Real-world statistics at two timescales and a mechanism for infant learning of object names.

Infants begin learning the visual referents of nouns before their first birthday. Despite considerable empirical and theoretical effort, little is known about the statistics of the experiences that enable infants to break into object­name learning. We used wearable sensors to collect infant experiences of visual objects and their heard names for 40 early-learned categories. The analyzed data were from one context that occurs multiple times a day and includes objects with early-learned names: mealtime. The statistics reveal two distinct timescales of experience. At the timescale of many mealtime episodes (n = 87), the visual categories were pervasively present, but naming of the objects in each of those categories was very rare. At the timescale of single mealtime episodes, names and referents did cooccur, but each name­referent pair appeared in very few of the mealtime episodes. The statistics are consistent with incremental learning of visual categories across many episodes and the rapid learning of name­object mappings within individual episodes. The two timescales are also consistent with a known cortical learning mechanism for one-episode learning of associations: new information, the heard name, is incorporated into well-established memories, the seen object category, when the new information cooccurs with the reactivation of that slowly established memory.

SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses.

BACKGROUND: The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained. RESULTS: To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers. CONCLUSIONS: The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature.

Request for an Opinion: conservation of the illegitimate prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980).

The prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980) is a later homonym of the protozoan genus name Proteus Müller, 1786 and therefore should be considered illegitimate and in need of replacement according to Rules 51b(4) and 54 of the International Code of Nomenclature of Prokaryotes. However, it would be unwelcome for medical and veterinary community to propose by anyone any replacement name and discontinue the current usage. To prevent from any unfavourable replacement, conservation of the illegitimate prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980) according to Rules 23a Note 4 and 56b is needed, and therefore, a request for conservation by the Judicial Commission over its earlier protozoan homonym is made here by the author, with Judicial Opinions 9 and 12 serving as precedents.

Proposal of Shuttleworthella gen. nov. and Nostocoides gen. nov. as replacement names for the illegitimate prokaryotic generic names Shuttleworthia and Tetrasphaera, respectively.

The prokaryotic generic name Shuttleworthia Downes et al. 2002 is illegitimate because it is a later homonym of the plant genus Shuttleworthia Meisner 1840 and the mollusk genus Shuttleworthia Baker 1941 (Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Shuttleworthella, with type species Shuttleworthella satelles comb. nov. The prokaryotic generic name Tetrasphaera Maszenan et al. 2000 is illegitimate because it is a later homonym of Tetrasphaera Popofsky 1913 (Protozoa, Radiolaria) and of Tetrasphaera Górka 1965 (a fossil dinoflagellate) (Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Nostocoides, with type species Nostocoides japonicum comb. nov.

Reclassification of Allomuricauda and Muricauda species as members of the genus Flagellimonas Bae et al. 2007 and emended description of the genus Flagellimonas.

The recently proposed genus Allomuricauda Deshmukh and Oren 2023 is illegitimate because it includes the type species of the genera Flagellimonas Bae et al. 2007 and Spongiibacterium Yoon and Oh 2012, contravening Rule 51b(1) of the International Code of Nomenclature of Prokaryotes. As Flagellimonas Bae et al. 2007 is the earlier described genus, we here reclassify 36 species earlier described as belonging to the illegitimate genus Muricauda as species of Flagellimonas. We also present an emended description of the genus Flagellimonas.

Formation of prokaryote names from personal names: a review of current practice and a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes.

The practice of naming elements from the natural world after notable individuals stretches back to ancient times. This practice of creating eponyms-terms derived from personal names-has been carried forward into prokaryotic nomenclature, where the International Code of Nomenclature of Prokaryotes (ICNP) sets guidelines for creating scientific names from personal names. However, these guidelines can be seen as culturally biased, disjointed and, on occasion, misguided. Here, with the goal of modernizing these recommendations to render them more user-friendly, coherent and inclusive, I review current practice in the light of precedents and key linguistic and cultural principles, while questioning the applicability of the first-name/last-name paradigm for many cultural traditions. Procedural challenges include romanization of the personal name (including handling of diacritics), creation of a short and agreeable latinized stem, assignment of the stem to a declension and addition of suffixes or compound word components to create genus names or species epithets, customizing the approach for names and stems that end in a vowel. I review the pros and cons of stem augmentation, which involves addition of an extra 'i' to the original stem. Next, I formulate a coherent workflow, which I incorporate into a Python script to enable computer-based automation of name creation. Rather than following the ICNP in limiting discussion to a few dozen mainly European names, I examine how these principles work out when applied to the tens of thousands of last names under which scientists publish in the PubMed database, focusing on edge cases where conventional approaches fail, particularly very short and very long names. Drawing on these explorations and analyses, I propose emendations to the advice currently presented in the ICNP to usher in a modern, consistent, pragmatic and globally inclusive approach to the creation of prokaryotic eponyms.

