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At least 145 records · Page 8

Machine learning prediction of incidence of Alzheimer’s disease using large-scale administrative health data

Nationwide population-based cohort provides a new opportunity to build an automated risk prediction model based on individuals’ history of health and healthcare beyond existing risk prediction models. We tested the possibility of machine learning models to predict future incidence of Alzheimer’s disease (AD) using large-scale administrative health data. From the Korean National Health Insurance Service database between 2002 and 2010, we obtained de-identified health data in elders above 65 years (N = 40,736) containing 4,894 unique clinical features including ICD-10 codes, medication codes, laboratory values, history of personal and family illness and socio-demographics. To define incident AD we considered two operational definitions: “definite AD” with diagnostic codes and dementia medication (n = 614) and “probable AD” with only diagnosis (n = 2026). We trained and validated random forest, support vector machine and logistic regression to predict incident AD in 1, 2, 3, and 4 subsequent years. For predicting future incidence of AD in balanced samples (bootstrapping), the machine learning models showed reasonable performance in 1-year prediction with AUC of 0.775 and 0.759, based on “definite AD” and “probable AD” outcomes, respectively; in 2-year, 0.730 and 0.693; in 3-year, 0.677 and 0.644; in 4-year, 0.725 and 0.683. The results were similar when the entire (unbalanced) samples were used. Important clinical features selected in logistic regression included hemoglobin level, age and urine protein level. This study may shed a light on the utility of the data-driven machine learning model based on large-scale administrative health data in AD risk prediction, which may enable better selection of individuals at risk for AD in clinical trials or early detection in clinical settings.

97 MATHEMATICS AND COMPUTING↗

Validation of the VUV-reflective coating for next-generation liquid xenon detectors

Abstract Coating detector materials with films highly reflective in the vacuum ultraviolet region improves sensitivity of the next-generation rare-event detectors that use liquid xenon. In this work, we investigate the MgF 2 -Al-MgF 2 coating designed to achieve high reflectance at 175 nm, the mean wavelength of liquid xenon (LXe) scintillation. The coating was applied to an unpolished, passivated copper substrate mimicking a realistic detector component of the proposed nEXO experiment, as well as to two unpassivated substrates with “high” and “average” levels of polishing. After confirming the composition and morphology of the thin-film coating using TEM and EDS, the samples underwent reflectance measurements in LXe and gaseous nitrogen (GN2). Measurements in LXe exposed the coated samples to -100°C for several hours. No peeling of the coatings was observed after several thermal cycles. Polishing is found to strongly correlate with the measured specular reflectance (R spec ). In particular, 5.8(5)% specular spike reflectance in LXe was measured for the realistic sample at 20° of incidence, while the values for similar angles of incidence on the high and average polish samples are 62.3(1.3)% and 27.4(7)%, respectively. At large angles (66°–75°), theR spec in LXe for the three samples increases to 23(5)%, 80(8)%, and 84(18)%, respectively. The R spec at around 45° was measured in both GN2 and LXe for average polish sample and shows a reasonable agreement. Importantly, the total reflectance of the samples is comparable and estimated to be 92(8)%, 85(8)%, and 83(8)% in GN2 for the realistic, average, and high polish samples, respectively. This is considered satisfactory for the next-generation LXe experiments that could benefit from using reflective films, such as nEXO and DARWIN, thus validating the design of the coating.

Instruments & Instrumentation↗

A declining major merger fraction with redshift in the local Universe from the largest-yet catalogue of major and minor mergers in SDSS

It is difficult to accurately identify galaxy mergers and it is an even larger challenge to classify them by their mass ratio or merger stage. In previous work we used a suite of simulated mergers to create a classification technique that uses linear discriminant analysis to identify major and minor mergers. Here, we apply this technique to 1.3 million galaxies from the SDSS DR16 photometric catalogue and present the probability that each galaxy is a major or minor merger, splitting the classifications by merger stages (early, late, post-coalescence). We present publicly available imaging predictor values and all of the above classifications for one of the largest-yet samples of galaxies. We measure the major and minor merger fraction (f merg ) and build a mass-complete sample of galaxies, which we bin as a function of stellar mass and redshift. For the major mergers, we find a positive slope of fmerg with stellar mass and negative slope of f merg with redshift between stellar masses of 10.5 < M * (log M ⊙ ) < 11.6 and redshifts of 0.03 < z < 0.19. We are able to reproduce an artificial positive slope of the major merger fraction with redshift when we do not bin for mass or craft a complete sample, demonstrating the importance of mass completeness and mass binning. Further, we determine that the positive trend of the major merger fraction with stellar mass is consistent with a hierarchical assembly scenario. The negative trend with redshift requires that an additional assembly mechanism, such as baryonic feedback, dominates in the local Universe.

