Some thoughts on taxonomic terminology

There are gaps and inconsistencies in current taxonomic vocabulary which might benefit from some attention. To address these issues, some terminological standards are proposed and explained herein. The validity of terminology derived from clear grammatical patterns is not necessarily precluded by an absence of previous use. It is still, however, a worthwhile exercise to include such potential terms in a body of text that can serve as a reference to anyone wishing to employ terminology of this nature, with the secondary benefit that it may encourage more widespread use of these terms for a more consistent use of taxonomic terminology.     

The Compontents of the Water Potential in Plants and Soils

The analysis of water potential in terms of pressure, solute,and matric components should be abandoned as ambiguous; an analysistheoretically and experimentally sounder is suggested. The term‘suction potential’ should be retained as an acceptablealternative to water potential.     

Recommendations for using the standardized terminology of respiratory physiology in radiation research

A succinct review of the terminology and of correlations between basic quantities in respiration physiology is given with special regard to oxygen as the gas of topical interest in radiation research and tumor pathophysiology. The role of the oxygen partial pressure gradient as the driving force of O2 diffusion is emphasized. It is generally recommended that the O2 partial pressure be considered when investigating oxygen diffusion and distribution problems. During those studies the physical boundary conditions, in particular the temperature, the barometric pressure, and the water vapor saturation, have to be considered and should be indicated. During equilibration of suspensions containing oxygen-consuming sites the impact of geometry and fluid agitation on the efficiency of gas exchange has to be taken into account. Reviews on solutions of diffusion equations, on numerical data for relevant constants to be considered, and on terminology and units in respiration physiology are included.     

Molecular trait of follicular-patterned thyroid neoplasms defined by MALDI-imaging

In the field of thyroid neoplasms, the most interesting recent change regards the introduction of a new terminology for follicular-patterned thyroid tumors, named Noninvasive Thyroid Neoplasm with Papillary-like Nuclear Features (NIFTP). This pre-malignant tumor is considered to be the putative precursor of invasive carcinoma. However, given that several issues are still unresolved, the application of ancillary tools, based on omics-techniques, may improve the clinical management of these challenging cases. The present paper highlights the proteomic profiles of a series of NIFTPs submitted to Fine Needle Aspirations (FNAs) and analysed by MALDI-imaging in order to confirm the heterogeneous phenotype of nodules included in the present NIFTP terminology and to underline the necessity of more accurate biomarkers that can be used for their characterization.Ethical and economic implications in terms of healthcare costs, operative risks, morbidity, as well as the potential need for lifelong hormone replacement therapy, seem to be significant reasons to approach the characterization of NIFTPs using alternative tools such as MALDI-MSI.     

Mobilizing metaphors: the popular use of keystone,flagship and umbrella species concepts

Misrepresentation of terminology is a major impediment for attempts at enhancing public conservation literacy. Despite being critically important for improving conservation practice, there have been few systematic analyses of the popular use of conservation terminology. This paper draws from science communication studies and metaphor analysis, to examine how keystone, flagship and umbrella species concepts are used and represented in non-academic contexts. 557 news articles containing these terms were systematically analyzed. Mammals featured in 60% of articles on keystones, 55% on flagships and 63% on umbrella species. Number of articles explaining the terms keystone (35%) and flagship (31%) was low, and keystones were the most misrepresented term. Keystones were metaphorically linked with balance, flagships with representation and umbrella species with protection. These metaphors influenced public interpretation of scientific terminology, oriented actions towards select species, and led to a valuation of such actions. Together, the findings highlight three important aspects of popular use of conservation terminology: (1) communication is largely biased towards mammals, (2) everyday language plays a vital role in the interpretation of concepts, and (3) metaphors influence peoples’ actions and understanding. Conservation biologists need to engage with issues of language if public conservation literacy is to be improved. Further evaluations of concepts with high public and policy relevance, systematic identification of communication shortfalls, and linguistic assessments prior to promoting new terms are potential ways of achieving this.     

