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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 109 records · Page 6

Parabacteroides distasonis : intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health

Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.

59 BASIC BIOLOGICAL SCIENCES↗

Cutaneous and local radiation injuries

The threat of a large-scale radiological or nuclear (R/N) incident looms in the present-day climate, as noted most recently in an editorial in Scientific American (March 2021). These large-scale incidents are infrequent but affect large numbers of people. Smaller-scale R/N incidents occur more often, affecting smaller numbers of people. There is more awareness of acute radiation syndrome (ARS) in the medical community; however, ionising radiation-induced injuries to the skin are much less understood. Here, this article will provide an overview of radiation-induced injuries to the skin, deeper tissues, and organs. The history and nomenclature; types and causes of injuries; pathophysiology; evaluation and diagnosis; current medical management; and current research of the evaluation and management are presented. Cutaneous radiation injuries (CRI) or local radiation injuries (LRI) may lead to cutaneous radiation syndrome, a sub-syndrome of ARS. These injuries may occur from exposure to radioactive particles suspended in the environment (air, soil, water) after a nuclear detonation or an improvised nuclear detonation (IND), a nuclear power plant incident, or an encounter with a radioactive dispersal or exposure device. These incidents may also result in a radiation-combined injury; a chemical, thermal, or traumatic injury, with radiation exposure. Skin injuries from medical diagnostic and therapeutic imaging, medical misadministration of nuclear medicine or radiotherapy, occupational exposures (including research) to radioactive sources are more common but are not the focus of this manuscript. Diagnosis and evaluation of injuries are based on the scenario, clinical picture, and dosimetry, and may be assisted through advanced imaging techniques. Research-based multidisciplinary therapies, both in the laboratory and clinical trial environments, hold promise for future medical management. Great progress is being made in recognising the extent of injuries, understanding their pathophysiology, as well as diagnosis and management; however, research gaps still exist.

61 RADIATION PROTECTION AND DOSIMETRY↗

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

Three approaches for the classification of protoneutron star oscillation modes

ABSTRACT The future detection of gravitational waves (GWs) from a Galactic core-collapse supernova will provide information on the physics inside protoneutron stars (PNS). In this work, we apply three different classification methods for the PNS non-radial oscillation modes: Cowling classification, Generalized Cowling Nomenclature (GCN), and a classification based on modal properties (CBMP). Using PNS models from 3D simulations of core-collapse supernovae, we find that in the early stages of the PNS evolution, typically 0.4 s after the bounce, the Cowling classification is inconsistent, but the GCN and the CBMP provide complementary information that helps to understand the evolution of the modes. In the GCN, we note several avoided crossings as the mode frequencies evolve at early times, while the CBMP tracks the modes across the avoided crossings. We verify that the strongest emission of GWs by the PNS corresponds to the f mode in the GCN, indicating that the mode trapping region alternates between the core and the envelope at each avoided crossing. At later times, approximately 0.4 s after the bounce, the three classification methods present a similar description of the mode spectrum. We use our results to test universal relations for the PNS modes according to their classification and find that the behaviour of the universal relations for f and p modes is remarkably simple in the CBMP.

Astronomy & Astrophysics↗

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Illustrated formalisms for total scattering data: a guide for new practitioners

The total scattering method is the simultaneous study of both the real- and reciprocal-space representations of diffraction data. While conventional Bragg-scattering analysis (employing methods such as Rietveld refinement) provides insight into the average structure of the material, pair distribution function (PDF) analysis allows for a more focused study of the local atomic arrangement of a material. Generically speaking, a PDF is generated by Fourier transforming the total measured reciprocal-space diffraction data (Bragg and diffuse) into a real-space representation. However, the details of the transformation employed and, by consequence, the resultant appearance and weighting of the real-space representation of the system can vary between different research communities. As the worldwide total scattering community continues to grow, these subtle differences in nomenclature and data representation have led to conflicting and confusing descriptions of how the PDF is defined and calculated. This paper provides a consistent derivation of many of these different forms of the PDF and the transformations required to bridge between them. Some general considerations and advice for total scattering practitioners in selecting and defining the appropriate choice of PDF in their own research are presented. This contribution aims to benefit people starting in the field or trying to compare their results with those of other researchers.

