Nomenclatural Issues Research Articles

Meeting Necessity instead of Serendipity: Miscellaneous Nomenclatural Notes on Asteraceae

While compiling a continuously updated checklist of families and genera of world embryophytes, the authors find it necessary to resolve some nomenclatural issues in Asteraceae (Compositae). Here we propose a new supertribal classification for Asteroideae with five supertribes, two of which (Calendulodae and Anthemidodae) are new and one (Ambrosiodae) is a replacement name. A new tribe Leucomerideae in Stifftioideae is described, with the monotypic Nouelia newly treated as a synonym. Two older generic names, Anacis and Epilepis, are resurrected to follow the revision of Coreopsis s.l. and to avoid later homonymy or superfluity, alongside with necessary new combinations. A new nothogenus ×Coreacis is thereby established. The correct spelling Malacotrichinae of the subtribe ‘Malacothricinae’ is discussed.

A new atlas to study embryonic cell types in Xenopus.

This paper introduces a single-cell atlas for pivotal developmental stages in Xenopus, encompassing gastrulation, neurulation, and early tailbud. Notably surpassing its predecessors, the new atlas enhances gene mapping, read counts, and gene/cell type nomenclature. Leveraging the latest Xenopus tropicalis genome version, alongside advanced alignment pipelines and machine learning for cell type assignment, this release maintains consistency with previous cell type annotations while rectifying nomenclature issues. Employing an unbiased approach for cell type assignment proves especially apt for embryonic contexts, given the considerable number of non-terminally differentiated cell types. An alternative cell type attribution here adopts a fuzzy, non-deterministic stance, capturing the transient nature of early embryo progenitor cells by presenting an ensemble of types in superposition. The value of the new resource is emphasized through numerous examples, with a focus on previously unexplored germ cell populations where we uncover novel transcription onset features. Offering interactive exploration via a user-friendly web portal and facilitating complete data downloads, this atlas serves as a comprehensive and accessible reference.

Catalog of Anaedus Blanchard, 1842 with nomenclatural notes (Coleoptera: Tenebrionidae: Lagriinae)

The genus Anaedus Blanchard, 1842 in the tribe Goniaderini Lacordaire, 1859 has experienced drastic genus-level change where seven other genera were subsumed as synonyms by Aalbu et al. (2023). That study addressed multiple nomenclatural issues including several replacement names, but did not provide a full species-group catalog. This study presents a full catalog for the 142 species-group names currently belonging to Anaedus and rectifies several nomenclatural issues missed within the previous study. The catalog includes full nomenclatural histories and type localities for all taxa. The following New Combinations are established: Anaedus keralensis (Kaszab, 1979), An. madrensis (Kaszab, 1979), An. philippinus (Schawaller, 1994), An. setosus (Kaszab, 1979), An. simillimus (Kaszab, 1979). The following New Replacement Names are established for the species listed in parentheses: Anaedus fairmairei Kanda & Johnston (replaces An. fulvipennis Fairmaire, 1889), An. pici Kanda & Johnston (replaces An. rufipes Pic, 192), An. pictus Kanda & Johnston (replaces Spinolyprops maculatus Kulzer, 1954), An. neorufescens Kanda & Johnston (replaces Aspisoma rufescens Pic, 1951).

Wagler vs. Fitzinger: Leposternon microcephalus, a fight over gender (Sauria, Amphisbaenidae)

This short note provides some insight into an academic “battle” between early 19th century herpetologists about a small but interesting nomenclatural issue, namely the grammatically correct gender of a species epithet. Most texts used in the current note (Wagler in Spix 1824; Fitzinger 1826a‒b; Schlegel 1826; Wagler 1827) were published in 19th century German, which sometimes made use of vocabulary that is no longer employed nowadays. The old German texts are translated here into English in a way that they reflect modern language as much as possible.

Alpha-fetoprotein producing endometrioid carcinoma arising in an adenomyoma of the uterus.

