Valid Publication Research Articles

Options and considerations for validation of prokaryotic names under the SeqCode

Stable taxon names for Bacteria and Archaea are essential for capturing and documenting prokaryotic diversity. They are also crucial for scientific communication, effective accumulation of biological data related to the taxon names and for developing a comprehensive understanding of prokaryotic evolution. However, after more than a hundred years, taxonomists have succeeded in valid publication of only around 30 000 species names, based mostly on pure cultures under the International Code of Nomenclature of Prokaryotes (ICNP), out of the millions estimated to reside in the biosphere. The vast majority of prokaryotic species have not been cultured and are becoming increasingly known to us via culture-independent sequence-based approaches. Until recently, such taxa could only be addressed nomenclaturally via provisional names such as Candidatus or alphanumeric identifiers. Here, we present options and considerations to facilitate validation of names for these taxa using the recently established Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Community engagement and participation of relevant taxon specialists are critical and encouraged for the success of endeavours to formally name the uncultured majority.

Validation List no. 219. Valid publication of new names and new combinations effectively published outside the IJSEM.

Validation List no. 219. Valid publication of new names and new combinations effectively published outside the IJSEM.

OligoM-Cancer: A multidimensional information platform for deep phenotyping of heterogenous oligometastatic cancer

Patients with oligometastatic cancer (OMC) exhibit better response to local therapeutic interventions and a more treatable tendency than those with polymetastatic cancers. However, studies on OMC are limited and lack effective integration for systematic comparison and personalized application, and the diagnosis and precise treatment of OMC remain controversial. The application of large language models in medicine remains challenging because of the requirement of high-quality medical data. Moreover, these models must be enhanced using precise domain-specific knowledge. Therefore, we developed the OligoM-Cancer platform (http://oligo.sysbio.org.cn), pioneering knowledge curation that depicts various aspects of oligometastases spectrum, including markers, diagnosis, prognosis, and therapy choices. A user-friendly website was developed using HTML, FLASK, MySQL, Bootstrap, Echarts, and JavaScript. This platform encompasses comprehensive knowledge and evidence of phenotypes and their associated factors. With 4059 items of literature retrieved, OligoM-Cancer includes 1345 valid publications and 393 OMC-associated factors. Additionally, the included clinical assistance tools enhance the interpretability and credibility of clinical translational practice. OligoM-Cancer facilitates knowledge-guided modeling for deep phenotyping of OMC and potentially assists large language models in supporting specialised oligometastasis applications, thereby enhancing their generalization and reliability.

Bibliometric Analysis of the Research Status and Global Trends in Behavioral and Psychological Symptoms of Dementia in Alzheimer's Disease from 2002 to 2022.

Several reviews on behavioral and psychological symptoms (BPSDs) in patients with Alzheimer's disease (AD) have summarized the current state of this field, but global trends are unclear. This study utilized CiteSpace to provide a global overview of the current state of research on AD and its BPSDs and to predict future research trends in the field. Data were retrieved from the Web of Science Core Collection. Bibliometric and cooccurrence analyses were performed using CiteSpace software. In total, 787 valid publications were included in the analysis. Publications on AD and BPSD have shown an increasing trend since 2002. The United States and the University of Toronto were the countries and institutions with the highest total number of publications, respectively. Japan and China were the second and third most influential in the field. Clive Ballard was the top author in terms of the number of publications. Journal of Alzheimer's Disease had the highest number of publications on this topic. Co-occurrence analysis showed that AD, behavioral symptoms, cognitive impairment, and early markers are hot topics in this area. Non-drug management of BPSDs, pharmacological treatment, and physiotherapy will be a hot topic in this field in the future. Our study visualized the relevant articles over the past 21 years to detect global hotspots and trends. Our findings may help researchers to identify research hotspots in this field and will help in the selection of appropriate research topics, while possibly leading to cross-regional cooperation.

Validation List no. 218. Valid publication of new names and new combinations effectively published outside the IJSEM.

Validation List no. 218. Valid publication of new names and new combinations effectively published outside the IJSEM.

SeqCode: A Nomenclatural Code for Prokaryotes.

SeqCode is a nomenclatural code for naming prokaryotes based on genetic information. With the majority of prokaryotes being inaccessible as pure cultures, they are not eligible for naming under the International Code of Nomenclature of Prokaryotes. To address this challenge, a new concept that is SeqCode, which assign names to prokaryotes on the basis of genome sequence, has been announced in 2022. The valid publication of names for prokaryotes based on isolated genome, metagenome-assembled genomes, or single-amplified genome sequences. It operates through a registration portal, SeqCode Registry, where metadata is linked to names and nomenclatural types. This code provides a framework for reproducible nomenclature for all prokaryotes, either culturable or not and facilitates communication across all microbiological disciplines. Additionally, the SeqCode includes provisions for updating and revising names as new data becomes available. By providing a standardized system for naming and classifying these microorganisms based on their genetic information, the SeqCode will facilitate the discovery, understanding and comparison of these microorganisms, helping us to understand their role in the environment and how they contribute to the functioning of the Earth.

