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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Classification of bacterial plasmid and chromosome derived sequences using machine learning

Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer—including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements—were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A portable application framework for energy management and information systems (EMIS) solutions using Brick semantic schema

This paper introduces a portable framework for developing, scaling and maintaining energy management and information systems (EMIS) applications using an ontology-based approach. Key contributions include an interoperable layer based on Brick schema, the formalization of application constraints pertaining metadata and data requirements, and a field demonstration. The framework allows for querying metadata models, fetching data, preprocessing, and analyzing data, thereby offering a modular and flexible workflow for application development. Its effectiveness is demonstrated through a case study involving the development and implementation of a data-driven anomaly detection tool for the photovoltaic systems installed at the Politecnico di Torino, Italy. During eight months of testing, the framework was used to tackle practical challenges including: (i) developing a machine learning-based anomaly detection pipeline, (ii) replacing data-driven models during operation, (iii) optimizing model deployment and retraining, (iv) handling critical changes in variable naming conventions and sensor availability (v) extending the pipeline from one system to additional ones.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Outlook for artificial intelligence and machine learning at the NSLS-II

Abstract We describe the current and future plans for using artificial intelligence and machine learning (AI/ML) methods at the National Synchrotron Light Source II (NSLS-II), a scientific user facility at the Brookhaven National Laboratory. We discuss the opportunity for using the AI/ML tools and techniques developed in the data and computational science areas to greatly improve the scientific output of large scale experimental user facilities. We describe our current and future plans in areas including from detecting and recovering from faults, optimizing the source and instrument configurations, streamlining the pipeline from measurement to insight, through data acquisition, processing, analysis. The overall strategy and direction of the NSLS-II facility in relation to AI/ML is presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Usable Data Abstractions for Next-Generation Scientific Workflows

Data- and computationally-intensive scientific research, such as numerical simulations and inversions or the training of large neural networks in machine learning applications, that are well suited for HPC environments also often require expert insight and evaluation throughout the computation which can be greatly facilitated with the use of interactive computing tools, such as those in the Jupyter ecosystem. HPC workflows and interactive workflows are typically treated as orthogonal, however, the next generation of research will require both. The first challenge we face in this project is thus designing the right level of abstractions to allow interactive capabilities in the JupyterLab environment to allow the working scientist to flexibly explore and query their data at multiple levels, with a minimal amount of customization required of the underlying optimized codes. In addition to these questions regarding the high-level representation of data for interactive use in HPC, we tackled two additional issues that are part of the entire lifecycle of research and that become particularly acute in HPC contexts: how to improve the experience of interfacing with the HPC system's scheduling environment for a scientist focused on exploratory questions, and how can that scientist then best share the results of their work with others in a self-contained, reproducible manner.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Process Anomaly Detection for Sparsely Labeled Events in Nuclear Power Plants