79 ASTRONOMY AND ASTROPHYSICS↗

Size-Dependent Nucleation in Crystal Phase Transition from Machine Learning Metadynamics

In this Letter, we present a framework that combines machine learning potential (MLP) and metadynamics to investigate solid-solid phase transition. Here, based on the spectral descriptors and neural networks regression, we develop a scalable MLP model to warrant an accurate interpolation of the energy surface where two phases coexist. Applying it to the simulation of B4–B1 phase transition of GaN under 50 GPa with different model sizes, we observe sequential change of the phase transition mechanism from collective modes to nucleation and growths. When the size is at or below 128 000 atoms, the nucleation and growth appear to follow a preferred direction. At larger sizes, the nuclei occur at multiple sites simultaneously and grow to microstructures by passing the critical size. The observed change of the atomistic mechanism manifests the importance of statistical sampling with large system size in phase transition modeling.

36 MATERIALS SCIENCE↗

Study of a linear surface wave plasma source for tin removal in an extreme ultraviolet source

Tin deposition mitigation employs hydrogen radicals and ions, formed in a hydrogen plasma, to interact with tin to form tin hydride (SnH 4 ) in the gaseous state, which is then pumped away. Surface wave plasma (SWP) technology developed at Illinois generates hydrogen radicals and ions, resulting in tin etch rates that are high enough to keep extreme ultraviolet (EUV) lithographic tools clean. An advantage of an SWP antenna is the ability to generate a high density of hydrogen radicals and hydrogen ions directly at the desired etching location. In situ etching of tin enables high availability EUV tools by maintaining high reflectivity of the multilayer mirror of the collector. Additionally, the SWP is characterized with low ion energies and low electron temperature, such that the multilayer mirror does not suffer any damage from sputtering or implantation of hydrogen ions during operation. Here, experiments elucidating the fundamental processes of tin removal are conducted by varying pressure, power, surface temperature, and gas flow rate in order to observe the etch rate behavior. Our results have shown that the presence of hydrogen ions increases etch rates because ion bombardment weakens Sn–Sn bonds, which, in turn, allows for a higher rate of chemical etching by the radicals. The ion bombardment reduces the number of radicals needed to etch a single tin atom to the range of 10 2 –10 3 . The linear SWP antenna yields plasma densities on the order of 10 17 to 10 18 m -3 and radical densities on the order of 10 18 to 10 19 m -3 , allowing for greater utilization of ion etch enhancement. Etch rates of up to 200 nm/min have been achieved. The surface temperature of the samples is an important factor in the etching process such that the decrease in the surface temperature increases the etch rates and decreases the hydrogen desorption rates. In addition, a kinetic etch model is developed to explain the behavior of etch rates as a function of surface temperature. Furthermore, results from experiments performed in an Illinois NXE:3100 chamber will be discussed.

42 ENGINEERING↗

Recovering new viruses from New Mexico soils

Here, we utilized metagenomic and size-filtered virome sequencing to recover 4,157 medium, high, or complete quality viral genomes from soils taken from three high elevation sites in New Mexico, USA. Among recovered viral genomes, 90% were from size-filtered samples, indicating the importance of this enrichment in assessments of complex viromes.

