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At least 757 records · Page 42

Density-Aware Clustering Based on Aggregated Heat Kernel and Its Transformation

Current spectral clustering algorithms suffer from the sensitivity to existing noise, and parameter scaling, and may not be aware of different density distributions across clusters. If these problems are left untreated, the consequent clustering results cannot accurately represent true data patterns, in particular, for complex real world datasets with heterogeneous densities. This paper aims to solve these problems by proposing a diffusion-based Aggregated Heat Kernel (AHK) to improve the clustering stability, and a Local Density Affinity Transformation (LDAT) to correct the bias originating from different cluster densities. AHK statistically\ models the heat diffusion traces along the entire time scale, so it ensures robustness during clustering process, while LDAT probabilistically reveals local density of each instance and suppresses the local density bias in the affinity matrix. Our proposed framework integrates these two techniques systematically. As a result, not only does it provide an advanced noise-resisting and density-aware spectral mapping to the original dataset, but also demonstrates the stability during the processing of tuning the scaling parameter (which usually controls the range of neighborhood). Furthermore, our framework works well with the majority of similarity kernels, which ensures its applicability to many types of data and problem domains. The systematic experiments on different applications show that our proposed algorithms outperform state-of-the-art clustering algorithms for the data with heterogeneous density distributions, and achieve robust clustering performance with respect to tuning the scaling parameter and handling various levels and types of noise.

97 MATHEMATICS AND COMPUTING↗

Efficient data IO for a Parallel Global Cloud Resolving Model

Execution of a Global Cloud Resolving Model (GCRM) at target resolutions of 2-4 km will generate, at a minimum, 10s of Gigabytes of data per variable per snapshot. Writing this data to disk without creating a serious bottleneck in the execution of the GCRM code while also supporting efficient post-execution data analysis is a significant challenge. This paper discusses an Input/Output (IO) application programmer interface (API) for the GCRM that efficiently moves data from the model to disk while maintaining support for community standard formats, avoiding the creation of very large numbers of files, and supporting efficient analysis. Several aspects of the API will be discussed in detail. First, we discuss the output data layout which linearizes the data in a consistent way that is independent of the number of processors used to run the simulation and provides a convenient format for subsequent analyses of the data. Second, we discuss the flexible API interface that enables modelers to easily add variables to the output stream by specifying where in the GCRM code these variables are located and to flexibly configure the choice of outputs and distribution of data across files. The flexibility of the API is designed to allow model developers to add new data fields to the output as the model develops and new physics is added and also provides a mechanism for allowing users of the GCRM code itself to adjust the output frequency and the number of fields written depending on the needs of individual calculations. Third, we describe the mapping to the NetCDF data model with an emphasis on the grid description. Fourth, we describe our messaging algorithms and IO aggregation strategies that are used to achieve high bandwidth while simultaneously writing concurrently from many processors to shared files. We conclude with initial performance results.

99 GENERAL AND MISCELLANEOUS↗

Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy

Highlights: Black-Right-Pointing-Pointer Bile acid binding proteins from different constructs retain structural integrity. Black-Right-Pointing-Pointer NMR {sup 15}N-T{sub 1} relaxation data of BABPs show differences if LVPR extension is present. Black-Right-Pointing-Pointer Deviations from a {sup 15}N-T{sub 1}/molecular-weight calibration curve indicate aggregation. -- Abstract: The use of a recombinant protein to investigate the function of the native molecule requires that the former be obtained with the same amino acid sequence as the template. However, in many cases few additional residues are artificially introduced for cloning or purification purposes, possibly resulting in altered physico-chemical properties that may escape routine characterization. For example, increased aggregation propensity without visible protein precipitation is hardly detected by most analytical techniques but its investigation may be of great importance for optimizing the yield of recombinant protein production in biotechnological and structural biology applications. In this work we show that bile acid binding proteins incorporating the common C-terminal LeuValProArg extension display different hydrodynamic properties from those of the corresponding molecules without such additional amino acids. The proteins were produced enriched in nitrogen-15 for analysis via heteronuclear NMR spectroscopy. Residue-specific spin relaxation rates were measured and related to rotational tumbling time and molecular size. While the native-like recombinant proteins show spin-relaxation rates in agreement with those expected for monomeric globular proteins of their mass, our data indicate the presence of larger adducts for samples of proteins with very short amino acid extensions. The used approach is proposed as a further screening method for the quality assessment of biotechnological protein products.

