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At least 433 records · Page 24

A Load Switching Group based Feeder-level Microgrid Energy Management Algorithm for Service Restoration in Power Distribution System

This paper presents a load switching group based energy management system (LSG-EMS) for operating microgrids on a distribution feeder powered by one or multiple grid-forming distributed energy resources. Loads on a distribution feeder are divided into load switching groups that can be remotely switched on and off. The LSG-EMS algorithm, formulated as a mixed-integer linear programming (MILP) problem, has an objective function of maximizing the served loads while minimizing the total number of switching actions. A new set of topology constraints are developed for allowing multiple microgrids to be formed on the feeder and selecting the optimal supply path. Customer comfort is accounted for by maximizing the supply duration in the customer preferred service period and enforcing a minimum service duration. The proposed method is demonstrated on a modified IEEE 33-bus system using actual customer data. Simulation results show that the LSG-EMS successfully coordinates multiple grid-forming sources by selecting an optimal supply topology that maximizes the supply period of both the critical and noncritical loads while minimizing customer service interruptions in the service restoration process.

Hu, Rongxing↗

Probing Quantum Telecloning on Superconducting Quantum Processors

Quantum information cannot be perfectly cloned, but approximate copies of quantum information can be generated. Quantum telecloning combines approximate quantum cloning, more typically referred to as quantum cloning, and quantum teleportation. Quantum telecloning allows approximate copies of quantum information to be constructed by separate parties, using the classical results of a Bell measurement made on a prepared quantum telecloning state. Quantum telecloning can be implemented as a circuit on quantum computers using a classical coprocessor to compute classical feedforward instructions using if statements based on the results of a midcircuit Bell measurement in real time. We present universal symmetric optimal 1 → M telecloning circuits and experimentally demonstrate these quantum telecloning circuits for M = 2 up to M = 10, natively executed with real-time classical control systems on IBM Quantum superconducting processors, known as dynamic circuits. We perform the cloning procedure on many different message states across the Bloch sphere, on seven IBM Quantum processors, optionally using the error suppression technique X–X sequence digital dynamical decoupling. Two circuit optimizations are utilized: one that removes ancilla qubits for M = 2,3 , and one that reduces the total number of gates in the circuit but still uses ancilla qubits. Parallel single-qubit tomography with maximum likelihood estimation density matrix reconstruction is used in order to compute the mixed-state density matrices of the clone qubits, and clone quality is measured using quantum fidelity. These results present one of the largest and most comprehensive noisy intermediate-scale quantum computer experimental analyses on (single qubit) quantum telecloning to date. The clone fidelity sharply decreases to 0.5 for M > 5 , but for M = 2 , we are able to achieve a mean clone fidelity of up to 0.79 using dynamical decoupling.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Surrogate Modeling for Capacity Planning of Charging Station Equipped with PV and Hydropneumatic Energy Storage

Due to the promising potential for environmental sustainability, there has been a significant increase of electric vehicles (EVs) and plug-in hybrid electric vehicles (PHEV) in the market. To support this increasing demand for EVs and PHEVs, challenges related to capacity planning and investment costs of public charging infrastructure must be addressed. Hence, in this paper, a capacity planning problem for EV charging stations is developed and aims to balance current capital investment costs and future operational revenue. The charging station considered in this work is assumed to be equipped with solar photovoltaic panel (PV) and an energy storage system which could be electric battery or the recently invented hydro-pneumatic energy storage (GLIDES, Ground-Level Integrated Diverse Energy Storage) system. A co-optimization model that minimizes investment and operation cost is established to determine the global optimal solution while combining the capacity and operational decision making. The operational decision making considers EV mobility which is modeled as an Erlang-loss system. Meanwhile, stochastic programming is adopted to capture uncertainties from solar radiation and charging demand of the EV fleet. To provide a more general and computationally efficient model, main configuration parameters are sampled in the design space and then fixed in solving the co-optimization model. The model can be used to provide insights for charging station placement in different practical situations. The sampled parameters include: the total number of EV charging slots, the PV area, the maximum capacity of the energy storage system, and daily mean EV arrival number in the Erlang-loss system. Based on the sampled parameter combinations and its responses, black-box mappings are then constructed using surrogate models (RBF, Kriging etc). The effectiveness of proposed surrogate modeling approach is demonstrated in the numerical experiments.