36 MATERIALS SCIENCE↗

Magnetic structure determination of multiple phases in the multiferroic candidate GdCrO 3

Due to their potential applications in low-power consumption and/or multistate memory devices, multiferroic materials have attracted a lot of attention in the condensed matter community. As part of the effort to identify new multiferroic compounds, perovskite-based GdCrO 3 was studied in both bulk and thin film samples. A strong enhancement of the capacitance in a field suggested ferroelectric behaviour but significant leakage and no well developed P–E hysteresis loops were observed. Measurements clearly indicate the existence of a polar phase but only below 2 K (likely connected to Gd ordering). Here the determination of the magnetic structure through neutron diffraction collected on an isotopic 160 GdCrO 3 sample at the WISH diffractometer at ISIS is reported. The presence of three successive magnetic phases as a function of temperature (commensurate, spin re-orientation and incommensurate phases once the Gd order), previously only seen by magnetization, is confirmed. Using the most recent guidelines for reporting the determined structures, we highlight the benefits of using such nomenclature for discussing physical properties and consider possible mechanisms and couplings that led this seemingly rather isotropic system to display the complex structures observed.

incommensurate magnetic structure↗

Fundamentals of Three-Terminal Tandem Solar Cells: a Comprehensive Taxonomy

Three-terminal tandem (3TT) solar cells can overcome some of the limitations of two- and four-terminal tandem designs. However, the coupled nature of the cells adds a degree of complexity to the devices themselves and the ways that their performance can be measured and reported. To facilitate understanding, we have developed a taxonomy which encompasses all types of 3TT devices, enabling a common nomenclature for discussing devices and performance. Once the physical devices, contact nodes, and loading circuitry have been self-consistently described, it becomes apparent that a wide range of 3TT devices share a common set of design and operating principles.

3T↗

Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions

Many biotic and abiotic processes contribute to nitrous oxide (N 2 O) production in the biosphere, but N 2 O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N 2 O reductase enzyme, NosZ, responsible for N 2 O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N 2 O reducers could play an important, previously unrecognized role in controlling N 2 O emissions for several reasons, including: (1) the consumption of N 2 O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N 2 O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N 2 O reducers. Furthermore, we provide recommendations to accelerate advances in understanding the role of the diversity of N 2 O reducers in regulating soil N 2 O emissions.

59 BASIC BIOLOGICAL SCIENCES↗

Description of Freudenthalidium gen. nov. and Halluxium gen. nov. to Formally Recognize Clades Fr3 and H as Genera in the Family Symbiodiniaceae (Dinophyceae)

The Symbiodiniaceae are a family of marine dinoflagellates known mostly for their endosymbiotic interactions with invertebrates and protists, but facultatively and exclusively free‐living life histories in this family are also evident. A recent systematic revision of the Symbiodiniaceae replaced the clade‐based nomenclature of seven divergent lineages of “ Symbiodinium ” sensu lato with one based on formally described genera. The revised taxonomy was not extended to the whole group because type species to describe a new genus for each of the remaining clades and subclades were lacking. In an effort to characterize benthic habitats of symbiodiniaceans in sediments at Heron Island (Great Barrier Reef, Australia), we isolated >100 monoclonal Symbiodiniaceae cultures. Four of these belonged to Symbiodiniaceae ‘subclade’ Fr3, and three to Clade H, based on nucleotide sequence similarity (ITS2, LSU, cp23S, and mtCOB), representing the first cultures of these taxa. Based on these isolates, we propose two new genera: Freudenthalidium gen. nov. and Halluxium gen. nov., circumscribing Clades Fr3 and H, respectively. Three new species are described: Freudenthalidium heronense , F. endolithicum , and Halluxium pauxillum . Kofoidian tabulations of motile cells confirm previous observations that amphiesmal vesicle arrangements are generally conserved across the family. These descriptions are an important step toward completing the systematic revision of the Symbiodiniaceae. That this contribution was enabled by isolates from an endopsammic habitat highlights the potential of discovering new symbiodiniacean species in the environment, the study of which will lead to a deeper understanding of free‐living versus symbiotic life histories in this ecologically important family of dinoflagellates.