We report a case of alpha-fetoprotein-producing endometrioid carcinoma (AFP-EC) that originated within an adenomyoma of the uterine corpus. A 76-year-old Japanese woman was incidentally discovered to have a uterine tumor along with multiple lung nodules. Upon surgical removal of the uterus, it was revealed that the tumor was situated within the adenomyoma. The tumor exhibited microfollicular structures and solid growth patterns, with hyaline globules, clear cell glands, and primitive tumor cells. Immunohistochemical analysis indicated the presence of germ cell markers, including AFP, SALL4, and glypican3, leading to final diagnosis of AFP-EC. Histopathologically, AFP-ECs exhibit characteristics similar to those of AFP-producing neoplasms in other organs. Furthermore, a nomenclature issue arises when distinguishing AFP-ECs from yolk sac tumors of the endometrium in older patients due to their shared features. The concept of retrodifferentiation or neometaplasia suggests that "endometrioid carcinoma with yolk sac tumor differentiation" or "endometrioid carcinoma with a primitive phenotype" may serve as more fitting terms for the diverse spectrum of AFP-producing neoplasms in the endometrium. In conclusion, this case underscores the diagnostic challenges posed by AFP-ECs arising from adenomyomas and emphasizes the need for refining the nomenclature and classification of AFP-producing neoplasms within the endometrium.

Translating nanoEHS data using EPA NaKnowBase and the resource description framework

Background The U.S. Federal Government has supported the generation of extensive amounts of nanomaterials and related nano Environmental Health and Safety (nanoEHS) data, there is a need to make these data available to stakeholders. With recent efforts, a need for improved interoperability, translation, and sustainability of Federal nanoEHS data in the United States has been realized. The NaKnowBase (NKB) is a relational database containing experimental results generated by the EPA Office of Research and Development (ORD) regarding the actions of engineered nanomaterials on environmental and biological systems. Through the interaction of the National Nanotechnology Initiative’s Nanotechnology Environmental Health Implications (NEHI) Working Group, and the Database and Informatics Interest Group (DIIG), a U.S. Federal nanoEHS Consortium has been formed. Methods The primary goal of this consortium is to establish a “common language” for nanoEHS data that aligns with FAIR data standards. A second goal is to overcome nomenclature issues inherent to nanomaterials data, ultimately allowing data sharing and interoperability across the diverse U.S. Federal nanoEHS data compendium, but also in keeping a level of consistency that will allow interoperability with U.S. and European partners. The most recent version of the EPA NaKnowBase (NKB) has been implemented for semantic integration. Computational code has been developed to use each NKB record as input, modify and filter table data, and subsequently output each modified record to a Research Description Framework (RDF). To improve the accuracy and efficiency of this process the EPA has created the OntoSearcher tool. This tool partially automates the ontology mapping process, thereby reducing onerous manual curation. Conclusions Here we describe the efforts of the US EPA in promoting FAIR data standards for Federal nanoEHS data through semantic integration, as well as in the development of NAMs (computational tools) to facilitate these improvements for nanoEHS data at the Federal partner level.

Proceedings of the 2023 Division of Translational Toxicology Satellite Symposium.

The 2023 annual Division of Translational Toxicology (DTT) Satellite Symposium, entitled "Pathology Potpourri," was held in Summerlin, Nevada, at the Society of Toxicologic Pathology's 41st annual meeting. The goal of this symposium was to present and discuss challenging diagnostic pathology and/or nomenclature issues. This article presents summaries of the speakers' talks along with select images that were used by the audience for voting and discussion. Various lesions and topics covered during the symposium included induced and spontaneous neoplastic and nonneoplastic lesions in the mouse liver, infectious and proliferative lesions in nonhuman primates, interesting presentations of mononuclear cell infiltrates in various animal models and a complex oral tumor in a rat.

