Formal Name Research Articles

PARMALES (CHRYSOPHYCEAE) FROM THE GULF OF TEHUANTEPEC, MEXICO, INCLUDING THE DESCRIPTION OF A NEW SPECIES, TETRAPARMA INSECTA SP. NOV., AND A PROPOSAL TO THE TAXONOMY OF THE GROUP1

There are few studies dedicated to species of the Order Parmales all over the world. All 12 taxa described are part of the marine ultraplankton (less than 5 μm). Analysis of filtered samples from the Gulf of Tehuantepec yielded specimens of two taxa of the group. One is a new species, belonging to the genus Tetraparma. Tetraparma insecta sp. nov. is solitary and spherical (2.8–3.8 μm diameter), and all plates lack ornamentations or knobs, the walls are smooth, and only the plate junctions are seen. The shield plates are convex and show a conspicuous rim, some of them with an indentation. This species shows superficial similarities with Tetraparma pelagica, the other species described of the genus, and is very similar to siliceous forms, previously found, with no formal name. The other species is the taxon Triparma laevis form mexicana (Kosman) stat. nov., earlier described for Mexican waters, which has an irregular ala, the shield plates have knobs at the center, the triradiate plates show a “Y”‐shaped keel, and the walls of plates and ala show minute granules. Tetraparma insecta was distributed widely in the study area and was relatively abundant, reaching a density of 4 × 104·L−1, with an evident preference for subsurface waters (10–20 m depth), whereas T. laevis form mexicana was rare and scarce. Both species seem to be restricted to tropical–subtropical waters. We discuss the taxonomy of Parmales, especially concerning the category of subspecies within the group. Parmales is a widespread group in cold and tropical waters.

LOINC, a universal standard for identifying laboratory observations: a 5-year update.

The Logical Observation Identifier Names and Codes (LOINC) database provides a universal code system for reporting laboratory and other clinical observations. Its purpose is to identify observations in electronic messages such as Health Level Seven (HL7) observation messages, so that when hospitals, health maintenance organizations, pharmaceutical manufacturers, researchers, and public health departments receive such messages from multiple sources, they can automatically file the results in the right slots of their medical records, research, and/or public health systems. For each observation, the database includes a code (of which 25 000 are laboratory test observations), a long formal name, a "short" 30-character name, and synonyms. The database comes with a mapping program called Regenstrief LOINC Mapping Assistant (RELMA(TM)) to assist the mapping of local test codes to LOINC codes and to facilitate browsing of the LOINC results. Both LOINC and RELMA are available at no cost from http://www.regenstrief.org/loinc/. The LOINC medical database carries records for >30 000 different observations. LOINC codes are being used by large reference laboratories and federal agencies, e.g., the CDC and the Department of Veterans Affairs, and are part of the Health Insurance Portability and Accountability Act (HIPAA) attachment proposal. Internationally, they have been adopted in Switzerland, Hong Kong, Australia, and Canada, and by the German national standards organization, the Deutsches Instituts für Normung. Laboratories should include LOINC codes in their outbound HL7 messages so that clinical and research clients can easily integrate these results into their clinical and research repositories. Laboratories should also encourage instrument vendors to deliver LOINC codes in their instrument outputs and demand LOINC codes in HL7 messages they get from reference laboratories to avoid the need to lump so many referral tests under the "send out lab" code.

Future-proofing biological nomenclature.