Menstrual Cramps in Anovulatory versus Normally Ovulatory Cycles - SARS-COV-2 Pandemic Daily Data Plus a Meta-Analysis of Cramps and Anovulation.

It is asserted that primary dysmenorrhea/menstrual cramps only occur in ovulatory menstrual cycles. Our first objective was to present detailed menstrual cramps information in normally ovulatory versus anovulatory cycles from a single-cycle cohort study during the SARS-CoV-2 Pandemic. Secondly, we reviewed the literature for cohort studies documenting both menstrual cramps and ovulation. The Menstruation and Ovulation Study 2 recruited 108 women ages 19-35 years to a prospective, observational single-cycle study, recording cramps daily (0-4 scale) in the Menstrual Cycle Diary© and assessing normal ovulation (luteal length ≥10 days) by the validated Quantitative Basal Temperature© (Mean Temperature Method). We searched databases for «primary dysmenorrhea» /» menstrual cramps»; «menstrual cycles»; «anovulation», finding four valid publications. In 75 women/cycles during the Pandemic, mean age was 28.5, body mass index 23.5, and higher education (16 years); 40 normally ovulatory and 35 anovulatory cycles had similar lengths (29.5-30.0 days), respectively (P=0.571). However, anovulatory cycles recorded significantly worse menstrual cramps versus normally ovulatory cycles;anovulatory median intensity was 1.9 versus 1.6, and Cramp Score was 8 versus 6 in normally ovulatory cycles (P=0.017). Four publications in 273 women (991 cycles) showed cramps in both anovulatory and ovulatory cycles; three were in adolescent/young adult women, one of which documented a significantly greater percentage of cramps in ovulatory cycles. The 694 cycles in premenopausal women (20-41 years) showed similar percentages of symptomatic cramps in cycles of both ovulatory types. Meta-analysis documented significantly higher cramp prevalence in ovulatory cycles (OR 2.10; 95% CI 1.31, 3.37; P=0.002). This is the first documentation of more intense and frequent cramps in anovulatory cycles. However, meta-analysis showing the presence of symptomatic cramps in both ovulatory and anovulatory cycles documented they were twice as prevalent in ovulatory menstrual cycles.

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.

Validation List no. 217. Valid publication of new names and new combinations effectively published outside the IJSEM.

Validation List no. 217. Valid publication of new names and new combinations effectively published outside the IJSEM.

Reinstatement of the East African Asplenium aequilaterale (Aspleniaceae), and resolution of its synonymy

Following the valid publication in 1894 of the name Asplenium [‘Asplenum’] anisophyllum Kunze (1836: 511) var. aequilaterale Hieronymus in Engler (1894: 45) in the fern family Aspleniaceae for an East African taxon, and the further valid publication of this varietal name in Engler’s Die Pflanzenwelt Ost-Afrikas und der Nachbargebiete, Deutsch-Ost-Afrika the following year (Hieronymus 1895: 82), as Asplenium [again as ‘Asplenum’] anisophyllum Kunze (1836: 511) var. aequilaterale [‘aequilateralis’] Hieronymus in Engler (1895: 82), it seemingly remained unnoticed by pteridologists for nearly a century. Viane & Reichstein (1992) have pointed out that the name was not even listed in the Index Filicum of Christensen (1906) and Supplements, on which account it may have been overlooked in later relevant literature that includes Peter (1929), Faden (1973, 1974), and Jacobsen & Jacobsen (1989). Along with a specimen accessioned to Herb. B (Holst 2491), Viane & Reichstein (1992) relied on material collected by R.R. Schippers, held at Wageningen (Herb. WAG), to assess the status and position of Hieronymus’s variety. They deemed it recognisable at species rank and, accordingly, Viane published the name A. aequilaterale (Hieronymus in Engler 1895: 82) Viane in Viane & Reichstein (1992: 157), with Holst 2491 at Herb. B cited as the “holotype”. They recognised that the affinity of their species was not with A. anisophyllum in its present circumscription, but rather with the tropical African A. macrophlebium Baker in Hooker & Baker (1874: 485). The terrestrial A. aequilaterale was considered to grow in mid-montane forests between elevations of 1350 and 1950 m, within the South Pare and West Usambara mountains (Viane 1992). Schippers (1993) shortly thereafter extended the range of A. aequilaterale to include the North Pare mountains of Tanzania, and the Teita Hills of Kenya. He described it as a relatively common steep forest floor inhabitant, particularly in the South Pare and West Usambara mountains.

Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM.

Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM.

Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode

Codes of nomenclature that provide well-regulated and stable frameworks for the naming of taxa are a fundamental underpinning of biological research. These Codes themselves require systems that govern their administration, interpretation and emendment. Here we review the provisions that have been made for the governance of the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which provides a nomenclatural framework for the valid publication of names of Archaea and Bacteria using isolate genome, metagenome-assembled genome or single-amplified genome sequences as type material. The administrative structures supporting the SeqCode are designed to be open and inclusive. Direction is provided by the SeqCode Community, which we encourage those with an interest in prokaryotic systematics to join.