Nomenclatural updates in the sedge-flora of western Uttar Pradesh

Establishing all plant’s correct identity and nomenclature is crucial in the current context. Therefore, an updated list and nomenclature status of sedges of western Uttar Pradesh, India has been provided in this article. This research paper incorporates extensive consultation of taxonomic databases, examination of type specimens and scrutiny of published works, including Ph.D thesis, research papers, books, and floras. To ensure the accuracy of binomial nomenclature, a systematic approach is adopted, starting with the utilization of search engines to cross-verify and validate taxonomic information. This includes a rigorous examination of online databases and repositories to access up-to-date information on botanical nomenclature. This paper aims to provideaccepted binomials with correct author citations of the sedges growing in western Uttar Pradesh because several names in the published literature are not accepted now. Such publications include several synonyms as accepted name, as well as mistakes in authority. A pivotal aspect of this work involves the verification of binomial identities through the examination of protologues and type specimens. Keeping this in mind, a comprehensive study for solving and updating nomenclature issues hasbeen carried out using different databases, websites and recent publications. We updated the nomenclature of all sedges of western Uttar Pradesh included in publications after 1959. Review of literature and field studies shows that western Uttar Pradesh includes a total of 91 species belonging to 14 genera published in 18 publications. In this study, 25 names of past publications were corrected. This is the first report on updated name changes in the floristic component of western Uttar Pradesh, where 41 names of sedges have been updated. This research paper covers the accepted name, synonym, taxonomic treatment, and typification.

Contribution to the knowledge of Gongolaria barbata (Sargassaceae, Fucales) from the Mediterranean: insights into infraspecific diversity

Gongolaria barbata (Sargassaceae, Fucales) is a widespread species for which several infraspecific taxa have been described, indicating its polymorphism. This study contributes to the understanding of the molecular, nomenclatural, morphological and ecological aspects of G. barbata in the Mediterranean and sheds light on the infraspecific diversity and its implications for the taxonomy of this species. Molecular analyses were performed using sequencing of the mitochondrial cox1 gene on both haptophytic and pleustophytic forms from different sites in the Adriatic and Tyrrhenian Seas. Vegetative and reproductive morphology was studied on thalli samples from the Adriatic. Our results showed that there are different morphotypes within G. barbata populations related to specific environmental conditions, suggesting infraspecific variation. In contrast, molecular analyses showed no differences between samples, regardless of whether individuals are growing “attached” to a substrate or “unattached”. We also discussed the taxonomic status and nomenclatural issues related to certain infraspecific taxa previously proposed for G. barbata. In particular, the confusion surrounding Cystoseira aurantia is clarified.  

Impostor Phenomenon in Racially/Ethnically Minoritized Groups: Current Knowledge and Future Directions.

In recent years there has been a surge of research conducted on the impostor phenomenon, with approximately half of all impostor phenomenon articles being published between 2020 and 2022 and growing interest in understanding how the impostor phenomenon affects racially and ethnically minoritized individuals. Questions around intersectionality remain about how to apply the impostor phenomenon to the experiences of minoritized individuals. In this review, we revisit the historical context of the impostor phenomenon. We address issues of nomenclature and current controversies regarding whether the impostor phenomenon (a) blames the victim, (b) should be included in the Diagnostic and Statistical Manual of Mental Disorders (DSM), and (c) is beneficial for individuals. In addition, we address the limitations of current research on racially and ethnically minoritized individuals, especially women of color. Finally, we conclude by discussing the need for a reconceptualized racialized impostor phenomenon as well as the need to establish new impostor phenomenon measures, conduct more quantitative research with diverse samples, and create culturally tailored interventions. Expected final online publication date for the Annual Review of Clinical Psychology, Volume 20 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Is the bacterial genus name Rhodococcus Zopf 1891 illegitimate? Request for an Opinion.

In 2014, it was reported that the bacterial genus name Rhodococcus Zopf 1891 was illegitimate due to the priority of the cyanobacterial genus name Rhodococcus Hansgirg 1884. Since that time, the consequences of this conclusion have been largely ignored, whilst changes have been made to relevant Rules of the International Code of Nomenclature of Prokaryotes, including significant changes to the way in which the Code treats the names of members of Cyanobacteriota. Given the complexity of the nomenclatural issues, we request the opinion of the Judicial Commission of the International Committee on Systematics of Prokaryotes as to whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate.

GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis.

Amplicon-based 16S ribosomal RNA sequencing remains a widely used method to profile microbial communities, especially in low biomass samples, due to its cost-effectiveness and low-complexity approach. Reference databases are a mainstay for taxonomic assignments, which typically rely on popular databases such as SILVA, Greengenes, Genome Taxonomy Database (GTDB), or Ribosomal Database Project (RDP). However, the inconsistency of the nomenclature across databases and the presence of shortcomings in the annotation of these databases are limiting the resolution of the analysis. To overcome these limitations, we created the GSR database (Greengenes, SILVA, and RDP database), an integrated and manually curated database for bacterial and archaeal 16S amplicon taxonomy analysis. Unlike previous integration approaches, this database creation pipeline includes a taxonomy unification step to ensure consistency in taxonomical annotations. The database was validated with three mock communities, two real data sets, and a 10-fold cross-validation method and compared with existing 16S databases such as Greengenes, Greengenes 2, GTDB, ITGDB, SILVA, RDP, and MetaSquare. Results showed that the GSR database enhances taxonomical annotations of 16S sequences, outperforming current 16S databases at the species level, based on the evaluation of the mock communities. This was confirmed by the 10-fold cross-validation, except for Greengenes 2. The GSR database is available for full-length 16S sequences and the most commonly used hypervariable regions: V4, V1-V3, V3-V4, and V3-V5.IMPORTANCETaxonomic assignments of microorganisms have long been hindered by inconsistent nomenclature and annotation issues in existing databases like SILVA, Greengenes, Greengenes2, Genome Taxonomy Database, or Ribosomal Database Project. To overcome these issues, we created Greengenes-SILVA-RDP database (GSR-DB), accurate and comprehensive taxonomic annotations of 16S amplicon data. Unlike previous approaches, our innovative pipeline includes a unique taxonomy unification step, ensuring consistent and reliable annotations. Our evaluation analyses showed that GSR-DB outperforms existing databases in providing species-level resolution, especially based on mock-community analysis, making it a game-changer for microbiome studies. Moreover, GSR-DB is designed to be accessible to researchers with limited computational resources, making it a powerful tool for scientists across the board. Available for full-length 16S sequences and commonly used hypervariable regions, including V4, V1-V3, V3-V4, and V3-V5, GSR-DB is a go-to database for robust and accurate microbial taxonomy analysis.

Precise Terminology and Specified Catheter Insertion Length in Ultrasound-Guided Infraclavicular Central Vein Catheterization.

Background and Objectives: As the latest research encourages the ultrasound-guided infraclavicular central venous approach, due to the lateral puncture site displacement, in comparison to the anatomical landmark technique based on subclavian vein catheterization, the need to re-calculate the optimal catheter insertion length and possibly to rename the punctuated vessel emerges. Although naming a particular anatomical structure is a nomenclature issue, a suboptimal catheter position can be associated with multiple life-threatening complications and must be avoided. The main study objective is to determine the optimal catheter insertion length by the most proximal ultrasound-guided, in-plane infraclavicular central vein approach, to compare results with the anatomical landmark technique based on subclavian vein catheterization and to clarify the punctuated anatomical structure. Materials and Methods: 109 patients were enrolled in this study. All procedures were performed according to the same catheterization protocol. In order to determine optimal insertion length, chest X-ray scans with an existing catheter were performed. The definition of punctuated vessel was based on computer tomography and evaluated by radiologists. Independent predictors for optimal insertion length were identified, prediction equations were generated. Results: The optimal catheter insertion length is approximately 1.5 cm longer than estimated by Pere's formula and can be accurately calculated based on anthropometric data. Computed tomography revealed: five cases with subclavian vein puncture and three cases with axillary vein puncture. Conclusions: Even the most proximal ultrasound-guided infraclavicular central vein access does not guarantee subclavian vein catheterization. A more accurate term could be infraclavicular central venous access, with the implication that the entry point could be through either subclavian or axillary veins. The optimal insertion length is approximately 1.5 cm deeper than the length determined for the anatomical landmark technique based on subclavian vein catheterization.

