List of new names and new combinations previously effectively, but not validly, published.
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ABSTRACT:
SUBMITTER: Oren A
PROVIDER: S-EPMC5817221 | biostudies-literature | 2017 Sep
REPOSITORIES: biostudies-literature
Publications
List of new names and new combinations previously effectively, but not validly, published.
Oren Aharon A Garrity George M GM
International journal of systematic and evolutionary microbiology 20170901 9
Similar Datasets
Project description:The List of Available Names in Zoology (LAN) is an inventory of names with specific scope in time and content, presented and approved in parts, and constituted as a cumulative index of names available for use in zoological nomenclature. It was defined in Article 79 in the fourth edition of the International Code of Zoological Nomenclature. The LAN is likely to gain importance with the development of the online Official Registry for Zoological Nomenclature (ZooBank) as it is potentially a source of many nomenclaturally certified names. Article 79 describes the deliberative process for adding large numbers of names to the LAN simultaneously, detailing steps and chronology for submission of a candidate Part to the LAN and consideration of a candidate Part by the public and Commission, but it is largely mute about the contents of a candidate Part. It does make clear that a name within the scope of a Part but not on the LAN has no nomenclatural standing, even if it had previously been considered available, thereby preventing long-forgotten names from displacing accepted ones and the accumulation of nomina dubia. Thus, for taxa on the LAN, nomenclatural archaeology - the resurrecting of old unused names to replace by priority names in current usage - will not be worthwhile. Beyond that, it has been unclear if Article 79 is intended to document every available name known within the scope of the Part, or if its intention is to pare the inventory of available names within the scope of the Part. Consideration by the Commission and two committees to deal with the LAN have defined steps to implement Article 79 with the latter intent. Procedures for consideration of a candidate Part are defined in a manual, published as an appendix in this volume.
| S-EPMC4741223 | biostudies-other
Project description:Calcareous dinophytes produce exoskeletal calcified structures during their life history (a unique character among the alveolates) and are subsumed under the Thoracosphaeraceae as part of the Peridiniales. We provide a brief synopsis about the taxonomic history of the group, from the first descriptions of fossils in the 19th century through to the results of molecular phylogenetics studies undertaken during the past two decades. Delimitation and circumscription of the Thoracosphaeraceae are challenging, as they comprise both phototrophic (presumably including endosymbiotic) as well as heterotrophic (and even parasitic) dinophytes from marine and freshwater environments, respectively. However, calcareous structures are not known from all members of the Thoracosphaeraceae, and the corresponding species and groups are considered to have lost the capacity to calcify. Five years ago, a taxonomic list of 99 generic names assigned to the Thoracosphaeraceae was published, and we update this compendium with 19 additional names based on recent studies.
| S-EPMC5029491 | biostudies-literature
Project description:Elatostema (Urticaceae) comprises several hundred herbaceous species distributed in tropical and subtropical Africa, Asia, Australia and Oceania. The greatest species richness occurs on limestone karst in Southeast Asia. Taxonomic revisions of Elatostema are largely out of date and contradict each other with respect to the delimitation of Elatostema and Pellionia. Most herbaria in SE Asia and worldwide contain significant amounts of unidentified material. As part of a broader revision of Elatostema in SE Asia, we present an updated checklist for Vietnam based on field visits, a review of specimens in herbaria worldwide, a review of type material and nomenclature. We recognize 77 taxa (75 species and two infraspecific taxa) of Elatostema in Vietnam, 23 of which were previously ascribed to Pellionia. Nineteen of these are new records for the country, i.e., E. attenuatoides, E. austrosinense, E. backeri, E. brunneinerve, E. crassiusculum, E. crenatum, E. fengshanense, E. glochidioides, E. malacotrichum, E. nanchuanense, E. oblongifolium, E. obtusum, E. oppositum, E. pergameneum, E. prunifolium, E. pseudolongipes, E. pycnodontum, E. salvinioides and E. xichouense. We place E. baviensis in synonymy of E. platyphyllum, E. colaniae in synonymy of E. myrtillus, P. macroceras in synonymy of E. hookerianum, and P. tetramera in synonymy of E. dissectum for the first time. Fourteen taxa (18% of all the recognized taxa) are endemic to Vietnam, which makes Elatostema one of the richest genera for endemic species in this country; this level of endemism is comparable to levels observed in Orchidaceae. Our checklist suggests that the highest diversity and endemism of Elatostema occurs in northern Vietnam, and that there is the greatest floristic similarity of northern Vietnam to SW China. The relationship among floristic regions is also investigated. We could find no records of Elatostema for 33 out of 63 provincial units of Vietnam, including all the southernmost provinces. We propose that further studies on the diversity of Elatostema in central and southern Vietnam are severely needed.
| S-EPMC6330208 | biostudies-literature
Project description:Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.
| S-EPMC5941136 | biostudies-literature
Project description:Antibiotic-resistant bacteria are a significant threat to human health, with one estimate suggesting they will cause 10 million worldwide deaths per year by 2050, surpassing deaths due to cancer1. Because new antibiotic development can take a decade or longer, it is imperative to effectively use currently available drugs. Antibiotic combination therapy offers promise for treating highly resistant bacterial infections, but the factors governing the sporadic efficacy of such regimens have remained unclear. Dogma suggests that antibiotics ineffective as monotherapy can be effective in combination2. Here, using carbapenem-resistant Enterobacteriaceae (CRE) clinical isolates, we reveal the underlying basis for the majority of effective combinations to be heteroresistance. Heteroresistance is a poorly understood mechanism of resistance reported for different classes of antibiotics3-6 in which only a subset of cells are phenotypically resistant7. Within an isolate, the subpopulations resistant to different antibiotics were distinct, and over 88% of CRE isolates exhibited heteroresistance to multiple antibiotics ('multiple heteroresistance'). Combinations targeting multiple heteroresistance were efficacious, whereas those targeting homogenous resistance were ineffective. Two pan-resistant Klebsiella isolates were eradicated by combinations targeting multiple heteroresistance, highlighting a rational strategy to identify effective combinations that employs existing antibiotics and could be clinically implemented immediately.