Chen, Yang↗

Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions

ABSTRACT Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context—propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)—is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering. IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

59 BASIC BIOLOGICAL SCIENCES↗

Atomistic Simulation of the Fission-Fragment-Induced Formation of Defects in a Uranium–Molybdenum Alloy

The formation of defects in a uranium–molybdenum alloy induced by xenon and zirconium ion irradiation with energies typical of fission fragments has been simulated within the two-temperature atomistic model and Monte Carlo method. This has allowed estimating the total number of primary radiation defects formed at the “thermal spike” stage and in collision cascades for different temperatures. The calculated threshold stopping powers of ions responsible for the formation of defects at the thermal spike stage are in good agreement with the available theoretical and experimental data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Measurement of $W^\pm$ boson production in Pb+Pb collisions at $\sqrt{s_{\mathrm{NN}}} = 5.02~\text {Te}\text {V}$ with the ATLAS detector

A measurement of W ± boson production in Pb+Pb collisions at √s NN =5.02 TeV is reported using data recorded by the ATLAS experiment at the LHC in 2015, corresponding to a total integrated luminosity of 0.49nb -1 . The W ± bosons are reconstructed in the electron or muon leptonic decay channels. Production yields of leptonically decaying W ± bosons, normalised by the total number of minimum-bias events and the nuclear thickness function, are measured within a fiducial region defined by the detector acceptance and the main kinematic requirements. These normalised yields are measured separately for W + and W - bosons, and are presented as a function of the absolute value of pseudorapidity of the charged lepton and of the collision centrality. The lepton charge asymmetry is also measured as a function of the absolute value of lepton pseudorapidity. In addition, nuclear modification factors are calculated using the W ± boson production cross-sections measured in pp collisions. The results are compared with predictions based on next-to-leading-order calculations with CT14 parton distribution functions as well as with predictions obtained with the EPPS16 and nCTEQ15 nuclear parton distribution functions. No dependence of normalised production yields on centrality and a good agreement with predictions are observed for mid-central and central collisions. For peripheral collisions, the data agree with predictions within 1.7 (0.9) standard deviations for W - (W + ) bosons.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Luminosity determination using Z boson production at the CMS experiment

The measurement of Z boson production is presented as a method to determine the integrated luminosity of CMS data sets. The analysis uses proton–proton collision data, recorded by the CMS experiment at the CERN LHC in 2017 at a center-of-mass energy of 13 TeV. Events with Z bosons decaying into a pair of muons are selected. The total number of Z bosons produced in a fiducial volume is determined, together with the identification efficiencies and correlations from the same data set, in small intervals of 20 pb –1 of integrated luminosity, thus facilitating the efficiency and rate measurement as a function of time and instantaneous luminosity. Using the ratio of the efficiency-corrected numbers of Z bosons, the precisely measured integrated luminosity of one data set is used to determine the luminosity of another. For the first time, a full quantitative uncertainty analysis of the use of Z bosons for the integrated luminosity measurement is performed. The uncertainty in the extrapolation between two data sets, recorded in 2017 at low and high instantaneous luminosity, is less than 0.5%. We show that the Z boson rate measurement constitutes a precise method, complementary to traditional methods, with the potential to improve the measurement of the integrated luminosity.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

ArborX: A Performance Portable Geometric Search Library

Searching for geometric objects that are close in space is a fundamental component of many applications. The performance of search algorithms comes to the forefront as the size of a problem increases both in terms of total object count as well as in the total number of search queries performed. Scientific applications requiring modern leadership-class supercomputers also pose an additional requirement of performance portability, i.e., being able to efficiently utilize a variety of hardware architectures. In this article, we introduce a new open-source C++ search library, ArborX, which we have designed for modern supercomputing architectures. Herein, we examine scalable search algorithms with a focus on performance, including a highly efficient parallel bounding volume hierarchy implementation, and propose a flexible interface making it easy to integrate with existing applications. We demonstrate the performance portability of ArborX on multi-core CPUs and GPUs and compare it to the state-of-the-art libraries such as Boost.Geometry.Index and nanoflann.