Cracking the glass‐perchlet code: Integrative taxonomy uncovers high species‐level diversity within the glass‐perchlet genus Ambassis (Ambassidae) in tropical Asia

AbstractGlass‐perchlets of the genus Ambassis (Teleostei; Ambassidae) form an important component of the brackish and marine coastal fish communities of tropical Asia. However, their species‐level diversity is still poorly documented because of the absence of recent taxonomic revisions in this region and the limited availability of specimens for research. In addition, long‐standing taxonomic and nomenclatural issues complicate the studies of this genus. Herein, we examine the diversity of Ambassis in Peninsular Malaysia using an integrative taxonomic approach and a large set of recently collected specimens from this region. Our initial morphological observations of 260 specimens revealed the presence of eight species, identified as Ambassis dussumieri, Ambassis interrupta, Ambassis kopsii, Ambassis macracanthus, Ambassis nalua, Ambassis octava, Ambassis urotaenia and Ambassis vachellii. We then sequenced the barcode fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene for 122 of our specimens, representing all eight morpho‐species. Automatic species delimitation methods recovered nine Molecular Operational Taxonomic Units (MOTUs) because A. interrupta is made of two MOTUs. Morphological re‐examination within A. interrupta detected variation at one character, congruent with molecular delimitation. Overall, our integrative approach unveiled rich species‐level diversity within the genus Ambassis in Peninsular Malaysia, with the presence of nine species. Further comparisons between our COI dataset and the COI sequences archived in the Barcode of Life Data System (BOLD) from specimens of Ambassis broadly collected in tropical Asian regions, indicated regional‐scale hidden diversity and identification conflicts, triggering the need for a complete taxonomic revision of this genus.

Lumping three nominal species into one: taxonomic revision of amphibian parasitic leeches of Torix in Far East Asia (Hirudinea: Glossiphoniidae)

Although most members of the freshwater leech family Glossiphoniidae have mid-body somites divided into three annuli, the genus Torix Blanchard, 1893 is distinguished by two-annuli somites. Torix has high species richness in Far East Asia, and three nominal species have been recognised in the Japanese Archipelago and adjacent regions that can be distinguished by a combination of both internal and external morphological characteristics. However, recent studies have shown that these diagnostic features are ontogenetically variable and this has resulted in taxonomic confusion among Torix species endemic to the Japanese Archipelago. In this study, we revisit the taxonomic accounts of T. orientalis (Oka, 1925) and T. tagoi (Oka, 1925), in addition to that of the recently redescribed T. tukubana (Oka, 1935) to clarify the diagnostic characteristics for each of the three species. Our morphological and molecular phylogenetic analyses demonstrated that the three Torix species in Japan are indistinguishable. We therefore conclude that these species should be synonymised and treated as a single species. The specific names orientalis and tagoi were simultaneously established under the genus Oligobdella Moore, 1918, therefore we acted as First Reviser and gave precedence to the name O. tagoi, thus the valid name for the Far East Asian Torix species is T. tagoi unless T. orientalis and T. tagoi are treated as distinct species. There are several type localities for T. tagoi and the name-bearing types have been lost, therefore we designate a neotype for this species to obviate zoological and nomenclatural issues. ZooBank: urn:lsid:zoobank.org:pub:E2DBF999-3B51-456F-AB04-A7D138E0AF2D

Description of fifty-one new species and new taxonomic arrangement for the E. sexdens group of the subgenus Edessa (Heteroptera, Pentatomidae, Edessinae, Edessa).

