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At least 271 records · Page 15

Analysis of Electric Vehicle Charging Behavior Patterns with Function Principal Component Analysis Approach

This manuscript focused on analyzing electric vehicles’ (EV) charging behavior patterns with a functional data analysis (FDA) approach, with the goal of providing theoretical support to the EV infrastructure planning and regulation, as well as the power grid load management. 5-year real-world charging log data from a total of 455 charging stations in Kansas City, Missouri, was used. The focuses were placed on analyzing the daily usage occupancy variability, daily energy consumption variability, and station-level usage variability. Compared with the traditional discrete-based analysis models, the proposed FDA modeling approach had unique advantages in preserving the smooth function behavior of the data, bringing more flexibility in the modeling process with little required assumptions or background knowledge on independent variables, as well as the capability of handling time series data with different lengths or sizes. In addition to the patterns revealed in the EV charging station’s occupancy and energy consumption, the differences between EV driver’s charging time and parking time were analyzed and called for the needs for parking regulation and enforcement. The different usage patterns observed at charging stations located on different land-use types were also analyzed.

Engineering↗

Functional Data Analysis in NTCP Modeling: A New Method to Explore the Radiation Dose-Volume Effects

Purpose/Objective(s): To describe a novel method to explore radiation dose-volume effects. Functional data analysis is used to investigate the information contained in differential dose-volume histograms. The method is applied to the normal tissue complication probability modeling of rectal bleeding (RB) for patients irradiated in the prostatic bed by 3-dimensional conformal radiation therapy. Methods and Materials: Kernel density estimation was used to estimate the individual probability density functions from each of the 141 rectum differential dose-volume histograms. Functional principal component analysis was performed on the estimated probability density functions to explore the variation modes in the dose distribution. The functional principal components were then tested for association with RB using logistic regression adapted to functional covariates (FLR). For comparison, 3 other normal tissue complication probability models were considered: the Lyman-Kutcher-Burman model, logistic model based on standard dosimetric parameters (LM), and logistic model based on multivariate principal component analysis (PCA). Results: The incidence rate of grade ≥2 RB was 14%. V{sub 65Gy} was the most predictive factor for the LM (P=.058). The best fit for the Lyman-Kutcher-Burman model was obtained with n=0.12, m = 0.17, and TD50 = 72.6 Gy. In PCA and FLR, the components that describe the interdependence between the relative volumes exposed at intermediate and high doses were the most correlated to the complication. The FLR parameter function leads to a better understanding of the volume effect by including the treatment specificity in the delivered mechanistic information. For RB grade ≥2, patients with advanced age are significantly at risk (odds ratio, 1.123; 95% confidence interval, 1.03-1.22), and the fits of the LM, PCA, and functional principal component analysis models are significantly improved by including this clinical factor. Conclusion: Functional data analysis provides an attractive method for flexibly estimating the dose-volume effect for normal tissues in external radiation therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Structural analysis and functional evaluation of the disordered ß–hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis

Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1–110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region’s impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%–97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.

59 BASIC BIOLOGICAL SCIENCES↗

Functional Data Analysis Applied to Modeling of Severe Acute Mucositis and Dysphagia Resulting From Head and Neck Radiation Therapy