TO MOST BIOLOGISTS, it seems inconceivable that the simple act of naming a biological entity has any more significance than identifying a personal achievement or staking a claim to a territory of research interest, akin to carving one’s initials into the tree of life. However, this simple act has potentially far-reaching and long-lived consequences. Names, especially those ascribed to organisms, serve as a primary entry point into the scientific, medical, and technical literature and figure prominently in countless laws and regulations governing various aspects of commerce, public safety and public health. These names also serve as a primary entry point into many of the central databases that the scientific community and the general public now rely upon. Even well-formed and properly applied names can serve as a source of confusion and considerable frustration. This is hardly a new problem. In the mid 18th century, Carl von Linne proposed the use of latinized binomial names and a hierarchical classification scheme as an alternative to trivial and colloquial names, which were a constant source of confusion among his contemporaries (Linne, 1735). The Linnaean system of nomenclature was widely accepted and has subsequently been codified into four separate legalistic frameworks (the codes of botanical [Greuter, 2000], zoological [Ride, 1985], prokaryotic [Sneath, 1992], and viral nomenclature [Buchen-Osmond, 2002]), describing the rules for forming and ascribing names to species and higher taxa, circumscription and emendation, priority and citation, synonymy and more recently homonymy, correction of orthographic errors and adjudication of disputes in nomenclature. Chief among the stated objectives of these codes is stability and order in the nomenclature of the taxa covered by each. Achieving this goal, however, remains elusive. There are a variety of reasons. Relatively few contemporary biologists are actively engaged in systematic studies and have reason to formally propose names for new biological entities. Rather, they are end-users of the classifications and nomenclature produced by a small group of specialists. Most biologists fail to recognize that taxonomic proposals are expert opinions, arising from comparative studies of small numbers of species that may or may not be representative of larger natural groups and that the opinions rendered by these experts are subject to acceptance or rejection by the larger community of biologists. They also fail to recognize that the Codes of Nomenclature do not govern the process of biological classification or identification, only the formation and assignment of names to proposed taxa. Legitimate and valid names may be ascribed to poorly formed taxa and illegitimate and invalid names may be assigned to well formed taxa. The name ascribed to a given group is fixed in both time and scope and may or may not be revised when new information is available. When taxonomic revisions do occur, resulting in the division or joining of previously described taxa, authors frequently fail to address synonymies or formally emend the descriptions of higher taxa that are affected. Whereas the different codes of nomenclature guarantee persistence of a formal name, the serial, cumulative nature of effective and valid publication allows the name to obsolesce in relation to the taxon it originally denoted. In contrast, it is the taxon itself that persists, and the granularity with which it is defined increases over time. The formal name provides an archival record of taxonomic definition only for a single point in time—the date of publication. A robust and persistent taxonomy requires taxonomic definition to

3407 機械機構模型のデータベース構築

Kyoto University imported machine mechanism models from Gustav Voigt. Co., Germany in 1903. But, only a copy of the purchase slip where German explanation was written in "Katakana" that are Japanese characters is preserved, and the original formal names were lost. Recently it has been made clear that the names of most models in the purchase slip are contained in the catalog in Cornell University, and author reported about it in the last annual meeting of JSME. In this research, a database will be built in order to make easy collation with the models and the names that are described in the purchase slip, or to make easy comparison examination with other machine mechanism models in the future.

Helicobacter cetorum sp. nov., a urease-positive Helicobacter species isolated from dolphins and whales.

A novel helicobacter with the proposed name Helicobacter cetorum, sp. nov. (type strain MIT 99-5656; GenBank accession number AF 292378), was cultured from the main stomach of two wild, stranded Atlantic white-sided dolphins (Lagenorhynchus acutus) and from the feces of three captive cetaceans (a Pacific white-sided dolphin [Lagenorhynchus obliquidens]; an Atlantic bottlenose dolphin [Tursiops truncatus]; and a beluga whale [Delphinapterus leucas]). The infected captive cetaceans were either subclinical, or clinical signs included intermittent regurgitation, inappetance, weight loss, and lethargy. Ulcers were observed in the esophagus and forestomach during endoscopic examination in two of the three captive animals. In the third animal, esophageal linear erosions were visualized endoscopically, and histopathological evaluation of the main stomach revealed multifocal lymphoplasmacytic gastritis with silver-stained spiral-shaped bacteria. Helicobacter cetorum is a fusiform gram-negative bacterium with a single bipolar flagellum. The isolates grow under microaerobic conditions at 37 and 42 degrees C but not at 25 degrees C. H. cetorum is urease, catalase, and oxidase positive, and it is sensitive to cephalothin. The isolates from the wild, stranded dolphins were sensitive to nalidixic acid, whereas the isolates from the collection animals were resistant. By 16S rRNA sequencing it was determined that H. cetorum represented a distinct taxon that clusters most closely with H. pylori. Further studies are necessary to determine the role of H. cetorum in the development of gastric ulcers and gastritis of cetaceans. This is the first description and formal naming of a novel Helicobacter species from a marine mammal.