Carl Friedrich Naumann and the introduction of enantio terminology: a review and analysis on the 150th anniversary

Enantiomorphism and enantiomorphous were the first enantio-based terms, introduced 150 years ago, by Carl Friedrich Naumann, a German crystallographer, to refer to non-superposable mirror-image crystals. The terminology was not adopted by Pasteur, the discoverer of molecular chirality, and was not embraced at first in the stereochemical context, until it was accepted in 1877 by Van't Hoff in the German edition of his proposal for the tetrahedral asymmetric carbon atom. In the 1890s the use of enantio terms began to spread in the research literature, and many new derivatives of Naumann's original two terms were subsequently introduced. Problems in the usage of some of the terms are often found in the literature, e.g., enantiomorphism is sometimes confused with chirality; enantiomeric is often misused; the meaning of some of the many derived terms, e.g., enantiosymmetric, enantioposition, etc., is unclear. All in all, Naumann should be remembered as the creator of essential terminology in the realm of chirality.     

A neutral terminology to define 'invasive' species

The use of simple terms to articulate ecological concepts can confuse ideological debates and undermine management efforts. This problem is particularly acute in studies of nonindigenous species, which alternatively have been called ‘exotic’, ‘introduced’, ‘invasive’ and ‘naturalised’, among others. Attempts to redefine commonly used terminology have proven difficult because authors are often partial to particular definitions. In an attempt to form a consensus on invasion terminology, we synthesize an invasional framework based on current models that break the invasion process into a series of consecutive, obligatory stages. Unlike previous efforts, we propose a neutral terminology based on this framework. This ‘stage‐based’ terminology can be used to supplement terms with ambiguous meanings (e.g. invasive, introduced, naturalized, weedy, etc.), and thereby improve clarity of future studies. This approach is based on the concept of ‘propagule pressure’ and has the additional benefit of identifying factors affecting the success of species at each stage. Under this framework, invasions can be more objectively understood as biogeographical, rather than taxonomic, phenomena; and author preferences in the use of existing terminology can be addressed. An example of this recommended protocol might be: ‘We examined distribution data to contrast the characteristics of invasive species (stages IVa and V) and noninvasive species (stages III and IVb)’.     

Response to Preuss and Zuccarello (2020): biological definitions that can be unambiguously applied for red algal parasites

In response to a comment in this issue on our proposal of new terminology to distinguish red algal parasites, we clarify a few key issues. The terms adelphoparasite and alloparasite were previously used to identify parasites that infected close or distant relatives. However, most red algal parasites have only been studied morphologically, and molecular tools have shown that these binary terms do a poor job at representing the range of parasite–host relationships. We recognize the need to clarify inferred misconceptions that appear to be drawing from historical terminology to contaminate our new definitions. We did not intend to replace the term adelphoparasite with neoplastic parasites and the term alloparasites with archaeplastic parasites. Rather, we seek to establish new terms for discussing red algal parasites, based on the retention of a native plastid, a binary biological trait that is relatively easy to identify using modern methods and has biological implications for the interactions between a parasite and its host. The new terminology can better account for the spectrum of relationships and developmental patterns found among the many independently evolved red algal parasites, and it is intended to inspire new research, particularly the role of plastids in the survival and evolution of red algal parasites.     

Embryology and disorders of sexual development

Recent consensus is that individuals with atypical male or female phenotype are to be considered to have a "disorder of sexual development." The goal is to eliminate previous terminology that included the terms intersex, hermaphrodite, or pseudohermaphrodite. However, the teaching of embryology, and particularly teaching about the development of the reproductive system, still has not made the change to the new terminology. If those who teach embryology to health-care professionals remain unaware of the controversies associated with the old terminology and continue to use it, they will perpetuate a nomenclature that can be destructive. Any terminology must be used carefully to avoid dehumanizing the individual to a disease or a medical state. We should be able to state clearly the variations in morphology that exist, attend to the immediate health of the individual, and avoid any attempt to stigmatize gender-atypical individuals.     

Clarifying the Nomenclature in Microbial Weed Control

Correct terminology is essential to promote the concepts of biological control. In the current literature there are many terms used interchangeably and often inappropriately. The purpose of this paper is to examine the overlapping and sometimes contradictory terms used in biological weed control and to suggest a standardized usage to clarify existing terms. This is achieved through a hierarchical classification of existing terms (bioherbicide, mycoherbicide) and the introduction of new terms such as biopestistat (an inundatively applied, living organism which reduces the competitive ability of the target weed to below a desired threshold) and microbially derived phytotoxin (secondary metabolite used in weed management practices as an analogue of a chemical herbicide).     