Purpose: Current normal tissue complication probability modeling using logistic regression suffers from bias and high uncertainty in the presence of highly correlated radiation therapy (RT) dose data. This hinders robust estimates of dose-response associations and, hence, optimal normal tissue–sparing strategies from being elucidated. Using functional data analysis (FDA) to reduce the dimensionality of the dose data could overcome this limitation. Methods and Materials: FDA was applied to modeling of severe acute mucositis and dysphagia resulting from head and neck RT. Functional partial least squares regression (FPLS) and functional principal component analysis were used for dimensionality reduction of the dose-volume histogram data. The reduced dose data were input into functional logistic regression models (functional partial least squares–logistic regression [FPLS-LR] and functional principal component–logistic regression [FPC-LR]) along with clinical data. This approach was compared with penalized logistic regression (PLR) in terms of predictive performance and the significance of treatment covariate–response associations, assessed using bootstrapping. Results: The area under the receiver operating characteristic curve for the PLR, FPC-LR, and FPLS-LR models was 0.65, 0.69, and 0.67, respectively, for mucositis (internal validation) and 0.81, 0.83, and 0.83, respectively, for dysphagia (external validation). The calibration slopes/intercepts for the PLR, FPC-LR, and FPLS-LR models were 1.6/−0.67, 0.45/0.47, and 0.40/0.49, respectively, for mucositis (internal validation) and 2.5/−0.96, 0.79/−0.04, and 0.79/0.00, respectively, for dysphagia (external validation). The bootstrapped odds ratios indicated significant associations between RT dose and severe toxicity in the mucositis and dysphagia FDA models. Cisplatin was significantly associated with severe dysphagia in the FDA models. None of the covariates was significantly associated with severe toxicity in the PLR models. Dose levels greater than approximately 1.0 Gy/fraction were most strongly associated with severe acute mucositis and dysphagia in the FDA models. Conclusions: FPLS and functional principal component analysis marginally improved predictive performance compared with PLR and provided robust dose-response associations. FDA is recommended for use in normal tissue complication probability modeling.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Application of Gaussian Process Modeling to Analysis of Functional Unreliability

This paper applies Gaussian Process (GP) modeling to analysis of the functional unreliability of a “passive system.” GPs have been used widely in many ways [1]. The present application uses a GP for emulation of a system simulation code. Such an emulator can be applied in several distinct ways, discussed below. All applications illustrated in this paper have precedents in the literature; the present paper is an application of GP technology to a problem that was originally analyzed [2] using neural networks (NN), and later [3, 4] by a method called “Alternating Conditional Expectations” (ACE). This exercise enables a multifaceted comparison of both the processes and the results. Given knowledge of the range of possible values of key system variables, one could, in principle, quantify functional unreliability by sampling from their joint probability distribution, and performing a system simulation for each sample to determine whether the function succeeded for that particular setting of the variables. Using previously available system simulation codes, such an approach is generally impractical for a plant-scale problem. It has long been recognized, however, that a well-trained code emulator or surrogate could be used in a sampling process to quantify certain performance metrics, even for plant-scale problems. “Response surfaces” were used for this many years ago. But response surfaces are at their best for smoothly varying functions; in regions of parameter space where key system performance metrics may behave in complex ways, or even exhibit discontinuities, response surfaces are not the best available tool. This consideration was one of several that drove the work in [2]. In the present paper, (1) the original quantification of functional unreliability using NN [2], and later ACE [3], is reprised using GP; (2) additional information provided by the GP about uncertainty in the limit surface, generally unavailable in other representations, is discussed; (3) a simple forensic exercise is performed, analogous to the inverse problem of code calibration, but with an accident management spin: given an observation about containment pressure, what can we say about the system variables? References 1. For an introduction to GPs, see (for example) Gaussian Processes for Machine Learning, C. E. Rasmussen and C. K. I. Williams (MIT, 2006). 2. Reliability Quantification of Advanced Reactor Passive Safety Systems, J. J. Vandenkieboom, PhD Thesis (University of Michigan, 1996). 3. Z. Cui, J. C. Lee, J. J. Vandenkieboom, and R. W. Youngblood, “Unreliability Quantification of a Containment Cooling System through ACE and ANN Algorithms,” Trans. Am. Nucl. Soc. 85, 178 (2001). 4. Risk and Safety Analysis of Nuclear Systems, J. C. Lee and N. J. McCormick (Wiley, 2011). See especially §11.2.4.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.

59 BASIC BIOLOGICAL SCIENCES↗

Functional Group Analysis for Diesel-like Mixing-Controlled Compression Ignition Combustion Blendstocks

This report addresses the suitability of hydrocarbon and oxygenate functional groups for use as a diesel-like fuel blending component in an advanced, mixing-controlled, compression ignition combustion engine. The functional groups are chosen from those that could be derived from a biomass feedstock, and represent a full range of chemistries. This first systematic analysis of functional groups will be of value to all who are pursuing new bio-blendstocks for diesel-like fuels.