Emendation of Appendix 9 of the International Code of Nomenclature of Prokaryotes to provide guidelines for naming genera after geographical locations.

Following a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes with guidelines for the naming of genera after geographical locations, I here report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes and present the guidelines to be incorporated in Appendix 9.

Visual word identification beyond common words: The role of font and letter case in brand names.

While abstractionist theories of visual word recognition propose that perceptual elements like font and letter case are filtered out during lexical access, instance-based theories allow for the possibility that these surface details influence this process. To disentangle these accounts, we focused on brand names embedded in logotypes. The consistent visual presentation of brand names may render them much more susceptible to perceptual factors than common words. In the present study, we compared original and modified brand logos, varying in font or letter case. In Experiment 1, participants decided whether the stimuli corresponded to existing brand names or not, regardless of graphical information. In Experiment 2, participants had to categorize existing brand names semantically - whether they corresponded to a brand in the transportation sector or not. Both experiments showed longer response times for the modified brand names, regardless of font or letter-case changes. These findings challenge the notion that only abstract units drive visual word recognition. Instead, they favor those models that assume that, under some circumstances, the traces in lexical memory may contain surface perceptual information.

Competition accumulates in successive retrieval of proper names.

Proper names are especially prone to retrieval failures and tip-of-the-tongue states (TOTs)-a phenomenon wherein a person has a strong feeling of knowing a word but cannot retrieve it. Current research provides mixed evidence regarding whether related names facilitate or compete with target-name retrieval. We examined this question in two experiments using a novel paradigm where participants either read a prime name aloud (Experiment 1) or classified a written prime name as famous or non-famous (Experiment 2) prior to naming a celebrity picture. Successful retrievals decreased with increasing trial number (and was dependent on the number of previously presented similar famous people) in both experiments, revealing a form of accumulating interference between multiple famous names. However, trial number had no effect on TOTs, and within each trial famous prime names increased TOTs only in Experiment 2. These results can be explained within a framework that assumes competition for selection at the point of lexical retrieval, such that successful retrievals decrease after successive retrievals of proper names of depicted faces of semantically similar people. By contrast, the effects of written prime words only occur when prime names are sufficiently processed, and do not provide evidence for competition but may reflect improved retrieval relative to a "don't know" response.

Allergens grouping names on packaging: Are the substances similar enough to ensure safety? The worst case scenarios question this.

OBJECTIVE: European Commission Regulation (EU) n°2023/1545 introduced the concept of grouping names in the cosmetics sector in July 2023. These groups bring together allergenic substances with the same level of skin sensitization. Their purpose is to lighten the list of ingredients on cosmetic packaging, by grouping together substances deemed to be similar under the same name. As this classification is based on a single toxic effect - skin sensitization - the present study aims to analyse the relevance of these groupings with regard to other toxic effects of substances in the same group. METHODS: This study was carried out by consulting an available database, various reports from 5 committees, 2 books and 5 articles in order to complete the toxicological profile of each substance. Then, in order to highlight any discrepancies within the classification, the worst cases were identified. For this purpose, the data for each substance in a group were compared, and in the event of greater criticality for a toxic effect, this was qualified as a worst case. In addition, similar toxic effects between several substances within the same group were also recorded. The aim of this additional research was to validate the definition of the grouping name and the similarities between substances in the same group. RESULTS: From the 17 grouping names, 5 presented worst cases. Two groups had 2 worst cases and the others only one. In total, from the 7 worst cases detected, 3 were due to the toxic effect "skin irritation". In most cases, the substances in the groupings shared the presence or absence of risk. Only the degree of risk criticality varied. CONCLUSION: Classification by grouping names appears justified regarding the similarities between substances, particularly in terms of skin sensitization. However, the presence of worst cases qualifies it and highlights the importance of being vigilant when assessing the risk of cosmetic products including these grouping names in their list of ingredients.