Within the subfamily Edessinae, Edessa Fabricius, 1803 is the genus with the most nomenclatural and taxonomic issues, basically related to the large number of poorly described species and the large number of new species. Furthermore, for many groups of morphologically similar species, certain names are used as tag names, adding to confusion and misidentification. The genus Edessa has been studied in small groups of species, either informal morphological groups within the genus or formal subgenera. Recently the nominal subgenus was revised and delimited, including the group E. sexdens. The E. sexdens group is diagnosed by a combination of characters such as anterior arms of metasternal process with excavated apex; connexival segments with a pair of dark spots; ventral surface of abdomen elevated medially; presence of a shallow rounded excavation near each spiracle; pygophore with union of dorsal rim and posterolateral angles with a groove, superior processes of the genital cup laminar, oblique to the paramere and continued ventrally by a carina; and paramere with three lobes. The biology of species in this group is almost unknown and most species have been collected in the Amazon region, particularly in the Brazilian Amazon. This group is the largest, in number of species, within the subgenus Edessa, presenting a surprising number of new species. In this article, fifty-one species new to science are described and Olbia magnifica Pirn, 1958 is transferred to Edessa. The composition of the E. sexdens group is updated to 74 species (23 previously described and 51 described here). The identification key to the species of the E. sexdens group is updated, and maps with the distribution of the new species are presented.

On the specific epithet “vaccinii” of Ashmead, 1887 and Burks, 1979 (Hymenoptera, Cynipidae)

Ashmead (1887) provided descriptions of two species of Cynipidae with “vaccinii” as the specific epithet: Solenozopheria vaccinii Ashmead, 1887 and Acraspis vaccinii Ashmead, 1887. There are numerous nomenclatural issues that have arisen from these descriptions. To resolve them, we have examined all relevant primary types and provide images of these specimens, as well as their labels. We recognize as valid the two “vaccinii” species, Loxaulus vaccinii (Ashmead, 1887) and Zopheroteras vaccinii (Ashmead, 1887), and list their synonyms. We also include the following new nomenclatural and taxonomic acts: Acraspis vaccinii Ashmead, 1887: lectotype by present designation; Callirhytis vaccinii Burks, 1979: species incertae sedis; Andricus impositus Beutenmüller, 1918: revalidated status; Andricus verifactor Kinsey, 1922: new status.

Creating convict criminology in the UK: a response to Aresti, Darke and Ross from members of the British Convict Criminology group

Responding to an earlier article (Aresti et al, 2023) by two scholars involved in convict criminology at Westminster University and a third from the US, this article mounts a defence of the British Convict Criminology group against the analysis and conclusions of the first article. We argue that convict criminology is diverse and needs to embrace different approaches that correspond to national circumstances, both in prisons and universities. We suggest that far from stagnating, convict criminology in the UK is beginning to thrive and has much to offer critical criminology. This offer is strengthened by adopting critical and convivial academic practice supportive of people’s various efforts and experiences in British prisons and British universities. Our article offers a critical engagement with issues of nomenclature, convictism and coloniality which we believe will be important for an inclusive convict criminology for the future.

Network of GRAS transcription factors in plant development, fruit ripening and stress responses

Abstract The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition.

Hot Is Rich—An Enormous Diversity of Simple Trichal Cyanobacteria from Yellowstone Hot Springs

In 2019, cyanobacterial samples were collected from thermal sites in Yellowstone National Park. In this paper, we discuss the considerable richness of representatives of simple filamentous cyanobacteria. Using a polyphasic approach, one new genus, Copelandiella, with two species (C. yellowstonensis and C. thermalis) and eight additional new species Albertania prattii, K. anagnostidisii, Kovacikia brockii, Leptolyngbya tildenae, L. vaporiphila, Nodosilinea calida, N. igneolacustris, and Oculatella castenholzii were described. At the same time, by analyzing our new molecular data, we concluded that other genera of trichal cyanobacteria can be merged with existing genera: species within the genus Plectolyngbya are herein transferred to Leptolyngbya, and if some nomenclatural issues are resolved, species within the genus Leptothermofonsia will be subsequently transferred to the genus Kovacikia, an earlier synonym.