60 APPLIED LIFE SCIENCES↗

An Elegant Sufficiency: Load-Aware Differentiated Scheduling of Data Transfers

We investigate the file transfer scheduling problem, where transfers among different endpoints must be scheduled to maximize pertinent metrics. We propose two new algorithms that exploit the fact that the aggregate bandwidth obtained over a network or at a storage system tends to increase with the number of concurrent transfers—but only up to a certain limit. The first algorithm, SEAL, uses runtime information and data-driven models to approximate system load and adapt transfer schedules and concurrency so as to maximize performance while avoiding saturation. We implement this algorithm using GridFTP as the transfer protocol and evaluate it using real transfer logs in a production WAN environment. Results show that SEAL can improve average slowdowns and turnaround times by up to 25% and worst-case slowdown and turnaround times by up to 50%, compared with the best-performing baseline scheme. Our second algorithm, STEAL, further leverages user-supplied categorization of transfers as either “interactive” (requiring immediate processing) or “batch” (less time-critical). Results show that STEAL reduces the average slowdown of interactive transfers by 63% compared to the best-performing baseline and by 21% compared to SEAL. For batch transfers, compared to the best-performing baseline, STEAL improves by 18% the utilization of the bandwidth unused by interactive transfers. By elegantly ensuring a sufficient, but not excessive, allocation of concurrency to the right transfers, we significantly improve overall performance despite constraints.

Kettimuthu, Rajkumar↗

Updated U.S. Low-Temperature Heating and Cooling Demand by County and Sector

This dataset includes U.S. low-temperature heating and cooling demand at the county level in major end-use sectors: residential, commercial, manufacturing, agricultural, and data centers. Census division-level end-use energy consumption, expenditure, and commissioned power database were dis-aggregated to the county level. The county-level database was incorporated with climate zone, numbers of housing units and farms, farm size, and coefficient of performance (COP) for heating and cooling demand analysis. This dataset also includes a paper containing a full explanation of the methodologies used and maps. Residential data were updated from the latest Residential Energy Consumption Survey (RECS) dataset (2015) using 2020 census data. Commercial data were baselined off the latest Commercial Building Energy Consumption Survey (CBECS) dataset (2012). Manufacturing data were baselined off the latest Manufacturing Energy Consumption Survey (MECS) dataset (2021).

15 GEOTHERMAL ENERGY↗

Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel

Abstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classification models that can require substantial ground truth datasets for training. We explore the potential of an unsupervised approach, autoencoders, to extract meaningful traits from plant hyperspectral reflectance data using measurements of the reflectance of 2151 individual wavelengths of light from the leaves of maize ( Zea mays ) plants harvested from 1658 field plots in a replicated field trial. A subset of autoencoder‐derived variables exhibited significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by difference between maize genotypes, while other autoencoder variables appear to capture variation resulting from changes in leaf reflectance between different batches of data collection. Several of the repeatable latent variables were significantly correlated with other traits scored from the same maize field experiment, including one autoencoder‐derived latent variable (LV8) that predicted plant chlorophyll content modestly better than a supervised model trained on the same data. In at least one case, genome‐wide association study hits for variation in autoencoder‐derived variables were proximal to genes with known or plausible links to leaf phenotypes expected to alter hyperspectral reflectance. In aggregate, these results suggest that an unsupervised, autoencoder‐based approach can identify meaningful and genetically controlled variation in high‐dimensional, high‐throughput phenotyping data and link identified variables back to known plant traits of interest.