09 BIOMASS FUELS↗

Microstructure of multistage annealed nanocrystalline SmCo 2 Fe 2 B alloy with enhanced magnetic properties

The microstructure and chemistry of SmCo 2 Fe 2 B melt-spun alloy after multistage annealing was investigated using high resolution transmission electron microscopy (HRTEM) and 3D atom probe tomography. The multistage annealing resulted in an increase in both the coercivity and magnetization. The presence of Sm(Co,Fe) 4 B (1:4:1) and Sm 2 (Co,Fe) 17 B x (2:17:x) magnetic phases were confirmed using both techniques. Fe 2 B at a scale of -5 nm was found by HRTEM precipitating within the 1:4:1 phase after the second-stage annealing. Ordering within the 2:17:x phase was directly identified both by the presence of antiphase boundaries observed by TEM and the interconnected isocomposition surface network found in 3D atom probe results in addition to radial distribution function analysis. The variations in the local chemistry after the secondary annealing were considered pivotal in improving the magnetic properties.

Environmental Molecular Sciences Laboratory↗

X-ray nano-imaging of defects in thin film catalysts via cluster analysis

Functional properties of transition-metal oxides strongly depend on crystallographic defects; crystallographic lattice deviations can affect ionic diffusion and adsorbate binding energies. Scanning x-ray nanodiffraction enables imaging of local structural distortions across an extended spatial region of thin samples. Yet, localized lattice distortions remain challenging to detect and localize using nanodiffraction, due to their weak diffuse scattering. Here, in this study, we apply an unsupervised machine learning clustering algorithm to isolate the low-intensity diffuse scattering in as-grown and alkaline-treated thin epitaxially strained SrIrO 3 films. We pinpoint the defect locations, find additional strain variation in the morphology of electrochemically cycled SrIrO 3 , and interpret the defect type by analyzing the diffraction profile through clustering. Our findings demonstrate the use of a machine learning clustering algorithm for identifying and characterizing hard-to-find crystallographic defects in thin films of electrocatalysts and highlight the potential to study electrochemical reactions at defect sites in operando experiments.

42 ENGINEERING↗

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, F. graminearum, F. oxysporum and Nectria haematococca (anamorph F. solani) identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted a phylogenomic and functional domain analysis. The resulting genealogy suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-of-function due to nucleotide mutations. Transcriptional analysis indicate that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and Functional Proteomic Analysis of a Developing Energy Transducing Membrane

While much is known about the light reactions of photosynthesis in purple bacteria, comparatively little information is available on how the requisite integral membrane proteins are assembled, their patterns of cellular localization are established or their apoproteins cooperate with numerous assembly factors in their insertion into the growing intracytoplasmic membrane (ICM). This problem was approached through a detailed structural and functional proteomic analysis of ICM assembly process in the well-characterized purple bacterium Rhodobacter sphaeroides. Proteomic approaches have focused upon identification of membrane proteins temporally expressed during ICM development and spatially localized in both membrane growth initiation sites and in mature ICM vesicles. Protocols were established for ICM induction under reduced aeration and ICM remodeling in cells adapting to low intensity illumination, which permitted isolation, in sucrose density gradients, of ICM growth initiation sites as an upper pigmented band (UPB) and mature ICM vesicles as the main (chromatophore) band. Non-denaturing clear native gel electrophoresis (CNE) of these isolated membrane fractions gave rise to pigmented bands containing the peripheral light-harvesting 2 (LH2) antenna and the reaction center-light-harvesting 1 (RC-LH1) core complex, together with a full array of other ICM proteins, which were subjected to proteomic analysis.

