Quid significat nomen? (What's in a name?)

For the purposes of classification and effective communication among scientists, organisms must have unequivocal names. The binomial naming system of species was devised and popularized by Linnaeus in the 18th Century. His "Botanical Latin" is an artificial language first adopted for naming plants and is now internationally accepted as a naming system for both plants and animals. Genus and species names are based on Latin and Greek words which describe characteristics of the organism, as well as words from more modern sources, such as the name of the discoverer or place of discovery. Naming follows certain rules and all of the word endings are Latinized. The history of naming parasites is interesting and the molecular age may influence naming in the future.     

Guidelines for managing datasets,programs and printouts in scientific research

This paper presents guidelines and naming conventions to assist in managing datasets, programs and printouts for small to medium sized research projects. First, the limits and nature of the type of project are considered. A number of definitions are included to help further specify the problem. Four main areas are addressed. First, a consistent set of rules for naming programs and datasets is presented. Next, techniques for storing and archiving the programs and datasets are presented, using the naming conventions just developed. Third, rules for printout management are given, based on the naming rules. Finally, the documentation of all components of the project is discussed. Although trivial to implement, adherence to the naming rules provides a sound basis for a high quality, easy-to-use documentation system.     

Mining fatty acid databases for detection of novel compounds in aerobic bacteria

This study examines how the discriminatory power of an automated bacterial whole-cell fatty acid identification system can be significantly enhanced by exploring the vast amounts of information accumulated during 15 years of routine gas chromatographic analysis of the fatty acid content of aerobic bacteria. Construction of a global peak occurrence histogram based upon a large fatty acid database is shown to serve as a highly informative tool for assessing the delineation of the naming windows used during the automatic recognition of fatty acid compounds. Along the lines of this data mining application, it is suggested that several naming windows of the Sherlock MIS TSBA50 peak naming method may need to be re-evaluated in order to fit more closely with the bulk of observed fatty acid profiles. At the same time, the global peak occurrence histogram has put forward the delineation of 32 new peak naming windows, accounting for a 26% increase in the total number of fatty acid features taken into account for bacterial identification. By scrutinizing the relationships between the newly delineated naming windows and the many taxonomic units covered within a proprietary fatty acid database, all new naming windows were proven to correspond with stable features of some specific groups of microorganisms. This latter analysis clearly underscores the impact of incorporating the new fatty acid compounds for improving the resolution of the bacterial identification system and endorses the applicability of knowledge discovery in databases within the field of microbiology.     

Problems in nomenclature of craniofacial disorders

The diverse background of clinical geneticists may lead to problems of communication unless attention is paid to nomenclature. In this paper, consensus is sought on terms for normal and abnormal development, a system for labeling developmental defects of dentin is proposed, and terms for patterns of coexistent variations are defined. The major methods for naming coexistent variations are reviewed, with attention to the disadvantages of each. An informal study on recognition of patterns of variation based on the naming system used is also presented.     

SLAⅠ类基因最新命名进展

介绍了国际动物遗传学会（ISAG）SLA命名委员会2004年制定的依据基因测序及进化树分析的SLAⅠ类基因系统命名法,详细叙述了对SLAⅠ类基因座、等位基因组、等位基因及单倍型的命名规则,其中概括介绍了命名新等位基因对基因序列的具体要求。SLAⅠ类基因系统命名法对于人类移植免疫学、猪免疫遗传及抗病育种具有重要意义。     

Progressive loss of access to spoken word forms in a case of Alzheimer's disease.

We report the results of a longitudinal study of a progressive anomia in a patient with dementia of the Alzheimer type (DAT). The anomia cannot be attributed to a deficit within the semantic system, but appears instead to arise from impaired access to the phonological lexicon at a post-semantic stage of the naming process: a deficit that hitherto has not been reported in DAT. Specific naming responses were affected consistently by the disorder, showing that disorders of access are not invariably associated with inconsistent responding. Before specific responses disappeared from spontaneous use, there appeared to be an intervening stage at which some responses could be elicited by an initial phoneme cue, suggesting a low level of spontaneous activity of insufficient strength to elicit a response unaided. The frequency of the name affected naming performance, but did not appear to interact with the severity of the naming disorder, suggesting that the parameters of the normal naming system were unaffected. It is claimed that important new insights into the characteristics of progressive anomia have been obtained by taking a longitudinal approach.     