Tross, Michael C.↗

The Distributed Wind Cost Taxonomy

To date, there has been no standard method or tool to analyze the installed and operational costs for distributed wind turbine systems. This report describes the development of a classification system, or taxonomy, for distributed wind turbine project costs. The taxonomy establishes a framework to help collect, sort, and compare distributed wind cost data that mirrors how the industry categorizes information. The taxonomy organizes costs so they can be aggregated from installers, developers, vendors, and other sources without losing cost details. Developing a peer-reviewed taxonomy is valuable to industry stakeholders because a common understanding the details of distributed wind turbine costs and balance of station costs is a first step to identifying potential high-value cost reduction opportunities. Addressing cost reduction potential can help increase distributed wind's competitiveness and propel the U.S. distributed wind industry forward. The taxonomy can also be used to perform cost comparisons between technologies and track trends for distributed wind industry costs in the future. As an initial application and piloting of the taxonomy, preliminary cost data were collected for projects of different sizes and from different regions across the contiguous United States. Following the methods described in this report, these data are placed into the established cost categories.

17 WIND ENERGY↗

CMPLE: Correlation Modeling to Decode Photosynthesis Using the Minorize–Maximize Algorithm

In plant genomic experiments, correlations among various biological traits (phenotypes) give new insights into how genetic diversity may have tuned biological processes to enhance fitness under diverse conditions. Consequently, knowing how the correlations are affected by genetic (G) and environmental (E) factors helps develop climate-resilient plants. However, the current literature lacks any method for assessing the effect of predictors on pairwise correlations among multiple phenotypes together with easily interpretable model parameters. To address this need, we propose to model pairwise correlations directly in terms of G and E and develop a computationally efficient inference procedure. Two major novelties in our methodology are (1) the use of a composite pairwise likelihood method to avoid the positive definiteness restriction on the correlation matrix and (2) the use of a novel Minorize–Maximize (MM) algorithm for the efficient estimation of a large number of parameters. The proposed method shows excellent numerical performance on synthetic datasets. Here, the analysis of the motivating data on cowpea reveals that the rates of solar energy storage by photosynthesis (the aggregate trait) are differentially affected by different genetic loci through two distinct processes: “photoinhibition” which results from photodamage caused by excess light, and “photoprotection” which protects plants from photodamage but also results in energy loss.

Correlation modeling↗

Combinatorial appraisal of transition states for in situ pair distribution function analysis

In situ total scattering measurements are increasingly utilized to follow atomic and nanoscale structural details of phase transitions and other transient processes in materials. This contribution presents an automated method and associated tool set to analyze series of diffraction and pair distribution function data with a linear combination of end-member states. It is demonstrated that the combinatorial appraisal of transition states (CATS) software tracks phase changes, relative phase fractions and length scales of interest in experimental data series. Here it is further demonstrated, using a series of local structure data simulations, that the misfit of such a model can reveal details of phase aggregation and growth related to the pair distribution function's sensitivity to interphase correlations. CATS may be applied to quantitative evaluation of many transient processes, including amorphous-to-crystalline phase transitions, the evolution of solid-solution behaviors, the precipitation and growth of aggregates, and other atomic to nanoscale details of crystallization and phase transformation phenomena.

36 MATERIALS SCIENCE↗

Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging

Background: Slow-degrading, fossil fuel-derived plastics can have deleterious effects on the environment, especially marine ecosystems. The production of bio-based, biodegradable plastics from or in plants can assist in supplanting those manufactured using fossil fuels. Polyhydroxybutyrate (PHB) is one such biodegradable polyester that has been evaluated as a possible candidate for relinquishing the use of environmentally harmful plastics. Results: PHB, possessing similar properties to polyesters produced from non-renewable sources, has been previously engineered in sugarcane, thereby creating a high-value co-product in addition to the high biomass yield. This manuscript illustrates the coupling of a Fourier-transform infrared microspectrometer, equipped with a focal plane array (FPA) detector, with multivariate imaging to successfully identify and localize PHB aggregates. Principal component analysis imaging facilitated the mining of the abundant quantity of spectral data acquired using the FPA for distinct PHB vibrational modes. PHB was measured in the chloroplasts of mesophyll and bundle sheath cells, acquiescent with previously evaluated plant samples. Conclusion: This study demonstrates the power of IR microspectroscopy to rapidly image plant sections to provide a snapshot of the chemical composition of the cell. While PHB was localized in sugarcane, this method is readily transferable to other value-added co-products in different plants.