97 MATHEMATICS AND COMPUTING↗

PV Generation and Load Forecasting for Adjuntas PR Community Microgrids

Existing frameworks to forecast time-series photovoltaic (PV) output power and consumer load for microgrid operations and controls assume a near-continuous availability of real-time input features from the field assets such as PV inverters, energy meters, and weather station. These incoming data points are used to periodically retrain models and update forecast snapshots over a moving horizon window, be it one hour-ahead, one-day ahead, or one-week ahead. However, such frameworks are not resilient to disruptions in data availability caused by losses in communications between the field sensors and data loggers. Hence, there is a need for programs that assume no availability of real-time microgrid asset data and still make reliable forecasts that can be used for decision-making. Such programs would be apt to function in extreme weather events such as hurricanes and would use lightweight recursive time-series models to independently forecast solar irradiance and ambient temperature, then compute PV power from those forecasts, as well as independently forecast consumer load. The codebase performs forecasting for the scenario of when the microgrid does not have a reliable access to forecasts or real-time observations of solar irradiance (I) and ambient temperature (AT) and load (Load) to be able to adequately forecast, in real-time, the PV power production or a business' load. In this case, using historical values of PV power and load, a univariate forecasting of generation and consumption are respectively made. The use-case in particular has two sub-scenarios: one, a normal 7-day ahead forecast where the unavailability of real-time data is assumed due to infrastructure issues such as loss of communication or sensor maintenance or service downtimes. Whereas a hurricane-caused unavailability of real-time data requires a second model trained specifically on historical hurricane days to be able to capture the extreme day behavior of generation in particular, and load if applicable. A gradient boosted regression tree comprises an ensemble of additive models that map between the input of historical values (be it irradiance, temperature, or load) and their corresponding output forecasts of a given horizon such that the individual learner predictions are summed up over the total number of such learners in the ensemble to produce an aggregate forecast. A weighting mechanism is applied to the training data in each iteration, where actual and forecast values are compared to penalize incorrect forecasts by increasing the weight and reducing it to reward correct forecasts. The code's benefits are that it: (a) accounts for a contingency where communication loss renders newly measured real-time data unavailable for model tuning and snapshot updates; (b) presents blind forecasting that recursively determines the next time-step value in a horizon using the forecast of the same attribute from a prior step; and (c) employs lightweight models that, once trained, can reliably generalize for different horizons, which make them suitable for enhancing the resilience of field microgrids prone to extreme events that encounter disruptions to data availability.

Sundararajan, Aditya [Oak Ridge National Laborator↗

Estimating Ice Water Content for Winter Storms from Millimeter-Wavelength Radar Measurements Using a Synthesis of Polarimetric and Dual-Frequency Radar Observations

The potential of millimeter-wavelength radar-based ice water content (IWC) estimation is demonstrated using a Ka-band Scanning Polarimetric Radar (KASPR) for the U.S. northeast coast winter storms. Two IWC relations for Ka-band polarimetric radar measurements are proposed: one that uses a combination of the radar reflectivity Z and the estimated total number concentration of snow particles N t and the other based on the joint use of Z, specific differential phase K DP , and the degree of riming f rim . A key element of the algorithms is to obtain the “Rayleigh-equivalent” value of Z measured at the Ka band, i.e., the corresponding Z at a longer radar wavelength for which Rayleigh scattering takes place. This is achieved via polarimetric retrieval of the mean volume diameter D m and incorporating the relationship between the dual-wavelength ratio DWR S/Ka and D m . Those techniques allow for retrievals from single millimeter-wavelength radar measurements and do not necessarily require the dual-wavelength ratio (DWR) measurements, if the DWR–D m relation and Rayleigh assumption for Ka-band K DP are valid. Comparison between the quasivertical profile product obtained from KASPR and the columnar vertical profile product generated from the nearby WSR-88D S-band radar measurements demonstrates that the DWR S/Ka can be estimated from the two close radars without the need for collocated radar beams and synchronized antenna scanning and can be used for determining the Rayleigh-equivalent value of Z. As a result, the performance of the suggested techniques is evaluated for seven winter storms using surface disdrometer and snow accumulation measurements.

