New radiolarians from the Devonian of the southern Ural Mountains: 1. Early-Middle Devonian (Late Emsian-Early Eifelian)

Late Emsian-Early Eifelian radiolarians from the southern Ural Mountains are recorded and described for the first time. They come from the Kamennaya Gora section on the Tanalyk River near the town of Buribay, Bashkiria. The new Late Emsian-Early Eifelian radiolarian assemblage consists of 20 species of 11 genera of spherical, discoidal, spindle-shaped, pylomate, and spiny radiolarians. Four new species, i.e., Entactinia rostriformis sp. nov., Palaeodiscaleksus tumefactus sp. nov., Primaritripus buribayensis sp. nov., and P. chuvashovi sp. nov., are described. The diagnosis of the genus Primaritripus Afanasieva, 2000 is amended. The fact that the oryctocenosis is dominated by discoidal radiolarians suggests that, in the Late Emsian-Early Eifelian, the area under study was occupied by a relatively shallow marine basin. Based on radiolarians, a new Upper Emsian-Lower Eifelian biostraton, beds with Primaritripus buribayensis-Entactinia rostriformis, is established. The history of the study of Early Devonian radiolarians is considered.     

New radiolarians from the Devonian of the southern Ural Mountains: 2. Middle-Late Devonian

Middle-Late Devonian Radiolarians are recorded for the first time in the southern Ural Mountains in Bashkortostan, in a section of Kariukmas Mountain (Upper Eifelian) and on the southern slope of Argagan Mountain (Middle Frasnian). The new Late Eifelian assemblage is composed of 17 species of 11 genera, and Middle Frasnian radiolarians comprise 13 species of 7 genera of spherical, discoidal, pylomate, and spiny radiolarians. A new species, Primaritripus kariukmasensis, sp. nov., is described. The prevalence of discoidal forms in the oryctocenosis suggests shallow marine conditions in the Late Eifelian and Middle Frasnian basins. Two new biostratons, the Upper Eifelian beds with Primaritripus kariukmasensis and Middle Frasnian beds with Primaritripus chuvashovi, are established based on radiolarians.     

Bovine placenta: A review on morphology,components, and defects from terminology and clinical perspectives

The bovine placenta has been the subject of many studies. Concurrently, several specialized terms have been developed to describe its development, morphology, components, function, and pathology. Many of these terms are simple, some are difficult to understand and use, and others are antiquated and may not be scientifically accurate. Defining and adopting terminology for the bovine placenta that is clear, precise and understandable, and available in a single source is expected to facilitate exchange of clinical and research information. This review presents a brief overview of the current knowledge regarding the bovine placenta and attempts to define terms. In this process, conventional terminology is presented, and contemporary and novel terms are proposed from a biological perspective. For example, use of terms such as syndesmochorial, retained placenta, and large offspring syndrome should be revisited. Furthermore, the clinical relevance of the structure and function of the bovine placenta is reviewed. Finally, terms discussed in this review are summarized (in table format).     

Skeletal morphology of Opius dissitus and Biosteres carbonarius (Hymenoptera: Braconidae), with a discussion of terminology

The Braconidae, a family of parasitic wasps, constitute a major taxonomic challenge with an estimated diversity of 40,000 to 120,000 species worldwide, only 18,000 of which have been described to date. The skeletal morphology of braconids is still not adequately understood and the terminology is partly idiosyncratic, despite the fact that anatomical features form the basis for most taxonomic work on the group. To help address this problem, we describe the external skeletal morphology of Opius dissitus Muesebeck 1963 and Biosteres carbonarius Nees 1834, two diverse representatives of one of the least known and most diverse braconid subfamilies, the Opiinae. We review the terminology used to describe skeletal features in the Ichneumonoidea in general and the Opiinae in particular, and identify a list of recommend terms, which are linked to the online Hymenoptera Anatomy Ontology. The morphology of the studied species is illustrated with SEM-micrographs, photos and line drawings. Based on the examined species, we discuss intraspecific and interspecific morphological variation in the Opiinae and point out character complexes that merit further study.     

An Ichnotaxonomic Approach to Wrinkled Microbially Induced Sedimentary Structures

Microbially induced sedimentary structures (MISS) are an important facet of recent paleoichnological work because of their taphonomic implications. MISS are extensively studied in terms of their formation processes, recognition in the ancient record, and their diverse morphologies. Classification and terminology schemes are based on their appearance and mode of formation; however, the taxonomic treatment of MISS remains debated. Traditionally MISS have been considered sedimentary structures, and arguments have been made that they cannot be treated as trace fossils under the International Code of Zoological Nomenclature (ICZN) due to MISS being formed by communities of microbiota including algae, cyanobacteria, and others, rather than a single tracemaker. Here, we reexamine MISS using an ichnotaxonomic approach and apply ichnologic terminology and binomial names. Upon reexamining the holotype of Kinneyia Walcott, a genus commonly used to describe some MISS, we argue it cannot be used to correctly describe wrinkle or ripple-like features seen in MISS, and we agree with previous authors that Kinneyia is likely not biogenic in origin. We here assign a new ichnogenus and ichnospecies, Rugalichnus matthewii, to ripple-like sedimentary wrinkle marks known as MISS, separating them from the nomen dubium genus Kinneyia.     

