Lithological studies : a description and classification of the rocks of the Cordilleras / by M.E. Wadsworth. With eight plates.

v.11:no.1 (1884)

Human Endogenous Retrovirus (HERV) Insertional Polymorphisms

Human endogenous retroviruses (HERVs) are the result of ancient germ cell infections of human germ cells by exogenous retroviruses. HERVs belong to the long terminal repeat (LTR) group of retrotransposons that comprise ~8% of the human genome. The majority of the HERVs documented have been truncated and/or incurred lethal mutations and no longer encode functional genes; however a very small number of HERVs seem to maintain functional in making new copies by retrotranspositon as suggested by the identification of a handful of polymorphic HERV insertions in human populations. The objectives of this study were to identify novel insertion of HERVs via analysis of personal genomic data and survey the polymorphism levels of new and known HERV insertions in the human genome. Specifically, this study involves the experimental validation of polymorphic HERV insertion candidates predicted by personal genome-based computation prediction and survey the polymorphism level within the human population based on a set of 30 diverse human DNA samples. Based on computational analysis of a limited number of personal genome sequences, PCR genotyping aided in the identification of 15 dimorphic, 2 trimorphic and 5 fixed full-length HERV-K insertions not previously investigated. These results suggest that the proliferation rate of HERVKs, perhaps also other ERVs, in the human genome may be much higher than we previously appreciated and the recently inserted HERVs exhibit a high level of instability. Throughout this study we have observed the frequent presence of additional forms of genotypes for these HERV insertions, and we propose for the first time the establishment of new genotype reporting nomenclature to reflect all possible combinations of the pre-integration site, solo-LTR and full-length HERV alleles.

Post-collisional lamprophyric event in Sierra Norte, Cordoba, Argentina: Mineralogical, geochemical and isotopic characteristics

Over 20 lamprophyre dykes, varying in width between a few centimeters and several meters, have been identified in central Sierra Norte - Eastern Pampean Ranges, Cordoba, Argentina. Their mineralogy and chemistry indicate that they are part of the calc-alkaline lamprophyres clan (CAL). They contain phenocrysts of magnesiohomblende +/- augite set in a groundmass of magnesiohornblende, calcic-plagioclase, alkali feldspar, and opaque minerals, which designate them as spessartite-type lamprophyres. Alteration products include chlorite, calcite and iron oxides after malfic phenocrysts, though some are partially replaced by actinolite. Feldspars are replaced by carbonate and clay minerals. The dykes are relatively primitive, and show restricted major element variation (SiO(2) 51.1-55.3 wt.%, Al(2)O(3) 12-16.6 wt.%, total alkalies 1.5-4.7 wt.%), high Mg# (55-77), high Cr contents (27-988 ppm) and moderate to high Ni contents (60-190 ppm). Lamprophyre LILE (e.g. Rb averages 110 ppm, Sr 211-387 ppm, Ba 203-452 ppm) are high relative to HFSE (e.g., Ta 0.2-1.6 ppm, Nb 4-11 ppm, Y 17-21 ppm), and are enriched in LREE (30-70 times chondrite). They are characterized by relatively high (208)Pb/(204)Pb (38.8-39.9), (207)Pb/(204)Pb(similar to 15.7), and (206)Pb/(204)Pb (18.7-20.1), combined with low (epsilon)epsilon(Nd) (-4.69 to -1.52) and a relative moderately high ((87)Sr/(86)Sr)(i) of 0.7055-0.7074. The Rb-Sr whole rock isochron indicates an Early Ordovician age of 485 +/- 25 Ma. The calculated T(DM) (1.7 Ga) suggests that these rocks appear to have originated from a reservoir that was created during a mantle metasomatism event related to the Pampean orogeny. The Sierra Norte lamprophyres show affinities with a subduction-related magma in an active continental margin. Their geochemical and isotopic features suggest a multicomponent source, composed of enriched mantle material variably contaminated by crustal components. The lamprophyric suite emplacement occurred at the dawning stage of the Pampean orogeny, in a regional post-collisional extensional setting developed in the Sierra Norte-Ambargasta batholith (SNAB) in Early Ordovician times. (C) 2008 Published by Elsevier Ltd.

PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.

Nomenclature et classification pharmaceutiques : accompagnées d'une nouvelle méthode de formuler, et d'un grand nombre de formules rédigées d'après cette méthode ... /

Mode of access: Internet.

The birds of New England and adjacent states : ... arranged by a long-approved classification and nomenclature ... with illustrations of many species of the birds and accurate figures of their nests and eggs /

Mode of access: Internet.

Le système de classification adopté par la Commission Impériale : précéde d'une nomenclature alphabéthique des produits de l'agriculture, de l'industrie et de l'art, indiquant, pour chacun, la classe et la section auxquelles il se rapport, a l'usage des exposants, des comités et des jurys.

Mode of access: Internet.

Nouvelle nomenclature chimique d'après la classification adoptée par M. Thénard /

Mode of access: Internet.