36 MATERIALS SCIENCE↗

Status and Trends in the U.S. Voluntary Green Power Market (2013 Data)

Voluntary green power markets are those in which consumers and institutions voluntarily purchase renewable energy to match their electricity needs. This report surveys utilities, competitive suppliers, renewable energy certificate (REC) marketers, and, for the first time, the community choice aggregation market. This report finds that the voluntary market totaled 62 million megawatt-hours in 2013. Approximately 5.4 million customers are purchasing green power. This report presents data and analysis on voluntary market sales and customer participation, products and premiums, green pricing marketing, and administrative expenses. The report also details trends in REC tracking systems, REC pricing in voluntary and compliance markets, community and crowd-funded solar, and interest in renewable energy by the information and communication technologies sector.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A Retrospective Analysis of the Benefits and Impacts of U.S. Renewable Portfolio Standards

This is the second in a series of reports exploring the costs, benefits, and other impacts of state renewable portfolio standards (RPS), both retrospectively and prospectively. This report focuses on the benefits and impacts of all state RPS programs, in aggregate, for the year 2013 (the most-recent year for which the requisite data were available). Relying on a well-vetted set of methods, the study evaluates a number of important benefits and impacts in both physical and monetary terms, where possible, and characterizes key uncertainties. The prior study in this series focused on historical RPS compliance costs, and future work will evaluate costs, benefits, and other impacts of RPS policies prospectively.

54 ENVIRONMENTAL SCIENCES↗

Multi-Angle Snowflake Camera Value-Added Product

The Multi-Angle Snowflake Camera (MASC) addresses a need for high-resolution multi-angle imaging of hydrometeors in freefall with simultaneous measurement of fallspeed. As illustrated in Figure 1, the MASC consists of three cameras, separated by 36°, each pointing at an identical focal point approximately 10 cm away. Located immediately above each camera, a light aims directly at the center of depth of field for its corresponding camera. The focal point at which the cameras are aimed lies within a ring through which hydrometeors fall. The ring houses a system of near-infrared emitter-detector pairs, arranged in two arrays separated vertically by 32 mm. When hydrometeors pass through the lower array, they simultaneously trigger all cameras and lights. Fallspeed is calculated from the time it takes to traverse the distance between the upper and lower triggering arrays. The trigger electronics filter out ambient light fluctuations associated with varying sunlight and shadows. The microprocessor onboard the MASC controls the camera system and communicates with the personal computer (PC). The image data is sent via FireWire 800 line, and fallspeed (and camera control) is sent via a Universal Serial Bus (USB) line that relies on RS232-over-USB serial conversion. See Table 1 for specific details on the MASC located at the Oliktok Point Mobile Facility on the North Slope of Alaska. The value-added product (VAP) detailed in this documentation analyzes the raw data (Section 2.0) using Python: images rely on OpenCV image processing library and derived aggregated statistics rely on some clever averaging. See Sections 4.1 and 4.2 for more details on what variables are computed.

47 OTHER INSTRUMENTATION↗

Organic Speciation and Interactions in ALSEP. One Step Partitioning Process of MinorActinides, Lanthanides, and Fission Products

Research conducted in this project focused on speciation characterization of the ALSEP extraction system (similar to the TALSPEAK-like application) which addresses recovery of minor actinides and lanthanides from PUREX raffinate. The ALSEP (Actinide-Lanthanide Separation) system proposes a trivalent minor actinide/lanthanide group extraction followed by a selective actinide strip to effectively partition minor actinides, lanthanides, and other fission products. The group extraction is achieved by a mixed organic solvent, combining acidic and neutral extracting ligands. The objective of this work is investigation the interactions of the acidic and neutral ligands with each other in the extraction organic solvent and with desired metals. Four combinations of a cation-exchange ligand (either HDEHP or HEH[EHP]) and a neutral solvating ligand (either TODGA or T2EHDGA) in n-dodecane were studied. Interligand dimers in these combinations were investigated with NMR and FTIR, the strongest interaction was observed for HDEHP+TODGA and weakest for T2EHDGA+HEH[EHP]. Complexes of the trivalent Am and lanthanides Nd, Eu, Ho, Pr in these binary ligand mixtures were probed with spectroscopic (UV–vis, time-resolved fluorescence, XAFS and SAXS-spectroscopies) and extraction (Job’s plot, slope analysis) methods; co-extracted water and nitric acid were analyzed by titration methods. Comparison of the collected spectra showed significant shifting for both DGA ligands with HDEHP, while both combinations of HEH[EHP]+DGA displayed much smaller spectral changes. Data were modeled with HypSpec program, and stability constants for extracted complexes were calculated. Aggregation in these systems were studied by SAXS (small-angle X-ray scattering) spectroscopy and interfacial tension, size of aggregates were measured. Two PhD students graduated (2017, 2018) and one student continues her PhD study.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

