Towards Standardizing Nomenclature in Huntington's Disease Research.

The field of Huntington's disease research covers many different scientific disciplines, from molecular biology all the way through to clinical practice, and as our understanding of the disease has progressed over the decades, a great deal of different terminology has accrued. The field is also renowned for its collaborative spirit and use of standardized reagents, assays, datasets, models, and clinical measures, so the use of standardized terms is especially important. We have set out to determine, through a consensus exercise involving basic and clinical scientists working in the field, the most appropriate language to use across disciplines. Nominally, this article will serve as the style guide for the Journal of Huntington's Disease (JHD), the only journal devoted exclusively to HD, and we lay out the preferred and standardized terminology and nomenclature for use in JHD publications. However, we hope that this article will also serve as a useful resource to the HD research community at large and that these recommended naming conventions will be adopted widely.

Revisiting the infrageneric classification of Garcinia L. (Clusiaceae): an updated sectional name and new, legitimate names in Garcinia for Allanblackiagabonensis (Pellegr.) Bamps and A.parviflora A.Chev.

In a recent publication dealing with the sectional-level taxonomy of Garcinia, an illegitimate superfluous sectional name and two illegitimate homonyms were published. Herein we choose a legitimate sectional name, GarciniasectionRheediopsis Pierre, for the superfluous name GarciniasectionRheedia (L.) S.W.Jones ex P.W.Sweeney; and create two new legitimate names in Garcinia for Allanblackiagabonensis (Pellegr.) Bamps and A.parviflora A.Chev.

From non-alcoholic fatty liver disease to metabolic-associated steatotic liver disease: Rationale and implications for the new terminology.

Non-alcoholic fatty liver disease (NAFLD) was the term first used to describe hepatic steatosis in patients with the metabolic syndrome who did not consume excess amounts of alcohol. Alcoholic liver disease (ALD) has many similarities to NAFLD in both pathogenesis and histology. This entity is now the most prevalent chronic liver disease worldwide as a consequence of the epidemic of obesity. Attempts to incorporate the importance of the metabolic syndrome in the development of steatosis resulted in the renaming of NAFLD as metabolic-associated fatty liver disease. This new term, however, has the disadvantage of the use of terms that may be perceived as derogatory. The terms fatty and non-alcoholic have negative connotations in many cultures. In addition, non-alcoholic is not usually a term applicable to pediatric cases of hepatic steatosis. Recently, an international collaborative effort, with participants from 56 countries, after a global consultation process, recommended to change the nomenclature to steatotic liver disease -including metabolic dysfunction- associated steatotic liver disease, metabolic-associated steatohepatitis and metabolic dysfunction-associated ALD. The new terminology is consistent with most of the previously published epidemiological studies and will have a major impact on research into diagnosis, prognosis and treatment.

Clarifying the nomenclature of Strychnosbredemeyeri and Lasiostoma (Loganiaceae).

Strychnos (Loganiaceae, Gentianales) is a large and pantropical genus of woody plants, ethnobotanically important as a source of many toxic alkaloids, including strychnine. Unfortunately, the status of numerous names at various ranks of Strychnos remains unresolved, including that of many specific or infraspecific taxa in the Neotropics. In this study, we address Strychnosbredemeyeri (basionym Lasiostomabredemeyeri), a species described in 1827 based on type material collected in Venezuela during the poorly documented Austrian Märter expedition (1783-1788). Strychnosbredemeyeri is an unarmed liana with solitary tendrils and axillary inflorescences that occurs in Neotropical rainforests and savannas in Brazil, Guyana, Trinidad and Tobago, and Venezuela. We clarify here the nomenclatural status of Lasiostoma Schreb., an illegitimate and superfluous genus currently in synonymy under Strychnos, and its former species Lasiostomabredemeyeri [= Strychnosbredemeyeri]. Also, we lectotypify S.pedunculata and S.trinitensis, both taxa currently synonyms of S.bredemeyeri.

