost, while more extreme binning tunes a trade-off between sensitivity and specificity. We therefore advocate logarithmic binning as a simple essential step in power-law inference.

97 MATHEMATICS AND COMPUTING↗

Constraining cosmological parameters using the pairwise kinematic Sunyaev-Zel’dovich effect with CMB-S4 and future galaxy cluster surveys

We present a forecast of the pairwise kinematic Sunyaev-Zel’dovich (kSZ) measurement that will be achievable with the future CMB-S4 experiment. CMB-S4 is the next stage for ground-based cosmic microwave background experiments, with a planned wide-area survey that will observe approximately 50% of the sky. We construct a simulated sample of galaxy clusters that have been optically selected in a Legacy Survey of Space and Time–like survey and have spectroscopic redshifts. For this cluster sample, assuming the likelihood is Gaussian, we predict that CMB-S4 will reject the null hypothesis of zero pairwise kSZ signal at 36⁢𝜎. We estimate the effects of systematic uncertainties such as scatter in the mass-richness scaling relation and cluster miscentering. We find that these effects can reduce the signal-to-noise ratio of the CMB-S4 pairwise kSZ measurement by 20%. We explore the constraining power of the measured kSZ signal in combination with measurements of the galaxy clusters’ thermal SZ emission on two extensions to the standard cosmological model. The first extension allows the dark energy equation of state 𝑤 to vary. We find the CMB-S4 pairwise kSZ measurement yields a modest reduction in the uncertainty on 𝑤 by a factor of 1.36 over the Planck’s 2018 uncertainty. The second extension tests general relativity by varying the growth index 𝛾. In conclusion, we find that CMB-S4’s pairwise kSZ measurement will yield a 28⁢𝜎 constraint on 𝛾 and strongly constrain alternative theories of gravity.

79 ASTRONOMY AND ASTROPHYSICS↗

Optics-Free Chip-Scale Intraoperative Imaging Using NIR-Excited Upconverting Nanoparticles

Here we present an optics-free CMOS image sensor that incorporates a novel time-gated dual-photodiode pixel design to allow filter- and lens-less image acquisition of near-infrared-excited (NIR-excited) upconverting nanoparticles. Recent biomedical advances have highlighted the benefits of NIR excitation, but NIR interaction with silicon has remained a challenge, even with high-performance optical blocking filters. Using a secondary diode and a dual-photodiode design, this sensor is able to remove the 100s of mV of NIR background on pixels and bring it down to single-digit mV level, nearing its noise floor of 2.2 mV rms, not achievable with any optical filter. Non-linear effects of background cancellation using the diode pair has been mitigated using an initial one-time pixel-level curve fitting and calibration in a post-processing setting. This imager comprises a highly linear 11 fF metal-oxide-metal (MOM) capacitor and includes integrated angle-selective gratings to reject oblique light and enhance sharpness. Each pixel also includes two distinct correlated double sampling schemes, to remove low frequency flicker noise and systematic offset in the datapath. We demonstrate the performance of this imager using pulsed NIR-excited upconverting nanoparticles on standard United-States-Air-Force (USAF) resolution targets and achieve an SNR of 15 dB, while keeping NIR background below 6 mV. This 36-by-80-pixel array measures only 2.3 mm by 4.8 mm and can be thinned down to 25 µm, allowing it to become surgically compatible with intraoperative instruments and equipment, while remaining optics-free.