Nomenclature of precancerous lesions of the uterine cervix. A position paper

There is universal and almost unanimous belief that there is a need for a radical revision of the terminology relating to the epithelial abnormalities of the uterine cervix that precede invasive carcinoma. Although this belief has been held for some years, no generally accepted alternative system has, as yet, been devised. This position paper examines (1) the origin of the existing system of terminology, (2) the problems associated with this system and (3) the requirements of any new, alternative nomenclature. The various alternatives that have been suggested are considered with particular reference to their advantages and disadvantages. Only two such alternatives are considered to be acceptable, and it is suggested that neither is likely to gain universal acceptance at this time. However, it is possible that new diagnostic techniques, with their potential for a more accurate evaluation of cell abnormalities, may facilitate the development or application of an acceptable system of terminology.     

A reference model based interface terminology for generic observations in Anatomic Pathology Structured Reports

Background

Current terminology systems for structured reporting in pathology are more or less focused on tumor pathology. They have not been compiled in a systematic approach, therefore they gather terms of very different granularity. Generic models for terminology development could help in establishing reference terminologies for all fields of anatomic pathology.The core principle of those models is the ontological structure of native speaking terminology. By analyzing the PathLex interface a generic terminology model will be derived.

Methods

For each element template of PathLex its possible generic nature and its value set was analyzed, looking for the uniqueness or multiplicity of the values in the value sets.The generic terms were mapped to SNOMED-CT terms using "ArtDecor".

Results

The 488 PathLex element templates for Anatomic Pathology (AP) observations can be reduced to 53 generic templates, leaving out only 17 templates very specific for organ and/or disease. Among those 53 templates 28 are describing UICC-TNM staging, ICD-O-classification, and grading. Further 15 templates describe the results from marker investigations. Almost all of the terms, used in those templates could be mapped to SNOMED CT.All of the generic elements have their "organ specific" counterparts by assigning them to one of 20 organs and invasive or noninvasive cancer, respectively. Studying the structure of generic and specific terms it becomes obvious that any AP observation- occurs always in a context- consists of three basic elements (target of observation, property of observation, additional qualifiers, added by value sets for coded data).

Conclusions

If a machine-readable terminology is aimed to preserve all the information of native speaking, then two principal solutions exist:- ystematic consideration of all the aspects mentioned above in each single term- ocusing on the generic elements of terms and combining this with the structure of communication, reflecting the non-obvious elements of the terminology.The fastest way for establishing an interface terminology is the first approach, which lists all of the terms needed for e.g. a checklist in a comprehensive manner (precoordination).However, if the list of terms and problems increases, or new requirements have to be met, considerable difficulties may arise in keeping the terminology consistent and complete.The second, postcoordination approach offers some advantages. It does not have limitations in the organ- or disease specificity, and it keeps the number of terms limited, making them more easily to survey.

     

The Role of the Limnologist in Ground Water Studies

The following topics are discussed: the advantages of an interdisciplinary approach to ground water studies; the porous aquifer as an open system; the problem of the terminology used in ground water ecology; the interest of ecologists in hydrogeological terminology; biological activity in the unsaturated zone of porous aquifers; the distribution of ground water fauna in the saturated zone of porous aquifers; ground water animals as environmental indicators; the manipulation of ground water ecosystems; basic lines for the further development of ground water ecological studies.     

Consensus for experimental design in electromyography (CEDE) project: Terminology matrix

Consensus on the definition of common terms in electromyography (EMG) research promotes consistency in the EMG literature and facilitates the integration of research across the field. This paper presents a matrix developed within the Consensus for Experimental Design in Electromyography (CEDE) project, providing definitions for terms used in the EMG literature. The definitions for physiological and technical terms that are common in EMG research are included in two tables, with key information on each definition provided in a comment section. A brief outline of some basic principles for recording and analyzing EMG is included in an appendix, to provide researchers new to EMG with background and context for understanding the definitions of physiological and technical terms. This terminology matrix can be used as a reference to aid researchers new to EMG in reviewing the EMG literature.     