An essential aspect of online monitoring, subtle anomaly detection increases the detection lead time for equipment failure and enables a nuclear power plant (NPP) to mitigate unexpected partial or full outages, resulting in significant cost saving to the plant. Once an anomaly is detected by plant staff, its cause and severity are investigated. Because the vast majority of anomalies require some level of investigation, including some that require time-consuming examination, before they are passed over to the engineering organization for further analysis, plants are often equipped with tools to assist the staff in performing anomaly detection. Those tools operate as a black box and are often based on statistical methods that establish sensor correlations using preconfigured mathematical models and flag correlation deviations as anomalies. Due to the number of anomalies detected at a given NPP on a daily basis, a significant number of flagged anomalies usually await examination for days or weeks. A primary cause of this backlog is that the methods used by the tools generate many false positives. Though this is usually attributed to oversensitive model settings due to very narrow normal operation bands, it can also be associated with the model development being inadequate for the process being monitored, or with missing model inputs that could have explained misclassified positives. The performance of anomaly detection tools impacts their plant acceptance and utilization, especially when the effort to address false positives generated by the tool depletes the value or cost saved by using that tool. Thus, means to advance anomaly detection performance have been investigated by the Department of Energy’s Light Water Reactor Sustainability program. Previous and ongoing efforts have targeted unsupervised machine-learning (ML) methods, which do not require the labeling of any data fed into the ML model. By contrast, in supervised anomaly detection methods, every data point is labeled as either a normal or abnormal process condition, and the model is trained to replicate the classification process. Supervised methods usually outperform unsupervised methods, due to the added value in differentiating normal from anomalous states of the monitored process. An NPP’s corrective action program requires it to track and document, via a dedicated report, the resolution of any issues that occur within the plant. Once created, each report is reviewed by a plant screening committee, and several classifications and decisions are made. Recently, a collaborating NPP developed an artificial intelligence and ML-based classifier to categorize a condition report (CR) into classes that can serve to label the data as normal or anomalous. Applying CRs as labels represents a semi-supervised use case. Semi-supervised ML assumes that labels exist for some data points (i.e., labeled anomalies, in this case) but not for the rest. In this effort, semi-supervised ML methods were used to fuse data from CRs with anomaly detection methods in order to test the hypothesis that partially labeled anomalies would improve the accuracy of the anomaly detection methods. Specifically, two methods were used. The first is the deep Semi-supervised Anomaly Detection (deep SAD) method, which can handle labels ranging from fully unsupervised to fully supervised cases. The second is a newly designed ML method developed specifically for this effort and referred to as the high-order feature (HOF)-based method. To evaluate these two methods in controlled environments, synthetic data generators were developed and used. The first datasets used a spring-mass-damper (SMD) system simulator commonly found in mechanical engineering references. This was used to create two use cases: a one- and a three-mass system. Anomalies were introduced by changing the spring and damper coefficients while the system was actuated by random forces. The second datasets used the commercial Dymola-Modelica software to build a simplified nuclear reactor model. Anomalies were added in the form of corrupted sensor readings and/or control commands. The deep SAD method was tested using the SMD system, while the HOF method was tested using both datasets. Application of the deep SAD semi-supervised ML method demonstrated that labels can generate increased confidence in detecting true anomalies. This helped increase the number of true positives and decrease the number of false negatives—something that would aid in addressing the backlog of possible anomalies. Application of the HOF method demonstrated that labels can aid in down selecting from a candidate set of features to a more optimal subset in order to better differentiate between normal and anomalous conditions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
DOE OSTI2023

Performance Comparison of Object Detection Networks for Shrapnel Identification in Ultrasound Images

Ultrasound imaging is a critical tool for triaging and diagnosing subjects but only if images can be properly interpreted. Unfortunately, in remote or military medicine situations, the expertise to interpret images can be lacking. Machine-learning image interpretation models that are explainable to the end user and deployable in real time with ultrasound equipment have the potential to solve this problem. We have previously shown how a YOLOv3 (You Only Look Once) object detection algorithm can be used for tracking shrapnel, artery, vein, and nerve fiber bundle features in a tissue phantom. However, real-time implementation of an object detection model requires optimizing model inference time. Here, we compare the performance of five different object detection deep-learning models with varying architectures and trainable parameters to determine which model is most suitable for this shrapnel-tracking ultrasound image application. We used a dataset of more than 16,000 ultrasound images from gelatin tissue phantoms containing artery, vein, nerve fiber, and shrapnel features for training and evaluating each model. Every object detection model surpassed 0.85 mean average precision except for the detection transformer model. Overall, the YOLOv7tiny model had the higher mean average precision and quickest inference time, making it the obvious model choice for this ultrasound imaging application. Other object detection models were overfitting the data as was determined by lower testing performance compared with higher training performance. In summary, the YOLOv7tiny object detection model had the best mean average precision and inference time and was selected as optimal for this application. Next steps will implement this object detection algorithm for real-time applications, an important next step in translating AI models for emergency and military medicine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Where’s Swimmy?: Mining unique color features buried in galaxies by deep anomaly detection using Subaru Hyper Suprime-Cam data

Abstract We present the Swimmy (Subaru WIde-field Machine-learning anoMalY) survey program, a deep-learning-based search for unique sources using multicolored (grizy) imaging data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). This program aims to detect unexpected, novel, and rare populations and phenomena, by utilizing the deep imaging data acquired from the wide-field coverage of the HSC-SSP. This article, as the first paper in the Swimmy series, describes an anomaly detection technique to select unique populations as “outliers” from the data-set. The model was tested with known extreme emission-line galaxies (XELGs) and quasars, which consequently confirmed that the proposed method successfully selected $\sim\!\! 60\%$–$70\%$ of the quasars and $60\%$ of the XELGs without labeled training data. In reference to the spectral information of local galaxies at z = 0.05–0.2 obtained from the Sloan Digital Sky Survey, we investigated the physical properties of the selected anomalies and compared them based on the significance of their outlier values. The results revealed that XELGs constitute notable fractions of the most anomalous galaxies, and certain galaxies manifest unique morphological features. In summary, deep anomaly detection is an effective tool that can search rare objects, and, ultimately, unknown unknowns with large data-sets. Further development of the proposed model and selection process can promote the practical applications required to achieve specific scientific goals.