Phylogeny and taxonomy of thegenera of south-western North American Euctenizinae trapdoor spiders and their relatives (Araneae: Mygalomorphae, Cyrtaucheniidae)

The primary focus of this paper is to evaluate the monophylyand intergeneric relationships of the cyrtaucheniid subfamily Euctenizinaeand to a lesser degree the monophyly of Cyrtaucheniidae. Using 71morphological characters scored for 29 mygalomorph taxa our cladisticanalysis shows that Cyrtaucheniidae is likely paraphyletic withrespect to the Domiothelina, the clade that comprises the Migidae,Actinopodidae, Ctenizidae, and Idiopidae. Together, the Domiothelinaand Cyrtaucheniidae have been treated as the Rastelloidina clade.A strict interpretation of rastelloid classification based on ourcladogram would require the establishment of four additional spiderfamilies. However, we choose to use informal names for these cladesso that these taxa can be validated by subsequent studies of mygalomorphphylogeny before formal names are introduced. The phylogenetic analysisalso serves as a vehicle for examining the patterns of homoplasyobserved in mygalomorphs. The secondary focus of this paper is ataxonomic revision of Euctenizinae genera from the south-westernUnited States that includes a key to its genera. The cyrtaucheniid genera Enrico and Astrosoga areconsidered junior synonyms of Eucteniza. Actinoxia and Nemesoides arejunior ­synonyms of Aptostichus. At present theNorth American Euctenizinae comprises these seven nominal genera: Eucteniza,Neoapachella gen.nov. (Neoapachella rothi sp. nov.), Myrmekiaphila,Entychides, Promyrmekiaphila,Apomastus gen. nov. (Apomastusschlingeri sp. nov.), and Aptostichus. © 2002The Linnean Society of London. Zoological Journal of the LinneanSociety, 2002, 136, 487−534

Preventing Burkholderia cepacia complex infection in cystic fibrosis: Is there a middle ground?

Preventing Burkholderia cepacia complex infection in cystic fibrosis: Is there a middle ground?

Nature of the virus associated with endemic Balkan nephropathy.

Endemic Balkan nephropathy (EBN), a disease restricted to three Balkan countries (Bulgaria, Rumania, and Yugoslavia), is characterized by a progressive shrinking of the kidneys and, in some cases, tumors in the proximal regions of the urinary tract 1,2. A coronavirus was reported to be involved in the etiology of the disease, mostly on the basis of the isolation of a virus in cultures of kidney cells from a patient with EBN 1,3. In addition, EBN-associated virus is reported to share serologic homology with human coronaviruses OC43 and 229E, as well as the porcine transmissible gastroenteritis coronavirus (formal name: Transmissible gastroenteritis virus [TGEV]), a virus that our laboratory has been studying for 16 years 4,5. The objective of this commentary is to clarify whether the EBN-associated virus is in fact related to members of the Coronaviridae family 6.

Phylogenetic relationships of southern African West Nile virus isolates.

Phylogenetic relationships were examined for 29 southern African West Nile virus (formal name West Nile virus [WNV]) isolates from various sources in four countries from 1958 to 2001. In addition sequence data were retrieved from GenBank for another 23 WNV isolates and Kunjin and Japanese encephalitis viruses. All isolates belonged to two lineages. Lineage 1 isolates were from central and North Africa, Europe, Israel, and North America; lineage 2 isolates were from central and southern Africa and Madagascar. No strict correlation existed between grouping and source of virus isolate, pathogenicity, geographic distribution, or year of isolation. Some southern African isolates have been associated with encephalitis in a human, a horse, and a dog and with fatal hepatitis in a human and death of an ostrich chick.

The non-H pylori helicobacters: their expanding role in gastrointestinal and systemic diseases.

The number of species in the genus Helicobacter has rapidly expanded over the past decade. The genus now includes at least 24 formally named species as well as numerous other helicobacters awaiting formal naming. This review highlights the expanding role that other helicobacters, although not as well known as H pylori, play in gastrointestinal and systemic disease in humans.