14 SOLAR ENERGY↗

Harnessing Uncertainty through Functional Data Analysis in Gas Breakthrough Data

Detecting subsurface explosions from radionuclide gas migration through rock fractures is an effective way to identify nuclear activity. Los Alamos National Laboratory (LANL) has developed simulation methods, based on data from the 1962 Hardhat underground nuclear test, to predict gas breakthrough times at the surface. However, these methods rely on an imperfect understanding of the relationship between rock damage and fracture permeability. Our clinic project studies methods for predicting breakthrough curves that characterize total mass produced as a function of time, as well as quantifying the uncertainty associated with these predictions. The model that is currently employed to relate damage to permeability uses an empirically motivated power-law expression, with a range of parameter values that are compatible with the experimental Hardhat data. We develop emulators, built from functional data analysis techniques and trained on simulation data, that rapidly predict the gas breakthrough curve given a damage field and given the parameter values of the power-law equation. Using Bayesian regression, we address the problem of uncertainty quantification in our emulators. Finally, in order to test the robustness of the model, we further validate it on a damage field representing different physical conditions.

58 GEOSCIENCES↗

Isolation and characterization of ventricular-like cells derived from NKX2-5 eGFP/w and MLC2v mCherry/w double knock-in human pluripotent stem cells

Highlights: • NKX2-5{sup eGFP/w} and MLC2v{sup mCherry/w} hPSC double knock-ins were established. • Culture conditions mimic in vivo cardiac developmental process. • Subtype-specific cardiac development and functional analysis were possible. Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) are a promising source for cell transplantation into the damaged heart, which has limited regenerative ability. Many methods have been developed to obtain large amounts of functional CMs from hPSCs for therapeutic applications. However, during the differentiation process, a mixed population of various cardiac cells, including ventricular, atrial, and pacemaker cells, is generated, which hampers the proper functional analysis and evaluation of cell properties. Here, we established NKX2-5{sup eGFP/w} and MLC2v{sup mCherry/w} hPSC double knock-ins that allow for labeling, tracing, purification, and analysis of the development of ventricular cells from early to late stages. As with the endogenous transcriptional activities of these genes, MLC2v-mCherry expression following NKX2-5-eGFP expression was observed under previously established culture conditions, which mimic the in vivo cardiac developmental process. Patch-clamp and microelectrode array electrophysiological analyses showed that the NKX2-5 and MLC2v double-positive cells possess ventricular-like properties. The results demonstrate that the NKX2-5{sup eGFP/w} and MLC2v{sup mCherry/w} hPSCs provide a powerful model system to capture region-specific cardiac differentiation from early to late stages. Our study would facilitate subtype-specific cardiac development and functional analysis using the hPSC-derived sources.

60 APPLIED LIFE SCIENCES↗

The Functional Resonance Analysis Method for a systemic risk based environmental auditing in a sinter plant: A semi-quantitative approach

Environmental auditing is a main issue for any production plant and assessing environmental performance is crucial to identify risks factors. The complexity of current plants arises from interactions among technological, human and organizational system components, which are often transient and not easily detectable. The auditing thus requires a systemic perspective, rather than focusing on individual behaviors, as emerged in recent research in the safety domain for socio-technical systems. We explore the significance of modeling the interactions of system components in everyday work, by the application of a recent systemic method, i.e. the Functional Resonance Analysis Method (FRAM), in order to define dynamically the system structure. We present also an innovative evolution of traditional FRAM following a semi-quantitative approach based on Monte Carlo simulation. This paper represents the first contribution related to the application of FRAM in the environmental context, moreover considering a consistent evolution based on Monte Carlo simulation. The case study of an environmental risk auditing in a sinter plant validates the research, showing the benefits in terms of identifying potential critical activities, related mitigating actions and comprehensive environmental monitoring indicators. - Highlights: • We discuss the relevance of a systemic risk based environmental audit. • We present FRAM to represent functional interactions of the system. • We develop a semi-quantitative FRAM framework to assess environmental risks. • We apply the semi-quantitative FRAM framework to build a model for a sinter plant.

