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Robust framework and software implementation for fast speciation mapping

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. In this work, several authors have used different multivariate data processing strategies to establish speciation maps. Furthermore, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. Additionally, the algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.

47 OTHER INSTRUMENTATION↗

Vector wind and vector wind shear models 0 to 27 km altitude for Cape Kennedy, Florida, and Vandenberg AFB, California

The techniques are presented to derive several statistical wind models. The techniques are from the properties of the multivariate normal probability function. Assuming that the winds can be considered as bivariate normally distributed, then (1) the wind components and conditional wind components are univariate normally distributed, (2) the wind speed is Rayleigh distributed, (3) the conditional distribution of wind speed given a wind direction is Rayleigh distributed, and (4) the frequency of wind direction can be derived. All of these distributions are derived from the 5-sample parameter of wind for the bivariate normal distribution. By further assuming that the winds at two altitudes are quadravariate normally distributed, then the vector wind shear is bivariate normally distributed and the modulus of the vector wind shear is Rayleigh distributed. The conditional probability of wind component shears given a wind component is normally distributed. Examples of these and other properties of the multivariate normal probability distribution function as applied to Cape Kennedy, Florida, and Vandenberg AFB, California, wind data samples are given. A technique to develop a synthetic vector wind profile model of interest to aerospace vehicle applications is presented.

Smith, O. E.↗

Editorial: Applications of spectroscopy and chemometrics in nuclear materials analysis

Optical analysis techniques, including spectroscopy and image analysis, have many advantages when applied to the study of nuclear materials. They require small sample sizes, can be performed remotely, and can be proceduralized through consistent practice. Most importantly, they provide a wealth of information by generating multivariate data. For example, ultraviolet–visible–near-infrared absorbance spectroscopy of actinides in aqueous and organic solutions is dependent on the oxidation state, anionic complexation, and temperature. These variables are important for solution-based separation processes, and sensitivity to these factors, combined with online monitoring, can drive the efficiency and control of these processes. The morphology and chemical composition of actinide particles can also provide a vital clue to the mechanisms by which the particles were formed, providing forensic information on the origins of the particles.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

STITCHES: creating new scenarios of climate model output by stitching together pieces of existing simulations

Abstract. Climate model output emulation has long been attempted to support impact research, mainly to fill in gaps in the scenario space. Given the computational cost of running coupled earth system models (ESMs), which are usually the domain of supercomputers and require on the order of days to weeks to complete a century-long simulation, only a handful of different scenarios are usually chosen to externally force ESM simulations. An effective emulator, able to run on standard computers in times of the order of minutes rather than days could therefore be used to derive climate information under scenarios that were not run by ESMs. Lately, the necessity of accounting for internal variability has also made the availability of initial-condition ensembles, under a specific scenario, important, further increasing the computational demand. At least so far, emulators have been limited to simplified ESM-like output, either seasonal, annual, or decadal averages of basic quantities, like temperature and precipitation, often emulated independently of one another. With this work, we propose a more comprehensive solution to ESM output emulation. Our emulator, STITCHES, uses existing archives of earth system models' (ESMs) scenario experiments to construct ESM-like output under new scenarios or enrich existing initial-condition ensembles, which is what other emulators also aim to do. Importantly, however, STITCHES' output has the same characteristics of the ESM output it sets out to emulate: multivariate, spatially resolved, and high frequency, representing both the forced component and the internal variability around it. STITCHES extends the idea of time sampling – according to which climate outcomes are stratified by the global warming level at which they manifest themselves, irrespective of the scenario and time at which they occur – to the construction of a continuous history of ESM-like output over the whole 21st century, consistent with a 21st-century trajectory of global surface air temperature (GSAT) derived from the scenario that has been chosen as the target of the emulation. STITCHES does so by first splitting the target GSAT trajectory into decade-long windows, then matching each window in turn to a decade-long window within an existing model simulation from the available scenario runs according to its proximity to the target in absolute size of the temperature anomaly and its rate of change. A look-up table is therefore created of a sequence of existing experiment–time-window combinations that, when stitched together, create a GSAT trajectory “similar” to the target. Importantly, we can then stitch together much more than GSAT from these windows, i.e., any output that the ESM has saved for these existing experiment–time-window combinations, at any frequency and spatial scale available in its archive. We show that the stitching does not introduce artifacts in the great majority of cases (we look at temperature and precipitation at monthly frequency and on the native grid of the ESM and at an index of ENSO activity, the Southern Oscillation Index). This is true even if the criteria for the identification of the decades to be stitched together are chosen to work for a smoothed time series of annual GSAT, a result we expect given the larger amount of noise affecting most other variables at finer spatial scales and higher frequencies, which therefore are more “forgiving” of the stitching. We successfully test the method's performance over many ESMs and scenarios. Only a few exceptions surface, but these less-than-optimal outcomes are always associated with a scarcity of the archived simulations from which we can gather the decade-long windows that form the building blocks of the emulated time series. In the great majority of cases, STITCHES' performance is satisfactory according to metrics that reward consistency in trends, interannual and inter-ensemble variance, and autocorrelation structure of the time series stitched together. The method therefore can be used to create ESM-like output according to new scenarios, on the basis of a trajectory of GSAT produced according to that scenario, which could be easily obtained by a simple climate model. It can also be used to increase the size of existing initial-condition ensembles. There are aspects of our emulator that will immediately disqualify it for specific applications, like when climate information is needed whose characteristics result from accumulated quantities over windows of times longer than those used as pieces by STITCHES, droughts longer than a decade for example. But for many applications, we argue that a stitched product can satisfy the climate information needs of impact researchers. STITCHES cannot emulate ESM output from scenarios that result in GSAT trajectories outside of the envelope available in the archive, nor can it emulate trajectories with shapes different from existing ones (overshoots with negative derivative, for example). Therefore, the size and characteristics of the available archives of ESM output are the principal limitations for STITCHES' deployment. Thus, we argue for the possibility of designing scenario experiments within, for example, the next phase of the Coupled Model Intercomparison Project according to new principles, relieved of the need to produce a number of similar trajectories that vary only in radiative forcing strength but more strategically covering the space of temperature anomalies and rates of change.