OBJECTIF: Le règlement (UE) n°2023/1545 de la Commission européenne a introduit la notion de « grouping names ¼ dans le domaine des cosmétiques en juillet 2023. Ces groupes rassemblent des substances allergènes ayant le même niveau de sensibilisation cutanée. Ils ont pour objectif d'alléger la liste des ingrédients figurant sur les emballages des produits cosmétiques, en regroupant sous un même nom des substances jugées similaires. Cette classification étant fondée sur un seul effet toxique ­ la sensibilisation cutanée ­ la présente étude vise à analyser la pertinence de ces regroupements au regard des autres effets toxiques des substances d'un même groupe. MÉTHODES: Cette étude a été réalisée en consultant une base de données disponible, différents rapports de 5 comités, 2 livres et 5 articles afin de compléter le profil toxicologique de chaque substance. Ensuite, afin de mettre en évidence les divergences au sein de la classification, les cas de criticité plus importante ont été identifiés. Pour ce faire, les données de chaque substance d'un groupe ont été comparées, et en cas de criticité supérieure d'un effet toxique, celui­ci a été qualifié de « worst case ¼. En outre, les effets toxiques similaires entre plusieurs substances d'un même groupe ont également été enregistrés. L'objectif de cette recherche complémentaire était de valider la définition du « grouping name ¼ et les similitudes entre les substances d'un même groupe. RÉSULTATS: Sur les 17 « grouping names ¼, 5 présentaient des « worst cases ¼. Deux groupes présentaient deux « worst cases ¼ et les autres un seul. Au total, sur les 7 « worst cases ¼ détectés, 3 étaient dus à l'effet toxique "irritation cutanée". Dans la plupart des cas, les substances des groupes partagent la présence ou l'absence de risque. Seul le degré de criticité du risque variait. CONCLUSION: La classification par « grouping names ¼ semble justifiée au regard des similitudes entre les substances, notamment en termes de sensibilisation cutanée. Cependant, la présence de « worst cases ¼ la nuance et souligne l'importance d'être vigilant lors de l'évaluation du risque des produits cosmétiques incluant ces « grouping names ¼ dans leur liste d'ingrédients.

The fallacy of functional nomenclature in the kingdom of biological multifunctionality: physiological and evolutionary considerations on ion channels.

Living organisms are multiscale complex systems that have evolved high degrees of multifunctionality and redundancy in the structure-function relationship. A number of factors, only in part determined genetically, affect the jobs of proteins. The overall structural organization confers unique molecular properties that provide the potential to perform a pattern of activities, some of which are co-opted by specific environments. The variety of multifunctional proteins is expanding, but most cases are handled individually and according to the still dominant 'one structure-one function' approach, which relies on the attribution of canonical names typically referring to the first task identified for a given protein. The present topical review focuses on the multifunctionality of ion channels as a paradigmatic example. Mounting evidence reports the ability of many ion channels (including members of voltage-dependent, ligand-gated and transient receptor potential families) to exert biological effects independently of their ion conductivity. 'Functionally based' nomenclature (the practice of naming a protein or family of proteins based on a single purpose) is a conceptual bias for three main reasons: (i) it increases the amount of ambiguity, deceiving our understanding of the multiple contributions of biomolecules that is the heart of the complexity; (ii) it is in stark contrast to protein evolution dynamics, largely based on multidomain arrangement; and (iii) it overlooks the crucial role played by the microenvironment in adjusting the actions of cell structures and in tuning protein isoform diversity to accomplish adaptational requirements. Biological information in protein physiology is distributed among different entwined layers working as the primary 'locus' of natural selection and of evolutionary constraints.

Name Changes for Fungi of Medical Importance, 2020 to 2021.

The current article summarizes recent changes in nomenclature for fungi of medical importance published in the years 2020 to 2021, including new species and revised names for existing ones. Many of the revised names have been widely adopted without further discussion. However, those that concern common pathogens of humans may take longer to achieve general usage, with new and current names reported together to engender increasing familiarity with the correct taxonomic classification.

Naming the menagerie: creativity, culture and consequences in the formation of scientific names.

The coining of scientific names for newly described species is one of the most creative acts in science. We briefly review the history of species naming, with an emphasis on constraints and freedoms in the choice of new names and how they came to be. We then consider patterns in etymologies and linguistic origins of scientific names across clades and through time. Use of 'non-classical' languages (those other than Latin and Greek) in naming species has increased, as has the use of eponymous names (despite recent controversy around the practice). Finally, we consider ways in which creativity in naming has consequences for the conduct and outcome of scientific work. For example, sale of naming rights has funded research and conservation, while naming species after celebrities has increased media attention to the science of species discovery. Other consequences of naming are more surprising, including a strong effect of species-name etymology on the kinds of scientific studies conducted for plant-feeding arthropods. Scientific naming is a clear example of how science and scientists are socially situated, and how culturally influenced decisions such as what to name a new species can affect both public perception of science and the conduct of science itself.

Can species naming drive scientific attention? A perspective from plant-feeding arthropods.

How do researchers choose their study species? Some choices are based on ecological or economic importance, some on ease of study, some on tradition-but could the name of a species influence researcher decisions? We asked whether phytophagous arthropod species named after their host plants were more likely to be assayed for host-associated genetic differentiation (or 'HAD'; the evolution of cryptic, genetically isolated host specialists within an apparently more generalist lineage). We chose 30 arthropod species (from a Google Scholar search) for which a HAD hypothesis has been tested. We traced the etymologies of species names in the 30 corresponding genera, and asked whether HAD tests were more frequent among species whose etymologies were based on host-plant names (e.g. Eurosta solidaginis, which attacks Solidago) versus those with other etymologies (e.g. Eurosta fenestrata, from Latin fenestra, 'window'). Species with host-derived etymologies were more likely to feature in studies of HAD than those with other etymologies. We speculate that the etymology of a scientific name can draw a researcher's attention to aspects of life-history and thus influence the direction of our scientific gaze.