SoDaH: the SOils DAta Harmonization database, an open-source synthesis of soil data from research networks, version 1.0

Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information available for inquiry. Synthesizing these data is challenging, especially considering the legacy of soil data that have already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last access: 22 December 2020), a flexible database designed to harmonize diverse SOM datasets from multiple research networks. SoDaH is built on several network science efforts in the United States, but the tools built for SoDaH aim to provide an open-access resource to facilitate synthesis of soil carbon data. Moreover, SoDaH allows for individual locations to contribute results from experimental manipulations, repeated measurements from long-term studies, and local- to regional-scale gradients across ecosystems or landscapes. Finally, we also provide data visualization and analysis tools that can be used to query and analyze the aggregated database. The SoDaH v1.0 dataset is archived and available at https://doi.org/10.6073/pasta/9733f6b6d2ffd12bf126dc36a763e0b4 (Wieder et al., 2020).

54 ENVIRONMENTAL SCIENCES↗

Development of a Trip Energy Estimation Model Using Real-World Global Positioning System Driving Data: Preprint

A data-driven technique for estimation of energy requirements for a proposed vehicle trip has been developed. Based on over 700,000 miles of driving data, the technique has been applied to generate a model that estimates trip energy requirements. The model uses a novel binning approach to categorize driving by road type, traffic conditions, and driving profile. The trip-level energy estimations can easily be aggregated to any higher-level transportation system network desired. The model has been tested and validated on the Austin, Texas, data set used to build this model. Ground-truth energy consumption for the data set was obtained from Future Automotive Systems Technology Simulator (FASTSim) vehicle simulation results. The energy estimation model has demonstrated 12.1 percent normalized total absolute error. The energy estimation from the model can be used to inform control strategies in routing tools, such as change in departure time, alternate routing, and alternate destinations, to reduce energy consumption. The model can also be used to determine more accurate energy consumption of regional or national transportation networks if trip origin and destinations are known. Additionally, this method allows the estimation tool to be tuned to a specific driver or vehicle type.

33 ADVANCED PROPULSION SYSTEMS↗

How Driving Volatility in Time to Collision Relates to Crash Severity in a Naturalistic Driving Environment

The sequence of instantaneous driving decisions and its variations, known as driving volatility, can be a leading indicator of unsafe driving practices. The research issue is to characterize volatility in instantaneous driving decisions in longitudinal and lateral direction and to seek an understanding of how driving volatility relates to crash severity. By using a unique real-world naturalistic driving database from the SHRP 2, a test set of 671 crash events featuring around 0.2 million temporal samples of real-world driving are analyzed. Based on different driving performance measures, 16 different volatility indices are created. The volatility indices are then linked with individual crash events including information on crash severity, drivers’ pre-crash maneuvers and behaviors, secondary tasks and durations, and other factors. As driving volatility prior to crash involvement can have different components, an in-depth analysis is conducted using the aggregate as well as segmented (based on time to collision) real-world driving data. To account for the issues of observed and unobserved heterogeneity, fixed and random parameter ordered models with heterogeneity in parameter means are estimated. The findings suggest that greater driving volatility (both in longitudinal and lateral direction) prior to crash occurrence increases the likelihood of police reportable or severe crash events. Importantly, compared to the effect of volatility in longitudinal acceleration on crash outcomes, the effect of volatility in longitudinal deceleration is significantly greater in magnitude. Methodologically, the random parameter models with heterogeneity-in-means significantly outperformed both the fixed parameter and random parameter counterparts. The relevance of the findings to the development of proactive behavioral countermeasures for drivers is discussed.

Wali, Behram↗