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 requirethe 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.

Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM.

Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM.

Valid publication of names of two domains and seven kingdoms of prokaryotes.

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.

Against Over-reliance on PRISMA Guidelines for Meta-analytical Studies.

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were elaborated to allow authors of such papers to identify quality articles for inclusion in their scholarly work. However, we have identified several issues that point to an over-reliance on the PRISMA guidelines. Firstly, we question the rigor of implementation by authors and the rigor of verification by peer reviewers and editors, and whether they have screened papers to ensure adherence to the PRISMA guidelines. Secondly, we have identified cases where the PRISMA criteria led to as much as 99.97% of the published literature being ignored, suggesting that valid publications meeting these criteria might be at risk of being ignored. Thirdly, we have noted that exclusion is not only a quantitative problem-it is also a qualitative one, since the screening procedure groups all non-conforming literature into one basket. Fourthly, we have noted that seven copies of the PRISMA guidelines exist. This being the case, which one should be cited? To replace over-reliance on PRISMA screening, we encourage authors, peer reviewers, and editors to publish systematic reviews and meta-analyses that respect the dual criteria of scientific plausibility and diversity of included papers.

Proposal of three novel insect-associated Commensalibacter species: Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov.

A recent modification of the Note to Rule 25a of the International Code for Nomenclature of Bacteria is used a posteriori by the List Editors of the International Journal of Systematic and Evolutionary Microbiology to justify the refusal to validate species protologues published in supplementary material prior to this formal decision. Authors are therefore forced to ask permission to reuse published data for the valid publication of such names. In the present letter we re-publish the species protologues of Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov.

Current Trends in Chronic Non-Communicable Disease Management: A Bibliometric Analysis of the Past Two Decades.

In recent years, there has been a growing focus on chronic non-communicable diseases (NCD) and their impact on personal and social health. Effective management of NCD is essential for their prevention and treatment. This study aims to utilize bibliometric methods to analyze and summarize the current development and emerging trends in NCD management. A literature search and screening were conducted on the Web of Science Core Collection database from January 1, 2004, to December 31, 2023. VOSviewer and Citespace software was performed to examine publication volume, authors, institutions, countries, journals, citation frequencies, keywords, clustering, and burst terms, and to create a visual map. A total of 996 valid publications from 464 journals were included in the study. The number of publications exhibited a gradual growth trend over the years. The United States was the most productive and influential country, contributing the highest proportion of both publications and total citations. BMC Health Services Research, Toronto University, and Marshall, Bruce C. were identified as the most productive journal, institution, and author, respectively. Further analysis of keyword co-occurrence and burst detection revealed that the most prevalent keywords were "improving primary care" and "integrated care". This bibliometric analysis provides a comprehensive overview of the current status and trends in NCD management over the past two decades, providing valuable insights for future research directions. It indicates a potential shift towards enhancing primary healthy care, integrated care, and digital health.

Validation List no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM.

Validation List no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM.

A review of the infrageneric classifications proposed for Kalanchoe (Crassulaceae subfam. Kalanchooideae) from the earliest times up to 2000

The infrageneric classifications, especially at the ranks of subgenus, section, and subsection proposed for Kalanchoe (Crassulaceae subfam. Kalanchooideae) from the early 1800s up to the end of the 20th century, are analysed. The pertinent works of especially Haworth (1820s); Baillon (1880s); Raymond-Hamet, Koorders, and Berger (all three from the early 1900s to 1930s); Boiteau and as elaborated on by Boiteau and Mannoni (1940s); Raymond-Hamet and Marnier-Lapostolle (1960s); Maire (1970s); and Boiteau and Allorge-Boiteau (1990s) are assessed to clarify the use of infrageneric ranks by these authors. From this analysis of the infrageneric classification of Kalanchoe during a period of about 250 years, it is evident that, with the exception of: (1) one validly published unranked name published by Baillon in 1885; (2) one subgenus name validly published by Koorders in 1919; (3) several unranked names validly published by Alwin Berger in 1930; and (3) two new combinatons validly published by Boiteau in 1947 at the rank of section and two new combinatons validly published by Boiteau in 1947 at the rank of subsection, all other such designations that were proposed between 1 January 1935 and 1 January 1953 were not validly published. The dates 1 January 1935 (Art. 39.1 of the International Code of Nomenclature for algae, fungi, and plants [ICN], Latin requirement) and 1 January 1953 (aspects of Articles 35 and 41 of the ICN, on new combinations, names at new ranks, and replacement names) are significant in determining the valid publication of historically proposed new names and new combinations. Furthermore, all the names proposed for infrageneric groups in Kalanchoe that postdate 1 January 1953, and up to 2000, the cutoff date used in this paper, were not validly published (aspects of Art. 41 of the ICN, on new combinations, names at new ranks, and replacement names) or were proposed informally only and not intended for valid publication. Note, especially, that neither of the two infrageneric designations proposed in 1916 and 1933, respectively, by Raymond-Hamet, the undisputed authority on Kalanchoe during the 20th century, were validly published.