A standardised nomenclature for long non-coding RNAs.

The HUGO Gene Nomenclature Committee (HGNC) is the sole group with the authority to approve symbols for human genes, including long non-coding RNA (lncRNA) genes. Use of approved symbols ensures that publications and biomedical databases are easily searchable and reduces the risks of confusion that can be caused by using the same symbol to refer to different genes or using many different symbols for the same gene. Here, we describe how the HGNC names lncRNA genes and review the nomenclature of the seven lncRNA genes most mentioned in the scientific literature.

The big four of plant taxonomy - a comparison of global checklists of vascular plant names.

Taxonomic checklists used to verify published plant names and identify synonyms are a cornerstone of biological research. Four global authoritative checklists for vascular plants exist: Leipzig Catalogue of Vascular Plants, World Checklist of Vascular Plants, World Flora Online (successor of The Plant List, TPL), and WorldPlants. We compared these four checklists in terms of size and differences across taxa. We matched taxon names of these checklists and TPL against each other, identified differences across checklists, and evaluated the consistency of accepted names linked to individual taxon names. We assessed geographic and phylogenetic patterns of variance. All checklists differed strongly compared with TPL and provided identical information on c. 60% of plant names. Geographically, differences in checklists increased from low to high latitudes. Phylogenetically, we detected strong variability across families. A comparison of name-matching performance on taxon names submitted to the functional trait database TRY, and a check of completeness of accepted names evaluated against an independent, expert-curated checklist of the family Meliaceae, showed a similar performance across checklists. This study raises awareness on the differences in data and approach across these checklists potentially impacting analyses. We propose ideas on the way forward exploring synergies and harmonizing the four global checklists.

Proposal of Thalassovita gen. nov. and Alloyangia gen. nov. as replacement names for the illegitimate prokaryotic generic names Thalassobius and Yangia, respectively.

The prokaryotic generic names Thalassobius Arahal et al. 2005 and Yangia Dai et al. 2006 are illegitimate because they are later homonyms of the genus names Thalassobius Solier 1849 (Coleoptera) and Yangia Zheng 1997 (fossil Rodentia), respectively Principle two and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes]. We therefore propose the replacement generic names Thalassovita and Alloyangia, with type species Thalassovita gelatinovora and Alloyangia pacifica, respectively.

Proposal of Allopseudospirillum gen. nov. as a replacement name for the illegitimate prokaryotic generic name Pseudospirillum Satomi et al. 2002.

The prokaryotic generic name Pseudospirillum Satomi et al. 2002 is illegitimate because it is a later homonym of Pseudospirillum Alexeieff 1917, a genus of uncertain affiliation, possibly belonging to the Mesomycetozoa (Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Allopseudospirillum, with type species Allopseudospirillum japonicum.

Proposal of Allomuricauda gen. nov. and Allofranklinella gen. nov. as replacement names for the illegitimate prokaryotic generic names Muricauda and Franklinella, respectively.

The prokaryotic generic names Muricauda Bruns et al. 2001 and Franklinella Bernard et al. 2022 are illegitimate because they are later homonyms of the genus names Muricauda Small 1903 (synonym of Arisaema; Tracheophyta - Liliopsida - Araceae) and Franklinella Stewart and Hendrix 1945 (a Devonian ostracod genus) and Franklinella Lenz 1973 (a Devonian brachiopod genus), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic names Allomuricauda and Allofranklinella, with type species Allomuricauda ruestringensis and Allofrankinella schreckenbergeri, respectively.

Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively.

The prokaryotic generic names Eoetvoesia Felföldi et al. 2014, Paludicola Li et al. 2017, Rivicola Sheu et al. 2014 and Sala Song et al. 2023 are illegitimate because they are later homonyms of the genus names Eoetvoesia Schulzer et al. 1866 (Ascomycota), Paludicola Wagler 1830 (Amphibia) and Paludicola Hodgson 1837 (Aves), Rivicola Fitzinger 1833 (Mollusca) and Sala Walker 1867 (Hemiptera) and the subgenus name Sala Ross 1937 (Hymenoptera), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic names Eoetvoesiella, Paludihabitans, Rivihabitans and Salella, with type species Eoetvoesiella caeni, Paludihabitans psychrotolerans, Rivihabitans pingtungensis and Sallella cibi, respectively.