54 ENVIRONMENTAL SCIENCES↗

Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity

Here, we present Brain Modulyzer, an interactive visual exploration tool for functional magnetic resonance imaging (fMRI) brain scans, aimed at analyzing the correlation between different brain regions when resting or when performing mental tasks. Brain Modulyzer combines multiple coordinated views—such as heat maps, node link diagrams, and anatomical views—using brushing and linking to provide an anatomical context for brain connectivity data. Integrating methods from graph theory and analysis, e.g., community detection and derived graph measures, makes it possible to explore the modular and hierarchical organization of functional brain networks. Providing immediate feedback by displaying analysis results instantaneously while changing parameters gives neuroscientists a powerful means to comprehend complex brain structure more effectively and efficiently and supports forming hypotheses that can then be validated via statistical analysis. In order to demonstrate the utility of our tool, we also present two case studies—exploring progressive supranuclear palsy, as well as memory encoding and retrieval

59 BASIC BIOLOGICAL SCIENCES↗

Unraveling the convoluted and dynamic interphasial mechanisms on Li metal anode

Accurate understanding of the chemistry of solid-electrolyte interphase (SEI) is key to developing new electrolytes for high-energy batteries using lithium metal (Li-0) anodes(1). SEI is generally believed to be formed by the reactions between Li-0 and electrolyte(2,3). However, our new study shows this is not the whole story. Through synchrotron-based X-ray diffraction and pair distribution function analysis, we reveal a much more convoluted formation mechanism of SEI, which receives considerable contributions from electrolyte, cathode, moisture and native surface species on Li-0, with highly dynamic nature during cycling. Using isotope labelling, we traced the origin of LiH to electrolyte solvent, moisture and a new source: the native surface species (LiOH) on pristine Li-0. When lithium accessibility is very limited as in the case of anode-free cells, LiOH develops into plate-shaped large crystals during cycling. Alternatively, when the lithium source is abundant, as in the case of Li||NMC811 cells, LiOH reacts with Li-0 to form LiH and Li2O. While the desired anion-derived LiF-rich SEI is typically found in the concentrated electrolytes or their derivatives, we found it can also be formed in low-concentration electrolyte via the crosstalk effect, emphasizing the importance of formation cycle protocol and opening up opportunities for low-cost electrolyte development.

Polzin, Bryant J.↗

Functional Data Analysis for Extracting the Intrinsic Dimensionality of Spectra: Application to Chemical Homogeneity in the Open Cluster M67

High-resolution spectroscopic surveys of the Milky Way have entered the Big Data regime and have opened avenues for solving outstanding questions in Galactic archeology. However, exploiting their full potential is limited by complex systematics, whose characterization has not received much attention in modern spectroscopic analyses. In this work, we present a novel method to disentangle the component of spectral data space intrinsic to the stars from that due to systematics. Using functional principal component analysis on a sample of 18,933 giant spectra from APOGEE, we find that the intrinsic structure above the level of observational uncertainties requires ≈10 functional principal components (FPCs). Our FPCs can reduce the dimensionality of spectra, remove systematics, and impute masked wavelengths, thereby enabling accurate studies of stellar populations. To demonstrate the applicability of our FPCs, we use them to infer stellar parameters and abundances of 28 giants in the open cluster M67. We employ Sequential Neural Likelihood, a simulation-based Bayesian inference method that learns likelihood functions using neural density estimators, to incorporate non-Gaussian effects in spectral likelihoods. By hierarchically combining the inferred abundances, we limit the spread of the following elements in M67: Fe ≲ 0.02 dex; C ≲ 0.03 dex; O, Mg, Si, Ni ≲ 0.04 dex; Ca ≲ 0.05 dex; N, Al ≲ 0.07 dex (at 68% confidence). Our constraints suggest a lack of self-pollution by core-collapse supernovae in M67, which has promising implications for the future of chemical tagging to understand the star formation history and dynamical evolution of the Milky Way.

79 ASTRONOMY AND ASTROPHYSICS↗