The earliest discoveries of dinosaurs: the records re-examined

The history of English discoveries of dinosaurs is recounted, from Robert Plot's first illustration of a dinosaur bone in 1677 to the first formal scientific description and naming of a dinosaur genus by William Buckland in 1824. It is shown that the English discoveries were more numerous than recognized hitherto and that they amply predated the first finds in France and North America. Though bones of other dinosaur groups were discovered, the majority of English finds were of carnosaur (probably megalosaur) bones and teeth. It is considered probable that all the various bones and teeth of Megalosaurus , obtained piecemeal from the Stonesfield Slate at Stonesfield, Oxfordshire over 125 years, were the remains of a single individual dinosaur.

New and little‐known Mallomonas (Synurophyceae) taxa from Ontario, Canada

Mallomonas tonsurata var. coroniferoides var. nov. is described on the basis of material from four sites in Ontario Canada. It differs from M. tonsurata var. tonsurata by having posterior scales possessing a tubular outgrowth with a toothed, crownlike margin. Preliminary descriptions are provided for three other apparently undescribed Mallomonas species. However, complete description and formal naming of these three new species cannot be done at this time owing to omission of certain detailed structural information presently not available in the existing material. New information on the distribution and morphology of the peculiar M. retrorsa is also reported, and two other species, M. vannigera and M. clavus are reported for the first time from the Western Hemisphere; however, there is an unpublished report of M. vannigera from Nova Scotia. Because M. vannigera is common in the Baltic, it is possible that its discovery in North America indicates relatively recent trans‐Atlantic transport in ship ballast water as has been demonstrated recently for many other “exotic” protistan species.

Foodborne viruses and fresh produce.

Raw and minimally processed fruits and vegetables are typically sold to the consumer in a ready-to-use or ready-to-eat form. These products do not generally contain preservatives or antimicrobial agents and rarely undergo any heat processing prior to consumption. For many years raw fruits and vegetables have been implicated as vehicles for transmission of infectious micro-organisms. Although fresh produce can support the growth and/or survival of many pathogenic bacteria there is little published information on the stability of human pathogenic viruses on these food products. Viruses cannot grow in or on foods but may sometimes be present on fresh produce as a result of faecal contamination. This contamination can arise at source in the growth and harvesting area from contact with polluted water and inadequately or untreated sewage sludge used for irrigation and fertilization. Alternatively, fruits or vegetables handled by an infected person might become contaminated with virus and transmit infection. The most frequently reported foodborne viral infections are viral gastroenteritis and hepatitis A: both have been associated with the consumption of fresh fruit or vegetables.

March Field Reopens for Training, 1927-1931

U.S. Air Force base near Riverside, California, affectionately known as through several formal name changes, is the oldest operational base in California. The field opened for flying instructions on July 1 , 1918. It was first named as Alessandro Flying Training Field, but the name was changed to March Field on March 20, 1918 to honor 2nd Lieutenant Peyton C. March, Jr., killed a few days previously in a plane crash in Texas. He was the son of the then acting Army Chief of Staff, Major General Peyton C. March. After the installation's first training era, 1918-1921, the base was closed for five years.1

O mapeamento faciológico em rochas ígneas plutônicas

The mapping of plutonic igneous rocks poses special problems, since the usual stratigraphic laws are not applicable to such cases. Most igneous massifs are frequently the result of complex sequences of magma emplacement, to be unraveled by mapping procedures. Special care is thus needed with the definition of the several mapping units, and the mapping activity itself becomes a foremost tool for the interpretation of igneous processes and data. Initially, the igneous rock fades is recognized as the core mapping unit, each defined entirely by macroscopic-mesoscopic features (mineral content, texture, color and color index, structure). Most cannot be represented on a map, on the usual standard scales such as 1:10,000 or 1:25,000, so that the next step is to identify the mappable unit (or association), usually various that can clearly be grouped together, on account of similarities in composition, structure, and relative ages, as shown by crosscutting relationships. Mapping of these units outlines the igneous massif, its structure, geometry and emplacement behaviour. The term igneous body is here proposed as a synonym for this rheologic or emplacement unit, and the neutral name seems fit to identify any medium- or large-sized igneous occurrence. Facies and facies associations, or mappable units, should be named informally (e.g., A, B; of red granite; etc.), while a geographic addition identifies the entire massif (.e.g., Atibaia massif, etc.). All cited mapping categories (facies, association, body, massif) are informal and should therefore be clearly separated from lhe formal names defined in the official Stratigraphic Codes. Several geologically-geotectonically related massifs, grouped together, identify a still informal category of higher hierarchy, the magmatic or genetic unit, informally akin to the suites and supersuites of other authors, to be defined only after comprehensive regional studies.