59 BASIC BIOLOGICAL SCIENCES↗

Assessing Prior Emergent Constraints on Surface Albedo Feedback in CMIP6

An emergent constraint (EC) is a popular model evaluation technique, which offers the potential to reduce intermodel variability in projections of climate change. Two examples have previously been laid out for future surface albedo feedbacks (SAF) stemming from loss of Northern Hemisphere (NH) snow cover (SAF snow ) and sea ice (SAF ice ). These processes also have a modern-day analog that occurs each year as snow and sea ice retreat from their seasonal maxima, which is strongly correlated with future SAF across an ensemble of climate models. The newly released CMIP6 ensemble offers the chance to test prior constraints through out-of-sample verification, an important examination of EC robustness. Here, we show that the SAF snow EC is equally strong in CMIP6 as it was in past generations, while the SAF ice EC is also shown to exist in CMIP6, but with different, slightly weaker characteristics. We find that the CMIP6 mean NH SAF exhibits a global feedback of 0.25 ± 0.05 W m -2 K -1 , or ~61% of the total global albedo feedback, largely in line with prior generations despite its increased climate sensitivity. Additionally, the NH SAF can be broken down into similar contributions from snow and sea ice over the twenty-first century in CMIP6. Crucially, intermodel variability in seasonal SAF snow and SAF ice is largely unchanged from CMIP5 because of poor outlier simulations of snow cover, surface albedo, and sea ice thickness. These outliers act to mask the noted improvement from many models when it comes to SAF ice , and to a lesser extent SAF snow .

58 GEOSCIENCES↗

Conditional quantum plasmonic sensing

The possibility of using weak optical signals to perform sensing of delicate samples constitutes one of the main goals of quantum photonic sensing. Furthermore, the nanoscale confinement of electromagnetic near fields in photonic platforms through surface plasmon polaritons has motivated the development of highly sensitive quantum plasmonic sensors. Despite the enormous potential of plasmonic platforms for sensing, this class of sensors is ultimately limited by the quantum statistical fluctuations of surface plasmons. Indeed, the fluctuations of the electromagnetic field severely limit the performance of quantum plasmonic sensing platforms in which delicate samples are characterized using weak near-field signals. Furthermore, the inherent losses associated with plasmonic fields levy additional constraints that challenge the realization of sensitivities beyond the shot-noise limit. Here, we introduce a protocol for quantum plasmonic sensing based on the conditional detection of plasmons. We demonstrate that the conditional detection of plasmonic fields, via plasmon subtraction, provides a new degree of freedom to control quantum fluctuations of plasmonic fields. This mechanism enables improvement of the signal-to-noise ratio of photonic sensors relying on plasmonic signals that are comparable to their associated field fluctuations. Consequently, the possibility of using weak plasmonic signals to sense delicate samples, while preserving the sample properties, has important implications for molecule sensing, and chemical detection.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Cost of (In-) Accurate Waste Characterization in the U.S. Nuclear Power Industry - 20066

Proper disposal of waste has never been a human priority. Our history is full of examples of throwing away things with minimal effort or thought to consequence. That is until disease or toxicity become apparent and we realize we need to change. Unfortunately, we almost never have all the information we need at the time we make decisions. In addition to the technical and scientific issues, profits and politics are also factors. Newton's third law also applies to politics and so for every policy (action) put in place, there will be (opposite reaction) forces in play to push back against it. These forces are seldom balanced and so the reaction to the discovery of harm is to over-correct and destroy the benefit to be had. This of course causes those who want the benefit, or profit from it, to work to undermine or repeal those measures put in place to eliminate the harm. The issue is exacerbated when the problem to be solved is highly technical and at the edge of our science so that the harm and benefit cannot be easily or accurately quantified. At these times, reason often goes out the window and our decision makers are influenced by either greed or fear as these emotions are much easier to stoke. Those of us in the middle, with the charge to 'do the right thing for the least cost', are therefore frequently constrained and forced into actions that are neither technically the right thing to do and not cost effective. The cost of radioactive waste disposal is based on the concentrations of various radioisotopes in the waste. Some of these isotopes are relatively easy to quantify and some are not. Most laboratory methods for quantification are limited in the amount of activity that can be present during the measurement process. Current nuclear plants were not designed with the idea that taking truly representative waste samples would be important. The limits used to define waste class and therefore cost are precisely defined but the methods for determining those concentrations are far less precise. Improving the accuracy of radioactivity concentrations in waste and having consistent and reasonable oversight can reduce waste costs through active management of the process. So what can we do about it? Science may provide an answer. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Using low volume eDNA methods to sample pelagic marine animal assemblages

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380–1800 mL) collected at depths of 0–2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

59 BASIC BIOLOGICAL SCIENCES↗

Current and future federal and state sampling guidance for per- and polyfluoroalkyl substances in environmental matrices