54 ENVIRONMENTAL SCIENCES↗

Spatial land-use inventory, modeling, and projection/Denver metropolitan area, with inputs from existing maps, airphotos, and LANDSAT imagery

A landscape model was constructed with 34 land-use, physiographic, socioeconomic, and transportation maps. A simple Markov land-use trend model was constructed from observed rates of change and nonchange from photointerpreted 1963 and 1970 airphotos. Seven multivariate land-use projection models predicting 1970 spatial land-use changes achieved accuracies from 42 to 57 percent. A final modeling strategy was designed, which combines both Markov trend and multivariate spatial projection processes. Landsat-1 image preprocessing included geometric rectification/resampling, spectral-band, and band/insolation ratioing operations. A new, systematic grid-sampled point training-set approach proved to be useful when tested on the four orginal MSS bands, ten image bands and ratios, and all 48 image and map variables (less land use). Ten variable accuracy was raised over 15 percentage points from 38.4 to 53.9 percent, with the use of the 31 ancillary variables. A land-use classification map was produced with an optimal ten-channel subset of four image bands and six ancillary map variables. Point-by-point verification of 331,776 points against a 1972/1973 U.S. Geological Survey (UGSG) land-use map prepared with airphotos and the same classification scheme showed average first-, second-, and third-order accuracies of 76.3, 58.4, and 33.0 percent, respectively.

Tom, C.↗

Organic matter distribution in the icy environments of Taylor Valley, Antarctica

Glaciers can accumulate and release organic matter affecting the structure and function of associated terrestrial and aquatic ecosystems. Here we analyzed 18 ice cores collected from six locations in Taylor Valley (McMurdo Dry Valleys), Antarctica to determine the spatial abundance and quality of organic matter, and the spatial distribution of bacterial density and community structure from the terminus of the Taylor Glacier to the coast (McMurdo Sound). Our results showed that dissolved and particulate organic carbon (DOC and POC) concentrations in the ice core samples increased from the Taylor Glacier to McMurdo Sound, a pattern also shown by bacterial cell density. Fluorescence Excitation Emission Matrices Spectroscopy (EEMs) and multivariate parallel factor (PARAFAC) modeling identified one humic-like (C1) and one protein-like (C2) component in ice cores whose fluorescent intensities all increased from the Polar Plateau to the coast. The fluorescence index showed that the bioavailability of dissolved organic matter (DOM) also decreased from the Polar Plateau to the coast. Partial least squares path modeling analysis revealed that bacterial abundance was the main positive biotic factor influencing both the quantity and quality of organic matter. Marine aerosol influenced the spatial distribution of DOC more than katabatic winds in the ice cores. Certain bacterial taxa showed significant correlations with DOC and POC concentrations. Collectively, our results show the tight connectivity among organic matter spatial distribution, bacterial abundance and meteorology in the McMurdo Dry Valley ecosystem.