Rotational and hinge dynamics of discoidal high density lipoproteins probed by interchain disulfide bond formation

To develop a detailed double belt model for discoidal HDL, we previously scored inter-helical salt bridges between all possible registries of two stacked antiparallel amphipathic helical rings of apolipoprotein (apo) A-I. The top score was the antiparallel apposition of helix 5 with 5 followed closely by appositions of helix 5 with 4 and helix 5 with 6. The rationale for the current study is that, for each of the optimal scores, a pair of identical residues can be identified in juxtaposition directly on the contact edge between the two antiparallel helical belts of apoA-I. Further, these residues are always in the '9th position' in one of the eighteen 11-mer repeats that make up the lipid-associating domain of apoA-I. To illustrate our terminology, 129j (LL5/5) refers to the juxtaposition of the Cα atoms of G129 (in a '9th position') in the pairwise helix 5 domains. We reasoned that if identical residues in the double belt juxtapositions were mutated to a cysteine and kept under reducing conditions during disc formation, we would have a precise method for determining registration in discoidal HDL by formation of a disulfide-linked apoA-I homodimer. Using this approach, we conclude that 129j (LL5/5) is the major rotamer orientation for double belt HDL and propose that the small ubiquitous gap between the pairwise helix 5 portions of the double belt in larger HDL discoidal particles is significantly dynamic to hinge off the disc edge under certain conditions, e.g., in smaller particles or perhaps following binding of the enzyme LCAT. This article is part of a Special Issue entitled Advances in High Density Lipoprotein Formation and Metabolism: A Tribute to John F. Oram (1945-2010).     

Rotational and hinge dynamics of discoidal high density lipoproteins probed by interchain disulfide bond formation

To develop a detailed double belt model for discoidal HDL, we previously scored inter-helical salt bridges between all possible registries of two stacked antiparallel amphipathic helical rings of apolipoprotein (apo) A-I. The top score was the antiparallel apposition of helix 5 with 5 followed closely by appositions of helix 5 with 4 and helix 5 with 6. The rationale for the current study is that, for each of the optimal scores, a pair of identical residues can be identified in juxtaposition directly on the contact edge between the two antiparallel helical belts of apoA-I. Further, these residues are always in the ‘9th position’ in one of the eighteen 11-mer repeats that make up the lipid-associating domain of apoA-I. To illustrate our terminology, 129j (LL5/5) refers to the juxtaposition of the Cα atoms of G129 (in a ‘9th position’) in the pairwise helix 5 domains. We reasoned that if identical residues in the double belt juxtapositions were mutated to a cysteine and kept under reducing conditions during disc formation, we would have a precise method for determining registration in discoidal HDL by formation of a disulfide-linked apoA-I homodimer. Using this approach, we conclude that 129j (LL5/5) is the major rotamer orientation for double belt HDL and propose that the small ubiquitous gap between the pairwise helix 5 portions of the double belt in larger HDL discoidal particles is significantly dynamic to hinge off the disc edge under certain conditions, e.g., in smaller particles or perhaps following binding of the enzyme LCAT. This article is part of a Special Issue entitled Advances in High Density Lipoprotein Formation and Metabolism: A Tribute to John F. Oram (1945-2010).     

Early Cambrian radiolarians and sponge spicules from the Niujiaohe Formation in South China

Most of the reported Cambrian radiolarians are from middle Cambrian (Miaolingian Series, Wuliuan Stage) and onward, the radiolarians from lower Cambrian (Terreneuvian and Cambrian Series 2), on the other hand, are poorly documented, thus their morphological characteristics have not been well understood. In this study, we extracted spherical radiolarians and sponge spicules from the chert of the Cambrian Series 2 Niujiaohe Formation in southern Jiangxi Province, China. The well-preserved radiolarian fossils, identified as Paraantygopora porosa, consist of perforate plate shells pierced by dense pores with elevated rims, and display similarities to those from Lower Ordovician. Seven forms of sponge spicules are recognized, including monaxons, diaxons, tetractines, hexactines, triaxon tetractines, triaxon pentactines and irregular tetraxon tetractines, which are similar to those from the Qiongzhusian Stage in South China. Our results, combined with previously reported early Cambrian radiolarians from South China, indicate that the early Cambrian radiolarians developed advanced spherical skeletons.     