Uncovering trends in gene naming

We take stock of current genetic nomenclature and attempt to organize strange and notable gene names. We categorize, for instance, those that involve a naming system transferred from another context (for example, Pavlov’s dogs). We hope this analysis provides clues to better steer gene naming in the future.     

Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits

DNA polymerase III is one of the five eubacterial DNA polymerases that is re-sponsible for the replication of DNA duplex. Among the ten subunits of the DNApolymerase III core enzyme, the alpha subunit catalyzes the reaction for polymer-izing both DNA strands. In this study, we extracted genomic sequences of thealpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. We found that all eubacterial genomeshave one or more alpha subunits, which form either homodimers or heterodimers.Phylogenetic and domain structural analyses as well as copy number variations ofthe alpha subunit in each bacterium indicate the classification of alpha subunit intofour basic groups: polC, dnaE1, dnaE2, and dnaE3. This classification is of essencein genome composition analysis. We also consolidated the naming convention toavoid further confusion in gene annotations.     

A nomenclature and data model to describe NMR experiments

Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason for the absence of a universal naming system is that the information content of the coherence pathways is difficult to describe in full detail. We propose a system that describes the common and generic elements of the coherence pathways produced by pulse sequences. The system itself is formalised by an ‘NMR experiment protocol’ model, which is described in the Universal Modelling Language (UML) as part of the CCPN data model. Furthermore, normalized experiment names can be derived from this proposed model. We hope this article will stimulate discussion to organise the wealth of NMR experiments, and that by bringing this discussion into the public domain we can improve and expand our proposed system to include as much information and as many NMR experiments as possible. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Joint first authors     

Timed picture naming norms for Mandarin Chinese

The present study reports timed norms for 435 object pictures in Mandarin Chinese. These data include naming latency, name agreement, concept agreement, word length, and age of acquisition (AoA) based on children's naming and adult ratings, and several other adult ratings of concept familiarity, subjective word frequency, image agreement, image variability, and visual complexity. Furthermore, we examined factors that influence the naming latencies of the pictures. The results show that concept familiarity, AoA, concept agreement, name agreement, and image agreement are significant predictors of naming latencies, whereas subjective word frequency is not a reliable determinant. These results are discussed in light of picture naming data in other languages. An item-based index for the norms is provided in the Table S1.     

A nomenclature for restriction enzymes,DNA methyltransferases,homing endonucleases and their genes

A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.     

The biological basis of a universal constraint on color naming: cone contrasts and the two-way categorization of colors

Many studies have provided evidence for the existence of universal constraints on color categorization or naming in various languages, but the biological basis of these constraints is unknown. A recent study of the pattern of color categorization across numerous languages has suggested that these patterns tend to avoid straddling a region in color space at or near the border between the English composite categories of "warm" and "cool". This fault line in color space represents a fundamental constraint on color naming. Here we report that the two-way categorization along the fault line is correlated with the sign of the L- versus M-cone contrast of a stimulus color. Moreover, we found that the sign of the L-M cone contrast also accounted for the two-way clustering of the spatially distributed neural responses in small regions of the macaque primary visual cortex, visualized with optical imaging. These small regions correspond to the hue maps, where our previous study found a spatially organized representation of stimulus hue. Altogether, these results establish a direct link between a universal constraint on color naming and the cone-specific information that is represented in the primate early visual system.     

中国传统私家园林景点题名中的松柏意象研究

中国传统松柏文化源远流长,蔚为大观。深入挖掘中国古典园林中的松柏文化对于弘扬中国优秀传统文化和提升现代园林文化具有重要意义。现有松柏文化研究主要集中在诗词、绘画、民俗等领域,在园林品题领域的研究还不够系统和深入。以历代私家园林中的景点名称为研究对象,采用古籍文献查询和统计分析相结合的方法,对历代私家园林中的松柏景点、景点题名中的常见意象、松柏景题所表达的精神文化内涵进行研究。结果表明：1）唐代及以前私家园林中的松柏景题记载较少,题名意象也非常单一;2）宋元时期虽然记载的松柏景题仍然不多,但是题名意象已经非常丰富;3）明清时期松柏景题的数量最多,题名意象也最为多元;4）历代私家园林松柏景点除直接以松柏名称题名外,以松风意象题名最多,其次是数量意象、岁寒意象、松阴意象等;5）松柏景题的精神内涵主要表达了历代文人对隐逸理想的寄托、高洁人格的追求、佛理禅思的寓意和对健康长寿的企盼。     