Valid publication of names for bacterial species from the chicken gut.

This article is a follow-up to Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, et al. PeerJ 2021;9:e10941, detailing accession numbers from culture collections to ensure that names for 33 new species conform to the Rules of the International Code of Nomenclature of Prokaryotes required for valid publication of names for cultured species. The following species names are now proposed to be recognized as validly published: Acinetobacter pecorum sp. nov., Arthrobacter gallicola sp. nov., Arthrobacter pullicola sp. nov., Bacillus norwichensis sp. nov., Brevibacterium gallinarum sp. nov., Brevundimonas guildfordensis sp. nov., Cellulomonas avistercoris sp. nov., Clostridium gallinarum sp. nov., Comamonas avium sp. nov., Corynebacterium gallinarum sp. nov., Cytobacillus stercorigallinarum sp. nov., Escherichia whittamii sp. nov., Kaistella pullorum sp. nov., Luteimonas colneyensis sp. nov., Microbacterium commune sp. nov., Microbacterium gallinarum sp. nov., Microbacterium pullorum sp. nov., Oceanitalea stevensii sp. nov., Ochrobactrum gallinarum sp. nov., Oerskovia douganii sp. nov., Oerskovia gallyi sp. nov., Oerskovia merdavium sp. nov., Oerskovia rustica sp. nov., Paenibacillus gallinarum sp. nov., Phocaeicola gallinarum sp. nov., Planococcus wigleyi sp. nov., Psychrobacter communis sp. nov., Serpens gallinarum sp. nov., Solibacillus faecavium sp. nov., Sporosarcina gallistercoris sp. nov., Sporosarcina quadrami sp. nov., Stenotrophomonas pennii sp. nov. and Ureibacillus galli sp. nov.

25 years of the IPD-IMGT/HLA Database.

Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD-IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic.

A Cybertaxonomic Revision of the "Crocidura pergrisea" Species Complex with a Special Focus on Endemic Rocky Shrews: Crocidura armenica and Crocidura arispa (Soricidae).

The extraction of museum DNA from a unique collection of samples of the "Crocidura pergrisea" species complex, which comprises local endemics of Central and West Asia, allowed us to determine their inter- and intragroup relationships. The first step of this study was the re-evaluation of heavily damaged type specimens of C. armenica via a microcomputed-tomography-based cybertaxonomic approach (CTtax), which enabled a precise description of the species' morphology; three-dimensional models of the cybertypes were made available through the MorphoBank Repository. We developed the "AProMaDesU" pipeline on the basis of five requirements for micro-CT-based cyber-datasets in relation to mammalian collections. Our second step was a combination of several meticulous approaches to morphological investigation against a background of a cytb-based phylogeny, which helped us to make a taxonomic decision about the status of species of the "pergrisea" group, e.g., C. arispa, C. armenica, and C. serezkyensis, when the morphological results were partly incongruent with the molecular phylogeny. Nevertheless, under two assumptions, our findings preserved a separate species-level status of C. serezkyensis and C. arispa. In addition, we restored the species-level status of C. armenica. This taxonomic decision is based on our morphospace analysis, which revealed unique craniomandibular shape transformations within the rocky shrews that helped them with the transition to a new area of morphospace/trophic niches and consequently separated them from the other analyzed Crocidura groups.

SeqCode in the golden age of prokaryotic systematics.

The SeqCode is a new code of prokaryotic nomenclature that was developed to validate taxon names using genome sequences as type material. The present article provides an independent view about the SeqCode, highlighting its history, current status, basic features, pros and cons, and use to date. We also discuss important topics to consider for validation of novel prokaryotic taxon names using genomes as type material. Owing to significant advances in metagenomics and cultivation methods, hundreds of novel prokaryotic species are expected to be discovered in the coming years. This manuscript aims to stimulate and enrich the debate around the use of the SeqCode in the upcoming golden age of prokaryotic taxon discovery and systematics.