Mesozoic Radiolaria of Bosnia and Serbia: New data

Jurassic and Cretaceous radiolarian faunas were discovered in bedded chert of the Dinaric and Vardar tectonic zones of Bosnia and Herzegovina. Only Triassic radiolarians have previously been described in Bosnia and Herzegovina, while the finds of Bajocian, Bathonian-Callovian, Oxfordian-Kimmeridgian, Tithonian-Berriasian, and Campanian are new. Additional localities of Triassic and Jurassic radiolarians were investigated in Serbia. By correlation with radiolarians from the previous studies within Serbia, the Late Aalenian-Bajocian and Bathonian-Callovian Serbian radiolarian beds are newly dated. The first find of Cretaceous radiolarians in Serbia is reported. The oldest Mesozoic Radiolaria-bearing formations outcropping in the Western Belt of the Vardar Zone are dated Mid-Upper Triassic. The youngest radiolarians come from the Upper Cretaceous (Campanian) of the northern part of this belt of the Vardar Zone, where they co-occur with planktonic foraminifers. The distribution of 70 radiolarian samples within sections is shown. The taxonomic composition of 39 samples is analyzed. Radiolarian species extracted from 13 samples are described and figured. The list of 72 taxa and 3 plates of Jurassic radiolarians of Bosnia and Herzegovina, 3 plates of Triassic, 1 plate of Middle Jurassic, and 1 plate of Upper Cretaceous radiolarians of Serbia are presented.     

Terminology for the ageing of chondrichthyan fish using dorsal-fin spines

Dorsal-fin spines are becoming increasingly popular as a suitable structure for ageing some chondrichthyan fishes. However, the terminology used to describe dorsal-fin structure is often inconsistent between studies, and is consequently unclear. Standardised terms and definitions of the dorsal-fin spine structure are proposed, with particular focus on those areas that are used for age and growth studies.     

江苏仑山地区上奥陶统五峰组放射虫动物群及其地质意义

五峰组以盛产笔石动物群著称,时代为凯迪晚期(相当于英国的阿什极尔期),其中也发现了放射虫.该时期的放射虫在全球并不多见.本文首次描述江苏句容仑山地区五峰组的放射虫动物群,该动物群以不具刺的球形放射虫最为发育,并出现少量Inaniguttidae科的分子,化石保存较差,属种单调,分异度很低,这些特点与大西洋沿岸地区陆表海...     

DEVELOPMENT OF A LEXICON FOR THE DESCRIPTION OF PEANUT FLAVOR

A lexicon of terms to describe desirable as well as undesirable flavors in peanuts has been developed. The lexicon and an intensity rating scale was developed by a 13 member panel of flavor and peanut specialists representing industry and the USDA-Agricultural Research Service. This system is intended to provide definitive, common terminology for use in communicating differences in peanut flavor variables among all phases of peanut research and industry.     

Apolipoprotein AI tertiary structures determine stability and phospholipid‐binding activity of discoidal high‐density lipoprotein particles of different sizes

Human high‐density lipoprotein (HDL) plays a key role in the reverse cholesterol transport pathway that delivers excess cholesterol back to the liver for clearance. In vivo, HDL particles vary in size, shape and biological function. The discoidal HDL is a 140–240 kDa, disk‐shaped intermediate of mature HDL. During mature spherical HDL formation, discoidal HDLs play a key role in loading cholesterol ester onto the HDL particles by activating the enzyme, lecithin:cholesterol acyltransferase (LCAT). One of the major problems for high‐resolution structural studies of discoidal HDL is the difficulty in obtaining pure and, foremost, homogenous sample. We demonstrate here that the commonly used cholate dialysis method for discoidal HDL preparation usually contains 5–10% lipid‐poor apoAI that significantly interferes with the high‐resolution structural analysis of discoidal HDL using biophysical methods. Using an ultracentrifugation method, we quickly removed lipid‐poor apoAI. We also purified discoidal reconstituted HDL (rHDL) into two pure discoidal HDL species of different sizes that are amendable for high‐resolution structural studies. A small rHDL has a diameter of 7.6 nm, and a large rHDL has a diameter of 9.8 nm. We show that these two different sizes of discoidal HDL particles display different stability and phospholipid‐binding activity. Interestingly, these property/functional differences are independent from the apoAI α‐helical secondary structure, but are determined by the tertiary structural difference of apoAI on different discoidal rHDL particles, as evidenced by two‐dimensional NMR and negative stain electron microscopy data. Our result further provides the first high‐resolution NMR data, demonstrating a promise of structural determination of discoidal HDL at atomic resolution using a combination of NMR and other biophysical techniques.     

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.