42 ENGINEERING↗

Deep learning uncertainty quantification for clinical text classification

Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network’s confidence, in-depth analyses are needed to establish whether they are well calibrated. In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) population-based cancer registries. In particular, we introduce multiple methods for selective classification to achieve a target level of accuracy on multiple classification tasks while minimizing the rejection amount—that is, the number of electronic pathology reports for which the model’s predictions are unreliable. We evaluate the proposed methods by comparing our approach with the current in-house deep learning-based abstaining classifier. Overall, all the proposed selective classification methods effectively allow for achieving the targeted level of accuracy or higher in a trade-off analysis aimed to minimize the rejection rate. On in-distribution validation and holdout test data, with all the proposed methods, we achieve on all tasks the required target level of accuracy with a lower rejection rate than the deep abstaining classifier (DAC). Interpreting the results for the out-of-distribution test data is more complex; nevertheless, in this case as well, the rejection rate from the best among the proposed methods achieving 97% accuracy or higher is lower than the rejection rate based on the DAC. We show that although both approaches can flag those samples that should be manually reviewed and labeled by human annotators, the newly proposed methods retain a larger fraction and do so without retraining—thus offering a reduced computational cost compared with the in-house deep learning-based abstaining classifier.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of the scintillation response of water-based liquid scintillator to alpha particles, and implications for particle identification

Next-generation large-scale neutrino detectors, from EOS, at the 1 t scale, to THEIA, at the 10 s-of-kt scale, will utilize differences in both the scintillation and Cherenkov light emission for different particle species to perform background rejection. This manuscript presents measurements of the scintillation light yield and emission time profile of water-based liquid scintillator samples in response to α radiation. These measurements are used as input to simulation models used to make predictions for future detectors. In particular, we present the timing-based particle identification achievable in generic water-based scintillator detectors at the 4 t, 1 kt, and 100 kt scales. We find that α/β discrimination improves with increasing scintillation concentration and we identify better than 80% α rejection for 90% β acceptance in 10% water-based liquid scintillator, at the 4 t scale.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A stilbene–strontium iodide based radioxenon detection system for monitoring nuclear explosions

Atmospheric measurement of noble gases has been extensively used for monitoring clandestine nuclear weapon explosions for many years. The ratios of four xenon isotopes of interest ( 131 mXe, 133 mXe, 133 Xe, and 135 Xe) help in discriminating regular reactor operations from nuclear tests. A new coincidence-based detection system using stilbene and strontium iodide [SrI 2 (Eu)] for electron and photon detection respectively was developed at Oregon State University to address some of the challenges of the radioxenon systems deployed in the field such as memory effect, and poor energy resolution. Silicon photomultipliers (SiPMs) were used for sensing optical photons from all scintillation media. Real-time coincidence identification was achieved using the eight-channel digital pulse processor. The detection system was evaluated using lab check sources and Oregon State TRIGA reactor irradiated radioxenon samples. A 48-hour background coincidence spectrum was collected yielding a coincidence count rate and background rejection rate of 0.0174 ± 0.0003 counts per second (cps) and 98.9% respectively. The minimum detectable concentration (MDC) of the system was evaluated to be 0.11 ± 0.01, 0.13 ± 0.02, 0.20 ± 0.02, and 0.73 ± 0.08 for 131 mXe, 133 mXe, 133 Xe, and 135 Xe respectively. The memory effect of the detection system was found to be 0.069 ± 0.015%, which is almost a 70-fold reduction compared to traditional plastic scintillators. Here, the detection elements, custom-designed electronics, and the detector response to radioxenon are detailed in this work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

One-Component Nanocomposite Membranes from Polymer Grafted Cellulose Nanocrystals

Membrane filtration is an important industrial purification process used to access clean and potable water. The fabrication of the membranes used in these purification applications often involves expensive and energy-intensive processes that have a large negative impact on the environment. Sustainable alternatives with a high water flux and strong rejection performance are needed to purify water. Here, the focus of this work is to investigate the use of polymer-grafted cellulose nanocrystals (CNCs) in membrane applications. The impact of the polymer grafting density and polymer conformation was investigated and it is shown that by increasing the grafting density of PEG such that it adopts a semidilute polymer brush conformation, the water flux through the membranes could be increased from 3.5 to 2900 L h –1 m –2 for CNC membranes without and with grafted PEG, respectively. These membranes also exhibited rejection performances with molecular weight cutoffs between 62 and 100 kDa for all polymer-grafted samples, consistent with the ultrafiltration regime. Thus, the design of these one-component composite materials can enhance the water permeability of ultrafiltration membranes while maintaining effective selectivity.