Terminologia Anatomica in Latin-American countries: a systematic review.

Terminologia Anatomica (TA) is a unique collection of technical terms that allow communication in anatomy and medicine around the world. Considering this, we reviewed articles published by Latin American authors on Terminologia Anatomica and synthesized the main results found in this article. This study is a systematic review about Terminologia Anatomica that focuses on non-English-speaking countries in Latin America. The database used was Scopus via Elsevier. 207, and candidate articles were identified after applying the search strategy and with no restriction of year of publication. After the exclusion of articles whose authorship was not Latin American, 68 articles were filtered based on their titles and abstracts without the exclusion of any of them. These articles were fully evaluated resulting in 66 articles that met all the inclusion criteria of this review. We collected the following data: title of the article, year of publication, journal of publication, keywords of the study, country of origin, and aim of the article. Among the analyzed articles, 22 proposed changes to terms present in Terminologia Anatomica, 15 of them proposed the inclusion of terms for Terminologia Anatomica, and several articles sought to explain the existence of the existing terms. It is necessary to analyze the terms that are and their origins in the Latin America languages to evaluate their coherence and anatomical correspondence. A standard descriptor for Terminologia Anatomica was not obtained and it is a limitation since eventual articles may not have been obtained. As the study evaluates only articles that were published in journals indexed in Scopus, some articles published in non-indexed journals were not included.

A Standardized Nomenclature Design for Systematic Referencing and Identification of Animal Cellular Material.

The documentation, preservation and rescue of biological diversity increasingly uses living biological samples. Persistent associations between species, biosamples, such as tissues and cell lines, and the accompanying data are indispensable for using, exchanging and benefiting from these valuable materials. Explicit authentication of such biosamples by assigning unique and robust identifiers is therefore required to allow for unambiguous referencing, avoid identification conflicts and maintain reproducibility in research. A predefined nomenclature based on uniform rules would facilitate this process. However, such a nomenclature is currently lacking for animal biological material. We here present a first, standardized, human-readable nomenclature design, which is sufficient to generate unique and stable identifying names for animal cellular material with a focus on wildlife species. A species-specific human- and machine-readable syntax is included in the proposed standard naming scheme, allowing for the traceability of donated material and cultured cells, as well as data FAIRification. Only when it is consistently applied in the public domain, as publications and inter-institutional samples and data are exchanged, distributed and stored centrally, can the risks of misidentification and loss of traceability be mitigated. This innovative globally applicable identification system provides a standard for a sustainable structure for the long-term storage of animal bio-samples in cryobanks and hence facilitates current as well as future species conservation and biomedical research.

Why and how to use the SeqCode.

The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.

Fomes weberianus, 50 years of taxonomic confusion: lectotypification and taxonomic notes.

Fomes weberianus Bres. & Henn. ex Sacc. is currently the basionym of two very distinct polypores (Basidiomycota), Ganoderma weberianum (Polyporales) and Phylloporia weberiana (Hymenochaetales). This fact has led to almost fifty years of taxonomic confusion. Fomes weberianus was first lectotypified by Steyaert, who accepted the species as G. weberianum. However, studies of Weber's original material in B, duplicate material in S, the protologue, and early interpretations of the name have shown that Steyaert's choice conflicts with the protologue and early interpretations, and that his interpretation as a species of Ganoderma is erroneous. A new lectotype was designated and the species was re-described under the correct interpretation Phylloporia weberiana.

Golden spikes, scientific types, and the ma(r)king of deep time.