Per- and polyfluoroalkyl substances (PFAS) are a class of emerging contaminants composed of an estimated 5000 to 10,000 human-made, fluorinated, organic chemicals. Due to the complexity of PFAS, the need for multiple environmental matrix considerations and the absence of a promulgated federal standard for environmental sampling and analysis, U.S. states have begun developing health-based regulatory and/or guidance values for a limited number of PFAS in environmental matrices. As there is a growing body of science to inform PFAS sampling guidance standard development, it is important to understand which U.S. states are implementing sampling guidelines and how they plan to handle emerging PFAS. This critical review discusses the current and impending federal and state sampling guidelines for PFAS in environmental matrices, the data gaps surrounding PFAS sampling guidance in U.S. states, and the future impacts of impending guidance documents and regulations. Ten federal guidance documents are available for PFAS sampling guidance and analysis. The maximum number of PFAS covered in these guidance documents is 25 analytes spanning across 8 unique media. While the EPA has developed several different sampling and analytical guidelines for PFAS, there is no formal regulation of PFAS or requirements of states to enforce these guidelines. Consequently, only 31 states have informally adopted sampling guidelines, while the other 19 states have no guidance documentation in place for PFAS. The introduction of new PFAS sampling guidelines by the EPA, as well as updated analytical guidelines that target more PFAS or total organofluoride, is expected to continuously shift the landscape of federal and state guidance for PFAS sampling moving forward.

54 ENVIRONMENTAL SCIENCES↗

Sample preparation with sucrose cryoprotection dramatically alters Zn distribution in the rodent hippocampus, as revealed by elemental mapping

Transition metal ions (Fe, Mn, Cu, Zn) are essential for healthy brain function, but altered concentration, distribution, or chemical form of the metal ions has been implicated in numerous brain pathologies. Currently, it is not possible to image the cellular or sub-cellular distribution of metal ions in vivo and therefore, studying brain-metal homeostasis largely relies on ex vivo in situ elemental mapping. Sample preparation methods that accurately preserve the in vivo elemental distribution are essential if one wishes to translate the knowledge of elemental distributions measured ex vivo toward increased understanding of chemical and physiological pathways of brain disease. Furthermore, the choice of sample preparation is particularly important for metal ions that exist in a labile or mobile form, for which the in vivo distribution could be easily distorted by inappropriate sample preparation. One of the most widely studied brain structures, the hippocampus, contains a large pool of labile and mobile Zn. Herein, we describe how sucrose cryoprotection, the gold standard method of preparing tissues for immuno-histochemistry or immuno-fluorescence, which is also often used as a sample preparation method for elemental mapping studies, drastically alters hippocampal Zn distribution. Based on the results of this study, in combination with a comparison against the strong body of published literature that has used either rapid plunge freezing of brain tissue, or sucrose cryo-protection, we strongly urge investigators in the future to cease using sucrose cryoprotection as a method of sample preparation for elemental mapping, especially if Zn is an analyte of interest.

59 BASIC BIOLOGICAL SCIENCES↗

A Bayesian Approach for Quantifying Data Scarcity when Modeling Human Behavior via Inverse Reinforcement Learning

Computational models that formalize complex human behaviors enable study and understanding of such behaviors. However, collecting behavior data required to estimate the parameters of such models is often tedious and resource intensive. Thus, estimating dataset size as part of data collection planning (also known as Sample Size Determination) is important to reduce the time and effort of behavior data collection while maintaining an accurate estimate of model parameters. In this paper, we present a sample size determination method based on Uncertainty Quantification (UQ) for a specific Inverse Reinforcement Learning (IRL) model of human behavior, in two cases: 1) pre-hoc experiment design—conducted in the planning stage before any data is collected, to guide the estimation of how many samples to collect; and 2) post-hoc dataset analysis—performed after data is collected, to decide if the existing dataset has sufficient samples and whether more data is needed. Here, we validate our approach in experiments with a realistic model of behaviors of people with Multiple Sclerosis (MS) and illustrate how to pick a reasonable sample size target. Our work enables model designers to perform a deeper, principled investigation of effects of dataset size on IRL.