Nitschke, Matthew R.↗

Two novel Patescibacteria: Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov., both associated with microalgae optimized for carbon dioxide sequestration from flue gas

The functional roles of bacterial symbionts associated with microalgae remain understudied despite the importance of microalgae in biotechnology and environmental microbiology. 16S rRNA gene sequencing was conducted to analyze bacterial communities associated with two microalgae optimized for growth with flue gas containing 5%–10% CO 2 . Two dominant bacteria with no taxonomic classification beyond the class level (Paceibacteria) were discovered repeatedly in the most productive algal cultures. Long-read metagenomic sequencing was conducted to yield high-quality metagenomes, from which two novel species were discovered under the Seqcode (seqco.de/r:ywe1blo2), Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov. The genus Phycocordibacter gen. nov. was proposed as the nomenclatural type of the family Phycocordibacteraceae fam. nov. and the order Phycocordibacterales ord. nov. Both bacteria possessed features typical of Patescibacteria such as reduced genomes (<800 kbp), lack of complete glycolysis and tricarboxylic acid (TCA) cycle pathways, and inability to synthesize amino acids. Instead, they rely on the reductive pentose phosphate pathway (Calvin cycle) for essential biosynthesis and redox balance. P. aenigmaticus may also rely on elemental sulfur oxidation (sdo), partial nitrite reduction (nirK), and sulfur-related amino acid metabolism (SAMe → SAH). Both bacteria were found in high relative abundance in cultures of Tetradesmus obliquus HTB1 (freshwater) and Nannochloropsis oceanica IMET1 (marine), suggesting a tight association with microalgae in various environments. The absence of full metabolic pathways for energy production suggests extreme metabolic limitations and obligate symbiosis, most likely with other bacteria associated with the microalgae.

54 ENVIRONMENTAL SCIENCES↗

Virus species names have been standardized; virus names remain unchanged

Virus taxonomy, comprising classification and nomenclature, is regulated by the International Committee on Taxonomy of Viruses (ICTV). Taxon names are standardized to facilitate recognition and communication, with defined suffixes for each rank (e.g., the names of orders, families, and genera end in -virales, -viridae, and -virus, respectively). However, until recently, a standard format for species names was lacking. In 2021, following extensive discussion and community consultation, the ICTV decided to adopt a standardized binomial (Linnaean) format for virus species names, consisting of the genus name followed by a "freeform" species epithet. Previously assigned virus species names that were non-compliant with the binomial format have been fully updated. In contrast to taxon names regulated by the ICTV, the names of viruses, or "common" names, such as yellow fever virus or human immunodeficiency virus, are not under the remit of the ICTV and have not been changed.

Zerbini, F Murilo↗

$\gamma$-ray angular correlations, distributions and linear polarization in tracking arrays

With $\gamma $-ray tracking arrays, the angular correlation and, especially, the linear polarization of $\gamma $ rays can be measured with high precision. However, because of the complexity of these spectrometers, measuring angular distributions is more involved. The techniques and associated formalisms were developed and established in the 1950s. The experimental setups of that era were relatively simple when compared to the advanced $\gamma $-ray tracking arrays available today. This paper aims to review and refine these techniques, unify the nomenclatures and, specifically, adapt them for use with the newest tracking arrays. In addition, new methods for producing the required response functions for these arrays are introduced.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence↗

Four principles to establish a universal virus taxonomy

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

59 BASIC BIOLOGICAL SCIENCES↗

Polariton panorama

Abstract In this brief review, we summarize and elaborate on some of the nomenclature of polaritonic phenomena and systems as they appear in the literature on quantum materials and quantum optics. Our summary includes at least 70 different types of polaritonic light–matter dressing effects. This summary also unravels a broad panorama of the physics and applications of polaritons. A constantly updated version of this review is available at https://infrared.cni.columbia.edu .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