Proposed Nomenclature for Mutants of Adenoviruses

In accord with the nomenclature proposed for mutants of simian virus 40 the same rules, with minor modifications, are recommended for naming mutants of adenoviruses. It is further suggested that these rules, which pertain to a system of classification based primarily upon complementation analysis, also be applied to mutants of other DNA-containing animal viruses.     

On counting cranial nerves

The enumeration of the cranial nerves is traced briefly from Galen's seven to Willis' ten and to von S?mmerring's twelve. The system of von S?mmerring, which has been followed for some 200 years, is a useful convention, although it is merely one of several possibilities. The naming of the cranial nerves was standardized nearly 100 years ago.     

Proposal for Naming Host Cell-Derived Inserts in Retrovirus Genomes

We propose a system for naming inserted sequences in transforming retroviruses (i.e., onc genes), based on using trivial names derived from a prototype strain of virus.     

Mechanisms Explaining Variety Naming by Farmers and Name Consistency of Rice Varieties in The Gambia

Mechanisms Explaining Variety Naming by Farmers and Name Consistency of Rice Varieties in The Gambia. Understanding variety naming by farmers is important for better understanding crop genetic diversity in farmer fields and its management by farmers. This paper describes variety naming of rice by farmers in The Gambia and presents mechanisms that explain naming diversity and consistency. Three types of variety names can be distinguished, referring to common old varieties, common new varieties, and uncommon varieties. Interview and plant data suggest that variety exchange affects variety naming within villages. As a result, variety names give information on the period of time a variety is used in a village, and on the flow of varieties between and within villages. Name consistency within and between villages results from and illuminates the dynamics of variety exchange within and between villages.     

Odor recognition memory as a function of odor-naming performance

A series of experiments sought to clarify the relationship between odor naming and memory by manipulating odor label availability during a dual naming-memory task. Experiment 1 demonstrated that recognition memory and odor naming were both better when the naming task provided participants with odor label alternatives. Consistent and correct odor naming was associated with nearly perfect memory, whereas inconsistent or incorrect naming was associated with very weak memory if any at all. Experiment 2 showed that the availability of odor labels was effective at improving memory only if labels were available at both memory encoding and retrieval, suggesting that the labels were aiding memory by improving the identification of the odors. Odor naming was manipulated in Experiment 3 by varying the number of available labels from 4 to 16 during each odor-naming trial. As found in the previous experiments, naming and memory were strongly related in each of the labeling conditions. Experiment 4 showed that corrective naming feedback produced better memory performance but only when the feedback led to correct odor naming. It was concluded that perceptual processes related to matching olfactory input to acquired, multidimensional representations of odors play a critical role in both odor naming and episodic memory.     

Dai People’s Botanical Knowledge: Nomenclature Meaning and Classification

After analysis, statistics and conclude 1175 species (variety) of plants,1370 Dai names and 1691 meanings were obtained to elucidate how the Dai people recognize and define the plant. They used ‘hong e bin’, which means‘the things with life come out from the ground’ to define the plant. This is similar to the modern science which defined the plant as ‘anything that grows from the ground’. This is a highly synthesized scientific term that seldom seen in many other ethnics in the world. In their method of naming plants, they used the types of plant life form and economic type for ‘generic’ names, and used the meanings of plant morphogenesis and characters, economic uses, ecological distribution, and stories and legends etc. for ‘specific’ names. Among the 1691 meanings, they are occupied 60%, 30%, 8% and 2% respectively. This reflected that the naming method of Dai for plant ‘Just see what′s looking alike on naming them’ is similar to Linnaeus′ bi nomenclature of the modern botanical taxonomy. Moreover, the folk plant classification system based on the structure of Dai names is then established, including 5 categories as plant kingdom, tow ‘families’ of wild or cultivated plant, about 20 ‘genera’ of life forms and economic types, and more than 3000 species and over 1000 varieties, by the ‘two names’ in the paper as well.