97 MATHEMATICS AND COMPUTING↗

A device for volatile organic compound (VOC) analysis from skin using heated dynamic headspace sampling

Abstract Human skin is an important source of volatile organic compounds (VOCs) offering noninvasive methods to gain clinical metabolite information. This work was focused on the development of a skin sampling device based on a dynamic headspace sampling method with the addition of temperature to increase VOC metabolite recovery. The device preconcentrates skin VOC emissions onto a sorbent substrate, which can either be preserved for offline analysis or attached to a real time sensor downstream. In this work, skin VOC samples were analyzed offline using thermal desorption-gas chromatography-mass spectrometry. A list of 10 common skin VOCs was pre-selected to optimize parameters of sampling time, sampling temperature, and sorbent selection. Overall, this study highlights an effective skin VOC sampling technology with a heating dimension (40 °C, rather than 30 °C or no heating) with a sampling time of 15 min (rather than 5 or 30 mins) and onto Tenax TA sorbent (rather than PDMS), which collectively increases the recovery of compounds with lower vapor pressure and decreases the observed variability in skin VOC measurements. Finally, a list of 79 skin VOC compounds were detected and identified within a cohort of 20 young, healthy volunteers.

Biochemistry & Molecular Biology↗

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

Background: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

54 ENVIRONMENTAL SCIENCES↗

A lathe system for micrometre-sized cylindrical sample preparation at room and cryogenic temperatures

A simple two-spindle based lathe system for the preparation of cylindrical samples intended for X-ray tomography is presented. The setup can operate at room temperature as well as under cryogenic conditions, allowing the preparation of samples down to 20 and 50 µm in diameter, respectively, within minutes. Case studies are presented involving the preparation of a brittle biomineral brachiopod shell and cryogenically fixed soft brain tissue, and their examination by means of ptychographic X-ray computed tomography reveals the preparation method to be mainly free from causing artefacts. Since this lathe system easily yields near-cylindrical samples ideal for tomography, a usage for a wide variety of otherwise challenging specimens is anticipated, in addition to potential use as a time- and cost-saving tool prior to focused ion-beam milling. Fast sample preparation becomes especially important in relation to shorter measurement times expected in next-generation synchrotron sources.

36 MATERIALS SCIENCE↗

Bayesian Inference with Latent Hamiltonian Neural Networks (L-HNNs)

When sampling for Bayesian inference, one popular approach is to use Hamiltonian Monte Carlo (HMC) and the No-U-Turn Sampler (NUTS). However, HMC and NUTS can require numerous numerical gradients of the target density and can prove slow in practice. We propose Hamiltonian neural networks (HNNs) with HMC and NUTS for solving Bayesian inference problems [1, 2]. Once trained, HNNs do not require gradients of the target density while sampling. Moreover, they satisfy important properties such as perfect time reversibility and Hamiltonian conservation, making them well suited for use within HMC and NUTS because stationarity can be shown. We also propose an HNN extension called latent HNNs (L-HNNs), which predict latent variable outputs. Compared to HNNs, L-HNNs offer improved expressivity and a reduction in integration errors. Finally, we propose employing L-HNNs in NUTS with an online error monitoring scheme to prevent degeneracy of the sampling in regions of low probability density. We demonstrate L-HNNs in NUTS with online error monitoring by using several example cases involving complex, heavy-tailed, and high local curvature probability densities. Overall, L-HNNs in NUTS with online error monitoring satisfactorily inferred these probability densities. Compared to traditional NUTS, L-HNNs in NUTS with online error monitoring improved the effective sample size (ESS) per gradient by an order of magnitude.

97 MATHEMATICS AND COMPUTING↗

Local cation order and ferrimagnetism in compositionally complex spinel ferrites

We present an exploration of a family of compositionally complex cubic spinel ferrites featuring combinations of Mg, Fe, Co, Ni, Cu, Mn, and Zn cations, systematically investigating the average and local atomic structures, chemical short-range order, magnetic spin configurations, and magnetic properties. All compositions result in ferrimagnetic average structures with extremely similar local bonding environments; however, the samples display varying degrees of cation inversion and, therefore, differing apparent bulk magnetization. Additionally, first-order reversal curve analysis of the magnetic reversal behavior indicates varying degrees of magnetic ordering and interactions, including potentially local frustration. Finally, reverse Monte Carlo modeling of the spin orientation demonstrates a relationship between the degree of cation inversion and the spin collinearity. Collectively, these observations correlate with differences in synthesis procedures. This work provides a framework for understanding magnetic behavior reported for “high-entropy spinels,” revealing many are likely compositionally complex oxides with differing degrees of chemical short-range order—not meeting the community established criteria for high or medium entropy compounds. Moreover, this work highlights the importance of reporting complete sample processing histories and investigating local to long-range atomic arrangements when evaluating potential entropic mixing effects and assumed property correlations in high entropy materials.

36 MATERIALS SCIENCE↗