Astronomy & Astrophysics↗
DOE OSTI2022

Tsdat: An Open-Source Data Standardization Framework for Marine Energy and Beyond

Many organizations are tasked with the collection and processing of large quantities of data from various measurement devices. Data reported from these sources are often not interoperable with datasets and software used by analysts and other organizations in the same domain, introducing barriers for collaboration on large-scale projects. This poses a particular problem for cross-device comparisons and machine learning applications, which rely on large quantities of data from multiple sources. To address these challenges, the open-source Time-Series Data Pipelines (Tsdat) Python framework was developed by Pacific Northwest National Laboratory, with strategic guidance and direction provided by the National Renewable Energy Laboratory and Sandia National Laboratories to facilitate collaboration and accelerate advancements in the marine energy domain through the development of an open-source ecosystem of tools. This paper will describe the Tsdat framework and the data standards within which it operates. A beta version of Tsdat has been released and is being used by several projects in marine energy, wind energy, and building energy systems.

big data↗
DOE OSTI2022

Need for advanced research reactors for the next-generation reactor physics, analysis tools, and technology

Full text of publication follows. There is an urgent need for design and deployment of advanced research and test reactors in support of design, licensing and operation of advanced power reactors and education of next generation nuclear workforce. Existing research reactors mostly were designed and constructed decades ago with the main objectives of training operators, performing reactor physics experiments, and educating nuclear engineers and scientists. There are already gaps and significant concern about future capabilities for the existing research reactor facilities to address modern instrumentation and/or flexible environments for: performing reactor physics studies for advanced designs which have significantly different core materials forms and compositions, reactor shapes and size; validation of advanced high-fidelity software; development of machine learning algorithms for enhancement of human-machine collaboration in support of reactor monitoring, operation and safeguards; and, effective education of the next-generation workforce. The authors will focus on the need for advanced research reactors to improve and validate fast and accurate simulation tools for high-fidelity modeling and analysis of nuclear reactors in support of their design, optimization, licensing, operation, and monitoring. In the past, simulation tools were limited to relatively coarse models using approximate methodologies that benefited from two main factors: i) allowance for large margins and tolerances; ii) ability to construct prototype (e.g., zero power) reactors for adjustment of approximate methodologies. The next generation reactors have to be designed mainly by using novel high-fidelity computational tools that are accurate and fast, and therefore can be used for parametric studies and uncertainty quantification. To sufficiently demonstrate the accuracy of these tools, advanced research reactors are needed. The authors argue the need for new computational paradigms such as the MRT (Multistage, Response- function Transport) methodology which has resulted in the development of the novel high-fidelity RAPID (Real-time Analysis for Particle-transport and In-situ Detection) code system. Such code systems have to be robust in modeling any complex system, and should be fast and accurate, henceforth their uncertainties can be quantified at reasonable costs. Again, advanced research reactors are needed for the validation of the fidelity and accuracy of new computational tools. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2024