Cloud retrieval↗

Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome

Viruses are an understudied component of plant microbiomes. Identifying viruses that are shared between individual plants, or members of the “core virome”, could reveal stable viral populations with the potential to modulate the composition and function of the microbiome. Here, we examined the virome associated with Sphagnum mosses, a keystone species that has direct influence over the fate of peatland carbon stores. We analyzed bulk metagenomes and metatranscriptomes generated from Sphagnum field samples collected over a ten-month period to identify virus-like sequences shared among plants. Individual Sphagnum samples harbored distinct DNA and RNA viromes where only a small percentage (< 1%) of the total number of identified viral contigs were shared among all samples. Based on taxonomic classification, the shared viral contigs represent bacterial viruses, or phage (Caudoviricetes), as well as viruses of eukaryotes, namely nucleocytoplasmic large DNA viruses (Nucleocytoviricota) and RNA viruses (Riboviria). We linked the shared phage-like contigs to viral regions within sequenced genomes of bacterial taxa that are members of the Sphagnum core microbiome, suggesting that these contigs represent temperate phage or degraded prophage. The putative nucleocytoplasmic large DNA viruses and RNA viruses were phylogenetically diverse and showed sequence similarity to viruses associated with a broad range of hosts and environmental sources. The identification of shared viral contigs suggested that, despite the compositional heterogeneity between samples, Sphagnum mosses may harbor a core virome. Future work validating the presence of the core virome is warranted as it may aid in understanding how persistent viruses impact microbiome ecology and symbiont evolution within this climatically relevant keystone species.

Metagenomics↗

The Attraction Indian Buffet Distribution

We propose the attraction Indian buffet distribution (AIBD), a distribution for binary feature matrices influenced by pairwise similarity information. Binary feature matrices are used in Bayesian models to uncover latent variables (i.e., features) that explain observed data. The Indian buffet process (IBP) is a popular exchangeable prior distribution for latent feature matrices. In the presence of additional information, however, the exchangeability assumption is not reasonable or desirable. The AIBD can incorporate pairwise similarity information, yet it preserves many properties of the IBP, including the distribution of the total number of features. Thus, much of the interpretation and intuition that one has for the IBP directly carries over to the AIBD. A temperature parameter controls the degree to which the similarity information affects feature-sharing between observations. Unlike other nonexchangeable distributions for feature allocations, the probability mass function of the AIBD has a tractable normalizing constant, making posterior inference on hyperparameters straight-forward using standard MCMC methods. A novel posterior sampling algorithm is proposed for the IBP and the AIBD. We demonstrate the feasibility of the AIBD as a prior distribution in feature allocation models and compare the performance of competing methods in simulations and an application.

97 MATHEMATICS AND COMPUTING↗

Data from Managing Flowering Time in Miscanthus and Sugarcane to Facilitate Intra- and Intergeneric Crosses

Miscanthus is a close relative of saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between miscanthus and saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of saccharum and miscanthus genotypes. We found that day length was an important factor influencing when miscanthus and saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 miscanthus genotypes, including 28 M. sinensis , 2 M. floridulus , and 3 M. ×giganteus collected from 20.9° S to 44.9° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M. sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M. sinensis and M. floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M. sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M. sinensis , short days typically hastened floral induction, consistent with the expectations for a facultative short-day plant. However, for high latitude accessions of M. sinensis , days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M. sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas that the latter needs day lengths <12.5 h.