Eubiostratigraphic units, quasibiostratigraphic units, and “assemblage zones”

ABSTRACT A categorical distinction is made between two types of biostratigraphic units. In a given superposed section, a eubiostratigraphic unit is a thickness of strata whose boundaries are defined by the lowest and/or highest occurrences of fossils of one or more specified taxa. In contrast, a quasibiostratigraphic unit is a thickness of strata characterized by its fossil content, but whose boundaries are defined by other means. Eubiostratigraphic units include range, single-taxon interval, assemblage, and multiple-taxon interval fossilzones. Quasibiostratigraphic units include paleontologically distinct lithozones, metrizones, and “fuzzy” zones. Quasibiostratigraphic units serve to summarize the most distinctive changes in overall fossil content observed in individual sections, without necessary regard for the exact vertical ranges of particular taxa. Most quasibiostratigraphic units need not be given formal binomial names, but are best assigned alpha-numeric or informal descriptive designations. Assemblage fossilzones are multiple-taxon analogs of range fossilzones, in that they are defined by a single set of two or more taxa. Multiple-taxon interval fossilzones are multiple-taxon analogs of single-taxon interval fossilzones, in that their boundaries are defined by two different sets of two or more taxa. As such, multiple-taxon interval fossilzones are stratigraphically and temporally contiguous with one another by definition.

A cladistic view of the Monostilifera (Hoplonemertea) with interwoven rhynchocoel musculature: a preliminary assessment

A cladistic analysis was performed on 21 previously described and putative new genera comprising all hoplonemerteans having both monostilifery and interwoven rhynchocoel musculature. Traditional taxonomic methods have placed these genera into two existing families and one putative new family, but there has been active debate as to relationships within and between these groups. Sixty-one characters were employed. The intent of this study was to further elucidate relationships within and between these groups but without addressing their possible positions in the higher taxonomic scheme. The results suggest that the family Plectonemertidae (sensu Moore & Gibson, 1988) and the family Cratenemertidae are paraphyletic as is a new Antarctic form which appears to constitute a monotypic family. The results further suggest that Plectonemertes represents a monotypic family, the five `Group 2' terrestrial genera (Acteonemertes, Argonemertes, Antiponemertes, Leptonemertes and Katechonemertes) form a distinct family, and the freshwater genera Campbellonemertes and Potamonemertes represent either a single distinct family or two monotypic families. The family Cratenemertidae is seen as containing three subfamilies. The analysis also indicates that these groups, in which 10 of the 21 genera are highly habitat-adapted, exhibit no greater homoplasy than is evident in the animal and plant kingdoms generally. Formal designation and naming of the new family group entities suggested here must await publication of original descriptions or redescriptions of the underlying species and genera.

Snake origins and the need for scientific agreement on vernacular names

When transitional fossils blur previously clear boundaries between major groups, drawing that line can be problematic. While the need to rigorously define formal taxon names is widely acknowledged (e.g., de Queiroz and Gauthier 1992; Cantino et al. 1997), the need for similar precision in the scientific use of vernacular terms is not widely appreciated. The lack of accepted usages for common names has engendered endless arguments about when a fish becomes (also?) a tetrapod (e.g., Clack 1997), when a dinosaur becomes (also?) a bird (e.g., Padian and Chiappe 1998), and when a mammal-like reptile becomes (also?) a mammal (e.g., Rowe and Gauthier 1992). Recent descriptions of fossil snakes with well-developed hindlimbs have raised similar questions about where to draw the line between lizards and snakes and initiated a lively debate over the origin of snakes. However, lack of a precise definition of the vernacular term “snake,” as well as lack of a consensus on what constitutes a higher taxon's “origins,” has seriously hindered discussion of “snake origins.” Here, precise definitions of both terms are proposed and justified and their paleobiological implications discussed. The origin of higher taxa remains one of the most intriguing macroevolutionary problems, but scientists risk arguing at cross-purposes unless they agree on the exact boundaries of vernacular groups, and the exact meaning of the term “origin.”