| S-EPMC7205309 | biostudies-literature
Project description:[This corrects the article DOI: 10.1016/j.cegh.2021.100802.][This corrects the article DOI: 10.1016/j.cegh.2021.100904.][This corrects the article DOI: 10.1016/j.cegh.2021.100850.][This corrects the article DOI: 10.1016/j.cegh.2020.04.019.][This corrects the article DOI: 10.1016/j.cegh.2021.100813.][This corrects the article DOI: 10.1016/j.cegh.2020.02.016.][This corrects the article DOI: 10.1016/j.cegh.2020.100677.][This corrects the article DOI: 10.1016/j.cegh.2019.12.021.][This corrects the article DOI: 10.1016/j.cegh.2021.100786.][This corrects the article DOI: 10.1016/j.cegh.2020.05.017.][This corrects the article DOI: 10.1016/j.cegh.2021.100749.][This corrects the article DOI: 10.1016/j.cegh.2020.04.017.][This corrects the article DOI: 10.1016/j.cegh.2021.100784.][This corrects the article DOI: 10.1016/j.cegh.2021.100727.][This corrects the article DOI: 10.1016/j.cegh.2021.100737.].
| S-EPMC10250821 | biostudies-literature
Project description:There is a growing interest in standardizing gene-disease associations for the purpose of facilitating the proper classification of variants in the context of Mendelian diseases. One key line of evidence is the independent observation of pathogenic variants in unrelated individuals with similar phenotypes. Here, we expand on our previous effort to exploit the power of autozygosity to produce homozygous pathogenic variants that are otherwise very difficult to encounter in the homozygous state due to their rarity. The identification of such variants in genes with only tentative associations to Mendelian diseases can add to the existing evidence when observed in the context of compatible phenotypes. In this study, we report 20 homozygous variants in 18 genes (ADAMTS18, ARNT2, ASTN1, C3, DMBX1, DUT, GABRB3, GM2A, KIF12, LOXL3, NUP160, PTRHD1, RAP1GDS1, RHOBTB2, SIGMAR1, SPAST, TENM3, and WASHC5) that satisfy the ACMG classification for pathogenic/likely pathogenic if the involved genes had confirmed rather than tentative links to diseases. These variants were selected because they were truncating, founder with compelling segregation or supported by robust functional assays as with the DUT variant that we present its validation using yeast model. Our findings support the previously reported disease associations for these genes and represent a step toward their confirmation.
| S-EPMC7806527 | biostudies-literature
Project description:A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as "dark taxa" or "dark matter fungi". As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.
| S-EPMC5904500 | biostudies-literature
Project description:This study is aimed to shed light on the reliability of Sherborn's Index Animalium in terms of modern usage. The AnimalBase project spent several years' worth of teamwork dedicated to extracting new names from original sources in the period ranging from 1757 to the mid-1790s. This allowed us to closely analyse Sherborn's work and verify the completeness and correctness of his record. We found the reliability of Sherborn's resource generally very high, but in some special situations the reliability was reduced due to systematic errors or incompleteness in source material. Index Animalium is commonly used by taxonomists today who rely strongly on Sherborn's record; our study is directed most pointedly at those users. We recommend paying special attention to the situations where we found that Sherborn's data should be read with caution. In addition to some categories of systematic errors and mistakes that were Sherborn's own responsibility, readers should also take into account that nomenclatural rules have been changed or refined in the past 100 years, and that Sherborn's resource could eventually present outdated information. One of our main conclusions is that error rates in nomenclatoral compilations tend to be lower if one single and highly experienced person such as Sherborn carries out the work, than if a team is trying to do the task. Based on our experience with extracting names from original sources we came to the conclusion that error rates in such a manual work on names in a list are difficult to reduce below 2-4%. We suggest this is a natural limit and a point of diminishing returns for projects of this nature.
| S-EPMC4741220 | biostudies-other
Project description:BackgroundDexmedetomidine is a sedative and analgesic increasingly used in children supported with extracorporeal membrane oxygenation (ECMO). No data is available to describe the pharmacokinetics (PK) of dexmedetomidine in this population.MethodsWe performed a single-center prospective PK study. Children <18 years old, supported with ECMO, and on a dexmedetomidine infusion as part of their management were prospectively included. PK samples were collected. Dexmedetomidine dosing remained at the discretion of the clinical team. Six population PK models built in pediatrics were selected. Observed concentrations were compared with population predicted concentrations using the PK models.ResultsEight children contributed 30 PK samples. None of the PK models evaluated predicted the concentrations with acceptable precision and bias. Four of the six evaluated models overpredicted the concentrations. The addition of a correction factor on clearance improved models' fit. Two of the evaluated models were not applicable to our whole population age range because of their structure.ConclusionMost of the evaluated PK models overpredicted the concentrations, potentially indicating increased clearance on ECMO. Population PK models applicable to a broad spectrum of ages and pathologies are more practical in pediatric critical care settings but challenging to develop.
| S-EPMC9271626 | biostudies-literature