AEOLUS: Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems

Sustained advances in the mathematics of modeling and simulation have resulted in the capability today for routine simulation of a number of large scale complex DOE-relevant systems. As remarkable as this capability for solving the so-called forward problem is, it is typically only the first step-an inner loop within an outer loop that explores the simulation model's parameter space and decision space to characterize uncertainty in the model's predictions, learn unknown model parameters from data, design the most informative experiments, determine optimal control strategies, and create optimal designs. Broadly, what unifies all of these outer loop problems is that they are, in one form or another, optimization problems over parameter/control/design space that are constrained by complex uncertain models. To fully realize the power of scientific simulation as a basis for scientific discovery, technological innovation, and rational decision-making, it is imperative to move beyond simulation to tackle the outer loop of optimization for learning from data, experimental design, and control with complex uncertain models. When the models under consideration are large-scale and complex, and when the optimization variable and uncertain parameter spaces are high (or infinite) dimensional, this constitutes a grand challenge of the highest order, and is intractable with conventional methods. To overcome these challenges, the AEOLUS Center was established to develop a unified mathematical, computational, and statistical framework for (1) Learning predictive models from complex data via Bayesian inference and optimization, and (2) Optimizing experiments, processes, and designs using the resulting uncertain models. These problems are intractable with conventional methods, for several reasons: (1) The simulation problems that govern the inner loops of the optimization problems are expensive to execute (due to severe nonlinearity, heterogeneity, multiphysics/multiscale coupling); (2) The optimization variable and uncertain parameter spaces are high dimensional, often stemming from discretizations of infinite dimensional fields such as initial conditions, sources, or material properties. We argue that the key to overcoming these challenges is to develop new mathematical, computational, and statistical methods that exploit the structure of the Bayesian inference and optimization problems mediated by their underlying complex uncertain models. This structure includes the regularity, sparsity, geometry, low intrinsic dimensionality, and multifidelity nature of the maps from uncertain parameter/optimization variable spaces to the specific objectives targeted: Bayesian inference, optimal experimental design, and optimal control design. Black box methods developed as generic tools are incapable of exploiting this structure. To be successful, we must create, integrate, and cross-fertilize ideas across multiple areas of applied math--including approximation theory, Bayesian inference, data science, experimental design, information theory, machine learning, model reduction, optimal control theory, parallel algorithms, PDE-constrained optimization, randomized algorithms, stochastic optimization, and uncertainty quantification--all while exploiting the structure of the problems at hand. With this goal in mind, we have marshaled a team of leading authorities in these areas. While the methods we develop will be broadly applicable across a wide spectrum of DOE problems in which experiments inform models and the systems those models describe must be optimized under uncertainty, we have chosen a specific area, advanced manufacturing and materials, to drive our work. AMM is characterized by complex models across multiple scales, and is a rich source of challenging problems in inference, experimental design, and optimal control, requiring multifaceted and integrated advances in applied mathematics. As such, AMM serves as an excellent vehicle to motivate and demonstrate the advances in applied mathematics developed by our center.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Noisy intermediate-scale quantum algorithms

A universal fault-tolerant quantum computer that can efficiently solve problems such as integer factorization and unstructured database search requires millions of qubits with low error rates and long coherence times. While the experimental advancement toward realizing such devices will potentially take decades of research, noisy intermediate-scale quantum (NISQ) computers already exist. These computers are composed of hundreds of noisy qubits, i.e., qubits that are not error corrected, and therefore perform imperfect operations within a limited coherence time. In the search for achieving quantum advantage with these devices, algorithms have been proposed for applications in various disciplines spanning physics, machine learning, quantum chemistry, and combinatorial optimization. The overarching goal of such algorithms is to leverage the limited available resources to perform classically challenging tasks. In this review, a thorough summary of NISQ computational paradigms and algorithms is provided. The key structure of these algorithms and their limitations and advantages are discussed. Finally, a comprehensive overview of various benchmarking and software tools useful for programming and testing NISQ devices is additionally provided.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Machine learning for natural resource assessment: An application to the blind geothermal systems of Nevada

A study is underway to apply machine learning methods to evaluate natural resource potential. In particular, we are considering the search for blind geothermal systems in Nevada. Beginning with the data and experience from the previous Nevada play fairway analysis project, we are building models in TensorFlow/Keras and gaining experience toward predicting the geothermal resource potential as a probability map. During the first year of this project we have encountered several issues particular to using geological and geophysical data sets with these tools. Through an illustrative example we develop a promising workflow for future use as more data become available and are analyzed.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

Accelerating Discovery of Atomistic Defects via Machine Learning

The quantification of defects such as vacancies in crystalline structures is a cornerstone of materials science research. Traditional efforts often rely on manual detection, a process that is time-intensive, prone to human error, and challenging to scale. Here we leverage machine learning (ML) methods to identify and quantify vacancies within a crystalline lattice, aiming to expedite detection while improving accuracy. Additionally, we explore the transferability of these ML techniques, identifying characteristics of atomistic imaging data that complicate this task. We show how the integration of ML can drive innovation, providing a powerful tool that will play an increasingly crucial role in the future of materials science.