Statewide Tuskegee Alliance for clinical trials

BACKGROUND Cancer mortality rates for all sites are nearly 2.5 times greater for African-Americans compared with whites. In addition, there are data implying that cancer treatment outcomes for minorities are unfavorable compared with whites. Whether this is due to poor access to health care or a biologic property of malignancies occurring in specific populations remains to be determined. Because of these unknown factors, targeting minorities for clinical trials may contribute toward the reduction of the overall morbidity and mortality associated with specific cancers. METHODS The current study describes the establishment of a genuine collaborative partnership between the targeted minority community and clinical investigators at the University of Alabama at Birmingham. This partnership was formed for the purpose of identifying strategies that would enhance the accrual and retention of minority participants into current and future cancer prevention and control trials. Focus groups and key informant interviews were conducted to ascertain the community's perception of participating in clinical trials. RESULTS The majority of focus group participants were unclear regarding the nature of clinical trials. Participants indicated that they would participate in research studies if they received adequate information regarding the purpose and benefits of the study, and if the charge came from a pastor or physician. Barriers to participation included time commitments, family obligations, whether blood was involved, and past experiences. The majority of the participants indicated that their knowledge of the Tuskegee Syphilis Study did not influence their decision to participate in research. A major outcome of the conference was the formation of the Statewide Tuskegee Alliance Coalition. The planning coalition decided to continue their efforts to work with communities and promote cancer awareness among minorities. After the conference, the coalition conducted several meetings and in July 1998, 1 year after the conference, the coalition selected a chair, co-chair, and a formal name for the organized group. CONCLUSIONS The planning, development, and implementation of this conference provided a valuable experience for researchers and community members. It was discovered that community involvement in the early phase of this project contributed to its success. Furthermore, the partnership that developed between researchers (academic institutions) and communities successfully provided an infrastructure that supported the interest of both groups. Cancer 2001;91:237–41. © 2001 American Cancer Society.

Statewide Tuskegee Alliance for clinical trials. A community coalition to enhance minority participation in medical research.

Cancer mortality rates for all sites are nearly 2.5 times greater for African-Americans compared with whites. In addition, there are data implying that cancer treatment outcomes for minorities are unfavorable compared with whites. Whether this is due to poor access to health care or a biologic property of malignancies occurring in specific populations remains to be determined. Because of these unknown factors, targeting minorities for clinical trials may contribute toward the reduction of the overall morbidity and mortality associated with specific cancers. The current study describes the establishment of a genuine collaborative partnership between the targeted minority community and clinical investigators at the University of Alabama at Birmingham. This partnership was formed for the purpose of identifying strategies that would enhance the accrual and retention of minority participants into current and future cancer prevention and control trials. Focus groups and key informant interviews were conducted to ascertain the community's perception of participating in clinical trials. The majority of focus group participants were unclear regarding the nature of clinical trials. Participants indicated that they would participate in research studies if they received adequate information regarding the purpose and benefits of the study, and if the charge came from a pastor or physician. Barriers to participation included time commitments, family obligations, whether blood was involved, and past experiences. The majority of the participants indicated that their knowledge of the Tuskegee Syphilis Study did not influence their decision to participate in research. A major outcome of the conference was the formation of the Statewide Tuskegee Alliance Coalition. The planning coalition decided to continue their efforts to work with communities and promote cancer awareness among minorities. After the conference, the coalition conducted several meetings and in July 1998, 1 year after the conference, the coalition selected a chair, co-chair, and a formal name for the organized group. The planning, development, and implementation of this conference provided a valuable experience for researchers and community members. It was discovered that community involvement in the early phase of this project contributed to its success. Furthermore, the partnership that developed between researchers (academic institutions) and communities successfully provided an infrastructure that supported the interest of both groups.