54 ENVIRONMENTAL SCIENCES↗

High throughput crystal structure and composition mapping of crystalline nanoprecipitates in alloys by transmission Kikuchi diffraction and analytical electron microscopy

Statistically significant crystal structure and composition identification of nanocrystalline features such as nanoparticles/nanoprecipitates in materials chemistry and alloy designing using electron microscopy remains a grand challenge. In this paper, we reveal that differing crystallographic phases of nanoprecipitates in alloys can be mapped with unprecedented statistics using transmission Kikuchi diffraction (TKD), on typical carbon-based electron-transparent samples. Using a case of multiphase, multicomponent nanoprecipitates extracted from an improved version of 9% chromium Eurofer-97 reduced-activation ferritic-martensitic steel we show that TKD successfully identified more than thousand M 23 C 6 , MX, M 7 C 3 , and M 2 X ( M =Fe, Cr, W, V, Ta; X = C, N) nanoprecipitates in a single scan, something that is currently unachievable using a transmission electron microscope (TEM) without incorporating a precision electron diffraction (PED) system. Precipitates as small as ~20–25 nm were successfully phase identified by TKD. We verified the TKD phase identification using high-resolution transmission electron microscopy (HRTEM) and convergent beam electron diffraction (CBED) pattern analysis of a few precipitates that were identified by TKD on same sample. TKD study was combined with state-of-art analytical scanning transmission electron microscopy (STEM)-energy dispersive X-ray (EDX) spectroscopy and multivariate statistical analysis (MVSA) which provided the complete crystal structure and distinct chemistries of the precipitates in the steel in a high throughput automated way. This technique should be applicable to characterizing any multiphase crystalline nanoparticles or nanomaterials. Furthermore the results highlight that combining phase identification by TKD with analytical STEM and modern data analytics may open new pathways in big data material characterization at nanoscale that may be highly beneficial for characterizing existing materials and in designing new materials.

36 MATERIALS SCIENCE↗

Vegetation monitoring and classification using NOAA/AVHRR satellite data

A vegetation gradient model, based on a new surface hydrologic index and NOAA/AVHRR meteorological satellite data, has been analyzed along a 1300 km east-west transect across the state of Texas. The model was developed to test the potential usefulness of such low-resolution data for vegetation stratification and monitoring. Normalized Difference values (ratio of AVHRR bands 1 and 2, considered to be an index of greenness) were determined and evaluated against climatological and vegetation characteristics at 50 sample locations (regular intervals of 0.25 deg longitude) along the transect on five days in 1980. Statistical treatment of the data indicate that a multivariate model incorporating satellite-measured spectral greenness values and a surface hydrologic factor offer promise as a new technique for regional-scale vegetation stratification and monitoring.

Greegor, D. H., Jr.↗

Learning Planar Ising Models Software

Learning Planar Ising Models is a software package written in Matlab for learning relationships among variable in a dataset using graphical models. The software package implements a generally-applicable algorithm for learning planar Ising models from any multivariate dataset. The code provides an algorithm for learning the best planar Ising model to approximate an arbitrary collection of binary random variables (possibly from sample data). Given the set of all pairwise correlations among variables, we select a planar graph and optimal planar Ising model defined on this graph to best approximate that set of correlations. The software includes demonstrations of the algorithm in simulations and for applications on publicly available datasets. Details of the algorithm, demonstration simulations, and applications are given in Johnson, et al; 2016. Reference: Johnson, J. K., Oyen, D., Chertkov, M., and Netrapalli, P. (2016). Learning planar Ising models. Journal of Machine Learning Research.

Oyen, Diane↗

Cholesky-based experimental design for Gaussian process and kernel-based emulation and calibration.

Gaussian processes and other kernel-based methods are used extensively to construct approximations of multivariate data sets. The accuracy of these approximations is dependent on the data used. This paper presents a computationally efficient algorithm to greedily select training samples that minimize the weighted L p error of kernel-based approximations for a given number of data. The method successively generates nested samples, with the goal of minimizing the error in high probability regions of densities specified by users. The algorithm presented is extremely simple and can be implemented using existing pivoted Cholesky factorization methods. Training samples are generated in batches which allows training data to be evaluated (labeled) in parallel. For smooth kernels, the algorithm performs comparably with the greedy integrated variance design but has significantly lower complexity. Numerical experiments demonstrate the efficacy of the approach for bounded, unbounded, multi-modal and non-tensor product densities. We also show how to use the proposed algorithm to efficiently generate surrogates for inferring unknown model parameters from data using Bayesian inference.