Chronostratigraphy is the subfield of geology that studies the relative age of rock strata and that aims at producing a hierarchical classification of (global) divisions of the historical time-rock record. The 'golden spike' or 'GSSP' approach is the cornerstone of contemporary chronostratigraphic methodology. It is also perplexing. Chronostratigraphers define each global time-rock boundary extremely locally, often by driving a gold-colored pin into an exposed rock section at a particular level. Moreover, they usually avoid rock sections that show any meaningful sign of paleontological disruption or geological discontinuity: the less obvious the boundary, the better. It has been argued that we can make sense of this practice of marking boundaries by comparing the status and function of golden spikes to that of other concrete, particular reference standards from other sciences: holotypes from biological taxonomy and measurement prototypes from the metrology of weight and measures. Alisa Bokulich (2020b) has argued that these 'scientific types' are in an important sense one of a kind: they have a common status and function. I will argue that this picture of high-level conceptual unity is mistaken and fails to consider the diversity of aims and purposes of standardization and classification across the sciences. I develop an alternative, disunified account of scientific types that shows how differences in ontological attitudes and epistemic aims inform scientists' choices between different kinds of scientific types. This perspective on scientific types helps to make sense of an intriguing mid-twentieth-century debate among chronostratigraphers about the very nature of their enterprise. Should chronostratigraphers conventionally make boundaries by designating golden spikes, or should they attempt to mark pre-existing 'natural' boundaries with the help of a different kind of scientific type?

Ambiviricota, a novel ribovirian phylum for viruses with viroid-like properties.

Fungi harbor a vast diversity of mobile genetic elements (MGEs). Recently, novel fungal MGEs, tentatively referred to as 'ambiviruses,' were described. 'Ambiviruses' have single-stranded RNA genomes of about 4-5 kb in length that contain at least two open reading frames (ORFs) in non-overlapping ambisense orientation. Both ORFs are conserved among all currently known 'ambiviruses,' and one of them encodes a distinct viral RNA-directed RNA polymerase (RdRP), the hallmark gene of ribovirian kingdom Orthornavirae. However, 'ambivirus' genomes are circular and predicted to replicate via a rolling-circle mechanism. Their genomes are also predicted to form rod-like structures and contain ribozymes in various combinations in both sense and antisense orientations-features reminiscent of viroids, virusoids, ribozyvirian kolmiovirids, and yet-unclassified MGEs (such as 'epsilonviruses,' 'zetaviruses,' and some 'obelisks'). As a first step toward the formal classification of 'ambiviruses,' the International Committee on Taxonomy of Viruses (ICTV) recently approved the establishment of a novel ribovirian phylum, Ambiviricota, to accommodate an initial set of 20 members with well-annotated genome sequences.

Predicting concrete strength early age using a combination of machine learning and electromechanical impedance with nano-enhanced sensors.

To ensure the structural integrity of concrete and prevent unanticipated fracturing, real-time monitoring of early-age concrete's strength development is essential, mainly through advanced techniques such as nano-enhanced sensors. The piezoelectric-based electro-mechanical impedance (EMI) method with nano-enhanced sensors is emerging as a practical solution for such monitoring requirements. This study presents a strength estimation method based on Non-Destructive Testing (NDT) Techniques and Long Short-Term Memory (LSTM) and artificial neural networks (ANNs) as hybrid (NDT-LSTMs-ANN), including several types of concrete strength-related agents. Input data includes water-to-cement rate, temperature, curing time, and maturity based on interior temperature, allowing experimentally monitoring the development of concrete strength from the early steps of hydration and casting to the last stages of hardening 28 days after the casting. The study investigated the impact of various factors on concrete strength development, utilizing a cutting-edge approach that combines traditional models with nano-enhanced piezoelectric sensors and NDT-LSTMs-ANN enhanced with nanotechnology. The results demonstrate that the hybrid provides highly accurate concrete strength estimation for construction safety and efficiency. Adopting the piezoelectric-based EMI technique with these advanced sensors offers a viable and effective monitoring solution, presenting a significant leap forward for the construction industry's structural health monitoring practices.

Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World.