Feedstock Production↗

ORNL_AISD_NiPt_108atoms

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for crystal structures with 108 atoms with 1,900 configurations. The data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system 'MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001' [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in a compressed zipped folders atoms108.zip. The zipped folder contains the data structured in the following way: - Ni_ground_state.cfg --> atomic configuration for the pure nickel - Pt_ground_state.cfg --> atomic configuration for the pure platinum - Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder - Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms108.zip is 66,132. This dataset is an extension to the dataset ORNL_AISD_NiPt [5] that has been previously released with crystal structures of 256 atoms, 864 atoms, and 2,048 atoms, with the same methodology for data collection. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D [5] M. Karabin, M. Lupo Pasini, and M. Eisenbach. ORNL_AISD_NiPt. United States: N. p., 2023. Web. doi:10.13139/OLCF/1958172.

36 MATERIALS SCIENCE↗

EAGLE-I Power Outage Data 2023

The provided EAGLE-I historic dataset includes 1 year of power outage information at the county level for 2023 at 15-minute intervals collected by the EAGLE-I program at ORNL. The data has been collected from utility's public outage maps using an ETL process. The dataset details FIPS code, county name, state name, total number of customers without power, and a date/timestamp. Also included is the EAGLE-I coverage of each state for each year. For detailed metadata, refer to the metadata DOI.

24 POWER TRANSMISSION AND DISTRIBUTION↗

EAGLE-I Power Outage Data 2014 - 2022

The provided EAGLE-I historic dataset includes eight years of power outage information at the county level from 2014 to 2022 at 15-minute intervals collected by the EAGLE-I program at ORNL. The data has been collected from utility's public outage maps using an ETL process. The dataset details FIPS code, county name, state name, total number of customers without power, and a date/timestamp. Also included is the EAGLE-I coverage of each state for each year. For detailed metadata, refer to the metadata DOI.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Subcritical Multiplication with a Fixed Source

In a subcritical, multiplying medium, the system multiplication describes the expected total number of neutrons created by a single source neutron. Subcriticality plays a large role in criticality safety and thus it is vital for the subcritical multiplication factor be accurate, especially as a system approaches criticality. This work examines the accuracy of calculating the system multiplication using the MCNP6.2 ® k-eigenvalue power iteration (KCODE) method when a fixed-point source is present in a multiplying medium, for near critical systems. This work compares the standard approach for calculating system multiplication, using the fixed-source calculational approach, to a new, single k-eigenvalue power iteration approach that incorporates a fixed-source component and a fission-source component into a single calculation. For the remainder of this paper, some theoretical background and numerical results for an approximate k eigenvalue approach, an accurate fixed-source approach and a new and more accurate k-eigenvalue approach to computing system multiplication are provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling

Though chemical exposures are known to potentially have negative impacts on health, including contributing to chronic diseases such as cancer, the quantitative contribution of risk is not fully understood for every chemical. A commonly used approach to quantify levels of risk is to measure the proportion of organisms (such as a total number of zebrafish on a plate or mice in a cage) with abnormal behavioral responses or morphology at increasing concentrations of chemical exposure. A particular challenge with processing the proportional data from these assays is the appropriate estimation of chemical concentration levels that result in malformations or acute toxicity, as these values typically vary between experimental measurements. The recommended approach by the Environmental Protection Agency (EPA) is to fit benchmark dose curves with specific filters and model fitting steps, which are crucial to properly processing the proportional data. Several tools exist for the fitting of benchmark dose response curves, but none are standalone Python libraries built to process both morphological and behavioral data as proportions with all the EPA recommended filters, filter parameters, models, and model parameters. Thus, here we present the benchmark dose response curve (bmdrc) Python library, which was built to closely follow these EPA guidelines with helpful visualizations of filters and fitted model curves, and reports for reproducibility purposes. bmdrc is open-source and has demonstrated utility as a support package to an existing web portal for information on chemicals (https://srp.pnnl.gov). Our package will support any toxicology analysis where the response is a proportional value at increasing levels of a concentration of a chemical or chemical mixture.

Superfund↗