97 MATHEMATICS AND COMPUTING↗

Estimation of proportions of objects and determination of training sample-size in a remote sensing application

A multichannel scanning device may fail to observe objects because of obstructions blocking the view, or different categories of objects may make up a resolution element giving rise to a single observation. Ground truth will be required on any such categories of objects in order to estimate their expected proportions associated with various classes represented in the remote sensing data. Considering the classes to be distributed as multivariate normal with different mean vectors and common covariance, maximum likelihood estimates are given for the expected proportions of objects associated with different classes, using the Bayes procedure for classification of individuals obtained from these classes. An approximate solution for simultaneous confidence intervals on these proportions is given, and thereby a sample-size needed to achieve a desired amount of accuracy for the estimates is determined.

Chhikara, R. S.↗

Emergency department overcrowding and its associated factors at HARME medical emergency center in Eastern Ethiopia

Introduction: Emergency department (ED) overcrowding has become a significant concern as it can lead to compromised patient care in emergency settings. Various tools have been used to evaluate overcrowding in ED. However, there is a lack of data regarding this issue in resource-limited countries, including Ethiopia. This study aimed to validate NEDOCS, assess level of ED overcrowding and identify associated factors at HARME Medical Emergency Center, located in Hiwot Fana Comprehensive Specialized Hospital, Harar, Ethiopia. Methods: A cross-sectional study was conducted at the HARME Medical Emergency Center, Hiwot Fana Comprehensive Specialized Hospital, involving a total of 899 patients during 120 sampling intervals. The area under the receiver operating characteristic curves (AUC) was calculated to evaluate the agreement between objective and subjective assessments of ED overcrowding. A multivariable logistic regression analysis was employed to identify factors associated with ED overcrowding and statistically significant association was declared using 95% confidence level and a p-value < 0.05. Results: The interrater agreement showed a strong correlation with a Cohen's kappa (κ) of 0.80. The National Emergency Department Overcrowding Study Score demonstrated a strong association with subjective assessments from residents and case team nurses, with an AUC of 0.81 and 0.79, respectively. According to residents' perceptions, ED were considered overcrowded 65.8% of the time. Factors significantly associated with ED overcrowding included waiting time for triage (AOR: 2.24; 95% CI: 1.54–3.27), working time (AOR: 2.23; 95% CI: 1.52–3.26), length of stay (AOR: 2.40; 95% CI: 1.27–4.54), saturation level (AOR: 2.35; 95% CI: 1.31–4.20), chronic illness (AOR: 2.19; 95% CI: 1.37–3.53), and abnormal pulse rate (AOR: 1.52; 95% CI: 1.06–2.16). Conclusion: The study revealed that ED were overcrowded approximately two-thirds of the time.

60 APPLIED LIFE SCIENCES↗

Clinically applicable 53-Gene prognostic assay predicts chemotherapy benefit in gastric cancer: A multicenter study

BACKGROUND:We previously established a 53-gene prognostic signature for overall survival (OS) of gastric cancer patients. This retrospective multi-center study aimed to develop a clinically applicable gene expression detection assay and to investigate the prognostic value of this signature. METHODS:A TCGA gastric adenocarcinoma cohort (TCGA-STAD) was used for comparing 53-gene signature with other gene signatures. A high-throughput mRNA hybridization gene expression assay was developed to quantify the expression of 53-genes in formalin-fixed paraffin-embedded tissues of 540 patients enrolled from three hospitals. 180 patents were randomly selected from two hospitals to build a prognostic prediction model based on the 53-gene signature using leave-p-out (one-third out) cross-validation method together with Cox regression and Kaplan-Meier analysis, and the model was assessed on three validation cohorts. FINDINGS:In the evaluation phase, studies based on TCGA-STAD showed that the 53-gene signature was significantly superior to other three prognostic signatures and was independent of TCGA molecular subtypes and clinical factors. For clinical validation and utility, the prognostic scores were generated using the newly developed assay, which was reliable and sensitive, in 100 sampling training sets and were significantly associated with OS in 100 sampling validation sets. The scores were significantly associated with OS in three independent and combined validation cohorts, and in patients with stages II and III/IV. The multivariate Cox regression demonstrated that the prognostic power of the score was independent of clinical factors, consistent with those findings in the TCGA dataset. Finally, patients with good prognostic scores exhibited significantly a better 5-year OS rate from adjuvant FOLFOX chemotherapy after surgery than from other chemotherapies. INTERPRETATION:The 53-gene prognostic score system is clinically applicable for predicting the OS of patients independent of clinical factors in gastric cancers, which could also be a promising predictive biomarker for FOLFOX regimen. FUNDING:Chinese National Science and Technology, National Natural Science Foundation and Natural Science Foundation of Jiangsu Province.