This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (subtr. nov.). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for Amelanchier, Malus, Sorbus sensu lato, and Stranvaesia. In addition, we present a comprehensive taxonomic synopsis of Photinia and its morphological allies in the Old World, recognizing 27 species and ten varieties within Photinia, three species and two varieties within Stranvaesia, and two species and three varieties within Weniomeles. Furthermore, we also lectotypified 12 names and made two new combinations, Photiniamicrophylla (J.E.Vidal) B.B.Liu and Weniomelesatropurpurea (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.

Evaluation of SNOMED CT Grouper Accuracy and Coverage in Organizing the Electronic Health Record Problem List by Clinical System: Observational Study.

Background: The problem list (PL) is a repository of diagnoses for patients' medical conditions and health-related issues. Unfortunately, over time, our PLs have become overloaded with duplications, conflicting entries, and no-longer-valid diagnoses. The lack of a standardized structure for review adds to the challenges of clinical use. Previously, our default electronic health record (EHR) organized the PL primarily via alphabetization, with other options available, for example, organization by clinical systems or priority settings. The system's PL was built with limited groupers, resulting in many diagnoses that were inconsistent with the expected clinical systems or not associated with any clinical systems at all. As a consequence of these limited EHR configuration options, our PL organization has poorly supported clinical use over time, particularly as the number of diagnoses on the PL has increased. Objective: We aimed to measure the accuracy of sorting PL diagnoses into PL system groupers based on Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) concept groupers implemented in our EHR. Methods: We transformed and developed 21 system- or condition-based groupers, using 1211 SNOMED CT hierarchal concepts refined with Boolean logic, to reorganize the PL in our EHR. To evaluate the clinical utility of our new groupers, we extracted all diagnoses on the PLs from a convenience sample of 50 patients with 3 or more encounters in the previous year. To provide a spectrum of clinical diagnoses, we included patients from all ages and divided them by sex in a deidentified format. Two physicians independently determined whether each diagnosis was correctly attributed to the expected clinical system grouper. Discrepancies were discussed, and if no consensus was reached, they were adjudicated by a third physician. Descriptive statistics and Cohen κ statistics for interrater reliability were calculated. Results: Our 50-patient sample had a total of 869 diagnoses (range 4-59; median 12, IQR 9-24). The reviewers initially agreed on 821 system attributions. Of the remaining 48 items, 16 required adjudication with the tie-breaking third physician. The calculated κ statistic was 0.7. The PL groupers appropriately associated diagnoses to the expected clinical system with a sensitivity of 97.6%, a specificity of 58.7%, a positive predictive value of 96.8%, and an F1-score of 0.972. Conclusions: We found that PL organization by clinical specialty or condition using SNOMED CT concept groupers accurately reflects clinical systems. Our system groupers were subsequently adopted by our vendor EHR in their foundation system for PL organization.

Checklist of colourless euglenoids of the Czech Republic, with several taxonomic additions.

This study presents the results of a complex survey of freshwater heterotrophic euglenoids in the Czech Republic, including both literature data and own field surveys of 469 sites visited in the course of three years. The checklist includes 189 taxa in 28 genera: Anisonema (10), Astasia (26), Atraktomonas (1), Calycimonas (2), Chasmostoma (1), Dinematomonas (3), Distigma (8), Dylakosoma (1), Entosiphon (4), Euglena (1), Gyropaigne (1), Heteronema (19), Jenningsia (11), Khawkinea (1), Lepocinclis (1), Menoidium (7), Neometanema (3), Notosolenus (18), Petalomonas (40), Phacus (1), Ploeotia (2), Pseudoperanema (7), Rhabdomonas (5), Scytomonas (1), Sphenomonas (5), Teloprocta (1) Tropidocyphus (1), Urceolus (4), and 4 species of uncertain identity. In addition, a general description of habitat types in which the taxa were found and a review of the current taxonomy and nomenclature of included taxa are provided. Several taxonomic and nomenclatural novelties are proposed, based on the review of morphological features, mostly applying to the genera Notosolenus and Jenningsia.