Nomenclature and syntaxonomic notes on some high-rank syntaxa of the European grassland vegetation

We present descriptions of a new order (Ranunculo cortusifolii-Geranietalia reuteri and of a new alliance (Stachyo lusitanicae-Cheirolophion sempervirentis) for the herbaceous fringe communities of Macaronesia and of the southwestern Iberian Peninsula, respectively. A new alliance, the Polygalo mediterraneae-Bromion erecti (mesophilous post-cultural grasslands), was introduced for the Peninsular Italy. We further validate and typify the Armerietalia rumelicae (perennial grasslands supported by nutrient-poor on siliceous bedrocks at altitudes characterized by the submediterranean climate of central-southern Balkan Peninsula), the Securigero-Dasypyrion villosae (lawn and fallow-land tall-grass annual vegetation of Italy), and the Cirsio vallis-demoni-Nardion (acidophilous grasslands on siliceous substrates of the Southern Italy). Nomenclatural issues (validity, legitimacy, synonymy, formal corrections) have been discussed and clarified for the following names: Brachypodio-Brometalia, Bromo pannonici-Festucion csikhegyensis, Corynephoro-Plantaginion radicatae, Heleochloion, Hieracio-Plantaginion radicatae, Nardetea strictae, Nardetalia strictae, Nardo-Callunetea, Nardo-Galion saxatilis, Oligo-Bromion, Paspalo-Heleochloetalia, Plantagini-Corynephorion and Scorzoneret alia villosae. 

Understanding the Effects of Ionicity in Salts, Solvates, Co-Crystals, Ionic Co-Crystals, and Ionic Liquids, Rather than Nomenclature, Is Critical to Understanding Their Behavior

The incorporation of active pharmaceutical ingredients (APIs) into multicomponent solid forms (such as salts and co-crystals) or liquid forms (such as ionic liquids (ILs) or deep eutectic mixtures) is important in optimizing the efficacy and delivery of APIs. However, there is a current debate regarding the classification of these multicomponent systems based on their ionicity which could interfere with their consideration in important applications. Multicomponent systems of intermediate ionicity can show a combination of properties, leading to behavior that is neither strictly typical of either purely ionic or purely neutral compounds, nor easily described as intermediate between the two. In this perspective, we attempt to illustrate the problems in classifying multicomponent APIs based on one of two categories by discussing selected literature regarding solid and liquid multicomponent APIs and presenting the crystal structures of some relevant systems as case studies. It is clear that a focus on restrictive nomenclature carries with it the risk that a thorough examination of the physicochemical properties of the compounds will be overlooked.

Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012

In 2009, the Nomenclature Committee on Cell Death (NCCD) proposed a set of recommendations for the definition of distinct cell death morphologies and for the appropriate use of cell death-related terminology, including 'apoptosis', 'necrosis' and 'mitotic catastrophe'. In view of the substantial progress in the biochemical and genetic exploration of cell death, time has come to switch from morphological to molecular definitions of cell death modalities. Here we propose a functional classification of cell death subroutines that applies to both in vitro and in vivo settings and includes extrinsic apoptosis, caspase-dependent or -independent intrinsic apoptosis, regulated necrosis, autophagic cell death and mitotic catastrophe. Moreover, we discuss the utility of expressions indicating additional cell death modalities. On the basis of the new, revised NCCD classification, cell death subroutines are defined by a series of precise, measurable biochemical features.

Recommended Nomenclature for the Sapphirine and Surinamite Groups (Sapphirine Supergroup)

Minerals isostructural with sapphirine-1A, sapphirine-2M, and surinamite are closely related chain silicates that pose nomenclature problems because of the large number of sites and potential constituents, including several (Be, B, As, Sb) that are rare or absent in other chain silicates. Our recommended nomenclature for the sapphirine group (formerly-aenigmatite group) makes extensive use of precedent, but applies the rules to all known natural compositions, with flexibility to allow for yet undiscovered compositions such as those reported in synthetic materials. These minerals are part of a polysomatic series composed of pyroxene or pyroxene-like and spinel modules, and thus we recommend that the sapphirine supergroup should encompass the polysomatic series. The first level in the classification is based on polysome, i.e. each group within the supergroup Corresponds to a single polysome. At the second level, the sapphirine group is divided into subgroups according to the occupancy of the two largest M sites, namely, sapphirine (Mg), aenigmatite (Na), and rhonite (Ca). Classification at the third level is based on the occupancy of the smallest M site with most shared edges, M7, at which the dominant cation is most often Ti (aenigmatite, rhonite, makarochkinite), Fe(3+) (wilkinsonite, dorrite, hogtuvaite) or Al (sapphirine, khmaralite); much less common is Cr (krinovite) and Sb (welshite). At the fourth level, the two most polymerized T sites are considered together, e.g. ordering of Be at these sites distinguishes hogtuvaite, makarochkinite and khmaralite. Classification at the fifth level is based on X(Mg) = Mg/(Mg + Fe(2+)) at the M sites (excluding the two largest and M7). In principle, this criterion could be expanded to include other divalent cations at these sites, e.g. Mn. To date, most minerals have been found to be either Mg-dominant (X(mg) > 0.5), or Fe(2+)-dominant (X(Mg) < 0.5), at these M sites. However, X(mg) ranges from 1.00 to 0.03 in material described as rhonite, i.e. there are two species present, one Mg-dominant, the other Fe(2+)-dominant. Three other potentially new species are a Mg-dominant analogue of wilkinsonite, rhonite in the Allende meteorite, which is distinguished front rhonite and dorrite in that Mg rather than Ti or FC(3+) is dominant at M7, and an Al-dominant analogue of sapphirine, in which Al > Si at the two most polymerized T sites vs. Al < Si in sapphirine. Further splitting of the supergroup based on occupancies other than those specified above is not recommended.