60 APPLIED LIFE SCIENCES↗

Kullback-Leibler information function and the sequential selection of experiments to discriminate among several linear models

The error variance of the process prior multivariate normal distributions of the parameters of the models are assumed to be specified, prior probabilities of the models being correct. A rule for termination of sampling is proposed. Upon termination, the model with the largest posterior probability is chosen as correct. If sampling is not terminated, posterior probabilities of the models and posterior distributions of the parameters are computed. An experiment was chosen to maximize the expected Kullback-Leibler information function. Monte Carlo simulation experiments were performed to investigate large and small sample behavior of the sequential adaptive procedure.

Sidik, S. M.↗

Elemental Variation and Petrogenesis of Pyroxenes in HED Meteorites by Multivariable Discriminant Analysis Method

HED (Howardite, Eucrite and Diogenite) are meteorites with mafic and ultramafic igneous composition. Previous studies suggested HED came from asteroid (4) Vesta and they were generated by magmatic melting followed by differentiation crystallization, metamorphic, and impact. Uniform oxygen isotopic composition of HED samples favors global magma ocean for (4) Vesta. However, the petrological diversity of HED may indicate more complex magma processes in the meteorites. In general, most of the geochemical studies are using traditional methods (e.g. element to element or ratio to ratio plots) to classify the different rock type and groups. With the traditional methods, only limited elements can be shown in a figure. As such, some meteorites may have been identified as HED by a traditional method but found different either in isotopic composition or other elemental characteristic. These anomalous HED meteorites may or may not come from asteroid (4) Vesta. In fact, magma is a unit system where any elemental change should affect to all other elements as a whole, it would be reasonable to consider all elements together to look for the systematical changes. Using multivariable discriminant analysis (MDA) method is one of such testing for their geochemical variation. The method may be able to help us to better understand the petrologic processes and the relationship among elements. This study is to test the MDA method by focus mainly on pyroxene composition of eucrite and diogenite.

Peng, Z. X.↗

Monitoring task loading with multivariate EEG measures during complex forms of human-computer interaction

Electroencephalographic (EEG) recordings were made while 16 participants performed versions of a personal-computer-based flight simulation task of low, moderate, or high difficulty. As task difficulty increased, frontal midline theta EEG activity increased and alpha band activity decreased. A participant-specific function that combined multiple EEG features to create a single load index was derived from a sample of each participant's data and then applied to new test data from that participant. Index values were computed for every 4 s of task data. Across participants, mean task load index values increased systematically with increasing task difficulty and differed significantly between the different task versions. Actual or potential applications of this research include the use of multivariate EEG-based methods to monitor task loading during naturalistic computer-based work.

NASA Discipline Space Human Factors↗

A Deep Neural Network for Simultaneous Estimation of b Jet Energy and Resolution

We describe a method to obtain point and dispersion estimates for the energies of jets arising from b quarks produced in proton–proton collisions at an energy of $\sqrt{s}=13\,\text {TeV} $ at the CERN LHC. The algorithm is trained on a large sample of simulated b jets and validated on data recorded by the CMS detector in 2017 corresponding to an integrated luminosity of 41 $\,\text {fb}^{-1}$. A multivariate regression algorithm based on a deep feed-forward neural network employs jet composition and shape information, and the properties of reconstructed secondary vertices associated with the jet. The results of the algorithm are used to improve the sensitivity of analyses that make use of b jets in the final state, such as the observation of Higgs boson decay to $\hbox {b}\bar{\hbox {b}}$.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Monitoring the Caustic Dissolution of Aluminum Alloy in a Radiochemical Hot Cell Using Raman Spectroscopy

Chemical processing of highly radioactive materials commonly takes place in heavily shielded hot cells. The remote, real-time monitoring of chemical processing streams via optical spectroscopic techniques in hot cells may be particularly useful. Here in this paper, we describe the implementation of Raman spectroscopy and chemometric analysis to monitor the dissolution of aluminum-clad targets containing irradiated aluminum–neptunium oxide cermet pellets in caustic solutions in a hot cell environment. Partial least squares regression analysis was used to generate calibration models to quantify the concentration of dissolved aluminum, nitrate, and hydroxide in solutions within the radiochemical hot cell. This work explored a systematic approach to optimize a matrix of calibration standards using a D-optimal experimental design. The Design of Experiments-based regression model, in comparison to more traditional analytical approaches, was found to be the more practical method for building calibration models, with fewer samples, to obtain informative analytical data from Raman spectra.

36 MATERIALS SCIENCE↗