cellulose nanocrystals↗

Application of Markov Chain Monte Carlo Methods for Uncertainty Quantification in Inverse Transport Problems

Determination of the components of a radioactive source/shield system using the system’s radiation signature is of great importance in homeland security, material safeguards, and waste management. Although significant progress has been made toward solving this inverse transport problem in recent years, work remains to be done to quantify the uncertainty in reconstructed results. In this article we apply two Markov chain Monte Carlo (MCMC) approaches, the delayed rejection adaptive metropolis (DRAM) and differential evolution adaptive metropolis (DREAM) methods, to solve inverse problems and quantify uncertainty. The DRAM method uses delayed rejection combined with global adaptation of the proposal covariance matrix. Furthermore, the DREAM method hybridizes MCMC sampling with the differential evolution (DE) algorithm. In numerical test cases, the DRAM and DREAM methods are shown to be superior to a first-order inverse Hessian approach for problems with noisy data and multiple unknown quantities, with DREAM converging to the posterior distribution more quickly than DRAM. The DREAM and DRAM results indicate that a full posterior distribution is required to quantify uncertainty in many inverse transport problems.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

The Twins Embedding of Type Ia Supernovae. II. Improving Cosmological Distance Estimates

We show how spectra of Type Ia supernovae (SNe Ia) at maximum light can be used to improve cosmological distance estimates. In a companion article, we used manifold learning to build a three-dimensional parameterization of the intrinsic diversity of SNe Ia at maximum light that we call the "Twins Embedding."In this article, we discuss how the Twins Embedding can be used to improve the standardization of SNe Ia. With a single spectrophotometrically calibrated spectrum near maximum light, we can standardize our sample of SNe Ia with an rms of 0.101 0.007 mag, which corresponds to 0.084 0.009 mag if peculiar velocity contributions are removed and to 0.073 0.008 mag if a larger reference sample were obtained. Our techniques can standardize the full range of SNe Ia, including those typically labeled as peculiar and often rejected from other analyses. We find that traditional light-curve width + color standardization such as SALT2 is not sufficient. The Twins Embedding identifies a subset of SNe Ia, including, but not limited to, 91T-like SNe Ia whose SALT2 distance estimates are biased by 0.229 0.045 mag. Standardization using the Twins Embedding also significantly decreases host-galaxy correlations. We recover a host mass step of 0.040 0.020 mag compared to 0.092 0.026 mag for SALT2 standardization on the same sample of SNe Ia. These biases in traditional standardization methods could significantly impact future cosmology analyses if not properly taken into account.

79 ASTRONOMY AND ASTROPHYSICS↗

Using active learning to improve quasar identification for the DESI spectra processing pipeline

The Dark Energy Spectroscopic Instrument (DESI) survey uses an automatic spectral classification pipeline to classify spectra. QuasarNET is a convolutional neural network used as part of this pipeline originally trained using data from the Baryon Oscillation Spectroscopic Survey (BOSS). In this paper we implement an active learning algorithm to optimally select spectra to use for training a new version of the QuasarNET weights file using only DESI data, with the goal of improving classification accuracy. This active learning algorithm includes a novel outlier rejection step using a Self-Organizing Map to ensure we label spectra representative of the larger quasar sample observed in DESI. We perform two iterations of the active learning pipeline, assembling a final dataset of 5600 labeled spectra, a small subset of the approximately 1.3 million quasar targets in DESI's Data Release 1. When splitting the spectra into training and validation subsets we achieve similar performance to the previously trained weights file in completeness and purity calculated on the validation dataset but do so with less than one tenth of the amount of training data. The new weights also more consistently classify objects in the same way when used on unlabeled data compared to the old weights file. In the process of improving QuasarNET's classification accuracy we discovered a systemic error in QuasarNET's redshift estimation and used our findings to improve our understanding of QuasarNET's redshifts.

Machine learning↗