2D materials↗
DOE OSTI2021

CASTELO: clustered atom subtypes aided lead optimization—a combined machine learning and molecular modeling method

Background: Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined machine learning and molecular modeling approach that partially automates lead optimization workflow in silico, providing suggestions for modification hot spots. Results: The initial data collection is achieved with physics-based molecular dynamics simulation. Contact matrices are calculated as the preliminary features extracted from the simulations. To take advantage of the temporal information from the simulations, we enhanced contact matrices data with temporal dynamism representation, which are then modeled with unsupervised convolutional variational autoencoder (CVAE). Finally, conventional and CVAE-based clustering methods are compared with metrics to rank the submolecular structures and propose potential candidates for lead optimization. Conclusion: With no need for extensive structure-activity data, our method provides new hints for drug modification hotspots which can be used to improve drug potency and reduce the lead optimization time. It can potentially become a valuable tool for medicinal chemists.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Improving Trustworthiness of Data-Driven Power Grid Contingency Analysis With Bayesian Residual Graph Neural Networks

The evolving energy landscape requires novel tools to efficiently perform contingency analysis and reliability assessment of power grids, potentially in real-time. The high computational cost of traditional power flow solvers limits their applicability in practice. Machine learning (ML) surrogates such as deep neural networks (NNs) accelerate power flow solvers computations, enabling high-order contingency analysis and real-time decision-making by learning highly nonlinear functions and integrating grid topology via graph architectures. However, (graph) NNs lack predictive power away from training data and do not provide predictive confidence estimates. Here, we present a Bayesian residual graph NN that integrates knowledge from low-fidelity data via residual training and embeds granular quantification of uncertainties, improving trustworthiness critical for high-consequence decision-making. Applying Bayesian concepts to NNs is challenging due to the high-dimensionality of both the parameter space, complicating derivation of a meaningful prior, and the output space in large grid systems, requiring enhanced techniques to assess the predicted high-dimensional uncertainties. Our contributions include: (1) Deriving a prior for fully connected and graph NNs that leverages low-fidelity data to guide mean predictions and appropriately control prior predictive uncertainty. (2) Integrating this prior within an ensembling with anchoring scheme for efficient approximate posterior inference. (3) Deriving enhanced metrics to assess accuracy of both the mean and uncertainty predictions in high dimensions, appropriately accounting for correlations propagated through graph layers. The resulting Bayesian residual graph NN is tested on a contingency analysis task for 14-bus and 118-bus grids.

24 - POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

"Russians in the Grid" Enrichment Process

Threat intelligence sources are numerous, and the quality of their intelligence is equally variable. The need for quality, actionable, and shareable intelligence is becoming increasingly important as cyber-threats continue to increase. In this paper, we describe the process we used to enrich U.S. CERT’s Technical Alert entitled “Russian Government Cyber-Activity Targeting Energy and Other Critical Infrastructure Sectors,” affectionately referred to as “Russians In the Grid,” from a series of separate but related reports to a final, actionable, unified Structured Threat Information Expression (STIX) v2 representation of the report. In the process, we detail the tools and procedures we used, some of which are automated and others highly manual. We identify some of the limitations of current STIX enrichment tools and techniques, and propose enhancements to allow for more effective enrichment and better overall threat intelligence to be used for more effective threat data-sharing, as well as machine learning-based predictive threat work being conducted at Idaho National Laboratory.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2025

TGCM: (T)rait, (G)ene, and (C)rop Growth (M)odel Directed Targeted Gene Characterization in Sorghum (Final Technical Report)

Understanding which genes control important crop traits could help scientists develop better bioenergy and food crops more efficiently. However, plant genomes contain tens of thousands of genes, and testing each one individually is expensive and time-consuming. This project developed computational tools to predict which genes are most likely to matter, allowing researchers to focus their efforts where they will have the greatest impact. This project developed and validated integrated approaches combining machine learning, quantitative genetics, and crop growth modeling to improve the efficiency of functional gene characterization in sorghum (Sorghum bicolor), a critical bioenergy and food security crop. The research addressed a fundamental challenge in plant biology: the majority of genes in plant genomes lack experimentally validated functions, making it difficult to prioritize which genes to study using resource-intensive reverse genetics approaches.

60 APPLIED LIFE SCIENCES↗