COMPASS-FME Synoptic Site Characterization

This dataset contains soil biogeochemical and physicochemical characterization data for the COMPASS-FME synoptic sites.This dataset also contains data for the paper Patel et al. 2025 "Transition zones at the changing coastal terrestrial-aquatic interface", https://doi.org/10.1029/2025JG008978.Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience unique spatial and temporal variability in biogeochemical processes, driven by wetland-to-upland gradients and hydrological fluctuations. We studied drivers of coastal soil variability (a) at regional scales and (b) across transects from upland forest to wetland, in two contrasting regions — Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity-related analytes were a key driver of soil variability, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI – however, contrary to expectations, transition soils were not consistently intermediate between upland and wetland endmembers; the non-monotonic trends of carbon, phosphorus, iron along our transects suggest that these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients provide insights into which soil processes may act as precursors to ecosystem shifts. Our comprehensive soil characterization across the coastal transects provides essential data for mechanistic modeling of ecosystem dynamics.The data are provided as processed, csv files. Raw data and processing scripts can be accessed on GitHub (https://github.com/COMPASS-DOE/cmps-soil_characterization).A note on the nomenclature: the experimental design represents three points along the coastal gradient -- upland, transition, and wetland. "wetland" is referred to as "marsh" in the corresponding paper. The two terms can be used interchangeably for the sites in this study.

54 ENVIRONMENTAL SCIENCES↗

Cybersecurity for Distance Relay Protection

This project is a DOE follow-up effort on the CREDC workshop held on September 13, 2018 in Cambridge, MA to discuss cybersecurity of distance relays, which considered the benefits, vulnerabilities and risk mitigations for the use of communication systems in power system protection. The objectives of this project are to define the taxonomy of relay protection and associated communications; define use cases describing approaches to reduce the cyber-attack surface on those protective relays; and evaluate the loss of operational functional capability from changes to communication coverage. Mitigating controls will also be evaluated to understand if there are other approaches to reduce attack surfaces while maintaining communications or partial communications. Distance relays are used to protect transmission lines of approximately 10 to 300 miles in length, by detecting short circuits (i.e., faults) on the lines and then tripping circuit breakers in the substation. Such protection systems are a subset of the power system and they incorporate sensing, logic and communication functions. Protection system exposure to cyberattack could be drastically limited by disconnecting relays from all vulnerable communication systems, but this may adversely impact overall power system performance in the absence of cyberattack. This project began with a use case analysis of protection systems with communications, as summarized in this report. It continued with modeling, testing and evaluation in a miniature power system (MPS), located in the Western Area Power Administration (WAPA) Electric Power Training Center (EPTC). The project also incorporated feedback from two industry meetings held in February and September 2019. The suggested next steps account for and complement the work already underway with DOE/CESER funding: 1. Study the performance of LCD and PC vs. PUTT, which is less reliant on communication system performance and GPS timing references. The PUTT scheme could prove to be more resilient to cyberattack or communications-related disruption. It could also be more tolerant of message re-routing with SDN/SDR communication systems. On the other hand, it will be more vulnerable to false tripping during dynamic events or to loss of the voltage signal. The optimum choice of scheme may depend on the specific power system and risk assessment. This study could provide a new template for evaluation based on business functions. 2. Research and develop new methods to detect and monitor distributed physical attacks, possibly using drones, video sensors, thermal sensors, machine learning and other advanced techniques. This will help mitigate the impact of cyberattack on the protection system, and will also help mitigate the impact of wild fires. 3. Implement a scalable PKI for use in electric utility protection systems. This will encourage widespread adoption of secure authentication methods that are already available, but not widely used at present. This will help secure engineering access to the relays. 4. Investigate the use of SDN in combination with SDR to achieve better cybersecurity and electromagnetic security of the network, incorporating path variability. This would help secure both engineering access and peer-to-peer GOOSE messaging. 5. Perform additional testing, with operator evaluation of “red button” scenarios, PUTT vs. LCD, relay mis-operations, and other cyberattacks in the EPTC. This is an important advantage of testing in the EPTC rather than by computer simulation or even hardware-in-the-loop simulation; the EPTC is already dedicated to managing the situational awareness, operator response times and other human impacts. One of the project objectives was to settle on a common nomenclature for this problem space. We have concluded that the OSI layer model, supplemented by ANSI device numbers and other IEEE standards, is already well-accepted by the industry. The IEEE PSRC knowledge base provides a great deal of public information

24 POWER TRANSMISSION AND DISTRIBUTION↗