Lethal interactions among vertebrate top predators: a review of concepts,assumptions and terminology

Lethal interactions among large vertebrate predators have long interested researchers because of ecological and conservation issues. Research focusing on lethal interactions among vertebrate top predators has used several terms with a broad sense, and also introduced new terminology. We analysed the published literature with reference to the main underlying concepts and the use of terminology and its ecological context. The most frequently used terms in the literature were ‘predation’, ‘intraguild predation’, ‘interference competition’, and ‘interspecific killing’. Most studies presented evidence of the killing of the victim (77%), but information regarding its consumption was not given in 48% of cases. More than half of the analysed studies (56%) had no solid information on the degree of competition between interacting species. By reviewing definitions and their underlying assumptions, we demonstrate that lethal interactions among large vertebrate predators could be designated using four terms—‘predation’, ‘intraguild predation’, ‘interspecific competitive killing’, and ‘superpredation’—without the need to employ additional terminology that may increase confusion and misuse. For a correct framework of these lethal interactions it is critical to assess if the kill is consumed, if the victim is indeed a competitor of the killer, and if the prey is a high‐order predator. However, these elements of the framework are simultaneously the most common constraints to studies of lethal interactions, since they often require a great effort to obtain. The proper use of terms and concepts is fundamental to understanding the causes behind lethal interactions and, ultimately, what is actually happening in these complex interactions.     

Sexual reproduction: nuclear cycles and life-histories with particular reference to lower eukaryotes

Sexual reproduction is defined as the union of two haploid nuclei each derived from one of two different meioses. The implications of this definition for the interpretation of sexuality in coenocytes and homothallic haploids is discussed. The separation of the concept of the nuclear cycle from that of the life-history is advocated, and a new terminology for the nuclear cycle is proposed. The distinction between the terms life-cycle and life-history is reiterated.     

Applications of the compensating pressure theory of water transport

Some predictions of the recently proposed theory of long-distance water transport in plants (the Compensating Pressure Theory) have been verified experimentally in sunflower leaves. The xylem sap cavitates early in the day under quite small water stress, and the compensating pressure P (applied as the tissue pressure of turgid cells) pushes water into embolized vessels, refilling them during active transpiration. The water potential, as measured by the pressure chamber or psychrometer, is not a measure of the pressure in the xylem, but (as predicted by the theory) a measure of the compensating pressure P. As transpiration increases, P is increased to provide more rapid embolism repair. In many leaf petioles this increase in P is achieved by the hydrolysis of starch in the starch sheath to soluble sugars. At night P falls as starch is reformed. A hypothesis is proposed to explain these observations by pressure-driven reverse osmosis of water from the ground parenchyma of the petiole. Similar processes occur in roots and are manifested as root pressure. The theory requires a pump to transfer water from the soil into the root xylem. A mechanism is proposed by which this pump may function, in which the endodermis acts as a one-way valve and a pressure-confining barrier. Rays and xylem parenchyma of wood act like the xylem parenchyma of petioles and roots to repair embolisms in trees. The postulated root pump permits a re-appraisal of the work done by evaporation during transpiration, leading to the proposal that in tall trees there is no hydrostatic gradient to be overcome in lifting water. Some published observations are re-interpreted in terms of the theory: doubt is cast on the validity of measurements of hydraulic conductance of wood; vulnerability curves are found not to measure the cavitation threshold of water in the xylem, but the osmotic pressure of the xylem parenchyma; if measures of xylem pressure and of hydraulic conductance are both suspect, the accepted view of the hydraulic architecture of trees needs drastic revision; observations that xylem feeding insects feed faster as the water potential becomes more negative are in accord with the theory; tyloses, which have been shown to form in vessels especially vulnerable to cavitation, are seen as necessary for the maintenance of P, and to conserve the supplementary refilling water. Far from being a metastable system on the edge of disaster, the water transport system of the xylem is ultrastable: robust and self-sustaining in response to many kinds of stress.